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From: #CHEW B. L. A. <CHEW0357@e.ntu.edu.sg> - 2021-10-27 05:06:08
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Dear Scipion community, I had no issues using scipion3 until I have installed topaz under the installation instructions listed in cryosparc https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz I have tried reading through the troubleshooting guide but could not seem to find a solution to my problem here. I have attached various screenshots that show the path pointed out by "scipion3" command points to topaz, but this is not the case in my bashrc setting. Screenshots *_1 and *_2 are the list of documents in the Programme and anaconda env. I could not seem to find the scipion.conf file as well, I am unsure if setting the scipion.conf is the fix I need in my case or simply reinstall scipion3 by following the installation guide again? Thank you and hope to receive any useful advice on how to proceed. Best Regards Alvin CHEW | Ph.D. Student | Nanyang Technological University |<http://www.lkcmedicine.ntu.edu.sg/> "(You) who (have) a why to live can bear almost any how." ~Friedrich Nietzsche<http://www.brainyquote.com/quotes/quotes/f/friedrichn103819.html>~ |
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From: Charles C. <cha...@i2...> - 2021-10-14 11:41:48
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Hello Alberto, Uninstalling and installing the latest version of xmipp has indeed fixed the xmipp viewer issue. Thanks for your reply, Charles De: "Alberto Garcia Mena" <alb...@cn...> À: "scipion-users" <sci...@li...> Envoyé: Jeudi 14 Octobre 2021 12:42:05 Objet: [scipion-users] xmipp viewer issue after auto-picking Hello Charles, The first thing you could do, if you are working in devel mode is to [ https://github.com/I2PC/xmipp | update the xmipp version ] to ensure that all changes and bug fixes are included. It is possible that this will fix the bug. Thanks -- - Alberto GM - _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Alberto G. M. <alb...@cn...> - 2021-10-14 10:42:49
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Hello Charles, The first thing you could do, if you are working in devel mode is to update the xmipp version <https://github.com/I2PC/xmipp> to ensure that all changes and bug fixes are included. It is possible that this will fix the bug. Thanks -- - Alberto GM - |
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From: Estrella F. G. <me....@cn...> - 2021-10-13 07:45:44
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Hi Dmitry, I usually use xmipp3 - align volume with "local" search strategy, and it works fine for me in this kind of comparison workflow. To use local strategy the volumes must be close enough. I haven't use fast Fourier method nor exhaustive, but the help of the protocol says: "... Be aware that the Fast Fourier algorithm requires a special compilationof Xmipp (--cltomo flag)...", maybe that is the cause why it is not working properly. However, I can not tell you so much about xmipp3 - align volume, maybe someone from Xmipp with more experience can say something else. Regards, Estrella FG On 12/10/21 10:32, Dmitry Semchonok wrote: > Hi Estrella, > > I followed your suggestions for the volumes comparison. > But the xmipp-alignment doesn’t seem to do the good job for me. I used > the fast Fourier method (the default one was standby for the > indefinite time somehow). > > I downloaded and overlapped the refenence map and output of > xmipp-alignment map in Chimera. > So next I did Fit in model - the aligned map moved nicely to the position. > > > Do you have any clue why? > > > > Thank you. > > Sincerely, > Dmitry > > > > > > > > > > > >> On 8. Oct 2021, at 08:50, Estrella Fernández Giménez >> <me....@cn... <mailto:me....@cn...>> wrote: >> >> Hello Dmitry, >> >> I suggest you to use some of the new programs in Xmipp (and of course >> integrated in the correspondant Scipion plugin), which are actually >> implemented for this kind of task. >> The programs are: >> >> xmipp3 - volumes adjust: it allows you to have the volumes in the >> same numerical frame, thus, you can compare there in a reliable way >> (same threshold). >> >> xmipp3 - volumes subtraction: it performs the alignment described >> above and then it computes the subtraction between the volumes, thus, >> it result should be the differences between the volumes. >> >> xmipp3 - volume consensus: applying first "volume adjust protocol" >> described above, then this protocol is able to make a fusion of a set >> of volumes, taking the best parts of each one. The result will be a >> volume consensus between the input. The result is automatically >> displayed in chimera with a colormap that indicates you the degree of >> similarity among the input maps (what we call a "difference map"). >> >> You can find more details of these protocols in this paper: >> https://www.sciencedirect.com/science/article/pii/S104784772100085X?via%3Dihub >> >> This three protocols have to be applied once the set of volumes has >> the same box size and pixel size (you can use xmipp3 - crop/resize >> protocol to achive this). Also, the volumes have to be properly >> aligned (using xmipp3 - align volume, for example). >> >> Feel free to contact me in case you have any doubt. Hope it helps! >> >> Regards, >> Estrella FG >> >> >> Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> >> escribió: >> >>> <>Dear colleagues, >>> >>> >>> >>> My task is to compare 2 volume maps to see the differences. The maps >>> are biologically pretty similar. >>> >>> What strategy shall I undergo and tool to select? >>> >>> >>> >>> Apart from biological similarities they are different for the pixel >>> size, box size, resolution and volume threshold. >>> >>> >>> >>> Thank you >>> >>> >>> >>> Sincerely, >>> >>> <> >>> Dmitry >> >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Dmitry S. <Sem...@gm...> - 2021-10-12 08:32:21
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Hi Estrella, I followed your suggestions for the volumes comparison. But the xmipp-alignment doesn’t seem to do the good job for me. I used the fast Fourier method (the default one was standby for the indefinite time somehow). I downloaded and overlapped the refenence map and output of xmipp-alignment map in Chimera. So next I did Fit in model - the aligned map moved nicely to the position. Do you have any clue why? Thank you. Sincerely, Dmitry > On 8. Oct 2021, at 08:50, Estrella Fernández Giménez <me....@cn...> wrote: > > Hello Dmitry, > > I suggest you to use some of the new programs in Xmipp (and of course integrated in the correspondant Scipion plugin), which are actually implemented for this kind of task. > The programs are: > > xmipp3 - volumes adjust: it allows you to have the volumes in the same numerical frame, thus, you can compare there in a reliable way (same threshold). > > xmipp3 - volumes subtraction: it performs the alignment described above and then it computes the subtraction between the volumes, thus, it result should be the differences between the volumes. > > xmipp3 - volume consensus: applying first "volume adjust protocol" described above, then this protocol is able to make a fusion of a set of volumes, taking the best parts of each one. The result will be a volume consensus between the input. The result is automatically displayed in chimera with a colormap that indicates you the degree of similarity among the input maps (what we call a "difference map"). > > You can find more details of these protocols in this paper: https://www.sciencedirect.com/science/article/pii/S104784772100085X?via%3Dihub > > This three protocols have to be applied once the set of volumes has the same box size and pixel size (you can use xmipp3 - crop/resize protocol to achive this). Also, the volumes have to be properly aligned (using xmipp3 - align volume, for example). > > Feel free to contact me in case you have any doubt. Hope it helps! > > Regards, > Estrella FG > > > Dmitry Semchonok <Sem...@gm...> escribió: > >> <>Dear colleagues, >> >> >> >> My task is to compare 2 volume maps to see the differences. The maps are biologically pretty similar. >> >> What strategy shall I undergo and tool to select? >> >> >> >> Apart from biological similarities they are different for the pixel size, box size, resolution and volume threshold. >> >> >> >> Thank you >> >> >> >> Sincerely, >> >> <> >> Dmitry > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Linda F. <lin...@cs...> - 2021-10-11 17:52:50
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Dear Scipion, I'm currently trying to use the local rec filter on sub-particles generated from I1 symmetry. The picking indeed picks 60 sub-particles on each main particle, but when I try to get rid of overlapping particles it does not seem so straight-forward. I've played with many settings, but I was wondering if something goes wrong when using the Minimal distance between sub-particles option. am I correct in assuming that this option would limit overlap between boxes by x amount of pixels, calculating from the box centers? What I see is that the result is exactly the same if I set the extra option 'keep overlapping particles in symmetry axis' to no and to yes. There is no difference between the results for my 5 test particles which were tested setting the Minimal distance between sub-particles to 1, 20 and 40 pixels and so it doesn't seem to filter. Would this be something related to a specific installation? What I also would expect is that if I try to pick pentons, I would pick max ~ twelve clusters of 5 very closely localized boxes or less clusters with even more boxes. Then if I would set the Minimal distance between sub-particles option to say 40 pixels, that I would mostly keep the number of clusters and reduce the number of boxes within a cluser. This however does not look to be the case as I see clusters disappearing before I see everycluster having 1 particle. Could someone explain to me how to correctly filter the particles that I keep one particle from each cluster? Also, in the manual, the Angle to keep particles from sideviews option is used and set to 40 degrees and this seems to remove topviews. Could someone explain why this is desired? Thank you very much for your help. Best wishes, Linda |
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From: Dmitry S. <Sem...@gm...> - 2021-10-08 13:37:25
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Dear Alberto, Yes, I used C2 symmetry and the option - Calculate the noise bound for resolution “Yes”. Currently I will try what you kindly suggested. Thank you! Sincerely, Dmitry > On 8. Oct 2021, at 14:13, Alberto Garcia Mena <alb...@cn...> wrote: > > Hello Dmitry. > > Maybe there could be a problem with thread selection, selecting "No", it worked for me. What parametrization do you have in the protocol? Attached is my parametrization that worked for me in the TestValidateOverfitting > > Thanks and let's keep talking > > <jidbbilnhhjmfpci.png> > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Alberto G. M. <alb...@cn...> - 2021-10-08 12:13:40
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Hello Dmitry. Maybe there could be a problem with thread selection, selecting "No", it worked for me. What parametrization do you have in the protocol? Attached is my parametrization that worked for me in the TestValidateOverfitting Thanks and let's keep talking |
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From: Estrella F. G. <me....@cn...> - 2021-10-08 06:50:41
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Hello Dmitry, I suggest you to use some of the new programs in Xmipp (and of course integrated in the correspondant Scipion plugin), which are actually implemented for this kind of task. The programs are: xmipp3 - volumes adjust: it allows you to have the volumes in the same numerical frame, thus, you can compare there in a reliable way (same threshold). xmipp3 - volumes subtraction: it performs the alignment described above and then it computes the subtraction between the volumes, thus, it result should be the differences between the volumes. xmipp3 - volume consensus: applying first "volume adjust protocol" described above, then this protocol is able to make a fusion of a set of volumes, taking the best parts of each one. The result will be a volume consensus between the input. The result is automatically displayed in chimera with a colormap that indicates you the degree of similarity among the input maps (what we call a "difference map"). You can find more details of these protocols in this paper: https://www.sciencedirect.com/science/article/pii/S104784772100085X?via%3Dihub This three protocols have to be applied once the set of volumes has the same box size and pixel size (you can use xmipp3 - crop/resize protocol to achive this). Also, the volumes have to be properly aligned (using xmipp3 - align volume, for example). Feel free to contact me in case you have any doubt. Hope it helps! Regards, Estrella FG Dmitry Semchonok <Sem...@gm...> escribió: > <>Dear colleagues, > > > > My task is to compare 2 volume maps to see the differences. The maps > are biologically pretty similar. > > What strategy shall I undergo and tool to select? > > > > Apart from biological similarities they are different for the pixel > size, box size, resolution and volume threshold. > > > > Thank you > > > > Sincerely, > > <> > Dmitry |
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From: Dmitry S. <Sem...@gm...> - 2021-10-07 12:24:52
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<>Dear colleagues, My task is to compare 2 volume maps to see the differences. The maps are biologically pretty similar. What strategy shall I undergo and tool to select? Apart from biological similarities they are different for the pixel size, box size, resolution and volume threshold. Thank you Sincerely, <> Dmitry |
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From: Charles C. <cha...@i2...> - 2021-10-04 15:20:13
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Dear all,
I am not able to analyze results from xmipp3-autopicking, this error appear in the terminal :
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib/python3.8/tkinter/__init__.py", line 1892, in __call__
return self.func(*args)
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/pyworkflow/gui/project/viewprotocols.py", line 2261, in _analyzeResultsClicked
self._analyzeResults(prot)
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/pyworkflow/gui/project/viewprotocols.py", line 2232, in _analyzeResults
firstViewer.visualize(prot)
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/pyworkflow/viewer.py", line 144, in visualize
for view in self._visualize(obj, **kwargs):
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/xmipp3/viewers/viewer.py", line 244, in _visualize
micsfn = self._getExtraPath(micSet.getName() + '_micrographs.xmd')
AttributeError: 'XmippViewer' object has no attribute '_getExtraPath'
Does someone know how to fix this ?
Thank you very much for your help,
Charles CIRIO
--
Doctorant
Equipe Fonction et Architecture des Assemblages Macromoléculaires (FAAM)
Département de Biochimie, Biophysique, et Biologie Structurale (B3S)
Institut de Biologie Intégrative de la Cellule (I2BC) - UMR9198
Université Paris-Saclay, Bât. 430
91405 Orsay, France
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From: Grigory S. <sha...@gm...> - 2021-10-01 10:23:17
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Hi, I believe this has been finally fixed in devel branch: https://github.com/scipion-em/scipion-em-phenix/issues/51 Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Fri, Oct 1, 2021 at 11:20 AM Lugmayr, Wolfgang <w.l...@uk...> wrote: > Hi, > > I updated the plugin above today and when I open an existing project I get > the following error: > > $ scipion3 last > Scipion v3.0.9 - Eugenius > Failed to read settings. The reported error was: > While reading from > '/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/phenix/protocols.conf' > [line 4]: option '{"tag"' in section 'PROTOCOLS' already exists > To solve it, fix > /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/phenix/protocols.conf > and run again. > > Its not really clear how and what I should fix ;-) > Can you please give me a hint? > > Cheers, > Wolfgang > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Deutsches Elektronen-Synchrotron (DESY) > Notkestrasse 85 Gebäude 15 > 22607 Hamburg, Germany > Tel.: +49 40 8998-87652 > Email: wol...@cs... > http://www.cssb-hamburg.de/ > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Lugmayr, W. <w.l...@uk...> - 2021-10-01 10:19:47
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Hi,
I updated the plugin above today and when I open an existing project I get the following error:
$ scipion3 last
Scipion v3.0.9 - Eugenius
Failed to read settings. The reported error was:
While reading from '/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/phenix/protocols.conf' [line 4]: option '{"tag"' in section 'PROTOCOLS' already exists
To solve it, fix /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/phenix/protocols.conf and run again.
Its not really clear how and what I should fix ;-)
Can you please give me a hint?
Cheers,
Wolfgang
--
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Deutsches Elektronen-Synchrotron (DESY)
Notkestrasse 85 Gebäude 15
22607 Hamburg, Germany
Tel.: +49 40 8998-87652
Email: wol...@cs...
http://www.cssb-hamburg.de/
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From: Anastasina, M. <mar...@he...> - 2021-10-01 08:36:40
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Hi Grigory, Sure, I have this file, but it is about 28 MB, so I can’t send it by email, instead I shared it on google drive. If you’d prefer another method to get the file, please let me know. Best, Maria On 30. Sep 2021, at 21.54, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Hi, thank you for sending over the files from the original job. I'm afraid I will need the Runs/011346_ProtRelionClassify3D/extra/relion_it025_model.star as well. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Thu, Sep 30, 2021 at 5:25 PM Anastasina, Maria <mar...@he...<mailto:mar...@he...>> wrote: Hi Grigory, Thank you for looking into my files. Yes, this job is a continuation of another one where 25 iterations were completed, but CreateOutput step failed with exactly the same error message. This is why I put 0 iterations in the job, hoping that it will just manage to create the output (or was it a wrong idea?). Since the original job with 25 iterations also filed, it seems that the source of error is something else, or maybe was a problem with that original job that migrated to the next one (sorry if it sounds confusing)?. Just in case, I attach here .stderr and .stdout files form the original job too. There all 25 iterations were completed, but the CreateOutput failed. Best, Maria On 30. Sep 2021, at 11.50, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Hello Maria, srun `which relion_refine_mpi` --norm --scale --o Runs/012188_ProtRelionClassify3D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 4.0 --iter 25 --pad 2 --skip_gridding --healpix_order 4 --offset_range 5.0 --offset_step 2.0 --continue Runs/011346_ProtRelionClassify3D/extra/relion_it025_optimiser.star --dont_combine_weights_via_disc --pool 3 --gpu --j 4 You are running a job that will not do anything, continuing from iteration 25 until 25. Did you put 0 in number of iterations in the protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 6:07 PM Anastasina, Maria <mar...@he...<mailto:mar...@he...>> wrote: Dear Grigory, Here they go Best, Maria [masha@puhti-login2 ~]$ scipion3 config -p relion Scipion v3.0.8 - Eugenius Variables defined by plugin 'relion': RELION_HOME = /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.1 RELION_CUDA_LIB = /appl/spack/install-tree/gcc-8.3.0/cuda-10.1.168-mrdepn/lib64 These variables can be added/edited in '/appl/soft/math/scipion/3.0.7/config/scipion.conf' On 29. Sep 2021, at 18.28, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Dear Maria, could you please 1) post here the output of "scipion3 config -p relion" 2) attach run.stdout and run.stderr files from the failed protocol Thank you. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 4:08 PM Anastasina, Maria <mar...@he...<mailto:mar...@he...>> wrote: > > Hello, > > All my recent Relion 3D classification jobs the I run in Scipion fail at CreateOutput step with the error message "Protocol failed: 'Class3D' object has no attribute ‘_rlnClassDistribution’”. > > Jobs that I ran earlier (e.g. 10 days ago) in identical conditions used to finish successfully. I’m not aware of any changes or updates that have been done at our HPC server or Scipion installation (we use Scipion 3.0.8). > > Do you know what could be the reason for this error? > > Best regards, > Maria > _______________________________________________ > scipion-users mailing list > sci...@li...<mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-30 18:54:49
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Hi, thank you for sending over the files from the original job. I'm afraid I will need the Runs/011346_ProtRelionClassify3D/extra/relion_it025_model.star as well. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Sep 30, 2021 at 5:25 PM Anastasina, Maria < mar...@he...> wrote: > Hi Grigory, > > Thank you for looking into my files. Yes, this job is a continuation of > another one where 25 iterations were completed, but CreateOutput step > failed with exactly the same error message. This is why I put 0 iterations > in the job, hoping that it will just manage to create the output (or was it > a wrong idea?). > > Since the original job with 25 iterations also filed, it seems that the > source of error is something else, or maybe was a problem with that > original job that migrated to the next one (sorry if it sounds confusing)?. > Just in case, I attach here .stderr and .stdout files form the original job > too. There all 25 iterations were completed, but the CreateOutput failed. > > Best, > Maria > > > > > > > On 30. Sep 2021, at 11.50, Grigory Sharov <sha...@gm...> > wrote: > > Hello Maria, > > srun `which relion_refine_mpi` --norm --scale --o > Runs/012188_ProtRelionClassify3D/extra/relion --oversampling 1 > --flatten_solvent --tau2_fudge 4.0 --iter 25 --pad 2 --skip_gridding > --healpix_order 4 --offset_range 5.0 --offset_step 2.0 --continue > Runs/011346_ProtRelionClassify3D/extra/relion_it025_optimiser.star > --dont_combine_weights_via_disc --pool 3 --gpu --j 4 > > You are running a job that will not do anything, continuing from iteration > 25 until 25. Did you put 0 in number of iterations in the protocol? > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Wed, Sep 29, 2021 at 6:07 PM Anastasina, Maria < > mar...@he...> wrote: > > Dear Grigory, > > Here they go > > Best, > Maria > > [masha@puhti-login2 ~]$ scipion3 config -p relion > Scipion v3.0.8 - Eugenius > Variables defined by plugin 'relion': > > RELION_HOME = /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.1 > RELION_CUDA_LIB = > /appl/spack/install-tree/gcc-8.3.0/cuda-10.1.168-mrdepn/lib64 > > These variables can be added/edited in > '/appl/soft/math/scipion/3.0.7/config/scipion.conf' > > > On 29. Sep 2021, at 18.28, Grigory Sharov <sha...@gm...> > wrote: > > Dear Maria, > > could you please > > 1) post here the output of "scipion3 config -p relion" > 2) attach run.stdout and run.stderr files from the failed protocol > > Thank you. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > e-mail: gs...@mr... > > > On Wed, Sep 29, 2021 at 4:08 PM Anastasina, Maria < > mar...@he...> wrote: > > > > Hello, > > > > All my recent Relion 3D classification jobs the I run in Scipion fail at > CreateOutput step with the error message "Protocol failed: 'Class3D' > object has no attribute ‘_rlnClassDistribution’”. > > > > Jobs that I ran earlier (e.g. 10 days ago) in identical conditions used > to finish successfully. I’m not aware of any changes or updates that have > been done at our HPC server or Scipion installation (we use Scipion 3.0.8). > > > > Do you know what could be the reason for this error? > > > > Best regards, > > Maria > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2021-09-30 16:21:29
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Carlos, there is a chance that it may work if they haven't changed the "interface". For that, I think is better to move this discussion offline to avoid spamming others, and come back with a final solution. I'll write you a private email. On 30/9/21 15:52, Grigory Sharov wrote: > Hi, > > As I said earlier, the sphire plugin does not support cryolo 1.8, you > cannot install or/and use it inside Scipion. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I > removed it using pip uninstall cryolo) and put it to work inside > Scipion? > I tried to no use GPUs on cryolo picking, but I obtained the same > error. > Thanks again for the help. > Best regards, Carlos. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 3:26:53 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD > using Cryolo > > Hi Carlos, > you are using NVIDIA GeForce RTX 3090 which is only supported by > cryolo 1.8. > > Have a look here: > https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 > <https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11> > > AFAIK, Scipion does not support this version yet. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > Thanks for all support. Cryolo training worked very well; > however, I'm facing some problems with cryolo picking. > I obtain this error: > /Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py > -c Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w > /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 > -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ > -o Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ > -t 0.300 -g 1 -nc 4 --otf' returned non-zero exit status 1/ > > When I execute in bash *conda activate cryolo-1.7.6 && which > cryolo_predict.py*, I obtain a normal response > //home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py/ > > I'm sorry, I thought that the problems were solved... > I attached the run.stderr and run.stdout files > Thanks again for the support. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 2:08:45 PM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Oh, that's great that it worked! > You are welcome! > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > Thanks so so much! > Cryolo is running now in Scipion. > Best regards, > Carlos. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 12:18:43 PM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Hi Carlos, > ok, can you run *pip uninstall cryolo* and then execute in > that order: > 1) *which cryolo_train.py * > 2)***conda activate**cryolo-1.7.6 && which cryolo_train.py* > > The first one should fail but the second one should show > /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear Grigory, > > When I run *conda activate* *cryolo-1.7.6 && which > cryolo_train.py* and *which cryolo_train.py *in bash I > receive as response: > //home/impmc/.local/bin/cryolo_train.py/ > > And when I go to this address, I can run all cryolo > python files normally. Best regards, Carlos. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 11:58:30 AM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Can you run *conda activate cryolo-1.7.6 && which > cryolo_train.py* ? > Can you also run *which cryolo_train.py *? (in case > you installed cryolo into conda base env) > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE > FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dears Grigory and Pablo, > > Sorry for the problems with conda; these things > are very recent to me; I'm still learning how to > deal with them. > And, thanks again for the messages and for the > support. > > About libcudnn.so.8; indeed there is no > libcudnn.so.8 installed in cryolo-1.7.6 > environment lib folder. There is only > libcudnn.so.7.1.2: > /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 > /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 > /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 > It is possible to change to libcudnn.so.8 inside > these folders? > > About conda; Yes, cryolo 1.8 are using conda from > eman... I installed miniconda and anaconda3; > however when I type 'which conda', I have as only > response the conda from eman. > Best regards, > Carlos. > > ------------------------------------------------------------------------ > *From: *"Pablo Conesa" <pc...@cn... > <mailto:pc...@cn...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Thursday, September 30, 2021 10:29:11 AM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > I agree with Grigory, using eman2 conda is not a > good practice. > > Probably he did not decided that but Scipion > installer used the available one, and probably > that one was eman2 one. > > If you want to undo this you will need to install > miniconda, and have it available instead of eman2 one. > > "which conda" will tell you the available one. > > > On 29/9/21 18:54, Grigory Sharov wrote: > > Thanks! In run.stderr you can see the reason > it has failed: > > 2021-09-30 02:14:42.492074: W > tensorflow/stream_executor/platform/default/dso_loader.cc:64] > Could not load dynamic library > 'libcudnn.so.8'; dlerror: libcudnn.so.8: > cannot open shared object file: No such file > or directory; LD_LIBRARY_PATH: > /usr/local/cuda/lib64::/home/impmc/scipion/software/lib > > For some reason it's looking for libcudnn.so.8 > but the cryolo package should have installed > libcudnn.so.7.1.2 for you. Can you check that > a) you do have libcudnn8 in cryolo-1.7.6 > environment lib folder? I dont know where is > your env is installed. You can activate conda > and "check conda list env" > b) /home/impmc/.local/bin/cryolo_train.py does > not look like a correct path for cryolo env. > The previous command should tell you where it > should be > > In general, my advice would be to not use > eman2 conda for anything except eman. You'd be > better off using a separate miniconda3 > installation. Which conda did you use for > cryolo 1.8? From eman? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 5:37 PM Carlos > HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear Grigory, > > The files that you requested are attached. > Thanks so much again > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" > <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 > 6:18:12 PM > *Subject: *Re: [scipion-users] Problems > with CONDA_ACTIVATION_CMD using Cryolo > > Hi, > The config files look ok. Could you attach > run.stderr and run.stdout for the failed > protocol? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 5:15 PM Carlos > HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear Grigory, > > Thank you so much, fixing this space > solved the problem with > cryolo_1.7.6_installing (shame on me > for this). > However, I tried to run the cryolo > training and I obtained the same > previous error: > > eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&& conda > activate cryolo-1.7.6 && > cryolo_train.py -c config.json -w 5 -g > 0 1 -nc 4 -e 10 --fine_tune > 00022: Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&& conda > activate cryolo-1.7.6 && > cryolo_train.py -c config.json -w 5 -g > 0 1 -nc 4 -e 10 --fine_tune' returned > non-zero exit status 1. > 00023: FAILED: cryoloModelingStep, > step 3, time 2021-09-30 02:14:42.822982 > > Bellow, it is my current scipion.conf file > [PYWORKFLOW] > SCIPION_DOMAIN = pwem > SCIPION_FONT_NAME = Helvetica > SCIPION_GUI_REFRESH_IN_THREAD = False > SCIPION_LOG = > ~/ScipionUserData/logs/scipion.log > SCIPION_LOGO = scipion_logo.gif > SCIPION_LOGS = ~/ScipionUserData/logs > SCIPION_NOTES_FILE = notes.txt > SCIPION_NOTIFY = True > SCIPION_PLUGIN_REPO_URL = > http://scipion.i2pc.es/getplugins/ > <http://scipion.i2pc.es/getplugins/> > SCIPION_SOFTWARE = > ${SCIPION_HOME}/software > SCIPION_SUPPORT_EMAIL = > sc...@cn... > <mailto:sc...@cn...> > SCIPION_TESTS = ${SCIPION_HOME}/data/tests > SCIPION_TESTS_CMD = scipion3 tests > SCIPION_TESTS_OUTPUT = > ~/ScipionUserData/Tests > SCIPION_TMP = ~/ScipionUserData/tmp > SCIPION_URL = > http://scipion.cnb.csic.es/downloads/scipion > <http://scipion.cnb.csic.es/downloads/scipion> > SCIPION_URL_SOFTWARE = > http://scipion.cnb.csic.es/downloads/scipion/software > <http://scipion.cnb.csic.es/downloads/scipion/software> > SCIPION_URL_TESTDATA = > http://scipion.cnb.csic.es/downloads/scipion/data/tests > <http://scipion.cnb.csic.es/downloads/scipion/data/tests> > SCIPION_USER_DATA = ~/ScipionUserData > WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] > CONDA_ACTIVATION_CMD = eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)" > > [PLUGINS] > CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 > CISTEM_HOME = > %(EM_ROOT)s/cistem-1.0.0-beta > CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 > CRYOLO_ENV_ACTIVATION = conda activate > cryolo-1.7.6 > CRYOLO_ENV_ACTIVATION_CPU = conda > activate cryolo-1.7.6 > CRYOLO_GENERIC_DENOISED_MODEL = > %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > CRYOLO_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > CRYOLO_NS_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > CRYOSPARC_HOME = /home/impmc/ > CRYO_PROJECTS_DIR = scipion_projects > CTFFIND4_HOME = > %(EM_ROOT)s/ctffind4-4.1.14 > EMAN2SCRATCHDIR = /tmp > EMAN2_HOME = %(EM_ROOT)s/eman-2.91 > EM_ROOT = software/em > JANNI_GENERIC_MODEL = > %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 > MOTIONCOR2_CUDA_LIB = > /usr/local/cuda/lib64 > MOTIONCOR2_HOME = > %(EM_ROOT)s/motioncor2-1.4.0 > PHENIX_HOME = %(EM_ROOT)s/phenix- > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_HOME = %(EM_ROOT)s/relion-3.1.2 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > > > Thanks again. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" > <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 > 5:51:06 PM > *Subject: *Re: [scipion-users] > Problems with CONDA_ACTIVATION_CMD > using Cryolo > > Hello Carlos, > > to start, you are missing a space > between eval and the rest in: > CONDA_ACTIVATION_CMD = eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 4:47 PM Carlos > HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear Grigory, > > Thanks for the message. The all > output is bellow: > > Scipion v3.0.9 - Eugenius > Building scipion-em-sphire ... > /home/impmc/scipion/.scipion3/bin/python > -m pip install > scipion-em-sphire==3.0.7 > Looking in indexes: > https://pypi.org/simple > <https://pypi.org/simple>, > https://pypi.ngc.nvidia.com > <https://pypi.ngc.nvidia.com> > Requirement already satisfied: > scipion-em-sphire==3.0.7 in > ./scipion/.scipion3/lib/python3.8/site-packages > (3.0.7) > Requirement already satisfied: > scipion-em in > ./scipion/.scipion3/lib/python3.8/site-packages > (from scipion-em-sphire==3.0.7) > (3.0.13) > Requirement already satisfied: > biopython==1.76 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-em->scipion-em-sphire==3.0.7) > (1.76) > Requirement already satisfied: > tifffile in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-em->scipion-em-sphire==3.0.7) > (2021.4.8) > Requirement already satisfied: > scipion-pyworkflow>=3.0.15 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-em->scipion-em-sphire==3.0.7) > (3.0.17) > Requirement already satisfied: > numpy in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) > (1.18.4) > Requirement already satisfied: > mpi4py<=3.0.3 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (3.0.3) > Requirement already satisfied: > configparser<=5.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (5.0.0) > Requirement already satisfied: > psutil<=5.8.0 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (5.7.0) > Requirement already satisfied: > pillow<=8.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (7.1.2) > Requirement already satisfied: > bibtexparser<=1.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.2.0) > Requirement already satisfied: > requests<=2.25.1 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.25.1) > Requirement already satisfied: > matplotlib==3.2.2 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (3.2.2) > Requirement already satisfied: > tkcolorpicker<=2.1.3 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.1.3) > Requirement already satisfied: > cycler>=0.10 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.10.0) > Requirement already satisfied: > python-dateutil>=2.1 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.8.1) > Requirement already satisfied: > pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 > in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.4.7) > Requirement already satisfied: > kiwisolver>=1.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.3.1) > Requirement already satisfied: > future>=0.16.0 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.18.2) > Requirement already satisfied: six > in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.16.0) > Requirement already satisfied: > certifi>=2017.4.17 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2020.12.5) > Requirement already satisfied: > urllib3<1.27,>=1.21.1 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.26.4) > Requirement already satisfied: > chardet<5,>=3.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (4.0.0) > Requirement already satisfied: > idna<3,>=2.5 in > ./scipion/.scipion3/lib/python3.8/site-packages > (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.10) > Done (0.84 seconds) > Building cryolo-1.7.6 ... > Skipping command: wget -nv -c -O > /home/impmc/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz> > mv -v > /home/impmc/scipion/software/em/void.tgz.part > /home/impmc/scipion/software/em/void.tgz > All targets exist. > Skipping command: mkdir > /home/impmc/scipion/software/em/cryolo-1.7.6 > All targets exist. > Skipping command: tar -xf > void.tgz -C cryolo-1.7.6 > All targets exist. > cd > /home/impmc/scipion/software/em/cryolo-1.7.6 > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> > /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c > anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 > intel-openmp==2019.4 &&conda > activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed > /bin/sh: 1: evalexport > CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' > export _CE_M='' > export _CE_CONDA='' > export > CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' > > # Copyright (C) 2012 Anaconda, Inc > # SPDX-License-Identifier: > BSD-3-Clause > > __add_sys_prefix_to_path() { > # In dev-mode CONDA_EXE is > python.exe and on Windows > # it is in a different > relative location to condabin. > if [ -n "${_CE_CONDA}" ] && [ > -n "${WINDIR+x}" ]; then > SYSP=$(\dirname "${CONDA_EXE}") > else > SYSP=$(\dirname "${CONDA_EXE}") > SYSP=$(\dirname "${SYSP}") > fi > > if [ -n "${WINDIR+x}" ]; then > PATH="${SYSP}/bin:${PATH}" > PATH="${SYSP}/Scripts:${PATH}" > PATH="${SYSP}/Library/bin:${PATH}" > PATH="${SYSP}/Library/usr/bin:${PATH}" > PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" > PATH="${SYSP}:${PATH}" > else > PATH="${SYSP}/bin:${PATH}" > fi > \export PATH > } > > __conda_exe() ( > __add_sys_prefix_to_path > "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" > ) > > __conda_hashr() { > if [ -n "${ZSH_VERSION:+x}" ]; > then > \rehash > elif [ -n "${POSH_VERSION:+x}" > ]; then > : # pass > else > \hash -r > fi > } > > __conda_activate() { > if [ -n > "${CONDA_PS1_BACKUP:+x}" ]; then > # Handle transition from > shell activated with conda <= 4.3 > to a subsequent activation > # after conda updated to > >= 4.4. See issue #6173. > PS1="$CONDA_PS1_BACKUP" > \unset CONDA_PS1_BACKUP > fi > \local ask_conda > ask_conda="$(PS1="${PS1:-}" > __conda_exe shell.posix "$@")" || > \return > \eval "$ask_conda" > __conda_hashr > } > > __conda_reactivate() { > \local ask_conda > ask_conda="$(PS1="${PS1:-}" > __conda_exe shell.posix > reactivate)" || \return > \eval "$ask_conda" > __conda_hashr > } > > conda() { > \local cmd="${1-__missing__}" > case "$cmd" in > activate|deactivate) > __conda_activate "$@" > ;; > install|update|upgrade|remove|uninstall) > __conda_exe "$@" || \return > __conda_reactivate > ;; > *) > __conda_exe "$@" > ;; > esac > } > > if [ -z "${CONDA_SHLVL+x}" ]; then > \export CONDA_SHLVL=0 > # In dev-mode CONDA_EXE is > python.exe and on Windows > # it is in a different > relative location to condabin. > if [ -n "${_CE_CONDA:+x}" ] && > [ -n "${WINDIR+x}" ]; then > PATH="$(\dirname > "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" > else > PATH="$(\dirname "$(\dirname > "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" > fi > \export PATH > > # We're not allowing PS1 to be > unbound. It must at least be set. > # However, we're not exporting > it, which can cause problems when > starting a second shell > # via a first shell (i.e. > starting zsh from bash). > if [ -z "${PS1+x}" ]; then > PS1= > fi > fi > > conda activate base: not found > Traceback (most recent call last): > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', > numberProcessor]}) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' > not built (after " > AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> > /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c > anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 > intel-openmp==2019.4 &&conda > activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed') > Error at main: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> > /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c > anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 > intel-openmp==2019.4 &&conda > activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed') > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" > <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" > <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, > 2021 5:33:09 PM > *Subject: *Re: [scipion-users] > Problems with CONDA_ACTIVATION_CMD > using Cryolo > > Dear Carlos, > given the fact that the > installation has failed, could you > attach all output after "scipion3 > installp -p > scipion-em-sphire" command? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 4:03 PM > Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear all, > > I'm facing some problems using > cryolo training at Scipion. > I found the following error: > *Protocol failed: Command ' > source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& > conda activate cryolo-1.7.6 && > cryolo_train.py -c config.json > -w 5 -g 0 -nc 4 -e 10 > --fine_tune' returned non-zero > exit status 127. > * > * > * > I saw some discussion about > that at Scipion lists, but I'm > still little lost in how to > fix it. > In my scipion.conf file, I > inserted > /CONDA_ACTIVATION_CMD = source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh > /// > or even > CONDA_ACTIVATION_CMD = > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)"// > (I saw these pathways in my > bash.rc) > > Moreover, when I try to > install cryolo using command > line (scipion3 installp -p > scipion-em-sphire), the > following error apears: > *AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda > create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda > python=3.6 pyqt=5 cudnn=7.1.2 > numpy==1.14.5 cython > wxPython==4.0.4 > intel-openmp==2019.4 &&conda > activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 > &&touch cryolo_1.7.6_installed')* > > I am not sure if these errors > are related and hinder > performing cryolo in Scipion. > I have conda installed in the > computer and I'm able to use > cryolo 1.8 outside from > Scipion in the same computer > (using /source activate cryolo > /command). > > Anyone know what I'm doing > wrong? Thanks in advance, Carlos. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > -- > Pablo Conesa - *Madrid Scipion > <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sour... [truncated message content] |
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From: Jose M. de la R. T. <del...@gm...> - 2021-09-30 15:59:07
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Hi Caroline, I think the problem with 3090 cards is more specific to cryolo and topaz due to the cuda version requirements and also the dependency with tensorflow library. Other plugins should work. Best, José Miguel On Thu, Sep 30, 2021, 10:54 AM Caroline Ingeborg Jegerschöld <ci...@kt...> wrote: > Dear all, > > Is it so that for all plugins-versions within scipion3 one has to check > what hardware that is both necessary and possible to use? Before buying > e.g. such a computer with a card like nvidia 3090? Or just live with not > using some software. > > I was looking for some hardware suggestions for scipion3 but might not be > possible to do to accommodate all plugins? > > Best regards, > > Caroline > > > > *From:* Carlos HENRIQUE FERNANDES [mailto: > car...@so...] > *Sent:* Thursday, 30 September 2021 16:17 > *To:* scipion-users <sci...@li...> > *Subject:* Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Dear Grigory, > > Yes, you indeed said that, I realized now. > Thus, we have two problems, scipion does not support cryolo 1.8 and my > NVIDIA GeForce is not supported by cryolo 1.7. > So, as I understand, we can not solve this for now. > Thanks again. > Best regards, > Carlos. > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 3:52:48 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hi, > > As I said earlier, the sphire plugin does not support cryolo 1.8, you > cannot install or/and use it inside Scipion. > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it > using pip uninstall cryolo) and put it to work inside Scipion? > I tried to no use GPUs on cryolo picking, but I obtained the same error. > Thanks again for the help. > Best regards, Carlos. > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 3:26:53 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hi Carlos, > > you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo > 1.8. > > > > Have a look here: > https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 > > > > AFAIK, Scipion does not support this version yet. > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > Thanks for all support. Cryolo training worked very well; however, I'm > facing some problems with cryolo picking. > I obtain this error: > *Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c > Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w > /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 > -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o > Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc > 4 --otf' returned non-zero exit status 1* > > When I execute in bash *conda activate cryolo-1.7.6 && which > cryolo_predict.py*, I obtain a normal response > > */home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py* > > > > I'm sorry, I thought that the problems were solved... > > I attached the run.stderr and run.stdout files > > Thanks again for the support. > > > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 2:08:45 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Oh, that's great that it worked! > > You are welcome! > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > Thanks so so much! > Cryolo is running now in Scipion. > Best regards, > Carlos. > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 12:18:43 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hi Carlos, > > ok, can you run *pip uninstall cryolo* and then execute in that order: > > 1) *which cryolo_train.py * > > 2)* conda activate* *cryolo-1.7.6 && which cryolo_train.py* > > > > The first one should fail but the second one should > show /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > When I run *conda activate* *cryolo-1.7.6 && which cryolo_train.py* and *which > cryolo_train.py *in bash I receive as response: > */home/impmc/.local/bin/cryolo_train.py* > > And when I go to this address, I can run all cryolo python files normally. > Best regards, > Carlos. > > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 11:58:30 AM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Can you run *conda activate cryolo-1.7.6 && which cryolo_train.py* ? > > Can you also run *which cryolo_train.py *? (in case you installed cryolo > into conda base env) > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dears Grigory and Pablo, > > Sorry for the problems with conda; these things are very recent to me; I'm > still learning how to deal with them. > And, thanks again for the messages and for the support. > > About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in > cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: > /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 > /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 > > /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 > It is possible to change to libcudnn.so.8 inside these folders? > > About conda; Yes, cryolo 1.8 are using conda from eman... I installed > miniconda and anaconda3; however when I type 'which conda', I have as only > response the conda from eman. > Best regards, > Carlos. > ------------------------------ > > *From: *"Pablo Conesa" <pc...@cn...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 10:29:11 AM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > I agree with Grigory, using eman2 conda is not a good practice. > > Probably he did not decided that but Scipion installer used the available > one, and probably that one was eman2 one. > > If you want to undo this you will need to install miniconda, and have it > available instead of eman2 one. > > "which conda" will tell you the available one. > > > > On 29/9/21 18:54, Grigory Sharov wrote: > > Thanks! In run.stderr you can see the reason it has failed: > > > > 2021-09-30 02:14:42.492074: W > tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not > load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open > shared object file: No such file or directory; LD_LIBRARY_PATH: > /usr/local/cuda/lib64::/home/impmc/scipion/software/lib > > > > For some reason it's looking for libcudnn.so.8 but the cryolo package > should have installed libcudnn.so.7.1.2 for you. Can you check that > > a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I > dont know where is your env is installed. You can activate conda and "check > conda list env" > > b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct > path for cryolo env. The previous command should tell you where it should be > > > > In general, my advice would be to not use eman2 conda for anything except > eman. You'd be better off using a separate miniconda3 installation. Which > conda did you use for cryolo 1.8? From eman? > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > > > The files that you requested are attached. > > Thanks so much again > > > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 6:18:12 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hi, > > The config files look ok. Could you attach run.stderr and run.stdout for > the failed protocol? > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > Thank you so much, fixing this space solved the problem with > cryolo_1.7.6_installing (shame on me for this). > However, I tried to run the cryolo training and I obtained the same > previous error: > > eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json > -w 5 -g 0 1 -nc 4 -e 10 --fine_tune > 00022: Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json > -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. > 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 > 02:14:42.822982 > > Bellow, it is my current scipion.conf file > [PYWORKFLOW] > SCIPION_DOMAIN = pwem > SCIPION_FONT_NAME = Helvetica > SCIPION_GUI_REFRESH_IN_THREAD = False > SCIPION_LOG = ~/ScipionUserData/logs/scipion.log > SCIPION_LOGO = scipion_logo.gif > SCIPION_LOGS = ~/ScipionUserData/logs > SCIPION_NOTES_FILE = notes.txt > SCIPION_NOTIFY = True > SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ > SCIPION_SOFTWARE = ${SCIPION_HOME}/software > SCIPION_SUPPORT_EMAIL = sc...@cn... > SCIPION_TESTS = ${SCIPION_HOME}/data/tests > SCIPION_TESTS_CMD = scipion3 tests > SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests > SCIPION_TMP = ~/ScipionUserData/tmp > SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion > SCIPION_URL_SOFTWARE = > http://scipion.cnb.csic.es/downloads/scipion/software > SCIPION_URL_TESTDATA = > http://scipion.cnb.csic.es/downloads/scipion/data/tests > SCIPION_USER_DATA = ~/ScipionUserData > WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] > CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)" > > [PLUGINS] > CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 > CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta > CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 > CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 > CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 > CRYOLO_GENERIC_DENOISED_MODEL = > %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > CRYOLO_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > CRYOLO_NS_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > CRYOSPARC_HOME = /home/impmc/ > CRYO_PROJECTS_DIR = scipion_projects > CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 > EMAN2SCRATCHDIR = /tmp > EMAN2_HOME = %(EM_ROOT)s/eman-2.91 > EM_ROOT = software/em > JANNI_GENERIC_MODEL = > %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 > MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 > MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 > PHENIX_HOME = %(EM_ROOT)s/phenix- > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_HOME = %(EM_ROOT)s/relion-3.1.2 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > > > Thanks again. > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 5:51:06 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hello Carlos, > > > > to start, you are missing a space between eval and the rest in: > > CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > Thanks for the message. The all output is bellow: > > Scipion v3.0.9 - Eugenius > Building scipion-em-sphire ... > /home/impmc/scipion/.scipion3/bin/python -m pip install > scipion-em-sphire==3.0.7 > Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com > Requirement already satisfied: scipion-em-sphire==3.0.7 in > ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) > Requirement already satisfied: scipion-em in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em-sphire==3.0.7) (3.0.13) > Requirement already satisfied: biopython==1.76 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (1.76) > Requirement already satisfied: tifffile in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) > Requirement already satisfied: scipion-pyworkflow>=3.0.15 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (3.0.17) > Requirement already satisfied: numpy in > ./scipion/.scipion3/lib/python3.8/site-packages (from > biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) > Requirement already satisfied: mpi4py<=3.0.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) > Requirement already satisfied: configparser<=5.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) > Requirement already satisfied: psutil<=5.8.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) > Requirement already satisfied: pillow<=8.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) > Requirement already satisfied: requests<=2.25.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) > Requirement already satisfied: matplotlib==3.2.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) > Requirement already satisfied: tkcolorpicker<=2.1.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) > Requirement already satisfied: cycler>=0.10 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.10.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.8.1) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.4.7) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.3.1) > Requirement already satisfied: future>=0.16.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.18.2) > Requirement already satisfied: six in > ./scipion/.scipion3/lib/python3.8/site-packages (from > cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.16.0) > Requirement already satisfied: certifi>=2017.4.17 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2020.12.5) > Requirement already satisfied: urllib3<1.27,>=1.21.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.26.4) > Requirement already satisfied: chardet<5,>=3.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (4.0.0) > Requirement already satisfied: idna<3,>=2.5 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.10) > Done (0.84 seconds) > Building cryolo-1.7.6 ... > Skipping command: wget -nv -c -O > /home/impmc/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > mv -v /home/impmc/scipion/software/em/void.tgz.part > /home/impmc/scipion/software/em/void.tgz > All targets exist. > Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 > All targets exist. > Skipping command: tar -xf void.tgz -C cryolo-1.7.6 > All targets exist. > cd /home/impmc/scipion/software/em/cryolo-1.7.6 > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda > python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 > intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install > cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed > /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' > export _CE_M='' > export _CE_CONDA='' > export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' > > # Copyright (C) 2012 Anaconda, Inc > # SPDX-License-Identifier: BSD-3-Clause > > __add_sys_prefix_to_path() { > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then > SYSP=$(\dirname "${CONDA_EXE}") > else > SYSP=$(\dirname "${CONDA_EXE}") > SYSP=$(\dirname "${SYSP}") > fi > > if [ -n "${WINDIR+x}" ]; then > PATH="${SYSP}/bin:${PATH}" > PATH="${SYSP}/Scripts:${PATH}" > PATH="${SYSP}/Library/bin:${PATH}" > PATH="${SYSP}/Library/usr/bin:${PATH}" > PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" > PATH="${SYSP}:${PATH}" > else > PATH="${SYSP}/bin:${PATH}" > fi > \export PATH > } > > __conda_exe() ( > __add_sys_prefix_to_path > "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" > ) > > __conda_hashr() { > if [ -n "${ZSH_VERSION:+x}" ]; then > \rehash > elif [ -n "${POSH_VERSION:+x}" ]; then > : # pass > else > \hash -r > fi > } > > __conda_activate() { > if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then > # Handle transition from shell activated with conda <= 4.3 to a > subsequent activation > # after conda updated to >= 4.4. See issue #6173. > PS1="$CONDA_PS1_BACKUP" > \unset CONDA_PS1_BACKUP > fi > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return > \eval "$ask_conda" > __conda_hashr > } > > __conda_reactivate() { > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || > \return > \eval "$ask_conda" > __conda_hashr > } > > conda() { > \local cmd="${1-__missing__}" > case "$cmd" in > activate|deactivate) > __conda_activate "$@" > ;; > install|update|upgrade|remove|uninstall) > __conda_exe "$@" || \return > __conda_reactivate > ;; > *) > __conda_exe "$@" > ;; > esac > } > > if [ -z "${CONDA_SHLVL+x}" ]; then > \export CONDA_SHLVL=0 > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then > PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" > else > PATH="$(\dirname "$(\dirname > "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" > fi > \export PATH > > # We're not allowing PS1 to be unbound. It must at least be set. > # However, we're not exporting it, which can cause problems when > starting a second shell > # via a first shell (i.e. starting zsh from bash). > if [ -z "${PS1+x}" ]; then > PS1= > fi > fi > > conda activate base: not found > Traceback (most recent call last): > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > Error at main: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 5:33:09 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Dear Carlos, > > given the fact that the installation has failed, could you attach all > output after "scipion3 installp -p scipion-em-sphire" command? > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear all, > > > > I'm facing some problems using cryolo training at Scipion. > > I found the following error: > > *Protocol failed: Command ' source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate > cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 > --fine_tune' returned non-zero exit status 127.* > > > > I saw some discussion about that at Scipion lists, but I'm still little > lost in how to fix it. > > In my scipion.conf file, I inserted > *CONDA_ACTIVATION_CMD = source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * > > or even > > CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > > (I saw these pathways in my bash.rc) > > > > Moreover, when I try to install cryolo using command line (scipion3 > installp -p scipion-em-sphire), the following error apears: > > *AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 > numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate > cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed')* > > I am not sure if these errors are related and hinder performing cryolo in > Scipion. > > I have conda installed in the computer and I'm able to use cryolo 1.8 > outside from Scipion in the same computer (using *source activate cryolo * > command). > > Anyone know what I'm doing wrong? > > Thanks in advance, > > Carlos. > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Grigory S. <sha...@gm...> - 2021-09-30 15:10:06
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Dear Caroline, You are correct. Since Scipion is just a framework and does not do any image processing itself, you'd have to check compatibility for any software you want to use. In this particular case, I'm not the sphire plugin maintainer so I cannot estimate when cryolo 1.8beta will be supported there. I assume since 3090 cards are still quite rare, so there's not much demand for the latest unreleased cryolo version being available in Scipion... but I'm sure someone will add it soon! Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Sep 30, 2021 at 3:54 PM Caroline Ingeborg Jegerschöld <ci...@kt...> wrote: > Dear all, > > Is it so that for all plugins-versions within scipion3 one has to check > what hardware that is both necessary and possible to use? Before buying > e.g. such a computer with a card like nvidia 3090? Or just live with not > using some software. > > I was looking for some hardware suggestions for scipion3 but might not be > possible to do to accommodate all plugins? > > Best regards, > > Caroline > > > > *From:* Carlos HENRIQUE FERNANDES [mailto: > car...@so...] > *Sent:* Thursday, 30 September 2021 16:17 > *To:* scipion-users <sci...@li...> > *Subject:* Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Dear Grigory, > > Yes, you indeed said that, I realized now. > Thus, we have two problems, scipion does not support cryolo 1.8 and my > NVIDIA GeForce is not supported by cryolo 1.7. > So, as I understand, we can not solve this for now. > Thanks again. > Best regards, > Carlos. > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 3:52:48 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hi, > > As I said earlier, the sphire plugin does not support cryolo 1.8, you > cannot install or/and use it inside Scipion. > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it > using pip uninstall cryolo) and put it to work inside Scipion? > I tried to no use GPUs on cryolo picking, but I obtained the same error. > Thanks again for the help. > Best regards, Carlos. > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 3:26:53 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hi Carlos, > > you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo > 1.8. > > > > Have a look here: > https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 > > > > AFAIK, Scipion does not support this version yet. > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > Thanks for all support. Cryolo training worked very well; however, I'm > facing some problems with cryolo picking. > I obtain this error: > *Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c > Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w > /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 > -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o > Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc > 4 --otf' returned non-zero exit status 1* > > When I execute in bash *conda activate cryolo-1.7.6 && which > cryolo_predict.py*, I obtain a normal response > > */home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py* > > > > I'm sorry, I thought that the problems were solved... > > I attached the run.stderr and run.stdout files > > Thanks again for the support. > > > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 2:08:45 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Oh, that's great that it worked! > > You are welcome! > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > Thanks so so much! > Cryolo is running now in Scipion. > Best regards, > Carlos. > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 12:18:43 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hi Carlos, > > ok, can you run *pip uninstall cryolo* and then execute in that order: > > 1) *which cryolo_train.py * > > 2)* conda activate* *cryolo-1.7.6 && which cryolo_train.py* > > > > The first one should fail but the second one should > show /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > When I run *conda activate* *cryolo-1.7.6 && which cryolo_train.py* and *which > cryolo_train.py *in bash I receive as response: > */home/impmc/.local/bin/cryolo_train.py* > > And when I go to this address, I can run all cryolo python files normally. > Best regards, > Carlos. > > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 11:58:30 AM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Can you run *conda activate cryolo-1.7.6 && which cryolo_train.py* ? > > Can you also run *which cryolo_train.py *? (in case you installed cryolo > into conda base env) > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dears Grigory and Pablo, > > Sorry for the problems with conda; these things are very recent to me; I'm > still learning how to deal with them. > And, thanks again for the messages and for the support. > > About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in > cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: > /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 > /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 > > /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 > It is possible to change to libcudnn.so.8 inside these folders? > > About conda; Yes, cryolo 1.8 are using conda from eman... I installed > miniconda and anaconda3; however when I type 'which conda', I have as only > response the conda from eman. > Best regards, > Carlos. > ------------------------------ > > *From: *"Pablo Conesa" <pc...@cn...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 10:29:11 AM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > I agree with Grigory, using eman2 conda is not a good practice. > > Probably he did not decided that but Scipion installer used the available > one, and probably that one was eman2 one. > > If you want to undo this you will need to install miniconda, and have it > available instead of eman2 one. > > "which conda" will tell you the available one. > > > > On 29/9/21 18:54, Grigory Sharov wrote: > > Thanks! In run.stderr you can see the reason it has failed: > > > > 2021-09-30 02:14:42.492074: W > tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not > load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open > shared object file: No such file or directory; LD_LIBRARY_PATH: > /usr/local/cuda/lib64::/home/impmc/scipion/software/lib > > > > For some reason it's looking for libcudnn.so.8 but the cryolo package > should have installed libcudnn.so.7.1.2 for you. Can you check that > > a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I > dont know where is your env is installed. You can activate conda and "check > conda list env" > > b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct > path for cryolo env. The previous command should tell you where it should be > > > > In general, my advice would be to not use eman2 conda for anything except > eman. You'd be better off using a separate miniconda3 installation. Which > conda did you use for cryolo 1.8? From eman? > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > > > The files that you requested are attached. > > Thanks so much again > > > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 6:18:12 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hi, > > The config files look ok. Could you attach run.stderr and run.stdout for > the failed protocol? > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > Thank you so much, fixing this space solved the problem with > cryolo_1.7.6_installing (shame on me for this). > However, I tried to run the cryolo training and I obtained the same > previous error: > > eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json > -w 5 -g 0 1 -nc 4 -e 10 --fine_tune > 00022: Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json > -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. > 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 > 02:14:42.822982 > > Bellow, it is my current scipion.conf file > [PYWORKFLOW] > SCIPION_DOMAIN = pwem > SCIPION_FONT_NAME = Helvetica > SCIPION_GUI_REFRESH_IN_THREAD = False > SCIPION_LOG = ~/ScipionUserData/logs/scipion.log > SCIPION_LOGO = scipion_logo.gif > SCIPION_LOGS = ~/ScipionUserData/logs > SCIPION_NOTES_FILE = notes.txt > SCIPION_NOTIFY = True > SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ > SCIPION_SOFTWARE = ${SCIPION_HOME}/software > SCIPION_SUPPORT_EMAIL = sc...@cn... > SCIPION_TESTS = ${SCIPION_HOME}/data/tests > SCIPION_TESTS_CMD = scipion3 tests > SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests > SCIPION_TMP = ~/ScipionUserData/tmp > SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion > SCIPION_URL_SOFTWARE = > http://scipion.cnb.csic.es/downloads/scipion/software > SCIPION_URL_TESTDATA = > http://scipion.cnb.csic.es/downloads/scipion/data/tests > SCIPION_USER_DATA = ~/ScipionUserData > WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] > CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)" > > [PLUGINS] > CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 > CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta > CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 > CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 > CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 > CRYOLO_GENERIC_DENOISED_MODEL = > %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > CRYOLO_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > CRYOLO_NS_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > CRYOSPARC_HOME = /home/impmc/ > CRYO_PROJECTS_DIR = scipion_projects > CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 > EMAN2SCRATCHDIR = /tmp > EMAN2_HOME = %(EM_ROOT)s/eman-2.91 > EM_ROOT = software/em > JANNI_GENERIC_MODEL = > %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 > MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 > MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 > PHENIX_HOME = %(EM_ROOT)s/phenix- > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_HOME = %(EM_ROOT)s/relion-3.1.2 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > > > Thanks again. > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 5:51:06 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Hello Carlos, > > > > to start, you are missing a space between eval and the rest in: > > CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear Grigory, > > Thanks for the message. The all output is bellow: > > Scipion v3.0.9 - Eugenius > Building scipion-em-sphire ... > /home/impmc/scipion/.scipion3/bin/python -m pip install > scipion-em-sphire==3.0.7 > Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com > Requirement already satisfied: scipion-em-sphire==3.0.7 in > ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) > Requirement already satisfied: scipion-em in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em-sphire==3.0.7) (3.0.13) > Requirement already satisfied: biopython==1.76 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (1.76) > Requirement already satisfied: tifffile in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) > Requirement already satisfied: scipion-pyworkflow>=3.0.15 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (3.0.17) > Requirement already satisfied: numpy in > ./scipion/.scipion3/lib/python3.8/site-packages (from > biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) > Requirement already satisfied: mpi4py<=3.0.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) > Requirement already satisfied: configparser<=5.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) > Requirement already satisfied: psutil<=5.8.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) > Requirement already satisfied: pillow<=8.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) > Requirement already satisfied: requests<=2.25.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) > Requirement already satisfied: matplotlib==3.2.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) > Requirement already satisfied: tkcolorpicker<=2.1.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) > Requirement already satisfied: cycler>=0.10 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.10.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.8.1) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.4.7) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.3.1) > Requirement already satisfied: future>=0.16.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.18.2) > Requirement already satisfied: six in > ./scipion/.scipion3/lib/python3.8/site-packages (from > cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.16.0) > Requirement already satisfied: certifi>=2017.4.17 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2020.12.5) > Requirement already satisfied: urllib3<1.27,>=1.21.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.26.4) > Requirement already satisfied: chardet<5,>=3.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (4.0.0) > Requirement already satisfied: idna<3,>=2.5 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.10) > Done (0.84 seconds) > Building cryolo-1.7.6 ... > Skipping command: wget -nv -c -O > /home/impmc/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > mv -v /home/impmc/scipion/software/em/void.tgz.part > /home/impmc/scipion/software/em/void.tgz > All targets exist. > Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 > All targets exist. > Skipping command: tar -xf void.tgz -C cryolo-1.7.6 > All targets exist. > cd /home/impmc/scipion/software/em/cryolo-1.7.6 > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda > python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 > intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install > cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed > /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' > export _CE_M='' > export _CE_CONDA='' > export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' > > # Copyright (C) 2012 Anaconda, Inc > # SPDX-License-Identifier: BSD-3-Clause > > __add_sys_prefix_to_path() { > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then > SYSP=$(\dirname "${CONDA_EXE}") > else > SYSP=$(\dirname "${CONDA_EXE}") > SYSP=$(\dirname "${SYSP}") > fi > > if [ -n "${WINDIR+x}" ]; then > PATH="${SYSP}/bin:${PATH}" > PATH="${SYSP}/Scripts:${PATH}" > PATH="${SYSP}/Library/bin:${PATH}" > PATH="${SYSP}/Library/usr/bin:${PATH}" > PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" > PATH="${SYSP}:${PATH}" > else > PATH="${SYSP}/bin:${PATH}" > fi > \export PATH > } > > __conda_exe() ( > __add_sys_prefix_to_path > "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" > ) > > __conda_hashr() { > if [ -n "${ZSH_VERSION:+x}" ]; then > \rehash > elif [ -n "${POSH_VERSION:+x}" ]; then > : # pass > else > \hash -r > fi > } > > __conda_activate() { > if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then > # Handle transition from shell activated with conda <= 4.3 to a > subsequent activation > # after conda updated to >= 4.4. See issue #6173. > PS1="$CONDA_PS1_BACKUP" > \unset CONDA_PS1_BACKUP > fi > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return > \eval "$ask_conda" > __conda_hashr > } > > __conda_reactivate() { > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || > \return > \eval "$ask_conda" > __conda_hashr > } > > conda() { > \local cmd="${1-__missing__}" > case "$cmd" in > activate|deactivate) > __conda_activate "$@" > ;; > install|update|upgrade|remove|uninstall) > __conda_exe "$@" || \return > __conda_reactivate > ;; > *) > __conda_exe "$@" > ;; > esac > } > > if [ -z "${CONDA_SHLVL+x}" ]; then > \export CONDA_SHLVL=0 > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then > PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" > else > PATH="$(\dirname "$(\dirname > "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" > fi > \export PATH > > # We're not allowing PS1 to be unbound. It must at least be set. > # However, we're not exporting it, which can cause problems when > starting a second shell > # via a first shell (i.e. starting zsh from bash). > if [ -z "${PS1+x}" ]; then > PS1= > fi > fi > > conda activate base: not found > Traceback (most recent call last): > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > Error at main: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > ------------------------------ > > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 5:33:09 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > > > Dear Carlos, > > given the fact that the installation has failed, could you attach all > output after "scipion3 installp -p scipion-em-sphire" command? > > > Best regards, > Grigory > > > > > -------------------------------------------------------------------------------- > > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > > e-mail: gs...@mr... > > > > > > On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > > Dear all, > > > > I'm facing some problems using cryolo training at Scipion. > > I found the following error: > > *Protocol failed: Command ' source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate > cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 > --fine_tune' returned non-zero exit status 127.* > > > > I saw some discussion about that at Scipion lists, but I'm still little > lost in how to fix it. > > In my scipion.conf file, I inserted > *CONDA_ACTIVATION_CMD = source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * > > or even > > CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > > (I saw these pathways in my bash.rc) > > > > Moreover, when I try to install cryolo using command line (scipion3 > installp -p scipion-em-sphire), the following error apears: > > *AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 > numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate > cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed')* > > I am not sure if these errors are related and hinder performing cryolo in > Scipion. > > I have conda installed in the computer and I'm able to use cryolo 1.8 > outside from Scipion in the same computer (using *source activate cryolo * > command). > > Anyone know what I'm doing wrong? > > Thanks in advance, > > Carlos. > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Caroline I. J. <ci...@kt...> - 2021-09-30 14:54:29
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Dear all, Is it so that for all plugins-versions within scipion3 one has to check what hardware that is both necessary and possible to use? Before buying e.g. such a computer with a card like nvidia 3090? Or just live with not using some software. I was looking for some hardware suggestions for scipion3 but might not be possible to do to accommodate all plugins? Best regards, Caroline From: Carlos HENRIQUE FERNANDES [mailto:car...@so...] Sent: Thursday, 30 September 2021 16:17 To: scipion-users <sci...@li...> Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Dear Grigory, Yes, you indeed said that, I realized now. Thus, we have two problems, scipion does not support cryolo 1.8 and my NVIDIA GeForce is not supported by cryolo 1.7. So, as I understand, we can not solve this for now. Thanks again. Best regards, Carlos. ________________________________ From: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Thursday, September 30, 2021 3:52:48 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi, As I said earlier, the sphire plugin does not support cryolo 1.8, you cannot install or/and use it inside Scipion. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dear Grigory, So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it using pip uninstall cryolo) and put it to work inside Scipion? I tried to no use GPUs on cryolo picking, but I obtained the same error. Thanks again for the help. Best regards, Carlos. ________________________________ From: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Thursday, September 30, 2021 3:26:53 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi Carlos, you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo 1.8. Have a look here: https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 AFAIK, Scipion does not support this version yet. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dear Grigory, Thanks for all support. Cryolo training worked very well; however, I'm facing some problems with cryolo picking. I obtain this error: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc 4 --otf' returned non-zero exit status 1 When I execute in bash conda activate cryolo-1.7.6 && which cryolo_predict.py, I obtain a normal response /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py I'm sorry, I thought that the problems were solved... I attached the run.stderr and run.stdout files Thanks again for the support. ________________________________ From: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Thursday, September 30, 2021 2:08:45 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Oh, that's great that it worked! You are welcome! Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dear Grigory, Thanks so so much! Cryolo is running now in Scipion. Best regards, Carlos. ________________________________ From: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Thursday, September 30, 2021 12:18:43 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi Carlos, ok, can you run pip uninstall cryolo and then execute in that order: 1) which cryolo_train.py 2) conda activate cryolo-1.7.6 && which cryolo_train.py The first one should fail but the second one should show /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dear Grigory, When I run conda activate cryolo-1.7.6 && which cryolo_train.py and which cryolo_train.py in bash I receive as response: /home/impmc/.local/bin/cryolo_train.py And when I go to this address, I can run all cryolo python files normally. Best regards, Carlos. ________________________________ From: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Thursday, September 30, 2021 11:58:30 AM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Can you run conda activate cryolo-1.7.6 && which cryolo_train.py ? Can you also run which cryolo_train.py ? (in case you installed cryolo into conda base env) Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dears Grigory and Pablo, Sorry for the problems with conda; these things are very recent to me; I'm still learning how to deal with them. And, thanks again for the messages and for the support. About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 It is possible to change to libcudnn.so.8 inside these folders? About conda; Yes, cryolo 1.8 are using conda from eman... I installed miniconda and anaconda3; however when I type 'which conda', I have as only response the conda from eman. Best regards, Carlos. ________________________________ From: "Pablo Conesa" <pc...@cn...<mailto:pc...@cn...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Thursday, September 30, 2021 10:29:11 AM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo I agree with Grigory, using eman2 conda is not a good practice. Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one. If you want to undo this you will need to install miniconda, and have it available instead of eman2 one. "which conda" will tell you the available one. On 29/9/21 18:54, Grigory Sharov wrote: Thanks! In run.stderr you can see the reason it has failed: 2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env" b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dear Grigory, The files that you requested are attached. Thanks so much again ________________________________ From: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Wednesday, September 29, 2021 6:18:12 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi, The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dear Grigory, Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this). However, I tried to run the cryolo training and I obtained the same previous error: eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune 00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982 Bellow, it is my current scipion.conf file [PYWORKFLOW] SCIPION_DOMAIN = pwem SCIPION_FONT_NAME = Helvetica SCIPION_GUI_REFRESH_IN_THREAD = False SCIPION_LOG = ~/ScipionUserData/logs/scipion.log SCIPION_LOGO = scipion_logo.gif SCIPION_LOGS = ~/ScipionUserData/logs SCIPION_NOTES_FILE = notes.txt SCIPION_NOTIFY = True SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ SCIPION_SOFTWARE = ${SCIPION_HOME}/software SCIPION_SUPPORT_EMAIL = sc...@cn...<mailto:sc...@cn...> SCIPION_TESTS = ${SCIPION_HOME}/data/tests SCIPION_TESTS_CMD = scipion3 tests SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests SCIPION_TMP = ~/ScipionUserData/tmp SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion SCIPION_URL_SOFTWARE = http://scipion.cnb.csic.es/downloads/scipion/software SCIPION_URL_TESTDATA = http://scipion.cnb.csic.es/downloads/scipion/data/tests SCIPION_USER_DATA = ~/ScipionUserData WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" [PLUGINS] CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 CRYOSPARC_HOME = /home/impmc/ CRYO_PROJECTS_DIR = scipion_projects CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 EMAN2SCRATCHDIR = /tmp EMAN2_HOME = %(EM_ROOT)s/eman-2.91 EM_ROOT = software/em JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 PHENIX_HOME = %(EM_ROOT)s/phenix- RELION_CUDA_LIB = /usr/local/cuda/lib64 RELION_HOME = %(EM_ROOT)s/relion-3.1.2 XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src XMIPP_HOME = %(EM_ROOT)s/xmipp Thanks again. ________________________________ From: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Wednesday, September 29, 2021 5:51:06 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hello Carlos, to start, you are missing a space between eval and the rest in: CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dear Grigory, Thanks for the message. The all output is bellow: Scipion v3.0.9 - Eugenius Building scipion-em-sphire ... /home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7 Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13) Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76) Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17) Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1) Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2) Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0) Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10) Done (0.84 seconds) Building cryolo-1.7.6 ... Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz All targets exist. Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 All targets exist. Skipping command: tar -xf void.tgz -C cryolo-1.7.6 All targets exist. cd /home/impmc/scipion/software/em/cryolo-1.7.6 eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' export _CE_M='' export _CE_CONDA='' export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' # Copyright (C) 2012 Anaconda, Inc # SPDX-License-Identifier: BSD-3-Clause __add_sys_prefix_to_path() { # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then SYSP=$(\dirname "${CONDA_EXE}") else SYSP=$(\dirname "${CONDA_EXE}") SYSP=$(\dirname "${SYSP}") fi if [ -n "${WINDIR+x}" ]; then PATH="${SYSP}/bin:${PATH}" PATH="${SYSP}/Scripts:${PATH}" PATH="${SYSP}/Library/bin:${PATH}" PATH="${SYSP}/Library/usr/bin:${PATH}" PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" PATH="${SYSP}:${PATH}" else PATH="${SYSP}/bin:${PATH}" fi \export PATH } __conda_exe() ( __add_sys_prefix_to_path "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" ) __conda_hashr() { if [ -n "${ZSH_VERSION:+x}" ]; then \rehash elif [ -n "${POSH_VERSION:+x}" ]; then : # pass else \hash -r fi } __conda_activate() { if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then # Handle transition from shell activated with conda <= 4.3 to a subsequent activation # after conda updated to >= 4.4. See issue #6173. PS1="$CONDA_PS1_BACKUP" \unset CONDA_PS1_BACKUP fi \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return \eval "$ask_conda" __conda_hashr } __conda_reactivate() { \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return \eval "$ask_conda" __conda_hashr } conda() { \local cmd="${1-__missing__}" case "$cmd" in activate|deactivate) __conda_activate "$@" ;; install|update|upgrade|remove|uninstall) __conda_exe "$@" || \return __conda_reactivate ;; *) __conda_exe "$@" ;; esac } if [ -z "${CONDA_SHLVL+x}" ]; then \export CONDA_SHLVL=0 # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" else PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" fi \export PATH # We're not allowing PS1 to be unbound. It must at least be set. # However, we're not exporting it, which can cause problems when starting a second shell # via a first shell (i.e. starting zsh from bash). if [ -z "${PS1+x}" ]; then PS1= fi fi conda activate base: not found Traceback (most recent call last): File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') ________________________________ From: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> To: "scipion-users" <sci...@li...<mailto:sci...@li...>> Sent: Wednesday, September 29, 2021 5:33:09 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Dear Carlos, given the fact that the installation has failed, could you attach all output after "scipion3 installp -p scipion-em-sphire" command? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES <car...@so...<mailto:car...@so...>> wrote: Dear all, I'm facing some problems using cryolo training at Scipion. I found the following error: Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127. I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it. In my scipion.conf file, I inserted CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh or even CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" (I saw these pathways in my bash.rc) Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears: AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') I am not sure if these errors are related and hinder performing cryolo in Scipion. I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command). Anyone know what I'm doing wrong? Thanks in advance, Carlos. _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos H. F. <car...@so...> - 2021-09-30 14:26:46
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Dear Grigory, Thanks again for all your help. I wish you all the best. Best regards, Carlos. From: "Grigory Sharov" <sha...@gm...> To: "scipion-users" <sci...@li...> Sent: Thursday, September 30, 2021 4:18:28 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Yes you are correct. You can only use cryolo 1.8 outside Scipion. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 3:17 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: Dear Grigory, Yes, you indeed said that, I realized now. Thus, we have two problems, scipion does not support cryolo 1.8 and my NVIDIA GeForce is not supported by cryolo 1.7. So, as I understand, we can not solve this for now. Thanks again. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 3:52:48 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi, As I said earlier, the sphire plugin does not support cryolo 1.8, you cannot install or/and use it inside Scipion. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it using pip uninstall cryolo) and put it to work inside Scipion? I tried to no use GPUs on cryolo picking, but I obtained the same error. Thanks again for the help. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 3:26:53 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi Carlos, you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo 1.8. Have a look here: [ https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 | https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 ] AFAIK, Scipion does not support this version yet. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks for all support. Cryolo training worked very well; however, I'm facing some problems with cryolo picking. I obtain this error: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc 4 --otf' returned non-zero exit status 1 When I execute in bash conda activate cryolo-1.7.6 && which cryolo_predict.py , I obtain a normal response /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py I'm sorry, I thought that the problems were solved... I attached the run.stderr and run.stdout files Thanks again for the support. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 2:08:45 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Oh, that's great that it worked! You are welcome! Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks so so much! Cryolo is running now in Scipion. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 12:18:43 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi Carlos, ok, can you run pip uninstall cryolo and then execute in that order: 1) which cryolo_train.py 2) conda activate cryolo-1.7.6 && which cryolo_train.py The first one should fail but the second one should show /home/impmc/eman2-sphire- sparx/envs/cryolo-1.7.6/bin/... Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, When I run conda activate cryolo-1.7.6 && which cryolo_train.py and which cryolo_train.py in bash I receive as response: /home/impmc/.local/bin/cryolo_train.py And when I go to this address, I can run all cryolo python files normally. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 11:58:30 AM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Can you run conda activate cryolo-1.7.6 && which cryolo_train.py ? Can you also run which cryolo_train.py ? (in case you installed cryolo into conda base env) Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dears Grigory and Pablo, Sorry for the problems with conda; these things are very recent to me; I'm still learning how to deal with them. And, thanks again for the messages and for the support. About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 It is possible to change to libcudnn.so.8 inside these folders? About conda; Yes, cryolo 1.8 are using conda from eman... I installed miniconda and anaconda3; however when I type 'which conda', I have as only response the conda from eman. Best regards, Carlos. From: "Pablo Conesa" < [ mailto:pc...@cn... | pc...@cn... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 10:29:11 AM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo I agree with Grigory, using eman2 conda is not a good practice. Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one. If you want to undo this you will need to install miniconda, and have it available instead of eman2 one. "which conda" will tell you the available one. On 29/9/21 18:54, Grigory Sharov wrote: BQ_BEGIN Thanks! In run.stderr you can see the reason it has failed: 2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env" b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, The files that you requested are attached. Thanks so much again From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 6:18:12 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi, The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this). However, I tried to run the cryolo training and I obtained the same previous error: eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune 00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982 Bellow, it is my current scipion.conf file [PYWORKFLOW] SCIPION_DOMAIN = pwem SCIPION_FONT_NAME = Helvetica SCIPION_GUI_REFRESH_IN_THREAD = False SCIPION_LOG = ~/ScipionUserData/logs/scipion.log SCIPION_LOGO = scipion_logo.gif SCIPION_LOGS = ~/ScipionUserData/logs SCIPION_NOTES_FILE = notes.txt SCIPION_NOTIFY = True SCIPION_PLUGIN_REPO_URL = [ http://scipion.i2pc.es/getplugins/ | http://scipion.i2pc.es/getplugins/ ] SCIPION_SOFTWARE = ${SCIPION_HOME}/software SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ] SCIPION_TESTS = ${SCIPION_HOME}/data/tests SCIPION_TESTS_CMD = scipion3 tests SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests SCIPION_TMP = ~/ScipionUserData/tmp SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ] SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ] SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ] SCIPION_USER_DATA = ~/ScipionUserData WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" [PLUGINS] CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 CRYOSPARC_HOME = /home/impmc/ CRYO_PROJECTS_DIR = scipion_projects CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 EMAN2SCRATCHDIR = /tmp EMAN2_HOME = %(EM_ROOT)s/eman-2.91 EM_ROOT = software/em JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 PHENIX_HOME = %(EM_ROOT)s/phenix- RELION_CUDA_LIB = /usr/local/cuda/lib64 RELION_HOME = %(EM_ROOT)s/relion-3.1.2 XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src XMIPP_HOME = %(EM_ROOT)s/xmipp Thanks again. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:51:06 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hello Carlos, to start, you are missing a space between eval and the rest in: CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)" Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks for the message. The all output is bellow: Scipion v3.0.9 - Eugenius Building scipion-em-sphire ... /home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7 Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ] Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13) Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76) Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17) Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1) Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2) Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0) Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10) Done (0.84 seconds) Building cryolo-1.7.6 ... Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ] mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz All targets exist. Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 All targets exist. Skipping command: tar -xf void.tgz -C cryolo-1.7.6 All targets exist. cd /home/impmc/scipion/software/em/cryolo-1.7.6 eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' export _CE_M='' export _CE_CONDA='' export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' # Copyright (C) 2012 Anaconda, Inc # SPDX-License-Identifier: BSD-3-Clause __add_sys_prefix_to_path() { # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then SYSP=$(\dirname "${CONDA_EXE}") else SYSP=$(\dirname "${CONDA_EXE}") SYSP=$(\dirname "${SYSP}") fi if [ -n "${WINDIR+x}" ]; then PATH="${SYSP}/bin:${PATH}" PATH="${SYSP}/Scripts:${PATH}" PATH="${SYSP}/Library/bin:${PATH}" PATH="${SYSP}/Library/usr/bin:${PATH}" PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" PATH="${SYSP}:${PATH}" else PATH="${SYSP}/bin:${PATH}" fi \export PATH } __conda_exe() ( __add_sys_prefix_to_path "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" ) __conda_hashr() { if [ -n "${ZSH_VERSION:+x}" ]; then \rehash elif [ -n "${POSH_VERSION:+x}" ]; then : # pass else \hash -r fi } __conda_activate() { if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then # Handle transition from shell activated with conda <= 4.3 to a subsequent activation # after conda updated to >= 4.4. See issue #6173. PS1="$CONDA_PS1_BACKUP" \unset CONDA_PS1_BACKUP fi \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return \eval "$ask_conda" __conda_hashr } __conda_reactivate() { \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return \eval "$ask_conda" __conda_hashr } conda() { \local cmd="${1-__missing__}" case "$cmd" in activate|deactivate) __conda_activate "$@" ;; install|update|upgrade|remove|uninstall) __conda_exe "$@" || \return __conda_reactivate ;; *) __conda_exe "$@" ;; esac } if [ -z "${CONDA_SHLVL+x}" ]; then \export CONDA_SHLVL=0 # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" else PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" fi \export PATH # We're not allowing PS1 to be unbound. It must at least be set. # However, we're not exporting it, which can cause problems when starting a second shell # via a first shell (i.e. starting zsh from bash). if [ -z "${PS1+x}" ]; then PS1= fi fi conda activate base: not found Traceback (most recent call last): File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:33:09 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Dear Carlos, given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear all, I'm facing some problems using cryolo training at Scipion. I found the following error: Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127. I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it. In my scipion.conf file, I inserted CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh or even CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" (I saw these pathways in my bash.rc) Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears: AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') I am not sure if these errors are related and hinder performing cryolo in Scipion. I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command). Anyone know what I'm doing wrong? Thanks in advance, Carlos. _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END -- Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-30 14:20:03
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Yes you are correct. You can only use cryolo 1.8 outside Scipion. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Sep 30, 2021 at 3:17 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > Yes, you indeed said that, I realized now. > Thus, we have two problems, scipion does not support cryolo 1.8 and my > NVIDIA GeForce is not supported by cryolo 1.7. > So, as I understand, we can not solve this for now. > Thanks again. > Best regards, > Carlos. > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 3:52:48 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Hi, > As I said earlier, the sphire plugin does not support cryolo 1.8, you > cannot install or/and use it inside Scipion. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear Grigory, >> >> So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it >> using pip uninstall cryolo) and put it to work inside Scipion? >> I tried to no use GPUs on cryolo picking, but I obtained the same error. >> Thanks again for the help. >> Best regards, Carlos. >> >> ------------------------------ >> *From: *"Grigory Sharov" <sha...@gm...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Thursday, September 30, 2021 3:26:53 PM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> Hi Carlos, >> you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo >> 1.8. >> >> Have a look here: >> https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 >> >> AFAIK, Scipion does not support this version yet. >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dear Grigory, >>> >>> Thanks for all support. Cryolo training worked very well; however, I'm >>> facing some problems with cryolo picking. >>> I obtain this error: >>> *Protocol failed: Command ' eval >>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c >>> Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w >>> /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 >>> -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o >>> Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc >>> 4 --otf' returned non-zero exit status 1* >>> >>> When I execute in bash *conda activate cryolo-1.7.6 && which >>> cryolo_predict.py*, I obtain a normal response >>> */home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py* >>> >>> I'm sorry, I thought that the problems were solved... >>> I attached the run.stderr and run.stdout files >>> Thanks again for the support. >>> >>> ------------------------------ >>> *From: *"Grigory Sharov" <sha...@gm...> >>> *To: *"scipion-users" <sci...@li...> >>> *Sent: *Thursday, September 30, 2021 2:08:45 PM >>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >>> Cryolo >>> >>> Oh, that's great that it worked! >>> You are welcome! >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < >>> car...@so...> wrote: >>> >>>> Dear Grigory, >>>> >>>> Thanks so so much! >>>> Cryolo is running now in Scipion. >>>> Best regards, >>>> Carlos. >>>> >>>> ------------------------------ >>>> *From: *"Grigory Sharov" <sha...@gm...> >>>> *To: *"scipion-users" <sci...@li...> >>>> *Sent: *Thursday, September 30, 2021 12:18:43 PM >>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>> using Cryolo >>>> >>>> Hi Carlos, >>>> ok, can you run *pip uninstall cryolo* and then execute in that order: >>>> 1) *which cryolo_train.py * >>>> 2) *conda activate* *cryolo-1.7.6 && which cryolo_train.py* >>>> >>>> The first one should fail but the second one should show >>>> /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... >>>> >>>> Best regards, >>>> Grigory >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>> e-mail: gs...@mr... >>>> >>>> >>>> On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < >>>> car...@so...> wrote: >>>> >>>>> Dear Grigory, >>>>> >>>>> When I run *conda activate* *cryolo-1.7.6 && which cryolo_train.py* >>>>> and *which cryolo_train.py *in bash I receive as response: >>>>> */home/impmc/.local/bin/cryolo_train.py* >>>>> >>>>> And when I go to this address, I can run all cryolo python files normally. >>>>> Best regards, >>>>> Carlos. >>>>> >>>>> ------------------------------ >>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>> *To: *"scipion-users" <sci...@li...> >>>>> *Sent: *Thursday, September 30, 2021 11:58:30 AM >>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>> using Cryolo >>>>> >>>>> Can you run *conda activate cryolo-1.7.6 && which cryolo_train.py* ? >>>>> Can you also run *which cryolo_train.py *? (in case you installed >>>>> cryolo into conda base env) >>>>> >>>>> Best regards, >>>>> Grigory >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> Grigory Sharov, Ph.D. >>>>> >>>>> MRC Laboratory of Molecular Biology, >>>>> Francis Crick Avenue, >>>>> Cambridge Biomedical Campus, >>>>> Cambridge CB2 0QH, UK. >>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>> e-mail: gs...@mr... >>>>> >>>>> >>>>> On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < >>>>> car...@so...> wrote: >>>>> >>>>>> Dears Grigory and Pablo, >>>>>> >>>>>> Sorry for the problems with conda; these things are very recent to >>>>>> me; I'm still learning how to deal with them. >>>>>> And, thanks again for the messages and for the support. >>>>>> >>>>>> About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in >>>>>> cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: >>>>>> /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 >>>>>> >>>>>> /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 >>>>>> >>>>>> /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 >>>>>> It is possible to change to libcudnn.so.8 inside these folders? >>>>>> >>>>>> About conda; Yes, cryolo 1.8 are using conda from eman... I installed >>>>>> miniconda and anaconda3; however when I type 'which conda', I have as only >>>>>> response the conda from eman. >>>>>> Best regards, >>>>>> Carlos. >>>>>> >>>>>> ------------------------------ >>>>>> *From: *"Pablo Conesa" <pc...@cn...> >>>>>> *To: *"scipion-users" <sci...@li...> >>>>>> *Sent: *Thursday, September 30, 2021 10:29:11 AM >>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>> using Cryolo >>>>>> >>>>>> I agree with Grigory, using eman2 conda is not a good practice. >>>>>> >>>>>> Probably he did not decided that but Scipion installer used the >>>>>> available one, and probably that one was eman2 one. >>>>>> >>>>>> If you want to undo this you will need to install miniconda, and have >>>>>> it available instead of eman2 one. >>>>>> >>>>>> "which conda" will tell you the available one. >>>>>> >>>>>> >>>>>> On 29/9/21 18:54, Grigory Sharov wrote: >>>>>> >>>>>> Thanks! In run.stderr you can see the reason it has failed: >>>>>> >>>>>> 2021-09-30 02:14:42.492074: W >>>>>> tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not >>>>>> load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open >>>>>> shared object file: No such file or directory; LD_LIBRARY_PATH: >>>>>> /usr/local/cuda/lib64::/home/impmc/scipion/software/lib >>>>>> >>>>>> For some reason it's looking for libcudnn.so.8 but the cryolo package >>>>>> should have installed libcudnn.so.7.1.2 for you. Can you check that >>>>>> a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I >>>>>> dont know where is your env is installed. You can activate conda and "check >>>>>> conda list env" >>>>>> b) /home/impmc/.local/bin/cryolo_train.py does not look like a >>>>>> correct path for cryolo env. The previous command should tell you where it >>>>>> should be >>>>>> >>>>>> In general, my advice would be to not use eman2 conda for anything >>>>>> except eman. You'd be better off using a separate miniconda3 installation. >>>>>> Which conda did you use for cryolo 1.8? From eman? >>>>>> >>>>>> Best regards, >>>>>> Grigory >>>>>> >>>>>> >>>>>> -------------------------------------------------------------------------------- >>>>>> Grigory Sharov, Ph.D. >>>>>> >>>>>> MRC Laboratory of Molecular Biology, >>>>>> Francis Crick Avenue, >>>>>> Cambridge Biomedical Campus, >>>>>> Cambridge CB2 0QH, UK. >>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>> e-mail: gs...@mr... >>>>>> >>>>>> >>>>>> On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < >>>>>> car...@so...> wrote: >>>>>> >>>>>>> Dear Grigory, >>>>>>> >>>>>>> The files that you requested are attached. >>>>>>> Thanks so much again >>>>>>> >>>>>>> ------------------------------ >>>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>>> *To: *"scipion-users" <sci...@li...> >>>>>>> *Sent: *Wednesday, September 29, 2021 6:18:12 PM >>>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>>> using Cryolo >>>>>>> >>>>>>> Hi, >>>>>>> The config files look ok. Could you attach run.stderr and run.stdout >>>>>>> for the failed protocol? >>>>>>> >>>>>>> Best regards, >>>>>>> Grigory >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------------- >>>>>>> Grigory Sharov, Ph.D. >>>>>>> >>>>>>> MRC Laboratory of Molecular Biology, >>>>>>> Francis Crick Avenue, >>>>>>> Cambridge Biomedical Campus, >>>>>>> Cambridge CB2 0QH, UK. >>>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>>> e-mail: gs...@mr... >>>>>>> >>>>>>> >>>>>>> On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < >>>>>>> car...@so...> wrote: >>>>>>> >>>>>>>> Dear Grigory, >>>>>>>> >>>>>>>> Thank you so much, fixing this space solved the problem with >>>>>>>> cryolo_1.7.6_installing (shame on me for this). >>>>>>>> However, I tried to run the cryolo training and I obtained the same >>>>>>>> previous error: >>>>>>>> >>>>>>>> eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>>>>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune >>>>>>>> 00022: Protocol failed: Command ' eval >>>>>>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>>>>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. >>>>>>>> 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 >>>>>>>> 02:14:42.822982 >>>>>>>> >>>>>>>> Bellow, it is my current scipion.conf file >>>>>>>> [PYWORKFLOW] >>>>>>>> SCIPION_DOMAIN = pwem >>>>>>>> SCIPION_FONT_NAME = Helvetica >>>>>>>> SCIPION_GUI_REFRESH_IN_THREAD = False >>>>>>>> SCIPION_LOG = ~/ScipionUserData/logs/scipion.log >>>>>>>> SCIPION_LOGO = scipion_logo.gif >>>>>>>> SCIPION_LOGS = ~/ScipionUserData/logs >>>>>>>> SCIPION_NOTES_FILE = notes.txt >>>>>>>> SCIPION_NOTIFY = True >>>>>>>> SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ >>>>>>>> SCIPION_SOFTWARE = ${SCIPION_HOME}/software >>>>>>>> SCIPION_SUPPORT_EMAIL = sc...@cn... >>>>>>>> SCIPION_TESTS = ${SCIPION_HOME}/data/tests >>>>>>>> SCIPION_TESTS_CMD = scipion3 tests >>>>>>>> SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests >>>>>>>> SCIPION_TMP = ~/ScipionUserData/tmp >>>>>>>> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion >>>>>>>> SCIPION_URL_SOFTWARE = >>>>>>>> http://scipion.cnb.csic.es/downloads/scipion/software >>>>>>>> SCIPION_URL_TESTDATA = >>>>>>>> http://scipion.cnb.csic.es/downloads/scipion/data/tests >>>>>>>> SCIPION_USER_DATA = ~/ScipionUserData >>>>>>>> WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] >>>>>>>> CONDA_ACTIVATION_CMD = eval >>>>>>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" >>>>>>>> >>>>>>>> [PLUGINS] >>>>>>>> CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 >>>>>>>> CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 >>>>>>>> CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta >>>>>>>> CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 >>>>>>>> CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 >>>>>>>> CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 >>>>>>>> CRYOLO_GENERIC_DENOISED_MODEL = >>>>>>>> %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 >>>>>>>> CRYOLO_GENERIC_MODEL = >>>>>>>> %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 >>>>>>>> CRYOLO_NS_GENERIC_MODEL = >>>>>>>> %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 >>>>>>>> CRYOSPARC_HOME = /home/impmc/ >>>>>>>> CRYO_PROJECTS_DIR = scipion_projects >>>>>>>> CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 >>>>>>>> EMAN2SCRATCHDIR = /tmp >>>>>>>> EMAN2_HOME = %(EM_ROOT)s/eman-2.91 >>>>>>>> EM_ROOT = software/em >>>>>>>> JANNI_GENERIC_MODEL = >>>>>>>> %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 >>>>>>>> MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 >>>>>>>> MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 >>>>>>>> MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 >>>>>>>> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 >>>>>>>> PHENIX_HOME = %(EM_ROOT)s/phenix- >>>>>>>> RELION_CUDA_LIB = /usr/local/cuda/lib64 >>>>>>>> RELION_HOME = %(EM_ROOT)s/relion-3.1.2 >>>>>>>> XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src >>>>>>>> XMIPP_HOME = %(EM_ROOT)s/xmipp >>>>>>>> >>>>>>>> >>>>>>>> Thanks again. >>>>>>>> >>>>>>>> ------------------------------ >>>>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>>>> *To: *"scipion-users" <sci...@li...> >>>>>>>> *Sent: *Wednesday, September 29, 2021 5:51:06 PM >>>>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>>>> using Cryolo >>>>>>>> >>>>>>>> Hello Carlos, >>>>>>>> >>>>>>>> to start, you are missing a space between eval and the rest in: >>>>>>>> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>>>> shell.bash hook)" >>>>>>>> >>>>>>>> Best regards, >>>>>>>> Grigory >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------------- >>>>>>>> Grigory Sharov, Ph.D. >>>>>>>> >>>>>>>> MRC Laboratory of Molecular Biology, >>>>>>>> Francis Crick Avenue, >>>>>>>> Cambridge Biomedical Campus, >>>>>>>> Cambridge CB2 0QH, UK. >>>>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>>>> e-mail: gs...@mr... >>>>>>>> >>>>>>>> >>>>>>>> On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < >>>>>>>> car...@so...> wrote: >>>>>>>> >>>>>>>>> Dear Grigory, >>>>>>>>> >>>>>>>>> Thanks for the message. The all output is bellow: >>>>>>>>> >>>>>>>>> Scipion v3.0.9 - Eugenius >>>>>>>>> Building scipion-em-sphire ... >>>>>>>>> /home/impmc/scipion/.scipion3/bin/python -m pip install >>>>>>>>> scipion-em-sphire==3.0.7 >>>>>>>>> Looking in indexes: https://pypi.org/simple, >>>>>>>>> https://pypi.ngc.nvidia.com >>>>>>>>> Requirement already satisfied: scipion-em-sphire==3.0.7 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >>>>>>>>> Requirement already satisfied: scipion-em in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-em-sphire==3.0.7) (3.0.13) >>>>>>>>> Requirement already satisfied: biopython==1.76 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-em->scipion-em-sphire==3.0.7) (1.76) >>>>>>>>> Requirement already satisfied: tifffile in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >>>>>>>>> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >>>>>>>>> Requirement already satisfied: numpy in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >>>>>>>>> Requirement already satisfied: mpi4py<=3.0.3 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >>>>>>>>> Requirement already satisfied: configparser<=5.0.2 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >>>>>>>>> Requirement already satisfied: psutil<=5.8.0 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >>>>>>>>> Requirement already satisfied: pillow<=8.2.0 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >>>>>>>>> Requirement already satisfied: bibtexparser<=1.2.0 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >>>>>>>>> Requirement already satisfied: requests<=2.25.1 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >>>>>>>>> Requirement already satisfied: matplotlib==3.2.2 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >>>>>>>>> Requirement already satisfied: tkcolorpicker<=2.1.3 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >>>>>>>>> Requirement already satisfied: cycler>=0.10 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (0.10.0) >>>>>>>>> Requirement already satisfied: python-dateutil>=2.1 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (2.8.1) >>>>>>>>> Requirement already satisfied: >>>>>>>>> pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (2.4.7) >>>>>>>>> Requirement already satisfied: kiwisolver>=1.0.1 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (1.3.1) >>>>>>>>> Requirement already satisfied: future>=0.16.0 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (0.18.2) >>>>>>>>> Requirement already satisfied: six in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (1.16.0) >>>>>>>>> Requirement already satisfied: certifi>=2017.4.17 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (2020.12.5) >>>>>>>>> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (1.26.4) >>>>>>>>> Requirement already satisfied: chardet<5,>=3.0.2 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (4.0.0) >>>>>>>>> Requirement already satisfied: idna<3,>=2.5 in >>>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>>> (2.10) >>>>>>>>> Done (0.84 seconds) >>>>>>>>> Building cryolo-1.7.6 ... >>>>>>>>> Skipping command: wget -nv -c -O >>>>>>>>> /home/impmc/scipion/software/em/void.tgz.part >>>>>>>>> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >>>>>>>>> mv -v /home/impmc/scipion/software/em/void.tgz.part >>>>>>>>> /home/impmc/scipion/software/em/void.tgz >>>>>>>>> All targets exist. >>>>>>>>> Skipping command: mkdir >>>>>>>>> /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>>>>>> All targets exist. >>>>>>>>> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >>>>>>>>> All targets exist. >>>>>>>>> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>>>>> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >>>>>>>>> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >>>>>>>>> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >>>>>>>>> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >>>>>>>>> /bin/sh: 1: evalexport >>>>>>>>> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >>>>>>>>> export _CE_M='' >>>>>>>>> export _CE_CONDA='' >>>>>>>>> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >>>>>>>>> >>>>>>>>> # Copyright (C) 2012 Anaconda, Inc >>>>>>>>> # SPDX-License-Identifier: BSD-3-Clause >>>>>>>>> >>>>>>>>> __add_sys_prefix_to_path() { >>>>>>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>>>>>> # it is in a different relative location to condabin. >>>>>>>>> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >>>>>>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>>>>>> else >>>>>>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>>>>>> SYSP=$(\dirname "${SYSP}") >>>>>>>>> fi >>>>>>>>> >>>>>>>>> if [ -n "${WINDIR+x}" ]; then >>>>>>>>> PATH="${SYSP}/bin:${PATH}" >>>>>>>>> PATH="${SYSP}/Scripts:${PATH}" >>>>>>>>> PATH="${SYSP}/Library/bin:${PATH}" >>>>>>>>> PATH="${SYSP}/Library/usr/bin:${PATH}" >>>>>>>>> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >>>>>>>>> PATH="${SYSP}:${PATH}" >>>>>>>>> else >>>>>>>>> PATH="${SYSP}/bin:${PATH}" >>>>>>>>> fi >>>>>>>>> \export PATH >>>>>>>>> } >>>>>>>>> >>>>>>>>> __conda_exe() ( >>>>>>>>> __add_sys_prefix_to_path >>>>>>>>> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >>>>>>>>> ) >>>>>>>>> >>>>>>>>> __conda_hashr() { >>>>>>>>> if [ -n "${ZSH_VERSION:+x}" ]; then >>>>>>>>> \rehash >>>>>>>>> elif [ -n "${POSH_VERSION:+x}" ]; then >>>>>>>>> : # pass >>>>>>>>> else >>>>>>>>> \hash -r >>>>>>>>> fi >>>>>>>>> } >>>>>>>>> >>>>>>>>> __conda_activate() { >>>>>>>>> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >>>>>>>>> # Handle transition from shell activated with conda <= 4.3 >>>>>>>>> to a subsequent activation >>>>>>>>> # after conda updated to >= 4.4. See issue #6173. >>>>>>>>> PS1="$CONDA_PS1_BACKUP" >>>>>>>>> \unset CONDA_PS1_BACKUP >>>>>>>>> fi >>>>>>>>> \local ask_conda >>>>>>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || >>>>>>>>> \return >>>>>>>>> \eval "$ask_conda" >>>>>>>>> __conda_hashr >>>>>>>>> } >>>>>>>>> >>>>>>>>> __conda_reactivate() { >>>>>>>>> \local ask_conda >>>>>>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix >>>>>>>>> reactivate)" || \return >>>>>>>>> \eval "$ask_conda" >>>>>>>>> __conda_hashr >>>>>>>>> } >>>>>>>>> >>>>>>>>> conda() { >>>>>>>>> \local cmd="${1-__missing__}" >>>>>>>>> case "$cmd" in >>>>>>>>> activate|deactivate) >>>>>>>>> __conda_activate "$@" >>>>>>>>> ;; >>>>>>>>> install|update|upgrade|remove|uninstall) >>>>>>>>> __conda_exe "$@" || \return >>>>>>>>> __conda_reactivate >>>>>>>>> ;; >>>>>>>>> *) >>>>>>>>> __conda_exe "$@" >>>>>>>>> ;; >>>>>>>>> esac >>>>>>>>> } >>>>>>>>> >>>>>>>>> if [ -z "${CONDA_SHLVL+x}" ]; then >>>>>>>>> \export CONDA_SHLVL=0 >>>>>>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>>>>>> # it is in a different relative location to condabin. >>>>>>>>> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >>>>>>>>> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >>>>>>>>> else >>>>>>>>> PATH="$(\dirname "$(\dirname >>>>>>>>> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >>>>>>>>> fi >>>>>>>>> \export PATH >>>>>>>>> >>>>>>>>> # We're not allowing PS1 to be unbound. It must at least be >>>>>>>>> set. >>>>>>>>> # However, we're not exporting it, which can cause problems >>>>>>>>> when starting a second shell >>>>>>>>> # via a first shell (i.e. starting zsh from bash). >>>>>>>>> if [ -z "${PS1+x}" ]; then >>>>>>>>> PS1= >>>>>>>>> fi >>>>>>>>> fi >>>>>>>>> >>>>>>>>> conda activate base: not found >>>>>>>>> Traceback (most recent call last): >>>>>>>>> File >>>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>>>>>> line 470, in <module> >>>>>>>>> main() >>>>>>>>> File >>>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>>>>>> line 293, in main >>>>>>>>> installPluginMethods() >>>>>>>>> File >>>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>>>>>>>> line 232, in installPluginMethods >>>>>>>>> plugin.installBin({'args': ['-j', numberProcessor]}) >>>>>>>>> File >>>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>>>>>>>> line 166, in installBin >>>>>>>>> environment.execute() >>>>>>>>> File >>>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>>>> line 748, in execute >>>>>>>>> self._executeTargets(targetList) >>>>>>>>> File >>>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>>>> line 690, in _executeTargets >>>>>>>>> tgt.execute() >>>>>>>>> File >>>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>>>> line 221, in execute >>>>>>>>> command.execute() >>>>>>>>> File >>>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>>>> line 161, in execute >>>>>>>>> assert glob(t), ("target '%s' not built (after " >>>>>>>>> AssertionError: target >>>>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>>>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>>>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>>>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>>>>>> Error at main: target >>>>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>>>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>>>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>>>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>>>>>> >>>>>>>>> ------------------------------ >>>>>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>>>>> *To: *"scipion-users" <sci...@li...> >>>>>>>>> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >>>>>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>>>>> using Cryolo >>>>>>>>> >>>>>>>>> Dear Carlos, >>>>>>>>> given the fact that the installation has failed, could you attach >>>>>>>>> all output after "scipion3 installp -p scipion-em-sphire" command? >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> Grigory >>>>>>>>> >>>>>>>>> >>>>>>>>> -------------------------------------------------------------------------------- >>>>>>>>> Grigory Sharov, Ph.D. >>>>>>>>> >>>>>>>>> MRC Laboratory of Molecular Biology, >>>>>>>>> Francis Crick Avenue, >>>>>>>>> Cambridge Biomedical Campus, >>>>>>>>> Cambridge CB2 0QH, UK. >>>>>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>>>>> e-mail: gs...@mr... >>>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >>>>>>>>> car...@so...> wrote: >>>>>>>>> >>>>>>>>>> Dear all, >>>>>>>>>> >>>>>>>>>> I'm facing some problems using cryolo training at Scipion. >>>>>>>>>> I found the following error: >>>>>>>>>> >>>>>>>>>> *Protocol failed: Command ' source >>>>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>>>>>>>>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>>>>>>>>> --fine_tune' returned non-zero exit status 127. * >>>>>>>>>> >>>>>>>>>> I saw some discussion about that at Scipion lists, but I'm still >>>>>>>>>> little lost in how to fix it. >>>>>>>>>> In my scipion.conf file, I inserted >>>>>>>>>> *CONDA_ACTIVATION_CMD = source >>>>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>>>>>>>>> or even >>>>>>>>>> CONDA_ACTIVATION_CMD = >>>>>>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" >>>>>>>>>> (I saw these pathways in my bash.rc) >>>>>>>>>> >>>>>>>>>> Moreover, when I try to install cryolo using command line >>>>>>>>>> (scipion3 installp -p scipion-em-sphire), the following error apears: >>>>>>>>>> *AssertionError: target >>>>>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>>>>> built (after running 'source >>>>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>>>>>>>>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>>>>>>>>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>>>>>>>>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>>>>>>>>> cryolo_1.7.6_installed')* >>>>>>>>>> >>>>>>>>>> I am not sure if these errors are related and hinder performing >>>>>>>>>> cryolo in Scipion. >>>>>>>>>> I have conda installed in the computer and I'm able to use cryolo >>>>>>>>>> 1.8 outside from Scipion in the same computer (using *source >>>>>>>>>> activate cryolo *command). >>>>>>>>>> >>>>>>>>>> Anyone know what I'm doing wrong? >>>>>>>>>> Thanks in advance, >>>>>>>>>> Carlos. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> scipion-users mailing list >>>>>>>>>> sci...@li... >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> scipion-users mailing list >>>>>>>>> sci...@li... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>>> _______________________________________________ >>>>>>>>> scipion-users mailing list >>>>>>>>> sci...@li... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> scipion-users mailing list >>>>>>>> sci...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>> _______________________________________________ >>>>>>>> scipion-users mailing list >>>>>>>> sci...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> scipion-users mailing list >>>>>>> sci...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>> _______________________________________________ >>>>>>> scipion-users mailing list >>>>>>> sci...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> >>>>>> -- >>>>>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Carlos H. F. <car...@so...> - 2021-09-30 14:17:18
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Dear Grigory, Yes, you indeed said that, I realized now. Thus, we have two problems, scipion does not support cryolo 1.8 and my NVIDIA GeForce is not supported by cryolo 1.7. So, as I understand, we can not solve this for now. Thanks again. Best regards, Carlos. From: "Grigory Sharov" <sha...@gm...> To: "scipion-users" <sci...@li...> Sent: Thursday, September 30, 2021 3:52:48 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi, As I said earlier, the sphire plugin does not support cryolo 1.8, you cannot install or/and use it inside Scipion. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: Dear Grigory, So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it using pip uninstall cryolo) and put it to work inside Scipion? I tried to no use GPUs on cryolo picking, but I obtained the same error. Thanks again for the help. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 3:26:53 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi Carlos, you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo 1.8. Have a look here: [ https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 | https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 ] AFAIK, Scipion does not support this version yet. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks for all support. Cryolo training worked very well; however, I'm facing some problems with cryolo picking. I obtain this error: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc 4 --otf' returned non-zero exit status 1 When I execute in bash conda activate cryolo-1.7.6 && which cryolo_predict.py , I obtain a normal response /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py I'm sorry, I thought that the problems were solved... I attached the run.stderr and run.stdout files Thanks again for the support. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 2:08:45 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Oh, that's great that it worked! You are welcome! Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks so so much! Cryolo is running now in Scipion. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 12:18:43 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi Carlos, ok, can you run pip uninstall cryolo and then execute in that order: 1) which cryolo_train.py 2) conda activate cryolo-1.7.6 && which cryolo_train.py The first one should fail but the second one should show /home/impmc/eman2-sphire- sparx/envs/cryolo-1.7.6/bin/... Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, When I run conda activate cryolo-1.7.6 && which cryolo_train.py and which cryolo_train.py in bash I receive as response: /home/impmc/.local/bin/cryolo_train.py And when I go to this address, I can run all cryolo python files normally. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 11:58:30 AM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Can you run conda activate cryolo-1.7.6 && which cryolo_train.py ? Can you also run which cryolo_train.py ? (in case you installed cryolo into conda base env) Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dears Grigory and Pablo, Sorry for the problems with conda; these things are very recent to me; I'm still learning how to deal with them. And, thanks again for the messages and for the support. About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 It is possible to change to libcudnn.so.8 inside these folders? About conda; Yes, cryolo 1.8 are using conda from eman... I installed miniconda and anaconda3; however when I type 'which conda', I have as only response the conda from eman. Best regards, Carlos. From: "Pablo Conesa" < [ mailto:pc...@cn... | pc...@cn... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 10:29:11 AM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo I agree with Grigory, using eman2 conda is not a good practice. Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one. If you want to undo this you will need to install miniconda, and have it available instead of eman2 one. "which conda" will tell you the available one. On 29/9/21 18:54, Grigory Sharov wrote: BQ_BEGIN Thanks! In run.stderr you can see the reason it has failed: 2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env" b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, The files that you requested are attached. Thanks so much again From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 6:18:12 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi, The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this). However, I tried to run the cryolo training and I obtained the same previous error: eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune 00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982 Bellow, it is my current scipion.conf file [PYWORKFLOW] SCIPION_DOMAIN = pwem SCIPION_FONT_NAME = Helvetica SCIPION_GUI_REFRESH_IN_THREAD = False SCIPION_LOG = ~/ScipionUserData/logs/scipion.log SCIPION_LOGO = scipion_logo.gif SCIPION_LOGS = ~/ScipionUserData/logs SCIPION_NOTES_FILE = notes.txt SCIPION_NOTIFY = True SCIPION_PLUGIN_REPO_URL = [ http://scipion.i2pc.es/getplugins/ | http://scipion.i2pc.es/getplugins/ ] SCIPION_SOFTWARE = ${SCIPION_HOME}/software SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ] SCIPION_TESTS = ${SCIPION_HOME}/data/tests SCIPION_TESTS_CMD = scipion3 tests SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests SCIPION_TMP = ~/ScipionUserData/tmp SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ] SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ] SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ] SCIPION_USER_DATA = ~/ScipionUserData WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" [PLUGINS] CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 CRYOSPARC_HOME = /home/impmc/ CRYO_PROJECTS_DIR = scipion_projects CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 EMAN2SCRATCHDIR = /tmp EMAN2_HOME = %(EM_ROOT)s/eman-2.91 EM_ROOT = software/em JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 PHENIX_HOME = %(EM_ROOT)s/phenix- RELION_CUDA_LIB = /usr/local/cuda/lib64 RELION_HOME = %(EM_ROOT)s/relion-3.1.2 XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src XMIPP_HOME = %(EM_ROOT)s/xmipp Thanks again. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:51:06 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hello Carlos, to start, you are missing a space between eval and the rest in: CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)" Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks for the message. The all output is bellow: Scipion v3.0.9 - Eugenius Building scipion-em-sphire ... /home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7 Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ] Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13) Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76) Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17) Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1) Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2) Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0) Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10) Done (0.84 seconds) Building cryolo-1.7.6 ... Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ] mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz All targets exist. Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 All targets exist. Skipping command: tar -xf void.tgz -C cryolo-1.7.6 All targets exist. cd /home/impmc/scipion/software/em/cryolo-1.7.6 eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' export _CE_M='' export _CE_CONDA='' export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' # Copyright (C) 2012 Anaconda, Inc # SPDX-License-Identifier: BSD-3-Clause __add_sys_prefix_to_path() { # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then SYSP=$(\dirname "${CONDA_EXE}") else SYSP=$(\dirname "${CONDA_EXE}") SYSP=$(\dirname "${SYSP}") fi if [ -n "${WINDIR+x}" ]; then PATH="${SYSP}/bin:${PATH}" PATH="${SYSP}/Scripts:${PATH}" PATH="${SYSP}/Library/bin:${PATH}" PATH="${SYSP}/Library/usr/bin:${PATH}" PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" PATH="${SYSP}:${PATH}" else PATH="${SYSP}/bin:${PATH}" fi \export PATH } __conda_exe() ( __add_sys_prefix_to_path "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" ) __conda_hashr() { if [ -n "${ZSH_VERSION:+x}" ]; then \rehash elif [ -n "${POSH_VERSION:+x}" ]; then : # pass else \hash -r fi } __conda_activate() { if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then # Handle transition from shell activated with conda <= 4.3 to a subsequent activation # after conda updated to >= 4.4. See issue #6173. PS1="$CONDA_PS1_BACKUP" \unset CONDA_PS1_BACKUP fi \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return \eval "$ask_conda" __conda_hashr } __conda_reactivate() { \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return \eval "$ask_conda" __conda_hashr } conda() { \local cmd="${1-__missing__}" case "$cmd" in activate|deactivate) __conda_activate "$@" ;; install|update|upgrade|remove|uninstall) __conda_exe "$@" || \return __conda_reactivate ;; *) __conda_exe "$@" ;; esac } if [ -z "${CONDA_SHLVL+x}" ]; then \export CONDA_SHLVL=0 # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" else PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" fi \export PATH # We're not allowing PS1 to be unbound. It must at least be set. # However, we're not exporting it, which can cause problems when starting a second shell # via a first shell (i.e. starting zsh from bash). if [ -z "${PS1+x}" ]; then PS1= fi fi conda activate base: not found Traceback (most recent call last): File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:33:09 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Dear Carlos, given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear all, I'm facing some problems using cryolo training at Scipion. I found the following error: Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127. I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it. In my scipion.conf file, I inserted CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh or even CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" (I saw these pathways in my bash.rc) Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears: AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') I am not sure if these errors are related and hinder performing cryolo in Scipion. I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command). Anyone know what I'm doing wrong? Thanks in advance, Carlos. _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END -- Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-30 13:53:50
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Hi, As I said earlier, the sphire plugin does not support cryolo 1.8, you cannot install or/and use it inside Scipion. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it > using pip uninstall cryolo) and put it to work inside Scipion? > I tried to no use GPUs on cryolo picking, but I obtained the same error. > Thanks again for the help. > Best regards, Carlos. > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 3:26:53 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Hi Carlos, > you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo > 1.8. > > Have a look here: > https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 > > AFAIK, Scipion does not support this version yet. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear Grigory, >> >> Thanks for all support. Cryolo training worked very well; however, I'm >> facing some problems with cryolo picking. >> I obtain this error: >> *Protocol failed: Command ' eval >> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c >> Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w >> /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 >> -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o >> Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc >> 4 --otf' returned non-zero exit status 1* >> >> When I execute in bash *conda activate cryolo-1.7.6 && which >> cryolo_predict.py*, I obtain a normal response >> */home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py* >> >> I'm sorry, I thought that the problems were solved... >> I attached the run.stderr and run.stdout files >> Thanks again for the support. >> >> ------------------------------ >> *From: *"Grigory Sharov" <sha...@gm...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Thursday, September 30, 2021 2:08:45 PM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> Oh, that's great that it worked! >> You are welcome! >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dear Grigory, >>> >>> Thanks so so much! >>> Cryolo is running now in Scipion. >>> Best regards, >>> Carlos. >>> >>> ------------------------------ >>> *From: *"Grigory Sharov" <sha...@gm...> >>> *To: *"scipion-users" <sci...@li...> >>> *Sent: *Thursday, September 30, 2021 12:18:43 PM >>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >>> Cryolo >>> >>> Hi Carlos, >>> ok, can you run *pip uninstall cryolo* and then execute in that order: >>> 1) *which cryolo_train.py * >>> 2) *conda activate* *cryolo-1.7.6 && which cryolo_train.py* >>> >>> The first one should fail but the second one should show >>> /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... >>> >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < >>> car...@so...> wrote: >>> >>>> Dear Grigory, >>>> >>>> When I run *conda activate* *cryolo-1.7.6 && which cryolo_train.py* >>>> and *which cryolo_train.py *in bash I receive as response: >>>> */home/impmc/.local/bin/cryolo_train.py* >>>> >>>> And when I go to this address, I can run all cryolo python files normally. >>>> Best regards, >>>> Carlos. >>>> >>>> ------------------------------ >>>> *From: *"Grigory Sharov" <sha...@gm...> >>>> *To: *"scipion-users" <sci...@li...> >>>> *Sent: *Thursday, September 30, 2021 11:58:30 AM >>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>> using Cryolo >>>> >>>> Can you run *conda activate cryolo-1.7.6 && which cryolo_train.py* ? >>>> Can you also run *which cryolo_train.py *? (in case you installed >>>> cryolo into conda base env) >>>> >>>> Best regards, >>>> Grigory >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>> e-mail: gs...@mr... >>>> >>>> >>>> On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < >>>> car...@so...> wrote: >>>> >>>>> Dears Grigory and Pablo, >>>>> >>>>> Sorry for the problems with conda; these things are very recent to me; >>>>> I'm still learning how to deal with them. >>>>> And, thanks again for the messages and for the support. >>>>> >>>>> About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in >>>>> cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: >>>>> /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 >>>>> >>>>> /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 >>>>> >>>>> /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 >>>>> It is possible to change to libcudnn.so.8 inside these folders? >>>>> >>>>> About conda; Yes, cryolo 1.8 are using conda from eman... I installed >>>>> miniconda and anaconda3; however when I type 'which conda', I have as only >>>>> response the conda from eman. >>>>> Best regards, >>>>> Carlos. >>>>> >>>>> ------------------------------ >>>>> *From: *"Pablo Conesa" <pc...@cn...> >>>>> *To: *"scipion-users" <sci...@li...> >>>>> *Sent: *Thursday, September 30, 2021 10:29:11 AM >>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>> using Cryolo >>>>> >>>>> I agree with Grigory, using eman2 conda is not a good practice. >>>>> >>>>> Probably he did not decided that but Scipion installer used the >>>>> available one, and probably that one was eman2 one. >>>>> >>>>> If you want to undo this you will need to install miniconda, and have >>>>> it available instead of eman2 one. >>>>> >>>>> "which conda" will tell you the available one. >>>>> >>>>> >>>>> On 29/9/21 18:54, Grigory Sharov wrote: >>>>> >>>>> Thanks! In run.stderr you can see the reason it has failed: >>>>> >>>>> 2021-09-30 02:14:42.492074: W >>>>> tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not >>>>> load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open >>>>> shared object file: No such file or directory; LD_LIBRARY_PATH: >>>>> /usr/local/cuda/lib64::/home/impmc/scipion/software/lib >>>>> >>>>> For some reason it's looking for libcudnn.so.8 but the cryolo package >>>>> should have installed libcudnn.so.7.1.2 for you. Can you check that >>>>> a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I >>>>> dont know where is your env is installed. You can activate conda and "check >>>>> conda list env" >>>>> b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct >>>>> path for cryolo env. The previous command should tell you where it should be >>>>> >>>>> In general, my advice would be to not use eman2 conda for anything >>>>> except eman. You'd be better off using a separate miniconda3 installation. >>>>> Which conda did you use for cryolo 1.8? From eman? >>>>> >>>>> Best regards, >>>>> Grigory >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> Grigory Sharov, Ph.D. >>>>> >>>>> MRC Laboratory of Molecular Biology, >>>>> Francis Crick Avenue, >>>>> Cambridge Biomedical Campus, >>>>> Cambridge CB2 0QH, UK. >>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>> e-mail: gs...@mr... >>>>> >>>>> >>>>> On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < >>>>> car...@so...> wrote: >>>>> >>>>>> Dear Grigory, >>>>>> >>>>>> The files that you requested are attached. >>>>>> Thanks so much again >>>>>> >>>>>> ------------------------------ >>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>> *To: *"scipion-users" <sci...@li...> >>>>>> *Sent: *Wednesday, September 29, 2021 6:18:12 PM >>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>> using Cryolo >>>>>> >>>>>> Hi, >>>>>> The config files look ok. Could you attach run.stderr and run.stdout >>>>>> for the failed protocol? >>>>>> >>>>>> Best regards, >>>>>> Grigory >>>>>> >>>>>> >>>>>> -------------------------------------------------------------------------------- >>>>>> Grigory Sharov, Ph.D. >>>>>> >>>>>> MRC Laboratory of Molecular Biology, >>>>>> Francis Crick Avenue, >>>>>> Cambridge Biomedical Campus, >>>>>> Cambridge CB2 0QH, UK. >>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>> e-mail: gs...@mr... >>>>>> >>>>>> >>>>>> On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < >>>>>> car...@so...> wrote: >>>>>> >>>>>>> Dear Grigory, >>>>>>> >>>>>>> Thank you so much, fixing this space solved the problem with >>>>>>> cryolo_1.7.6_installing (shame on me for this). >>>>>>> However, I tried to run the cryolo training and I obtained the same >>>>>>> previous error: >>>>>>> >>>>>>> eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>>>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune >>>>>>> 00022: Protocol failed: Command ' eval >>>>>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>>>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. >>>>>>> 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 >>>>>>> 02:14:42.822982 >>>>>>> >>>>>>> Bellow, it is my current scipion.conf file >>>>>>> [PYWORKFLOW] >>>>>>> SCIPION_DOMAIN = pwem >>>>>>> SCIPION_FONT_NAME = Helvetica >>>>>>> SCIPION_GUI_REFRESH_IN_THREAD = False >>>>>>> SCIPION_LOG = ~/ScipionUserData/logs/scipion.log >>>>>>> SCIPION_LOGO = scipion_logo.gif >>>>>>> SCIPION_LOGS = ~/ScipionUserData/logs >>>>>>> SCIPION_NOTES_FILE = notes.txt >>>>>>> SCIPION_NOTIFY = True >>>>>>> SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ >>>>>>> SCIPION_SOFTWARE = ${SCIPION_HOME}/software >>>>>>> SCIPION_SUPPORT_EMAIL = sc...@cn... >>>>>>> SCIPION_TESTS = ${SCIPION_HOME}/data/tests >>>>>>> SCIPION_TESTS_CMD = scipion3 tests >>>>>>> SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests >>>>>>> SCIPION_TMP = ~/ScipionUserData/tmp >>>>>>> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion >>>>>>> SCIPION_URL_SOFTWARE = >>>>>>> http://scipion.cnb.csic.es/downloads/scipion/software >>>>>>> SCIPION_URL_TESTDATA = >>>>>>> http://scipion.cnb.csic.es/downloads/scipion/data/tests >>>>>>> SCIPION_USER_DATA = ~/ScipionUserData >>>>>>> WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] >>>>>>> CONDA_ACTIVATION_CMD = eval >>>>>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" >>>>>>> >>>>>>> [PLUGINS] >>>>>>> CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 >>>>>>> CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 >>>>>>> CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta >>>>>>> CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 >>>>>>> CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 >>>>>>> CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 >>>>>>> CRYOLO_GENERIC_DENOISED_MODEL = >>>>>>> %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 >>>>>>> CRYOLO_GENERIC_MODEL = >>>>>>> %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 >>>>>>> CRYOLO_NS_GENERIC_MODEL = >>>>>>> %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 >>>>>>> CRYOSPARC_HOME = /home/impmc/ >>>>>>> CRYO_PROJECTS_DIR = scipion_projects >>>>>>> CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 >>>>>>> EMAN2SCRATCHDIR = /tmp >>>>>>> EMAN2_HOME = %(EM_ROOT)s/eman-2.91 >>>>>>> EM_ROOT = software/em >>>>>>> JANNI_GENERIC_MODEL = >>>>>>> %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 >>>>>>> MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 >>>>>>> MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 >>>>>>> MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 >>>>>>> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 >>>>>>> PHENIX_HOME = %(EM_ROOT)s/phenix- >>>>>>> RELION_CUDA_LIB = /usr/local/cuda/lib64 >>>>>>> RELION_HOME = %(EM_ROOT)s/relion-3.1.2 >>>>>>> XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src >>>>>>> XMIPP_HOME = %(EM_ROOT)s/xmipp >>>>>>> >>>>>>> >>>>>>> Thanks again. >>>>>>> >>>>>>> ------------------------------ >>>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>>> *To: *"scipion-users" <sci...@li...> >>>>>>> *Sent: *Wednesday, September 29, 2021 5:51:06 PM >>>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>>> using Cryolo >>>>>>> >>>>>>> Hello Carlos, >>>>>>> >>>>>>> to start, you are missing a space between eval and the rest in: >>>>>>> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>>> shell.bash hook)" >>>>>>> >>>>>>> Best regards, >>>>>>> Grigory >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------------- >>>>>>> Grigory Sharov, Ph.D. >>>>>>> >>>>>>> MRC Laboratory of Molecular Biology, >>>>>>> Francis Crick Avenue, >>>>>>> Cambridge Biomedical Campus, >>>>>>> Cambridge CB2 0QH, UK. >>>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>>> e-mail: gs...@mr... >>>>>>> >>>>>>> >>>>>>> On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < >>>>>>> car...@so...> wrote: >>>>>>> >>>>>>>> Dear Grigory, >>>>>>>> >>>>>>>> Thanks for the message. The all output is bellow: >>>>>>>> >>>>>>>> Scipion v3.0.9 - Eugenius >>>>>>>> Building scipion-em-sphire ... >>>>>>>> /home/impmc/scipion/.scipion3/bin/python -m pip install >>>>>>>> scipion-em-sphire==3.0.7 >>>>>>>> Looking in indexes: https://pypi.org/simple, >>>>>>>> https://pypi.ngc.nvidia.com >>>>>>>> Requirement already satisfied: scipion-em-sphire==3.0.7 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >>>>>>>> Requirement already satisfied: scipion-em in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-em-sphire==3.0.7) (3.0.13) >>>>>>>> Requirement already satisfied: biopython==1.76 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-em->scipion-em-sphire==3.0.7) (1.76) >>>>>>>> Requirement already satisfied: tifffile in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >>>>>>>> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >>>>>>>> Requirement already satisfied: numpy in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >>>>>>>> Requirement already satisfied: mpi4py<=3.0.3 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >>>>>>>> Requirement already satisfied: configparser<=5.0.2 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >>>>>>>> Requirement already satisfied: psutil<=5.8.0 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >>>>>>>> Requirement already satisfied: pillow<=8.2.0 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >>>>>>>> Requirement already satisfied: bibtexparser<=1.2.0 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >>>>>>>> Requirement already satisfied: requests<=2.25.1 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >>>>>>>> Requirement already satisfied: matplotlib==3.2.2 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >>>>>>>> Requirement already satisfied: tkcolorpicker<=2.1.3 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >>>>>>>> Requirement already satisfied: cycler>=0.10 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (0.10.0) >>>>>>>> Requirement already satisfied: python-dateutil>=2.1 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (2.8.1) >>>>>>>> Requirement already satisfied: >>>>>>>> pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (2.4.7) >>>>>>>> Requirement already satisfied: kiwisolver>=1.0.1 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (1.3.1) >>>>>>>> Requirement already satisfied: future>=0.16.0 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (0.18.2) >>>>>>>> Requirement already satisfied: six in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (1.16.0) >>>>>>>> Requirement already satisfied: certifi>=2017.4.17 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (2020.12.5) >>>>>>>> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (1.26.4) >>>>>>>> Requirement already satisfied: chardet<5,>=3.0.2 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (4.0.0) >>>>>>>> Requirement already satisfied: idna<3,>=2.5 in >>>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>>> (2.10) >>>>>>>> Done (0.84 seconds) >>>>>>>> Building cryolo-1.7.6 ... >>>>>>>> Skipping command: wget -nv -c -O >>>>>>>> /home/impmc/scipion/software/em/void.tgz.part >>>>>>>> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >>>>>>>> mv -v /home/impmc/scipion/software/em/void.tgz.part >>>>>>>> /home/impmc/scipion/software/em/void.tgz >>>>>>>> All targets exist. >>>>>>>> Skipping command: mkdir >>>>>>>> /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>>>>> All targets exist. >>>>>>>> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >>>>>>>> All targets exist. >>>>>>>> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>>>> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >>>>>>>> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >>>>>>>> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >>>>>>>> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >>>>>>>> /bin/sh: 1: evalexport >>>>>>>> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >>>>>>>> export _CE_M='' >>>>>>>> export _CE_CONDA='' >>>>>>>> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >>>>>>>> >>>>>>>> # Copyright (C) 2012 Anaconda, Inc >>>>>>>> # SPDX-License-Identifier: BSD-3-Clause >>>>>>>> >>>>>>>> __add_sys_prefix_to_path() { >>>>>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>>>>> # it is in a different relative location to condabin. >>>>>>>> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >>>>>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>>>>> else >>>>>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>>>>> SYSP=$(\dirname "${SYSP}") >>>>>>>> fi >>>>>>>> >>>>>>>> if [ -n "${WINDIR+x}" ]; then >>>>>>>> PATH="${SYSP}/bin:${PATH}" >>>>>>>> PATH="${SYSP}/Scripts:${PATH}" >>>>>>>> PATH="${SYSP}/Library/bin:${PATH}" >>>>>>>> PATH="${SYSP}/Library/usr/bin:${PATH}" >>>>>>>> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >>>>>>>> PATH="${SYSP}:${PATH}" >>>>>>>> else >>>>>>>> PATH="${SYSP}/bin:${PATH}" >>>>>>>> fi >>>>>>>> \export PATH >>>>>>>> } >>>>>>>> >>>>>>>> __conda_exe() ( >>>>>>>> __add_sys_prefix_to_path >>>>>>>> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >>>>>>>> ) >>>>>>>> >>>>>>>> __conda_hashr() { >>>>>>>> if [ -n "${ZSH_VERSION:+x}" ]; then >>>>>>>> \rehash >>>>>>>> elif [ -n "${POSH_VERSION:+x}" ]; then >>>>>>>> : # pass >>>>>>>> else >>>>>>>> \hash -r >>>>>>>> fi >>>>>>>> } >>>>>>>> >>>>>>>> __conda_activate() { >>>>>>>> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >>>>>>>> # Handle transition from shell activated with conda <= 4.3 >>>>>>>> to a subsequent activation >>>>>>>> # after conda updated to >= 4.4. See issue #6173. >>>>>>>> PS1="$CONDA_PS1_BACKUP" >>>>>>>> \unset CONDA_PS1_BACKUP >>>>>>>> fi >>>>>>>> \local ask_conda >>>>>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || >>>>>>>> \return >>>>>>>> \eval "$ask_conda" >>>>>>>> __conda_hashr >>>>>>>> } >>>>>>>> >>>>>>>> __conda_reactivate() { >>>>>>>> \local ask_conda >>>>>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix >>>>>>>> reactivate)" || \return >>>>>>>> \eval "$ask_conda" >>>>>>>> __conda_hashr >>>>>>>> } >>>>>>>> >>>>>>>> conda() { >>>>>>>> \local cmd="${1-__missing__}" >>>>>>>> case "$cmd" in >>>>>>>> activate|deactivate) >>>>>>>> __conda_activate "$@" >>>>>>>> ;; >>>>>>>> install|update|upgrade|remove|uninstall) >>>>>>>> __conda_exe "$@" || \return >>>>>>>> __conda_reactivate >>>>>>>> ;; >>>>>>>> *) >>>>>>>> __conda_exe "$@" >>>>>>>> ;; >>>>>>>> esac >>>>>>>> } >>>>>>>> >>>>>>>> if [ -z "${CONDA_SHLVL+x}" ]; then >>>>>>>> \export CONDA_SHLVL=0 >>>>>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>>>>> # it is in a different relative location to condabin. >>>>>>>> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >>>>>>>> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >>>>>>>> else >>>>>>>> PATH="$(\dirname "$(\dirname >>>>>>>> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >>>>>>>> fi >>>>>>>> \export PATH >>>>>>>> >>>>>>>> # We're not allowing PS1 to be unbound. It must at least be set. >>>>>>>> # However, we're not exporting it, which can cause problems >>>>>>>> when starting a second shell >>>>>>>> # via a first shell (i.e. starting zsh from bash). >>>>>>>> if [ -z "${PS1+x}" ]; then >>>>>>>> PS1= >>>>>>>> fi >>>>>>>> fi >>>>>>>> >>>>>>>> conda activate base: not found >>>>>>>> Traceback (most recent call last): >>>>>>>> File >>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>>>>> line 470, in <module> >>>>>>>> main() >>>>>>>> File >>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>>>>> line 293, in main >>>>>>>> installPluginMethods() >>>>>>>> File >>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>>>>>>> line 232, in installPluginMethods >>>>>>>> plugin.installBin({'args': ['-j', numberProcessor]}) >>>>>>>> File >>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>>>>>>> line 166, in installBin >>>>>>>> environment.execute() >>>>>>>> File >>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>>> line 748, in execute >>>>>>>> self._executeTargets(targetList) >>>>>>>> File >>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>>> line 690, in _executeTargets >>>>>>>> tgt.execute() >>>>>>>> File >>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>>> line 221, in execute >>>>>>>> command.execute() >>>>>>>> File >>>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>>> line 161, in execute >>>>>>>> assert glob(t), ("target '%s' not built (after " >>>>>>>> AssertionError: target >>>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>>>>> Error at main: target >>>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>>>>> >>>>>>>> ------------------------------ >>>>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>>>> *To: *"scipion-users" <sci...@li...> >>>>>>>> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >>>>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>>>> using Cryolo >>>>>>>> >>>>>>>> Dear Carlos, >>>>>>>> given the fact that the installation has failed, could you attach >>>>>>>> all output after "scipion3 installp -p scipion-em-sphire" command? >>>>>>>> >>>>>>>> Best regards, >>>>>>>> Grigory >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------------- >>>>>>>> Grigory Sharov, Ph.D. >>>>>>>> >>>>>>>> MRC Laboratory of Molecular Biology, >>>>>>>> Francis Crick Avenue, >>>>>>>> Cambridge Biomedical Campus, >>>>>>>> Cambridge CB2 0QH, UK. >>>>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>>>> e-mail: gs...@mr... >>>>>>>> >>>>>>>> >>>>>>>> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >>>>>>>> car...@so...> wrote: >>>>>>>> >>>>>>>>> Dear all, >>>>>>>>> >>>>>>>>> I'm facing some problems using cryolo training at Scipion. >>>>>>>>> I found the following error: >>>>>>>>> >>>>>>>>> *Protocol failed: Command ' source >>>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>>>>>>>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>>>>>>>> --fine_tune' returned non-zero exit status 127. * >>>>>>>>> >>>>>>>>> I saw some discussion about that at Scipion lists, but I'm still >>>>>>>>> little lost in how to fix it. >>>>>>>>> In my scipion.conf file, I inserted >>>>>>>>> *CONDA_ACTIVATION_CMD = source >>>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>>>>>>>> or even >>>>>>>>> CONDA_ACTIVATION_CMD = >>>>>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" >>>>>>>>> (I saw these pathways in my bash.rc) >>>>>>>>> >>>>>>>>> Moreover, when I try to install cryolo using command line >>>>>>>>> (scipion3 installp -p scipion-em-sphire), the following error apears: >>>>>>>>> *AssertionError: target >>>>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>>>> built (after running 'source >>>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>>>>>>>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>>>>>>>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>>>>>>>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>>>>>>>> cryolo_1.7.6_installed')* >>>>>>>>> >>>>>>>>> I am not sure if these errors are related and hinder performing >>>>>>>>> cryolo in Scipion. >>>>>>>>> I have conda installed in the computer and I'm able to use cryolo >>>>>>>>> 1.8 outside from Scipion in the same computer (using *source >>>>>>>>> activate cryolo *command). >>>>>>>>> >>>>>>>>> Anyone know what I'm doing wrong? >>>>>>>>> Thanks in advance, >>>>>>>>> Carlos. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> scipion-users mailing list >>>>>>>>> sci...@li... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> scipion-users mailing list >>>>>>>> sci...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>> _______________________________________________ >>>>>>>> scipion-users mailing list >>>>>>>> sci...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> scipion-users mailing list >>>>>>> sci...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>> _______________________________________________ >>>>>>> scipion-users mailing list >>>>>>> sci...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> >>>>> -- >>>>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Carlos H. F. <car...@so...> - 2021-09-30 13:39:22
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Dear Grigory, So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it using pip uninstall cryolo) and put it to work inside Scipion? I tried to no use GPUs on cryolo picking, but I obtained the same error. Thanks again for the help. Best regards, Carlos. From: "Grigory Sharov" <sha...@gm...> To: "scipion-users" <sci...@li...> Sent: Thursday, September 30, 2021 3:26:53 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi Carlos, you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo 1.8. Have a look here: [ https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 | https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 ] AFAIK, Scipion does not support this version yet. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: Dear Grigory, Thanks for all support. Cryolo training worked very well; however, I'm facing some problems with cryolo picking. I obtain this error: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc 4 --otf' returned non-zero exit status 1 When I execute in bash conda activate cryolo-1.7.6 && which cryolo_predict.py , I obtain a normal response /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py I'm sorry, I thought that the problems were solved... I attached the run.stderr and run.stdout files Thanks again for the support. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 2:08:45 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Oh, that's great that it worked! You are welcome! Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks so so much! Cryolo is running now in Scipion. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 12:18:43 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi Carlos, ok, can you run pip uninstall cryolo and then execute in that order: 1) which cryolo_train.py 2) conda activate cryolo-1.7.6 && which cryolo_train.py The first one should fail but the second one should show /home/impmc/eman2-sphire- sparx/envs/cryolo-1.7.6/bin/... Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, When I run conda activate cryolo-1.7.6 && which cryolo_train.py and which cryolo_train.py in bash I receive as response: /home/impmc/.local/bin/cryolo_train.py And when I go to this address, I can run all cryolo python files normally. Best regards, Carlos. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 11:58:30 AM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Can you run conda activate cryolo-1.7.6 && which cryolo_train.py ? Can you also run which cryolo_train.py ? (in case you installed cryolo into conda base env) Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dears Grigory and Pablo, Sorry for the problems with conda; these things are very recent to me; I'm still learning how to deal with them. And, thanks again for the messages and for the support. About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 It is possible to change to libcudnn.so.8 inside these folders? About conda; Yes, cryolo 1.8 are using conda from eman... I installed miniconda and anaconda3; however when I type 'which conda', I have as only response the conda from eman. Best regards, Carlos. From: "Pablo Conesa" < [ mailto:pc...@cn... | pc...@cn... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Thursday, September 30, 2021 10:29:11 AM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo I agree with Grigory, using eman2 conda is not a good practice. Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one. If you want to undo this you will need to install miniconda, and have it available instead of eman2 one. "which conda" will tell you the available one. On 29/9/21 18:54, Grigory Sharov wrote: BQ_BEGIN Thanks! In run.stderr you can see the reason it has failed: 2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env" b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, The files that you requested are attached. Thanks so much again From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 6:18:12 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi, The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this). However, I tried to run the cryolo training and I obtained the same previous error: eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune 00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982 Bellow, it is my current scipion.conf file [PYWORKFLOW] SCIPION_DOMAIN = pwem SCIPION_FONT_NAME = Helvetica SCIPION_GUI_REFRESH_IN_THREAD = False SCIPION_LOG = ~/ScipionUserData/logs/scipion.log SCIPION_LOGO = scipion_logo.gif SCIPION_LOGS = ~/ScipionUserData/logs SCIPION_NOTES_FILE = notes.txt SCIPION_NOTIFY = True SCIPION_PLUGIN_REPO_URL = [ http://scipion.i2pc.es/getplugins/ | http://scipion.i2pc.es/getplugins/ ] SCIPION_SOFTWARE = ${SCIPION_HOME}/software SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ] SCIPION_TESTS = ${SCIPION_HOME}/data/tests SCIPION_TESTS_CMD = scipion3 tests SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests SCIPION_TMP = ~/ScipionUserData/tmp SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ] SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ] SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ] SCIPION_USER_DATA = ~/ScipionUserData WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" [PLUGINS] CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 CRYOSPARC_HOME = /home/impmc/ CRYO_PROJECTS_DIR = scipion_projects CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 EMAN2SCRATCHDIR = /tmp EMAN2_HOME = %(EM_ROOT)s/eman-2.91 EM_ROOT = software/em JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 PHENIX_HOME = %(EM_ROOT)s/phenix- RELION_CUDA_LIB = /usr/local/cuda/lib64 RELION_HOME = %(EM_ROOT)s/relion-3.1.2 XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src XMIPP_HOME = %(EM_ROOT)s/xmipp Thanks again. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:51:06 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hello Carlos, to start, you are missing a space between eval and the rest in: CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)" Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks for the message. The all output is bellow: Scipion v3.0.9 - Eugenius Building scipion-em-sphire ... /home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7 Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ] Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13) Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76) Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17) Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1) Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2) Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0) Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10) Done (0.84 seconds) Building cryolo-1.7.6 ... Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ] mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz All targets exist. Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 All targets exist. Skipping command: tar -xf void.tgz -C cryolo-1.7.6 All targets exist. cd /home/impmc/scipion/software/em/cryolo-1.7.6 eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' export _CE_M='' export _CE_CONDA='' export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' # Copyright (C) 2012 Anaconda, Inc # SPDX-License-Identifier: BSD-3-Clause __add_sys_prefix_to_path() { # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then SYSP=$(\dirname "${CONDA_EXE}") else SYSP=$(\dirname "${CONDA_EXE}") SYSP=$(\dirname "${SYSP}") fi if [ -n "${WINDIR+x}" ]; then PATH="${SYSP}/bin:${PATH}" PATH="${SYSP}/Scripts:${PATH}" PATH="${SYSP}/Library/bin:${PATH}" PATH="${SYSP}/Library/usr/bin:${PATH}" PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" PATH="${SYSP}:${PATH}" else PATH="${SYSP}/bin:${PATH}" fi \export PATH } __conda_exe() ( __add_sys_prefix_to_path "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" ) __conda_hashr() { if [ -n "${ZSH_VERSION:+x}" ]; then \rehash elif [ -n "${POSH_VERSION:+x}" ]; then : # pass else \hash -r fi } __conda_activate() { if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then # Handle transition from shell activated with conda <= 4.3 to a subsequent activation # after conda updated to >= 4.4. See issue #6173. PS1="$CONDA_PS1_BACKUP" \unset CONDA_PS1_BACKUP fi \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return \eval "$ask_conda" __conda_hashr } __conda_reactivate() { \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return \eval "$ask_conda" __conda_hashr } conda() { \local cmd="${1-__missing__}" case "$cmd" in activate|deactivate) __conda_activate "$@" ;; install|update|upgrade|remove|uninstall) __conda_exe "$@" || \return __conda_reactivate ;; *) __conda_exe "$@" ;; esac } if [ -z "${CONDA_SHLVL+x}" ]; then \export CONDA_SHLVL=0 # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" else PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" fi \export PATH # We're not allowing PS1 to be unbound. It must at least be set. # However, we're not exporting it, which can cause problems when starting a second shell # via a first shell (i.e. starting zsh from bash). if [ -z "${PS1+x}" ]; then PS1= fi fi conda activate base: not found Traceback (most recent call last): File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:33:09 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Dear Carlos, given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear all, I'm facing some problems using cryolo training at Scipion. I found the following error: Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127. I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it. In my scipion.conf file, I inserted CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh or even CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" (I saw these pathways in my bash.rc) Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears: AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') I am not sure if these errors are related and hinder performing cryolo in Scipion. I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command). Anyone know what I'm doing wrong? Thanks in advance, Carlos. _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END -- Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-30 13:27:22
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Hi Carlos, you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo 1.8. Have a look here: https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11 AFAIK, Scipion does not support this version yet. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > Thanks for all support. Cryolo training worked very well; however, I'm > facing some problems with cryolo picking. > I obtain this error: > *Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c > Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w > /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 > -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o > Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc > 4 --otf' returned non-zero exit status 1* > > When I execute in bash *conda activate cryolo-1.7.6 && which > cryolo_predict.py*, I obtain a normal response > */home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py* > > I'm sorry, I thought that the problems were solved... > I attached the run.stderr and run.stdout files > Thanks again for the support. > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 2:08:45 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Oh, that's great that it worked! > You are welcome! > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear Grigory, >> >> Thanks so so much! >> Cryolo is running now in Scipion. >> Best regards, >> Carlos. >> >> ------------------------------ >> *From: *"Grigory Sharov" <sha...@gm...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Thursday, September 30, 2021 12:18:43 PM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> Hi Carlos, >> ok, can you run *pip uninstall cryolo* and then execute in that order: >> 1) *which cryolo_train.py * >> 2) *conda activate* *cryolo-1.7.6 && which cryolo_train.py* >> >> The first one should fail but the second one should show >> /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dear Grigory, >>> >>> When I run *conda activate* *cryolo-1.7.6 && which cryolo_train.py* and *which >>> cryolo_train.py *in bash I receive as response: >>> */home/impmc/.local/bin/cryolo_train.py* >>> >>> And when I go to this address, I can run all cryolo python files normally. >>> Best regards, >>> Carlos. >>> >>> ------------------------------ >>> *From: *"Grigory Sharov" <sha...@gm...> >>> *To: *"scipion-users" <sci...@li...> >>> *Sent: *Thursday, September 30, 2021 11:58:30 AM >>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >>> Cryolo >>> >>> Can you run *conda activate cryolo-1.7.6 && which cryolo_train.py* ? >>> Can you also run *which cryolo_train.py *? (in case you installed >>> cryolo into conda base env) >>> >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < >>> car...@so...> wrote: >>> >>>> Dears Grigory and Pablo, >>>> >>>> Sorry for the problems with conda; these things are very recent to me; >>>> I'm still learning how to deal with them. >>>> And, thanks again for the messages and for the support. >>>> >>>> About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in >>>> cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: >>>> /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 >>>> >>>> /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 >>>> >>>> /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 >>>> It is possible to change to libcudnn.so.8 inside these folders? >>>> >>>> About conda; Yes, cryolo 1.8 are using conda from eman... I installed >>>> miniconda and anaconda3; however when I type 'which conda', I have as only >>>> response the conda from eman. >>>> Best regards, >>>> Carlos. >>>> >>>> ------------------------------ >>>> *From: *"Pablo Conesa" <pc...@cn...> >>>> *To: *"scipion-users" <sci...@li...> >>>> *Sent: *Thursday, September 30, 2021 10:29:11 AM >>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>> using Cryolo >>>> >>>> I agree with Grigory, using eman2 conda is not a good practice. >>>> >>>> Probably he did not decided that but Scipion installer used the >>>> available one, and probably that one was eman2 one. >>>> >>>> If you want to undo this you will need to install miniconda, and have >>>> it available instead of eman2 one. >>>> >>>> "which conda" will tell you the available one. >>>> >>>> >>>> On 29/9/21 18:54, Grigory Sharov wrote: >>>> >>>> Thanks! In run.stderr you can see the reason it has failed: >>>> >>>> 2021-09-30 02:14:42.492074: W >>>> tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not >>>> load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open >>>> shared object file: No such file or directory; LD_LIBRARY_PATH: >>>> /usr/local/cuda/lib64::/home/impmc/scipion/software/lib >>>> >>>> For some reason it's looking for libcudnn.so.8 but the cryolo package >>>> should have installed libcudnn.so.7.1.2 for you. Can you check that >>>> a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I >>>> dont know where is your env is installed. You can activate conda and "check >>>> conda list env" >>>> b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct >>>> path for cryolo env. The previous command should tell you where it should be >>>> >>>> In general, my advice would be to not use eman2 conda for anything >>>> except eman. You'd be better off using a separate miniconda3 installation. >>>> Which conda did you use for cryolo 1.8? From eman? >>>> >>>> Best regards, >>>> Grigory >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>> e-mail: gs...@mr... >>>> >>>> >>>> On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < >>>> car...@so...> wrote: >>>> >>>>> Dear Grigory, >>>>> >>>>> The files that you requested are attached. >>>>> Thanks so much again >>>>> >>>>> ------------------------------ >>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>> *To: *"scipion-users" <sci...@li...> >>>>> *Sent: *Wednesday, September 29, 2021 6:18:12 PM >>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>> using Cryolo >>>>> >>>>> Hi, >>>>> The config files look ok. Could you attach run.stderr and run.stdout >>>>> for the failed protocol? >>>>> >>>>> Best regards, >>>>> Grigory >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> Grigory Sharov, Ph.D. >>>>> >>>>> MRC Laboratory of Molecular Biology, >>>>> Francis Crick Avenue, >>>>> Cambridge Biomedical Campus, >>>>> Cambridge CB2 0QH, UK. >>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>> e-mail: gs...@mr... >>>>> >>>>> >>>>> On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < >>>>> car...@so...> wrote: >>>>> >>>>>> Dear Grigory, >>>>>> >>>>>> Thank you so much, fixing this space solved the problem with >>>>>> cryolo_1.7.6_installing (shame on me for this). >>>>>> However, I tried to run the cryolo training and I obtained the same >>>>>> previous error: >>>>>> >>>>>> eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune >>>>>> 00022: Protocol failed: Command ' eval >>>>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. >>>>>> 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 >>>>>> 02:14:42.822982 >>>>>> >>>>>> Bellow, it is my current scipion.conf file >>>>>> [PYWORKFLOW] >>>>>> SCIPION_DOMAIN = pwem >>>>>> SCIPION_FONT_NAME = Helvetica >>>>>> SCIPION_GUI_REFRESH_IN_THREAD = False >>>>>> SCIPION_LOG = ~/ScipionUserData/logs/scipion.log >>>>>> SCIPION_LOGO = scipion_logo.gif >>>>>> SCIPION_LOGS = ~/ScipionUserData/logs >>>>>> SCIPION_NOTES_FILE = notes.txt >>>>>> SCIPION_NOTIFY = True >>>>>> SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ >>>>>> SCIPION_SOFTWARE = ${SCIPION_HOME}/software >>>>>> SCIPION_SUPPORT_EMAIL = sc...@cn... >>>>>> SCIPION_TESTS = ${SCIPION_HOME}/data/tests >>>>>> SCIPION_TESTS_CMD = scipion3 tests >>>>>> SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests >>>>>> SCIPION_TMP = ~/ScipionUserData/tmp >>>>>> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion >>>>>> SCIPION_URL_SOFTWARE = >>>>>> http://scipion.cnb.csic.es/downloads/scipion/software >>>>>> SCIPION_URL_TESTDATA = >>>>>> http://scipion.cnb.csic.es/downloads/scipion/data/tests >>>>>> SCIPION_USER_DATA = ~/ScipionUserData >>>>>> WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] >>>>>> CONDA_ACTIVATION_CMD = eval >>>>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" >>>>>> >>>>>> [PLUGINS] >>>>>> CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 >>>>>> CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 >>>>>> CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta >>>>>> CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 >>>>>> CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 >>>>>> CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 >>>>>> CRYOLO_GENERIC_DENOISED_MODEL = >>>>>> %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 >>>>>> CRYOLO_GENERIC_MODEL = >>>>>> %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 >>>>>> CRYOLO_NS_GENERIC_MODEL = >>>>>> %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 >>>>>> CRYOSPARC_HOME = /home/impmc/ >>>>>> CRYO_PROJECTS_DIR = scipion_projects >>>>>> CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 >>>>>> EMAN2SCRATCHDIR = /tmp >>>>>> EMAN2_HOME = %(EM_ROOT)s/eman-2.91 >>>>>> EM_ROOT = software/em >>>>>> JANNI_GENERIC_MODEL = >>>>>> %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 >>>>>> MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 >>>>>> MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 >>>>>> MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 >>>>>> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 >>>>>> PHENIX_HOME = %(EM_ROOT)s/phenix- >>>>>> RELION_CUDA_LIB = /usr/local/cuda/lib64 >>>>>> RELION_HOME = %(EM_ROOT)s/relion-3.1.2 >>>>>> XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src >>>>>> XMIPP_HOME = %(EM_ROOT)s/xmipp >>>>>> >>>>>> >>>>>> Thanks again. >>>>>> >>>>>> ------------------------------ >>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>> *To: *"scipion-users" <sci...@li...> >>>>>> *Sent: *Wednesday, September 29, 2021 5:51:06 PM >>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>> using Cryolo >>>>>> >>>>>> Hello Carlos, >>>>>> >>>>>> to start, you are missing a space between eval and the rest in: >>>>>> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>> shell.bash hook)" >>>>>> >>>>>> Best regards, >>>>>> Grigory >>>>>> >>>>>> >>>>>> -------------------------------------------------------------------------------- >>>>>> Grigory Sharov, Ph.D. >>>>>> >>>>>> MRC Laboratory of Molecular Biology, >>>>>> Francis Crick Avenue, >>>>>> Cambridge Biomedical Campus, >>>>>> Cambridge CB2 0QH, UK. >>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>> e-mail: gs...@mr... >>>>>> >>>>>> >>>>>> On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < >>>>>> car...@so...> wrote: >>>>>> >>>>>>> Dear Grigory, >>>>>>> >>>>>>> Thanks for the message. The all output is bellow: >>>>>>> >>>>>>> Scipion v3.0.9 - Eugenius >>>>>>> Building scipion-em-sphire ... >>>>>>> /home/impmc/scipion/.scipion3/bin/python -m pip install >>>>>>> scipion-em-sphire==3.0.7 >>>>>>> Looking in indexes: https://pypi.org/simple, >>>>>>> https://pypi.ngc.nvidia.com >>>>>>> Requirement already satisfied: scipion-em-sphire==3.0.7 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >>>>>>> Requirement already satisfied: scipion-em in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-em-sphire==3.0.7) (3.0.13) >>>>>>> Requirement already satisfied: biopython==1.76 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-em->scipion-em-sphire==3.0.7) (1.76) >>>>>>> Requirement already satisfied: tifffile in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >>>>>>> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >>>>>>> Requirement already satisfied: numpy in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >>>>>>> Requirement already satisfied: mpi4py<=3.0.3 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >>>>>>> Requirement already satisfied: configparser<=5.0.2 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >>>>>>> Requirement already satisfied: psutil<=5.8.0 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >>>>>>> Requirement already satisfied: pillow<=8.2.0 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >>>>>>> Requirement already satisfied: bibtexparser<=1.2.0 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >>>>>>> Requirement already satisfied: requests<=2.25.1 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >>>>>>> Requirement already satisfied: matplotlib==3.2.2 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >>>>>>> Requirement already satisfied: tkcolorpicker<=2.1.3 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >>>>>>> Requirement already satisfied: cycler>=0.10 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (0.10.0) >>>>>>> Requirement already satisfied: python-dateutil>=2.1 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (2.8.1) >>>>>>> Requirement already satisfied: >>>>>>> pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (2.4.7) >>>>>>> Requirement already satisfied: kiwisolver>=1.0.1 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (1.3.1) >>>>>>> Requirement already satisfied: future>=0.16.0 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (0.18.2) >>>>>>> Requirement already satisfied: six in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (1.16.0) >>>>>>> Requirement already satisfied: certifi>=2017.4.17 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (2020.12.5) >>>>>>> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (1.26.4) >>>>>>> Requirement already satisfied: chardet<5,>=3.0.2 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (4.0.0) >>>>>>> Requirement already satisfied: idna<3,>=2.5 in >>>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>>> (2.10) >>>>>>> Done (0.84 seconds) >>>>>>> Building cryolo-1.7.6 ... >>>>>>> Skipping command: wget -nv -c -O >>>>>>> /home/impmc/scipion/software/em/void.tgz.part >>>>>>> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >>>>>>> mv -v /home/impmc/scipion/software/em/void.tgz.part >>>>>>> /home/impmc/scipion/software/em/void.tgz >>>>>>> All targets exist. >>>>>>> Skipping command: mkdir >>>>>>> /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>>>> All targets exist. >>>>>>> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >>>>>>> All targets exist. >>>>>>> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>>> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >>>>>>> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >>>>>>> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >>>>>>> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >>>>>>> /bin/sh: 1: evalexport >>>>>>> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >>>>>>> export _CE_M='' >>>>>>> export _CE_CONDA='' >>>>>>> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >>>>>>> >>>>>>> # Copyright (C) 2012 Anaconda, Inc >>>>>>> # SPDX-License-Identifier: BSD-3-Clause >>>>>>> >>>>>>> __add_sys_prefix_to_path() { >>>>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>>>> # it is in a different relative location to condabin. >>>>>>> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >>>>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>>>> else >>>>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>>>> SYSP=$(\dirname "${SYSP}") >>>>>>> fi >>>>>>> >>>>>>> if [ -n "${WINDIR+x}" ]; then >>>>>>> PATH="${SYSP}/bin:${PATH}" >>>>>>> PATH="${SYSP}/Scripts:${PATH}" >>>>>>> PATH="${SYSP}/Library/bin:${PATH}" >>>>>>> PATH="${SYSP}/Library/usr/bin:${PATH}" >>>>>>> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >>>>>>> PATH="${SYSP}:${PATH}" >>>>>>> else >>>>>>> PATH="${SYSP}/bin:${PATH}" >>>>>>> fi >>>>>>> \export PATH >>>>>>> } >>>>>>> >>>>>>> __conda_exe() ( >>>>>>> __add_sys_prefix_to_path >>>>>>> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >>>>>>> ) >>>>>>> >>>>>>> __conda_hashr() { >>>>>>> if [ -n "${ZSH_VERSION:+x}" ]; then >>>>>>> \rehash >>>>>>> elif [ -n "${POSH_VERSION:+x}" ]; then >>>>>>> : # pass >>>>>>> else >>>>>>> \hash -r >>>>>>> fi >>>>>>> } >>>>>>> >>>>>>> __conda_activate() { >>>>>>> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >>>>>>> # Handle transition from shell activated with conda <= 4.3 >>>>>>> to a subsequent activation >>>>>>> # after conda updated to >= 4.4. See issue #6173. >>>>>>> PS1="$CONDA_PS1_BACKUP" >>>>>>> \unset CONDA_PS1_BACKUP >>>>>>> fi >>>>>>> \local ask_conda >>>>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || >>>>>>> \return >>>>>>> \eval "$ask_conda" >>>>>>> __conda_hashr >>>>>>> } >>>>>>> >>>>>>> __conda_reactivate() { >>>>>>> \local ask_conda >>>>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" >>>>>>> || \return >>>>>>> \eval "$ask_conda" >>>>>>> __conda_hashr >>>>>>> } >>>>>>> >>>>>>> conda() { >>>>>>> \local cmd="${1-__missing__}" >>>>>>> case "$cmd" in >>>>>>> activate|deactivate) >>>>>>> __conda_activate "$@" >>>>>>> ;; >>>>>>> install|update|upgrade|remove|uninstall) >>>>>>> __conda_exe "$@" || \return >>>>>>> __conda_reactivate >>>>>>> ;; >>>>>>> *) >>>>>>> __conda_exe "$@" >>>>>>> ;; >>>>>>> esac >>>>>>> } >>>>>>> >>>>>>> if [ -z "${CONDA_SHLVL+x}" ]; then >>>>>>> \export CONDA_SHLVL=0 >>>>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>>>> # it is in a different relative location to condabin. >>>>>>> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >>>>>>> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >>>>>>> else >>>>>>> PATH="$(\dirname "$(\dirname >>>>>>> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >>>>>>> fi >>>>>>> \export PATH >>>>>>> >>>>>>> # We're not allowing PS1 to be unbound. It must at least be set. >>>>>>> # However, we're not exporting it, which can cause problems when >>>>>>> starting a second shell >>>>>>> # via a first shell (i.e. starting zsh from bash). >>>>>>> if [ -z "${PS1+x}" ]; then >>>>>>> PS1= >>>>>>> fi >>>>>>> fi >>>>>>> >>>>>>> conda activate base: not found >>>>>>> Traceback (most recent call last): >>>>>>> File >>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>>>> line 470, in <module> >>>>>>> main() >>>>>>> File >>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>>>> line 293, in main >>>>>>> installPluginMethods() >>>>>>> File >>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>>>>>> line 232, in installPluginMethods >>>>>>> plugin.installBin({'args': ['-j', numberProcessor]}) >>>>>>> File >>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>>>>>> line 166, in installBin >>>>>>> environment.execute() >>>>>>> File >>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>> line 748, in execute >>>>>>> self._executeTargets(targetList) >>>>>>> File >>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>> line 690, in _executeTargets >>>>>>> tgt.execute() >>>>>>> File >>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>> line 221, in execute >>>>>>> command.execute() >>>>>>> File >>>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>>> line 161, in execute >>>>>>> assert glob(t), ("target '%s' not built (after " >>>>>>> AssertionError: target >>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>>>> Error at main: target >>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>>>> >>>>>>> ------------------------------ >>>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>>> *To: *"scipion-users" <sci...@li...> >>>>>>> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >>>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>>> using Cryolo >>>>>>> >>>>>>> Dear Carlos, >>>>>>> given the fact that the installation has failed, could you attach >>>>>>> all output after "scipion3 installp -p scipion-em-sphire" command? >>>>>>> >>>>>>> Best regards, >>>>>>> Grigory >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------------- >>>>>>> Grigory Sharov, Ph.D. >>>>>>> >>>>>>> MRC Laboratory of Molecular Biology, >>>>>>> Francis Crick Avenue, >>>>>>> Cambridge Biomedical Campus, >>>>>>> Cambridge CB2 0QH, UK. >>>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>>> e-mail: gs...@mr... >>>>>>> >>>>>>> >>>>>>> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >>>>>>> car...@so...> wrote: >>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> I'm facing some problems using cryolo training at Scipion. >>>>>>>> I found the following error: >>>>>>>> >>>>>>>> *Protocol failed: Command ' source >>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>>>>>>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>>>>>>> --fine_tune' returned non-zero exit status 127. * >>>>>>>> >>>>>>>> I saw some discussion about that at Scipion lists, but I'm still >>>>>>>> little lost in how to fix it. >>>>>>>> In my scipion.conf file, I inserted >>>>>>>> *CONDA_ACTIVATION_CMD = source >>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>>>>>>> or even >>>>>>>> CONDA_ACTIVATION_CMD = >>>>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" >>>>>>>> (I saw these pathways in my bash.rc) >>>>>>>> >>>>>>>> Moreover, when I try to install cryolo using command line (scipion3 >>>>>>>> installp -p scipion-em-sphire), the following error apears: >>>>>>>> *AssertionError: target >>>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>>> built (after running 'source >>>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>>>>>>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>>>>>>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>>>>>>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>>>>>>> cryolo_1.7.6_installed')* >>>>>>>> >>>>>>>> I am not sure if these errors are related and hinder performing >>>>>>>> cryolo in Scipion. >>>>>>>> I have conda installed in the computer and I'm able to use cryolo >>>>>>>> 1.8 outside from Scipion in the same computer (using *source >>>>>>>> activate cryolo *command). >>>>>>>> >>>>>>>> Anyone know what I'm doing wrong? >>>>>>>> Thanks in advance, >>>>>>>> Carlos. >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> scipion-users mailing list >>>>>>>> sci...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> scipion-users mailing list >>>>>>> sci...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>> _______________________________________________ >>>>>>> scipion-users mailing list >>>>>>> sci...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>>> -- >>>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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