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From: Valérie B. <val...@ib...> - 2017-04-28 09:02:33
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Hello the test for 2D classification using CL2D worked and I tried to run the test for 2D classification using Relion which failed with an MPI error (see attached log file). Do you have any suggestion? thanks, best regards Valérie Biou Laboratoire de Biologie Physico-Chimique des Protéines Membranaires UMR 7099 CNRS/Univ. Paris Diderot P7 Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France |
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From: Valérie B. <bi...@ib...> - 2017-04-28 08:58:13
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Hello the test for 2D classification using CL2D worked and I tried to run the test for 2D classification using Relion which failed with an MPI error (see attached log file). Do you have any suggestion? thanks, best regards Valérie Biou Laboratoire de Biologie Physico-Chimique des Protéines Membranaires UMR 7099 CNRS/Univ. Paris Diderot P7 Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France |
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From: Pablo C. <pc...@cn...> - 2017-04-25 15:26:43
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Thanks Dmitry, Yaiza. Fix is already in release-1.1 branch. A git pull (providing you are already in release-1.1 branch should fix it). Cheers, Pablo. On 25/04/17 17:22, Yaiza Rancel wrote: > Hi Dmitry, > > Thanks for reporting this! Looks like there is a bug: scipion is > trying to get some arguments that are not supported in older > motioncor2 versions, only in the last one. A fix should be ready today > in branch release-1.1, try again after getting the latest code from > with git pull. You can also update motioncor2 to the latest version, > but that might require updating other dependencies (I think it > requires CUDA 8). > > Cheers, > > Yaiza Rancel > Scipion Team > > Activo Mar, 25 Abril at 12:04 PM , Dmitry Semchonok > <sem...@gm...> Escrito: > Dear colleagues, > > I have the issue with motioncorr2 protocol > > > It stops initially with the error > Protocol failed: 'ProtMotionCorr' object has no attribute 'doMagCor' > > Does anyone know why? > > Please see the image > > Встроенное изображение 1 > Sincerely, > Dmitry > > 116:553135 > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Yaiza R. <su...@bc...> - 2017-04-25 15:22:36
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Hi Dmitry,
Thanks for reporting this! Looks like there is a bug: scipion is trying to get some arguments that are not supported in older motioncor2 versions, only in the last one. A fix should be ready today in branch release-1.1, try again after getting the latest code from with git pull. You can also update motioncor2 to the latest version, but that might require updating other dependencies (I think it requires CUDA 8).
Cheers,
Yaiza Rancel
Scipion Team
Activo Mar, 25 Abril at 12:04 PM
, Dmitry Semchonok <sem...@gm...> Escrito:
Dear colleagues,
I have the issue with motioncorr2 protocol
It stops initially with the error Protocol failed: 'ProtMotionCorr' object has no attribute 'doMagCor'
Does anyone know why?
Please see the image
Sincerely,
Dmitry
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From: Dmitry S. <sem...@gm...> - 2017-04-25 10:04:15
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Dear colleagues, I have the issue with motioncorr2 protocol It stops initially with the error Protocol failed: 'ProtMotionCorr' object has no attribute 'doMagCor' Does anyone know why? Please see the image [image: Встроенное изображение 1] Sincerely, Dmitry |
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From: Grigory S. <sha...@gm...> - 2017-04-24 21:11:52
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Hi, Eman 1 box format saves bottom left corner of the box and box size, while Eman2 saves center of the boxes in json format On Apr 24, 2017 22:03, "Juha Huiskonen" <ju...@st...> wrote: > Hi Dennis, > > I believe xmipp is the center coordinate and EMAN is lower left followed > by the box size > > Best wishes, > Juha > > -- > Juha T. Huiskonen, PhD > Associate Professor > > Principal Investigator > Joint Head of Oxford Particle Imaging Centre > Division of Structural Biology > University of Oxford > > On 24 Apr 2017, at 15:35, Dennis Thomas <dt...@pr...> > wrote: > > Hi I very much like the xmipp particle picking in Scipion but wanted to > extract the particles in EMAN. The *.pos file is not read by EMAN so I > wrote a script to convert the file to an EMAN .box format. However the > particles extracted are wrong meaning nothing centered. Does xmipp save the > center, top left or are the micrograph coordinates defined differently from > EMAN? > > Thanks, > > Dennis > > > -- > Dr. Dennis Thomas > Cryo-EM Facility Manager > Center for Integrative Proteomics Research > Rutgers University > Phone: 848-445-5302 > > <dthomas.vcf> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Juha H. <ju...@st...> - 2017-04-24 21:03:00
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Hi Dennis, I believe xmipp is the center coordinate and EMAN is lower left followed by the box size Best wishes, Juha -- Juha T. Huiskonen, PhD Associate Professor Principal Investigator Joint Head of Oxford Particle Imaging Centre Division of Structural Biology University of Oxford > On 24 Apr 2017, at 15:35, Dennis Thomas <dt...@pr...> wrote: > > Hi I very much like the xmipp particle picking in Scipion but wanted to extract the particles in EMAN. The *.pos file is not read by EMAN so I wrote a script to convert the file to an EMAN .box format. However the particles extracted are wrong meaning nothing centered. Does xmipp save the center, top left or are the micrograph coordinates defined differently from EMAN? > > Thanks, > > Dennis > > > -- > Dr. Dennis Thomas > Cryo-EM Facility Manager > Center for Integrative Proteomics Research > Rutgers University > Phone: 848-445-5302 > > <dthomas.vcf> > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Jose M. de la R. T. <del...@gm...> - 2017-04-24 20:50:40
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Dear Dennis, Thanks a lot for your feedback. The coordinates in Xmipp/Scipion store the center of the coordinate. If you manage to write an script to convert the coordinates, I would encourage you to try to write a protocol in Scipion to extract particles with Eman (version 2 or 1, we only support Eman2). In that way other users that want to extract with Eman2 may greatly benefit. If you are interested I can help you with that. If not, I can also help with converting the SetOfCoordinates to EMAN .box files. Cheers, Jose Miguel On Mon, Apr 24, 2017 at 9:35 PM, Dennis Thomas < dt...@pr...> wrote: > Hi I very much like the xmipp particle picking in Scipion but wanted to > extract the particles in EMAN. The *.pos file is not read by EMAN so I > wrote a script to convert the file to an EMAN .box format. However the > particles extracted are wrong meaning nothing centered. Does xmipp save the > center, top left or are the micrograph coordinates defined differently from > EMAN? > > Thanks, > > Dennis > > > -- > Dr. Dennis Thomas > Cryo-EM Facility Manager > Center for Integrative Proteomics Research > Rutgers University > Phone: 848-445-5302 > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dennis T. <dt...@pr...> - 2017-04-24 19:53:12
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Hi I very much like the xmipp particle picking in Scipion but wanted to extract the particles in EMAN. The *.pos file is not read by EMAN so I wrote a script to convert the file to an EMAN .box format. However the particles extracted are wrong meaning nothing centered. Does xmipp save the center, top left or are the micrograph coordinates defined differently from EMAN? Thanks, Dennis -- Dr. Dennis Thomas Cryo-EM Facility Manager Center for Integrative Proteomics Research Rutgers University Phone: 848-445-5302 |
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From: Wolfgang L. <w.l...@uk...> - 2017-04-24 15:01:22
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dear jose miguel, the particles file is from relion2 after 3d. the alignment property says: _alignment = None 373 String the same star file has been successfully used via the localrec command line to extract sub-particles. cheers, wolfgang On 04/24/2017 04:34 PM, Jose Miguel de la Rosa Trevin wrote: > Hi Wolfgang, > > The 'hasAlignmentProj' is a property that SetOfParticles can have, it > means that particles have projection-alignment information, i.e, the > Euler angles to make a reconstruction. This information is required in > this protocol because localrec will take that information together > with the symmetry and the vectors to generate another SetOfParticles > (called sub-particles here) with another angular information (also > projection-alignment). Can you check that the 'projection-alignment' > is properly set after the import of particles. If you select the > import job, you can click in the 'db' icon and the 'alignment' > property under the outputParticles object. Have you imported the star > file of the particles after 3D refinement or classification? > > Hope this helps, > Jose Miguel. > > > On Mon, Apr 24, 2017 at 3:39 PM, Wolfgang Lugmayr > <wol...@im... > <mailto:wol...@im...>> wrote: > > dear all, > > we can run localrec in the given configuration from the > commandline (by > adding some environment settings). > > when we try to use it from the gui we have the following problem: > -> view: localized reconstruction > -> 1. compute sub-particles > -> input particles > > we cannot choose our imported particle file (from relion). > > what step must be done before that this particle set shows up? > or whats means "SetOfParticles (condition: hasAlignmentProj)"? > > thanks in advance for any related comments, > cheers, > wolfgang > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Institute of Molecular Biotechnology (IMBA) > Dr. Bohr-Gasse 3-7 (Room 6.14) > 1030 Vienna, Austria > Tel.: +43 (1) 790 44-4649 <tel:%2B43%20%281%29%20790%2044-4649> > Email: w.l...@uk... <mailto:w.l...@uk...> > http://www.cssb-hamburg.de/ > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > 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> > > -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.l...@uk... http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING |
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From: Jose M. de la R. T. <del...@gm...> - 2017-04-24 14:34:15
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Hi Wolfgang, The 'hasAlignmentProj' is a property that SetOfParticles can have, it means that particles have projection-alignment information, i.e, the Euler angles to make a reconstruction. This information is required in this protocol because localrec will take that information together with the symmetry and the vectors to generate another SetOfParticles (called sub-particles here) with another angular information (also projection-alignment). Can you check that the 'projection-alignment' is properly set after the import of particles. If you select the import job, you can click in the 'db' icon and the 'alignment' property under the outputParticles object. Have you imported the star file of the particles after 3D refinement or classification? Hope this helps, Jose Miguel. On Mon, Apr 24, 2017 at 3:39 PM, Wolfgang Lugmayr < wol...@im...> wrote: > dear all, > > we can run localrec in the given configuration from the commandline (by > adding some environment settings). > > when we try to use it from the gui we have the following problem: > -> view: localized reconstruction > -> 1. compute sub-particles > -> input particles > > we cannot choose our imported particle file (from relion). > > what step must be done before that this particle set shows up? > or whats means "SetOfParticles (condition: hasAlignmentProj)"? > > thanks in advance for any related comments, > cheers, > wolfgang > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Institute of Molecular Biotechnology (IMBA) > Dr. Bohr-Gasse 3-7 (Room 6.14) > 1030 Vienna, Austria > Tel.: +43 (1) 790 44-4649 > Email: w.l...@uk... > http://www.cssb-hamburg.de/ > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Wolfgang L. <wol...@im...> - 2017-04-24 14:14:37
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dear all, we can run localrec in the given configuration from the commandline (by adding some environment settings). when we try to use it from the gui we have the following problem: -> view: localized reconstruction -> 1. compute sub-particles -> input particles we cannot choose our imported particle file (from relion). what step must be done before that this particle set shows up? or whats means "SetOfParticles (condition: hasAlignmentProj)"? thanks in advance for any related comments, cheers, wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.l...@uk... http://www.cssb-hamburg.de/ |
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From: Pablo C. <pc...@cn...> - 2017-04-21 07:30:43
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Thanks David: scipion config --update is probably a misleading command. It does not touch already existing variables. It only adds those missing. So, not actually the right command for a "release" update. Sorry my bad!. We will come up with a something to make a smooth version update. So, you've manage to have everything running? Kind regards, Pablo. > On Thu, Apr 20, 2017 at 9:02 PM, David Belnap <db...@co... > <mailto:db...@co...>> wrote: > > Pablo, > > It seems that the ~/.config/scipion/scipion.conf is not getting > updated with the new directory names. I recompiled Scipion > release-1.1 (per your instructions in another email), deleted all > attached packages, and installed RELION 2.0.3. When I tried to > run a RELION routine inside Scipion, I got an error that the > RELION_HOME variable in ~/.config/scipion/scipion.conf was not > right. I renamed ~/.config/scipion/scipion.conf > to ~/.config/scipion/scipion.conf.old and ran "./scipion config > —update”. That gave me a new ~/.config/scipion/scipion.conf that > points to the right RELION directory. I think this should also > fix any need to make the link I mentioned earlier in this thread. > > David > > >> On Apr 17, 2017, at 11:12 PM, Pablo Conesa <pc...@cn... >> <mailto:pc...@cn...>> wrote: >> >> Thank you David for the feedback. >> >> >> On 17/04/17 20:09, David Belnap wrote: >>> Two minor problems when I installed release-1.1: >>> >>> 1. Many packages that I had installed were not recognized when I ran “./scipion install —help”. Only bsoft 1.9.0, dog picker, and chimera in one of my two installations. I deleted all packages (by deleting the directories and files in the software/em directory. Then I reinstalled the packages. Now, the ones I installed can be seen. >> >> Yes you are right, what happens here is that the config (at >> ~/.config/scipion/scipion.conf) points to the new installation >> paths while your previous installation has different folder names. >> >> As an example, and mainly for other in the list. >> >> In Scipion V1.0 path to relion was like >> <scipion_home>/software/em/relion >> whereas in new version is <scipion_home>/software/em/relion-2.0 >> (pattern is package-version) >> >> I guess you ended up with a new config file (with new pattern -> >> package-version) but your actual folder remain with old names. So >> renaming the folder to the new pattern would have been another >> way to fix it. >> >> We will think about this because, and at least document the >> "update" process and ideally come up with a smooth "migration" of >> the config files. >>> 2. I needed to make the following link to get CTFFIND4 to work in release-1.1 (in directory …/scipion/software/em): >>> ctffind4 -> ctffind4-4.1.5/ >> Same here. links will also work!. >> >> Thanks again for the feedback. >>> David >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites,Slashdot.org <http://slashdot.org>!http://sdm.link/slashdot >>> _______________________________________________ >>> 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> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org <http://slashdot.org>! >> http://sdm.link/slashdot_______________________________________________ >> <http://sdm.link/slashdot_______________________________________________> >> 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> > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ 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> > |
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From: Jose M. de la R. T. <del...@gm...> - 2017-04-20 19:13:44
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Thanks for the feedback David, I think we need to check this to facilitate the upgrade to other users. Cheers, Jose Miguel On Thu, Apr 20, 2017 at 9:02 PM, David Belnap <db...@co...> wrote: > Pablo, > > It seems that the ~/.config/scipion/scipion.conf is not getting updated > with the new directory names. I recompiled Scipion release-1.1 (per your > instructions in another email), deleted all attached packages, and > installed RELION 2.0.3. When I tried to run a RELION routine inside > Scipion, I got an error that the RELION_HOME variable > in ~/.config/scipion/scipion.conf was not right. I > renamed ~/.config/scipion/scipion.conf to ~/.config/scipion/scipion.conf.old > and ran "./scipion config —update”. That gave me a > new ~/.config/scipion/scipion.conf that points to the right RELION > directory. I think this should also fix any need to make the link I > mentioned earlier in this thread. > > David > > > On Apr 17, 2017, at 11:12 PM, Pablo Conesa <pc...@cn...> wrote: > > Thank you David for the feedback. > > On 17/04/17 20:09, David Belnap wrote: > > Two minor problems when I installed release-1.1: > > 1. Many packages that I had installed were not recognized when I ran “./scipion install —help”. Only bsoft 1.9.0, dog picker, and chimera in one of my two installations. I deleted all packages (by deleting the directories and files in the software/em directory. Then I reinstalled the packages. Now, the ones I installed can be seen. > > > Yes you are right, what happens here is that the config (at > ~/.config/scipion/scipion.conf) points to the new installation paths > while your previous installation has different folder names. > > As an example, and mainly for other in the list. > > In Scipion V1.0 path to relion was like <scipion_home>/software/em/relion > whereas in new version is <scipion_home>/software/em/relion-2.0 (pattern > is package-version) > > I guess you ended up with a new config file (with new pattern -> package- > version) but your actual folder remain with old names. So renaming the > folder to the new pattern would have been another way to fix it. > > We will think about this because, and at least document the "update" > process and ideally come up with a smooth "migration" of the config files. > > 2. I needed to make the following link to get CTFFIND4 to work in release-1.1 (in directory …/scipion/software/em): > ctffind4 -> ctffind4-4.1.5/ > > Same here. links will also work!. > > Thanks again for the feedback. > > David > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org>! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org>! > http://sdm.link/slashdot_______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: David B. <db...@co...> - 2017-04-20 19:02:49
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Pablo, It seems that the ~/.config/scipion/scipion.conf is not getting updated with the new directory names. I recompiled Scipion release-1.1 (per your instructions in another email), deleted all attached packages, and installed RELION 2.0.3. When I tried to run a RELION routine inside Scipion, I got an error that the RELION_HOME variable in ~/.config/scipion/scipion.conf was not right. I renamed ~/.config/scipion/scipion.conf to ~/.config/scipion/scipion.conf.old and ran "./scipion config —update”. That gave me a new ~/.config/scipion/scipion.conf that points to the right RELION directory. I think this should also fix any need to make the link I mentioned earlier in this thread. David On Apr 17, 2017, at 11:12 PM, Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote: Thank you David for the feedback. On 17/04/17 20:09, David Belnap wrote: Two minor problems when I installed release-1.1: 1. Many packages that I had installed were not recognized when I ran “./scipion install —help”. Only bsoft 1.9.0, dog picker, and chimera in one of my two installations. I deleted all packages (by deleting the directories and files in the software/em directory. Then I reinstalled the packages. Now, the ones I installed can be seen. Yes you are right, what happens here is that the config (at ~/.config/scipion/scipion.conf) points to the new installation paths while your previous installation has different folder names. As an example, and mainly for other in the list. In Scipion V1.0 path to relion was like <scipion_home>/software/em/relion whereas in new version is <scipion_home>/software/em/relion-2.0 (pattern is package-version) I guess you ended up with a new config file (with new pattern -> package-version) but your actual folder remain with old names. So renaming the folder to the new pattern would have been another way to fix it. We will think about this because, and at least document the "update" process and ideally come up with a smooth "migration" of the config files. 2. I needed to make the following link to get CTFFIND4 to work in release-1.1 (in directory …/scipion/software/em): ctffind4 -> ctffind4-4.1.5/ Same here. links will also work!. Thanks again for the feedback. David ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://slashdot.org>! http://sdm.link/slashdot _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://slashdot.org>! http://sdm.link/slashdot_______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2017-04-18 05:48:52
|
Thanks again, David On 17/04/17 23:27, David Belnap wrote: > I began using release-1.1 last week. I experienced an extreme slowdown of the Xmipp manual particle picking routine. My system administrator suggested I use different compiler and libraries. If I want to recompile everything in Scipion without deleting the files and redownloading everything, how do I do that? It seems the normal “./scipion install -j X” will only compile new code. If you want to compile just the java bits.....do: *rm software/em/xmipp/java/lib/Xmipp** and then *./scipion install -j 4* (number of CPUs to use for compilation) If you want to clean all, you have a clean script, run: *python <scipion_home>/scripts/clean.py* NOTE this will clean only Xmipp (.so, .os .o) files. If you want all installation then run: *python <scipion_home>/scripts/clean.py all* will make a deep clean of everything except EM packages and configuration files. It will be almost like a fresh start. and then *./scipion install -j 4* I'm also concerned about the "extreme slowdown of the Xmipp manual particle picking"..we haven't experienced it. So please, if reinstallation does not speeds it up, let us know to investigate. > Thanks. Thanks, Pablo. > David > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2017-04-18 05:12:33
|
Thank you David for the feedback. On 17/04/17 20:09, David Belnap wrote: > Two minor problems when I installed release-1.1: > > 1. Many packages that I had installed were not recognized when I ran “./scipion install —help”. Only bsoft 1.9.0, dog picker, and chimera in one of my two installations. I deleted all packages (by deleting the directories and files in the software/em directory. Then I reinstalled the packages. Now, the ones I installed can be seen. Yes you are right, what happens here is that the config (at ~/.config/scipion/scipion.conf) points to the new installation paths while your previous installation has different folder names. As an example, and mainly for other in the list. In Scipion V1.0 path to relion was like <scipion_home>/software/em/relion whereas in new version is <scipion_home>/software/em/relion-2.0 (pattern is package-version) I guess you ended up with a new config file (with new pattern -> package-version) but your actual folder remain with old names. So renaming the folder to the new pattern would have been another way to fix it. We will think about this because, and at least document the "update" process and ideally come up with a smooth "migration" of the config files. > 2. I needed to make the following link to get CTFFIND4 to work in release-1.1 (in directory …/scipion/software/em): > ctffind4 -> ctffind4-4.1.5/ Same here. links will also work!. Thanks again for the feedback. > David > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: David B. <db...@co...> - 2017-04-17 21:28:06
|
I began using release-1.1 last week. I experienced an extreme slowdown of the Xmipp manual particle picking routine. My system administrator suggested I use different compiler and libraries. If I want to recompile everything in Scipion without deleting the files and redownloading everything, how do I do that? It seems the normal “./scipion install -j X” will only compile new code. Thanks. David |
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From: David B. <db...@co...> - 2017-04-17 18:09:42
|
Two minor problems when I installed release-1.1: 1. Many packages that I had installed were not recognized when I ran “./scipion install —help”. Only bsoft 1.9.0, dog picker, and chimera in one of my two installations. I deleted all packages (by deleting the directories and files in the software/em directory. Then I reinstalled the packages. Now, the ones I installed can be seen. 2. I needed to make the following link to get CTFFIND4 to work in release-1.1 (in directory …/scipion/software/em): ctffind4 -> ctffind4-4.1.5/ David |
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From: Laura d. C. <su...@bc...> - 2017-04-17 09:58:20
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Hi Dmitry Semchonok, did you manage to proceed with the outputMicrographs in spite of the noDim message? you could also send us the output log of the xmipp3 movie alignment protocol to check if some movies had problems. thanks Laura Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/86 Activo Mar, 4 Abril at 5:32 PM , Biocomputing unit - National Center for Biotechnology <sc...@cn...> Escrito: Dear Dmitry, On 04/04/17 11:29, Dmitry Semchonok wrote: Dear colleagues, After running the xmipp3 movie alignment I got the result that I could not yet understand: I run xmipp3 movie alignment after xmipp3 correlation alignment using those file as an input. In the summary of xmipp3 movie alignment I got the following inputMovies (from xmipp3 - correlation alignment CPU/threads_no cluster 2 -> output SetOfMovies (5140 items ........) Output xmipp3 - movie alignment new 3 -> outputMicrographs SetOfMicrographs (4166 items, No-Dim ......A/px) This is strange in two ways (there is no dimension and the number of micrographs differ from the number of movies) xmipp3 - movie alignment new 3 -> outputMicrographsDoseWeighted SetOfMicrographs (5138 items, 3838 x 3710, ....A/px) Here also the number of micrographs is different. and then below SUMMARY Number of input movies 5140 So my questions are: 1. Why the input doesn't corresponds to output? (problems inside the stack?) I don't know, it is the first time I see this behavior, let's see if any of the other developers has seen it. 2. Which file to use for the CTF estimation - outputMicrographs (4166 items, No-Dim ) or outputMicrographsDoseWeighted (5138) I would use the outputMicrographs and hope that the no-dim message does not really mean an underlying error of the constructed set. Kind regards, Carlos Oscar Thank you! Sincerely, Dmitry ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Carlos O. S. <co...@cn...> - 2017-04-17 07:47:29
|
Hi Dmitry, thank you very much for the report. From the description below my guess is that the image FoilHole_144642_Data_31178828_31178829_20170202_1415_framestack.mrc is corrupted. Can you do an ls with its size and compare it to the size of other movies to check if the file is only half written? A different issue, which is on our side, is that the protocol should be robust to corrupted images. In which branch are you processing, so that we may try to reproduce the error and make the process more robust? Kind regards, Carlos Oscar On 04/16/17 19:01, Dmitry Semchonok wrote: > Dear colleagues, > > I still have an issue running xmipp3 - optical correction protocol. > > I tried to run it on GPU. It went fine until the image 3104 out of 5141. > > I tried to restart it but every time the same error appeared again. > > Could you please give any suggestion? > > Please see the error pictures in the attachment > > > > Thank you and have a nice Easter! > > Sincerely, > Dmitry > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Dmitry S. <sem...@gm...> - 2017-04-16 17:01:30
|
Dear colleagues, I still have an issue running xmipp3 - optical correction protocol. I tried to run it on GPU. It went fine until the image 3104 out of 5141. I tried to restart it but every time the same error appeared again. Could you please give any suggestion? Please see the error pictures in the attachment Thank you and have a nice Easter! Sincerely, Dmitry |
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From: David B. <db...@co...> - 2017-04-14 13:45:35
|
Jose Miguel,
Thank you for those instructions. I did the following:
1) git diff (see output below)
2) git stash (see output below)
3) git checkout release-1.1 (successful this time, see output below)
4) git pull (not necessary, “Already up-to-date.”)
5) ./scipion install -j 6 (Got immediate error "Warning: Missing section 'VARIABLES' in the configuration file ~/.config/scipion/scipion.conf”)
I did control-C to stop this process.
6) ./scipion config —update (Got message “All seems fine with ~/Programs/scipion/config/scipion.conf”)
7) ./scipion install -j 6 (Got error:
/usr/bin/ld: cannot find -lmpi_cxx
collect2: error: ld returned 1 exit status
scons: *** [software/em/xmipp/bin/xmipp_mpi_angular_continuous_assign2] Error 1
scons: building terminated because of errors.
8) git stash pop (see below)
9) ./scipion install -j 6 (“Congratulations, Scipion was installed successfully”)
Version 1.1 is now running. Thank you very much.
David
$ git diff
diff --git a/SConstruct b/SConstruct
index 3c8e2d8..ac366de 100644
--- a/SConstruct
+++ b/SConstruct
@@ -133,7 +133,7 @@ def CheckMPI(context, mpi_inc, mpi_libpath, mpi_lib, mpi_cc, mpi_cxx, mpi_link,
context.env.Append(LIBS=mpi_lib, LIBPATH=mpi_libpath,
CPPPATH=mpi_inc)
context.env.Replace(LINK=mpi_link)
- context.env.Replace(CC=mpi_cc, CXX=mpi_cxx)
+ context.env.Replace(CC=mpicc, CXX=mpicxx)
# Test only C++ mpi compiler
ret = context.TryLink('''
diff --git a/software/em/xmipp/scipion_sconscript b/software/em/xmipp/scipion_sconscript
index 275369d..426ff84 100644
--- a/software/em/xmipp/scipion_sconscript
+++ b/software/em/xmipp/scipion_sconscript
@@ -448,7 +448,7 @@ def addProg(progName, **kwargs):
if progName.startswith('mpi_'):
kwargs['mpi'] = True
- kwargs['libs'] += ['mpi', 'mpi_cxx', 'XmippParallel']
+ kwargs['libs'] += ['mpi', 'mpicxx', 'XmippParallel']
xmippProgName = 'xmipp_%s' % progName
$ git stash
Saved working directory and index state WIP on master: 1dfd3db Merge pull request #706 from I2PC/hotfix_java_compiling_utf_chars_error
HEAD is now at 1dfd3db Merge pull request #706 from I2PC/hotfix_java_compiling_utf_chars_error
$ git checkout release-1.1
Checking out files: 100% (773/773), done.
Branch release-1.1 set up to track remote branch release-1.1 from origin.
Switched to a new branch 'release-1.1'
$ git stash pop
Auto-merging software/em/xmipp/scipion_sconscript
Auto-merging SConstruct
# On branch release-1.1
# Changes not staged for commit:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# modified: SConstruct
# modified: software/em/xmipp/scipion_sconscript
#
# Untracked files:
# (use "git add <file>..." to include in what will be committed)
#
# SConstruct.old
# software/em/xmipp/scipion_sconscript.old
no changes added to commit (use "git add" and/or "git commit -a")
Dropped refs/stash@{0} (080c0d50247efc67c31ec99c4a9deb82a8fbda65)
On Apr 14, 2017, at 2:19 AM, Jose Miguel de la Rosa Trevin <del...@gm...<mailto:del...@gm...>> wrote:
Hi David,
It seems like you have some local modifications to the files:
SConstruct
software/em/xmipp/scipion_sconscript
Can you post the output of the command 'git diff', this should show the modifications
of these files, that could be some tweaks to make Scipion/Xmipp compile in your system.
It would be good to check if the modifications is something particular or a fix that
have been included in the more recent code.
Anyway, you can "store" the changes temporary by doing: 'git stash',
then getting the latest changes: 'git pull', and if needed, restore back the changes: 'git stash pop'
And if there are not conflicts you can proceed with the './scipion install -j 6'. Although you may
also update your config files with a './scipion config --update'
Maybe we should add this instruction in a wikipage since I guess more users will need this information.
Kind regards,
Jose Miguel
On Fri, Apr 14, 2017 at 5:55 AM, David Belnap <db...@co...<mailto:db...@co...>> wrote:
Pablo,
I tried to update my installation of Scipion (v1.0.1) to the release-1.1 branch by following the instructions below. I did “git pull” and “./scipion install -j 6” before I noticed the message below. When I did “git checkout release-1.1”, I get the following error message:
$ git checkout release-1.1
error: Your local changes to the following files would be overwritten by checkout:
SConstruct
software/em/xmipp/scipion_sconscript
Please, commit your changes or stash them before you can switch branches.
Aborting
What should I do to get past this problem?
Thanks.
David Belnap
On Mar 10, 2017, at 7:32 AM, Dmitry A. Semchonok <sem...@gm...<mailto:sem...@gm...>> wrote:
Dear Pablo,
I'm now at the particle picking stage.
We applied the fix for that updates of the protocols in the SCIPION 1.1. The problem still remains - some particles i can not delete pressing shift+left mouse button. But i noticed that if i use only the eraser tool then i can delete all the selections.
Sincerely,
Dmitry
Hi Dmitry, did this worked?
All the best, Pablo.
Scipion team
Activo Mar, 7 Marzo at 10:42 AM , Pablo Conesa <su...@bc...<mailto:su...@bc...>> Escrito:
Hi Dmitry,
May I recomend you to switch to release-1.1 branch. Reasons are:
Now devel and release-1.1 are almost similar. Differences are that release has more activity and bugfixes are pushed first to release-1.1 and after a while they end up un devel. Like in this case for the picking bug that is not yet in devel but soon will be.
You will also help us to test the future release while using it.
To do so, follow Jose Miguel steps but switch to release-1.1:
git pull # and this should bring the changes...and release-1.1 branch if not yet local.
git checkout release-1.1 #This switches you to release-1.1 branch
git pull # Again, this might not be needed, but I use to do it to be sure I have the latest changes.
scipion install -j N # replace N by an integer, it means how many CPUs you want to use to compile
scipion install is optimized and will only compile what has changed and EM packages are not reinstall. It should not take long.
Let us know how it goes?
All the best, Pablo.
Activo Lun, 6 Marzo at 5:08 PM , Dmitry Semchonok <sem...@gm...<mailto:sem...@gm...>> Escrito:
Dear colleagues,
If there an easy way to update the xmipp - particle picking protocol in
Scipion_dev (or any other protocol inside Scipion dev that was bug fixed)
without reinstalling everything?
Sincerely,
Dmitry
------------------------------------------------------------------------------
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dictionary content that is easy and intuitive to access. Sign up for an
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------------------------------------------------------------------------------
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|
From: Jose M. de la R. T. <del...@gm...> - 2017-04-14 08:19:35
|
Hi David, It seems like you have some local modifications to the files: SConstruct software/em/xmipp/scipion_sconscript Can you post the output of the command 'git diff', this should show the modifications of these files, that could be some tweaks to make Scipion/Xmipp compile in your system. It would be good to check if the modifications is something particular or a fix that have been included in the more recent code. Anyway, you can "store" the changes temporary by doing: 'git stash', then getting the latest changes: 'git pull', and if needed, restore back the changes: 'git stash pop' And if there are not conflicts you can proceed with the './scipion install -j 6'. Although you may also update your config files with a './scipion config --update' Maybe we should add this instruction in a wikipage since I guess more users will need this information. Kind regards, Jose Miguel On Fri, Apr 14, 2017 at 5:55 AM, David Belnap <db...@co...> wrote: > Pablo, > > I tried to update my installation of Scipion (v1.0.1) to the release-1.1 > branch by following the instructions below. I did “git pull” and > “./scipion install -j 6” before I noticed the message below. When I did > “git checkout release-1.1”, I get the following error message: > > $ git checkout release-1.1 > error: Your local changes to the following files would be overwritten by > checkout: > SConstruct > software/em/xmipp/scipion_sconscript > Please, commit your changes or stash them before you can switch branches. > Aborting > > What should I do to get past this problem? > > Thanks. > > David Belnap > > > On Mar 10, 2017, at 7:32 AM, Dmitry A. Semchonok <sem...@gm...> > wrote: > > Dear Pablo, > > I'm now at the particle picking stage. > > We applied the fix for that updates of the protocols in the SCIPION 1.1. > The problem still remains - some particles i can not delete pressing > shift+left mouse button. But i noticed that if i use only the eraser tool > then i can delete all the selections. > > Sincerely, > Dmitry > Hi Dmitry, did this worked? > > All the best, Pablo. > Scipion team > > Activo Mar, 7 Marzo at 10:42 AM , Pablo Conesa < > su...@bc...> Escrito: > Hi Dmitry, > > May I recomend you to switch to release-1.1 branch. Reasons are: > > Now devel and release-1.1 are almost similar. Differences are that release > has more activity and bugfixes are pushed first to release-1.1 and after a > while they end up un devel. Like in this case for the picking bug that is > not yet in devel but soon will be. > > You will also help us to test the future release while using it. > > To do so, follow Jose Miguel steps but switch to release-1.1: > > > *git pull # *and this should bring the changes...and release-1.1 branch > if not yet local. > > *git checkout release-1.1 *#This switches you to release-1.1 branch > > *git pull *# Again, this might not be needed, but I use to do it to be > sure I have the latest changes. > *scipion install -j N *# replace N by an integer, it means how many CPUs > you want to use to compile > > scipion install is optimized and will only compile what has changed and EM > packages are not reinstall. It should not take long. > > Let us know how it goes? > > All the best, Pablo. > > > Activo Lun, 6 Marzo at 5:08 PM , Dmitry Semchonok <sem...@gm...> > Escrito: > Dear colleagues, > > If there an easy way to update the xmipp - particle picking protocol in > Scipion_dev (or any other protocol inside Scipion dev that was bug fixed) > without reinstalling everything? > > Sincerely, > > Dmitry > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org <http://slashdot.org>! > http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > 52 > ------------------------------------------------------------ > ------------------ > Announcing the Oxford Dictionaries API! The API offers world-renowned > dictionary content that is easy and intuitive to access. Sign up for an > account today to start using our lexical data to power your apps and > projects. Get started today and enter our developer competition. > http://sdm.link/oxford_______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: David B. <db...@co...> - 2017-04-14 04:08:26
|
Pablo, I tried to update my installation of Scipion (v1.0.1) to the release-1.1 branch by following the instructions below. I did “git pull” and “./scipion install -j 6” before I noticed the message below. When I did “git checkout release-1.1”, I get the following error message: $ git checkout release-1.1 error: Your local changes to the following files would be overwritten by checkout: SConstruct software/em/xmipp/scipion_sconscript Please, commit your changes or stash them before you can switch branches. Aborting What should I do to get past this problem? Thanks. David Belnap On Mar 10, 2017, at 7:32 AM, Dmitry A. Semchonok <sem...@gm...<mailto:sem...@gm...>> wrote: Dear Pablo, I'm now at the particle picking stage. We applied the fix for that updates of the protocols in the SCIPION 1.1. The problem still remains - some particles i can not delete pressing shift+left mouse button. But i noticed that if i use only the eraser tool then i can delete all the selections. Sincerely, Dmitry Hi Dmitry, did this worked? All the best, Pablo. Scipion team Activo Mar, 7 Marzo at 10:42 AM , Pablo Conesa <su...@bc...<mailto:su...@bc...>> Escrito: Hi Dmitry, May I recomend you to switch to release-1.1 branch. Reasons are: Now devel and release-1.1 are almost similar. Differences are that release has more activity and bugfixes are pushed first to release-1.1 and after a while they end up un devel. Like in this case for the picking bug that is not yet in devel but soon will be. You will also help us to test the future release while using it. To do so, follow Jose Miguel steps but switch to release-1.1: git pull # and this should bring the changes...and release-1.1 branch if not yet local. git checkout release-1.1 #This switches you to release-1.1 branch git pull # Again, this might not be needed, but I use to do it to be sure I have the latest changes. scipion install -j N # replace N by an integer, it means how many CPUs you want to use to compile scipion install is optimized and will only compile what has changed and EM packages are not reinstall. It should not take long. Let us know how it goes? All the best, Pablo. Activo Lun, 6 Marzo at 5:08 PM , Dmitry Semchonok <sem...@gm...<mailto:sem...@gm...>> Escrito: Dear colleagues, If there an easy way to update the xmipp - particle picking protocol in Scipion_dev (or any other protocol inside Scipion dev that was bug fixed) without reinstalling everything? Sincerely, Dmitry ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org<http://slashdot.org>! http://sdm.link/slashdot _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users 52 ------------------------------------------------------------------------------ Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford_______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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