Menu
▾
▴
scipion-users — Mailing list for Scipion users
You can subscribe to this list here.
| 2016 |
Jan
(2) |
Feb
(13) |
Mar
(9) |
Apr
(4) |
May
(5) |
Jun
(2) |
Jul
(8) |
Aug
(3) |
Sep
(25) |
Oct
(7) |
Nov
(49) |
Dec
(15) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2017 |
Jan
(24) |
Feb
(36) |
Mar
(53) |
Apr
(44) |
May
(37) |
Jun
(34) |
Jul
(12) |
Aug
(15) |
Sep
(14) |
Oct
(9) |
Nov
(9) |
Dec
(7) |
| 2018 |
Jan
(16) |
Feb
(9) |
Mar
(27) |
Apr
(39) |
May
(8) |
Jun
(24) |
Jul
(22) |
Aug
(11) |
Sep
(1) |
Oct
|
Nov
|
Dec
|
| 2019 |
Jan
(4) |
Feb
(5) |
Mar
|
Apr
(1) |
May
(21) |
Jun
(13) |
Jul
(31) |
Aug
(22) |
Sep
(9) |
Oct
(19) |
Nov
(24) |
Dec
(12) |
| 2020 |
Jan
(30) |
Feb
(12) |
Mar
(16) |
Apr
(4) |
May
(37) |
Jun
(17) |
Jul
(19) |
Aug
(15) |
Sep
(26) |
Oct
(84) |
Nov
(64) |
Dec
(55) |
| 2021 |
Jan
(18) |
Feb
(58) |
Mar
(26) |
Apr
(88) |
May
(51) |
Jun
(36) |
Jul
(31) |
Aug
(37) |
Sep
(79) |
Oct
(15) |
Nov
(29) |
Dec
(8) |
| 2022 |
Jan
(5) |
Feb
(8) |
Mar
(29) |
Apr
(21) |
May
(11) |
Jun
(11) |
Jul
(18) |
Aug
(16) |
Sep
(6) |
Oct
(10) |
Nov
(23) |
Dec
(1) |
| 2023 |
Jan
(18) |
Feb
|
Mar
(4) |
Apr
|
May
(3) |
Jun
(10) |
Jul
(1) |
Aug
|
Sep
|
Oct
(1) |
Nov
(3) |
Dec
(5) |
| 2024 |
Jan
(2) |
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2025 |
Jan
(1) |
Feb
|
Mar
|
Apr
(5) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Carlos O. S. <co...@cn...> - 2021-02-23 19:17:45
|
Dear David, this compilation issue really goes out of my expertise. Which are the compilation errors you see? If they are solved by using different functions from Xmipp, we may try to solve them. If you want, we could have a separate call to see these errors in detail. Kind regards, Carlos Oscar On 2/23/21 12:40 PM, Pablo Conesa wrote: > > > -------- Forwarded Message -------- > Subject: Re: [scipion-users] make externally compiled HDF5 available > for xmipp compile > Date: Fri, 19 Feb 2021 11:22:13 -0500 > From: Hoover, David (NIH/CIT) [E] via scipion-users > <sci...@li...> > Reply-To: Mailing list for Scipion users > <sci...@li...> > To: sci...@li... > CC: Hoover, David (NIH/CIT) [E] <hoo...@hp...> > > > > Was it compiled with 1.8.x API compatibility macros? I am seeing > errors unless I compile HDF5 with --with-default-api-version=v18 option. > > https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html > > David > > On 2/19/2021 9:43 AM, Pablo Conesa wrote: >> Mine is linked to : >> >> libhdf5_serial.so.103 => >> /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f354a368000) >> libhdf5_cpp.so.103 => >> /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f354a2eb000) >> >> I think is 1.10.4 >> >> On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via scipion-users wrote: >>> One more question: what version of HDF5 does xmipp require? >>> >>> David >>> >>> On 2/19/2021 2:26 AM, Pablo Conesa wrote: >>>> Thanks Jason. >>>> >>>> There is a detailed "custom xmipp installation" page >>>> <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> >>>> where you can adapt xmipp to your system, providing default >>>> installation does not work. >>>> >>>> >>>> On 19/2/21 1:13, Jason Key wrote: >>>>> Hi David, >>>>> >>>>> On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via >>>>> scipion-users<sci...@li...> wrote: >>>>>> Is there any way of making HDF5 headers and libraries available >>>>>> for compiling xmipp? >>>>>> That is, must I install HDF5 with yum or apt-get into /usr/lib >>>>>> and /usr/include, or is there an environment variable or >>>>>> configuration setting that can be set to force the compile to >>>>>> look elsewhere for the header and library files? >>>>> I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables >>>>> to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". >>>>> >>>>> Best, >>>>> Jason >>>>> >>>> -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>>> >>>> >>>> _______________________________________________ >>>> 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 >> > > -- > David Hoover, Ph.D. > Computational Biologist > High Performance Computing Services, > Center for Information Technology, > National Institutes of Health > 12 South Dr., Rm 2N207 > Bethesda, MD 20892, USA > TEL: (+1) 301-435-2986 > Email:hoo...@hp... > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Carlos O. S. <co...@cn...> - 2021-02-23 19:14:43
|
Dear Dieter, I see two possible reasons: 1. --blobs and --fixed_Gaussian are mutually exclusive. Use only one of them as they point to different kinds of atom models. 2. --fixed_Gaussian if there is no parameter afterwards is taking the Gaussian sigma from the type of atom. If there is a type of atom in the PDB that is not explicitly encoded in the program, then the result may be undefined and that is why you are getting a segmentation fault. To me, the best atom conversion is the one without these two parameters. It is taking the electron atomic scattering factors. Kind regards, Carlos Oscar On 2/23/21 12:37 PM, Pablo Conesa wrote: > > Hi Dieter! > > I think xmipp team should know more about the current status. > > One question, how are you invoking the xmipp command, though > scipion3?, like scipion3 run xmipp_volume_from_pdb > > On 18/2/21 19:20, Dieter Blaas wrote: >> Hi, >> >> I am trying to make a kind of mean volume from many aligned pdb >> files. I appended all the pdbs and removed everything that is not a >> coordinate record. This file I feed into xmipp like so: >> xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" >> "--fixed_Gaussian". I am using an old version of this script but I >> believe that it has not have changed over the years. I get this: >> >> ############################################ >> >> PDB file: all_atoms.pdb >> >> Sampling rate: 1 >> High sampling rate: 0.0833333 >> Size: -1 >> Center PDB: 0 >> Do not Hetatm: 0 >> Use blobs: 1 >> Use poor Gaussian: 0 >> Use fixed Gaussian: 1 >> Intensity Col: occupancy >> Sigma: -1 >> >> Bus error (core dumped) >> Traceback (most recent call last): >> File "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", >> line 8, in <module> >> sys.exit(main()) >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", >> line 43, in main >> runProgram(program, params) >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", >> line 64, in runProgram >> pwutils.runJob(None, program, params, env=env) >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >> line 51, in runJob >> return runCommand(command, env, cwd) >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >> line 66, in runCommand >> check_call(command, shell=True, stdout=sys.stdout, >> stderr=sys.stderr, >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", >> line 364, in check_call >> raise CalledProcessError(retcode, cmd) >> subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb "-i" >> "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"' >> returned non-zero exit status 135. >> >> ############################################### >> >> What is wrong? What would be the best way for doing so? I want to use >> this volume to finally make a soft mask in relion.... >> >> Thanks a lot, best, Dieter >> >> >> ################################################### >> >> ------------------------------------------------------------------------ >> Dieter Blaas, >> Max Perutz Laboratories >> Medical University of Vienna, >> Inst. Med. Biochem., Vienna Biocenter (VBC), >> Dr. Bohr Gasse 9/3, >> A-1030 Vienna, Austria, >> Tel: 0043 1 4277 61630, >> Mobile: 0043 699 1942 1659 >> e-mail: die...@me... >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> 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 |
|
From: Pablo C. <pc...@cn...> - 2021-02-23 11:38:07
|
Hi Dieter! I think xmipp team should know more about the current status. One question, how are you invoking the xmipp command, though scipion3?, like scipion3 run xmipp_volume_from_pdb On 18/2/21 19:20, Dieter Blaas wrote: > Hi, > > I am trying to make a kind of mean volume from many aligned pdb files. > I appended all the pdbs and removed everything that is not a > coordinate record. This file I feed into xmipp like so: > xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" > "--fixed_Gaussian". I am using an old version of this script but I > believe that it has not have changed over the years. I get this: > > ############################################ > > PDB file: all_atoms.pdb > > Sampling rate: 1 > High sampling rate: 0.0833333 > Size: -1 > Center PDB: 0 > Do not Hetatm: 0 > Use blobs: 1 > Use poor Gaussian: 0 > Use fixed Gaussian: 1 > Intensity Col: occupancy > Sigma: -1 > > Bus error (core dumped) > Traceback (most recent call last): > File "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", > line 8, in <module> > sys.exit(main()) > File > "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", > line 43, in main > runProgram(program, params) > File > "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", > line 64, in runProgram > pwutils.runJob(None, program, params, env=env) > File > "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 51, in runJob > return runCommand(command, env, cwd) > File > "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 66, in runCommand > check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, > File > "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", > line 364, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb "-i" > "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"' returned > non-zero exit status 135. > > ############################################### > > What is wrong? What would be the best way for doing so? I want to use > this volume to finally make a soft mask in relion.... > > Thanks a lot, best, Dieter > > > ################################################### > > ------------------------------------------------------------------------ > Dieter Blaas, > Max Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Mobile: 0043 699 1942 1659 > e-mail: die...@me... > ------------------------------------------------------------------------ > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2021-02-23 11:23:41
|
Hi Dmitry, it's in the email I sent. Clearly I do not make myself clear enough or engage you to keep reading!! ;-) Try: *rm /tmp/outdated_cache_scipion-* && **scipion3 update* All the best, Pablo.* * * * "NOTE: It should install scipion-pyworkflow 3.0.10, informing clearly now which protocols are new or in beta: The version checking is cached so if it checked it recently is will not work. To remove the cached files type: rm /tmp/outdated_cache_scipion-* and then scipion3 update." On 23/2/21 11:34, Dmitry Semchonok wrote: > Dear Pablo, > > On the initial step — > > $ scipion update (in our case scipion3 update) > > I have this image > > > How can I get the 3.0.10? > > > Thank you > > Sincerely, > Dmitry > > > > > >> On 23. Feb 2021, at 11:03, Pablo Conesa <pc...@cn... >> <mailto:pc...@cn...>> wrote: >> >> Dear all! >> >> We have fixed this in scipion-pyworkflow package (this is not a >> plugin but a pip pacakge updatable through scipipn3 update). So to >> proceed run: >> >> scipion3 update >> >> You should see something like this-->The package scipion-pyworkflow >> is out of date. Your version is 3.0.9, the latest is 3.0.10. >> >> >> NOTE: It should install scipion-pyworkflow 3.0.10, informing clearly >> now which protocols are new or in beta: >> >> The version checking is cached so if it checked it recently is will >> not work. To remove the cached files type: >> >> rm /tmp/outdated_cache_scipion-* >> >> and then scipion3 update. >> >> NOTE2: What it brings you is a way to identify the development status >> of the protocolos: >> >> <icefhmmbcpapfdio.png> >> >> >> >> On 23/2/21 9:03, Pablo Conesa wrote: >>> >>> Hi, Wolfgang....rest, do not update cryosparc plugin yet. We >>> released a buggy version easy to solve. >>> >>> In the next hour we'll probably fix this. I'll send an email when ready. >>> >>> Apologies! >>> >>> On 22/2/21 13:01, Lugmayr, Wolfgang wrote: >>>> hi, >>>> >>>> i tried to combine scipion and cryosparc today on a local workstation and run into the error message below. >>>> >>>> $ scipion3 last >>>> Scipion v3.0.7 - Eugenius >>>> > error when importing from cryosparc2.protocols: cannot import name 'BETA' from 'pyworkflow' (/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/__init__.py) >>>> File "/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 33, in <module> >>>> Check the plugin manager (Configuration->Plugins in Scipion manager window) >>>> or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, >>>> it could be a versions compatibility issue. >>>> >>>> $ scipion3 update >>>> Scipion v3.0.7 - Eugenius >>>> The package scipion-pyworkflow is up to date. Your version is 3.0.9 >>>> The package scipion-em is up to date. Your version is 3.0.7 >>>> The package scipion-app is up to date. Your version is 3.0.7 >>>> >>>> i assume this has something to do with the recently updated workflow package and not with my yet not configured cryosparc configuration, right? >>>> >>>> cheers, >>>> wolfgang >>>> >>> -- >>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team* >>> >>> >>> _______________________________________________ >>> 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... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2021-02-23 11:18:57
|
yes, we (developers) should adapt this information accordingly. *Techy stuff for developers now:* Old versions of scipion described the "New" protocol status based on setting _lastUpdateVersion attribute to the latest scipion version. (https://github.com/scipion-em/scipion-pyworkflow/blob/devel/pyworkflow/protocol/protocol.py#L315) This is not useful anymore since each plugin has it's own "rythim", 100% independent from the scipion version. The way to proceed is described here: https://scipion-em.github.io/docs/docs/developer/creating-a-protocol.html?highlight=beta#protocol-development-status-definition If protocols were using _lastUpdateVersion and they are not new anymore, just removing the attribute will work. We can easily do de opposite, ignore _lastUpdateVersion, from now on so any current protocol that is new and "truly new" will have to use "_devStatus = NEW". Since the status is now "clearly" visible now we are seeing wrongly assigned attributes. Should we ignore _lastUpdateVersion? Will be this less confusing for users? And less work and urgency for developers? All the best, Pablo. On 23/2/21 11:28, Jose Miguel de la Rosa Trevin wrote: > Dear Pablo, > > There are many Relion protocols that are shown as "new" in your > screenshot and they have been there for a while. > > Best, > Jose Miguel > > > > On Tue, Feb 23, 2021 at 11:03 AM Pablo Conesa <pc...@cn... > <mailto:pc...@cn...>> wrote: > > Dear all! > > We have fixed this in scipion-pyworkflow package (this is not a > plugin but a pip pacakge updatable through scipipn3 update). So to > proceed run: > > scipion3 update > > You should see something like this-->The package > scipion-pyworkflow is out of date. Your version is 3.0.9, the > latest is 3.0.10. > > > NOTE: It should install scipion-pyworkflow 3.0.10, informing > clearly now which protocols are new or in beta: > > The version checking is cached so if it checked it recently is > will not work. To remove the cached files type: > > rm /tmp/outdated_cache_scipion-* > > and then scipion3 update. > > NOTE2: What it brings you is a way to identify the development > status of the protocolos: > > > > On 23/2/21 9:03, Pablo Conesa wrote: >> >> Hi, Wolfgang....rest, do not update cryosparc plugin yet. We >> released a buggy version easy to solve. >> >> In the next hour we'll probably fix this. I'll send an email when >> ready. >> >> Apologies! >> >> On 22/2/21 13:01, Lugmayr, Wolfgang wrote: >>> hi, >>> >>> i tried to combine scipion and cryosparc today on a local workstation and run into the error message below. >>> >>> $ scipion3 last >>> Scipion v3.0.7 - Eugenius >>> > error when importing from cryosparc2.protocols: cannot import name 'BETA' from 'pyworkflow' (/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/__init__.py) >>> File "/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 33, in <module> >>> Check the plugin manager (Configuration->Plugins in Scipion manager window) >>> or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, >>> it could be a versions compatibility issue. >>> >>> $ scipion3 update >>> Scipion v3.0.7 - Eugenius >>> The package scipion-pyworkflow is up to date. Your version is 3.0.9 >>> The package scipion-em is up to date. Your version is 3.0.7 >>> The package scipion-app is up to date. Your version is 3.0.7 >>> >>> i assume this has something to do with the recently updated workflow package and not with my yet not configured cryosparc configuration, right? >>> >>> cheers, >>> wolfgang >>> >> -- >> 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 > -- > 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... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Carlos O. S. <co...@cn...> - 2021-02-23 10:50:47
|
Dear Ana,
let us have a look at it and see what is happening.
Kind regards, Carlos Oscar
El 23/02/2021 a las 9:17, Ana Andreea ARTENI escribió:
> Morning,
>
> When using deep micrograph cleaner/analyse results/: when placing the value 0.97 in the program and clicking on the "eye" nothing happens but in the terminal I get the following error:
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/__init__.py", line 1883, in __call__
> return self.func(*args)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/gui/form.py", line 1281, in _visualizeVar
> self.visualizeCallback(self.paramName)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/viewer.py", line 265, in _visualizeParam
> views = self._getVisualizeDict()[paramName](paramName)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/viewers/viewer_deep_micrograph_cleaner.py", line 83, in _visualizeCoordinates
> newOutput = SetOfCoordinates(filename=coordsViewerFn)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pwem/objects/data.py", line 1437, in __init__
> EMSet.__init__(self, **kwargs)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/object.py", line 1096, in __init__
> self.load()
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/object.py", line 1196, in load
> self._mapper = self._MapperClass(fn, self._loadClassesDict(), prefix, self._indexes)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/mapper/sqlite.py", line 751, in __init__
> raise SqliteFlatMapperException('Error creating SqliteFlatMapper, '
> pyworkflow.mapper.sqlite.SqliteFlatMapperException: Error creating SqliteFlatMapper, dbName: Runs/001218_XmippProtDeepMicrographScreen/tmp/coordsViewer.sqlite, tablePrefix:
> error: unable to open database file
>
> How I can fix this?
> My kind regards,
> ana arteni.
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Dmitry S. <Sem...@gm...> - 2021-02-23 10:34:51
|
Dear Pablo, On the initial step — $ scipion update (in our case scipion3 update) I have this image How can I get the 3.0.10? Thank you Sincerely, Dmitry > On 23. Feb 2021, at 11:03, Pablo Conesa <pc...@cn...> wrote: > > Dear all! > > We have fixed this in scipion-pyworkflow package (this is not a plugin but a pip pacakge updatable through scipipn3 update). So to proceed run: > > scipion3 update > > You should see something like this-->The package scipion-pyworkflow is out of date. Your version is 3.0.9, the latest is 3.0.10. > > > > NOTE: It should install scipion-pyworkflow 3.0.10, informing clearly now which protocols are new or in beta: > > The version checking is cached so if it checked it recently is will not work. To remove the cached files type: > > rm /tmp/outdated_cache_scipion-* > > and then scipion3 update. > > NOTE2: What it brings you is a way to identify the development status of the protocolos: > > <icefhmmbcpapfdio.png> > > > > > > On 23/2/21 9:03, Pablo Conesa wrote: >> Hi, Wolfgang....rest, do not update cryosparc plugin yet. We released a buggy version easy to solve. >> >> In the next hour we'll probably fix this. I'll send an email when ready. >> >> Apologies! >> >> On 22/2/21 13:01, Lugmayr, Wolfgang wrote: >>> hi, >>> >>> i tried to combine scipion and cryosparc today on a local workstation and run into the error message below. >>> >>> $ scipion3 last >>> Scipion v3.0.7 - Eugenius >>> > error when importing from cryosparc2.protocols: cannot import name 'BETA' from 'pyworkflow' (/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/__init__.py) >>> File "/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 33, in <module> >>> Check the plugin manager (Configuration->Plugins in Scipion manager window) >>> or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, >>> it could be a versions compatibility issue. >>> >>> $ scipion3 update >>> Scipion v3.0.7 - Eugenius >>> The package scipion-pyworkflow is up to date. Your version is 3.0.9 >>> The package scipion-em is up to date. Your version is 3.0.7 >>> The package scipion-app is up to date. Your version is 3.0.7 >>> >>> i assume this has something to do with the recently updated workflow package and not with my yet not configured cryosparc configuration, right? >>> >>> cheers, >>> wolfgang >>> >> -- >> 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> > -- > Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es/> team > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Jose M. de la R. T. <del...@gm...> - 2021-02-23 10:28:32
|
Dear Pablo, There are many Relion protocols that are shown as "new" in your screenshot and they have been there for a while. Best, Jose Miguel On Tue, Feb 23, 2021 at 11:03 AM Pablo Conesa <pc...@cn...> wrote: > Dear all! > > We have fixed this in scipion-pyworkflow package (this is not a plugin but > a pip pacakge updatable through scipipn3 update). So to proceed run: > > scipion3 update > > You should see something like this-->The package scipion-pyworkflow is out > of date. Your version is 3.0.9, the latest is 3.0.10. > > > NOTE: It should install scipion-pyworkflow 3.0.10, informing clearly now > which protocols are new or in beta: > > The version checking is cached so if it checked it recently is will not > work. To remove the cached files type: > > rm /tmp/outdated_cache_scipion-* > > and then scipion3 update. > > NOTE2: What it brings you is a way to identify the development status of > the protocolos: > > > > On 23/2/21 9:03, Pablo Conesa wrote: > > Hi, Wolfgang....rest, do not update cryosparc plugin yet. We released a > buggy version easy to solve. > > In the next hour we'll probably fix this. I'll send an email when ready. > > Apologies! > On 22/2/21 13:01, Lugmayr, Wolfgang wrote: > > hi, > > i tried to combine scipion and cryosparc today on a local workstation and run into the error message below. > > $ scipion3 last > Scipion v3.0.7 - Eugenius > > error when importing from cryosparc2.protocols: cannot import name 'BETA' from 'pyworkflow' (/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/__init__.py) > File "/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 33, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager window) > or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, > it could be a versions compatibility issue. > > $ scipion3 update > Scipion v3.0.7 - Eugenius > The package scipion-pyworkflow is up to date. Your version is 3.0.9 > The package scipion-em is up to date. Your version is 3.0.7 > The package scipion-app is up to date. Your version is 3.0.7 > > i assume this has something to do with the recently updated workflow package and not with my yet not configured cryosparc configuration, right? > > cheers, > wolfgang > > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > 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 > |
|
From: Pablo C. <pc...@cn...> - 2021-02-23 10:03:23
|
Dear all! We have fixed this in scipion-pyworkflow package (this is not a plugin but a pip pacakge updatable through scipipn3 update). So to proceed run: scipion3 update You should see something like this-->The package scipion-pyworkflow is out of date. Your version is 3.0.9, the latest is 3.0.10. NOTE: It should install scipion-pyworkflow 3.0.10, informing clearly now which protocols are new or in beta: The version checking is cached so if it checked it recently is will not work. To remove the cached files type: rm /tmp/outdated_cache_scipion-* and then scipion3 update. NOTE2: What it brings you is a way to identify the development status of the protocolos: On 23/2/21 9:03, Pablo Conesa wrote: > > Hi, Wolfgang....rest, do not update cryosparc plugin yet. We released > a buggy version easy to solve. > > In the next hour we'll probably fix this. I'll send an email when ready. > > Apologies! > > On 22/2/21 13:01, Lugmayr, Wolfgang wrote: >> hi, >> >> i tried to combine scipion and cryosparc today on a local workstation and run into the error message below. >> >> $ scipion3 last >> Scipion v3.0.7 - Eugenius >> > error when importing from cryosparc2.protocols: cannot import name 'BETA' from 'pyworkflow' (/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/__init__.py) >> File "/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 33, in <module> >> Check the plugin manager (Configuration->Plugins in Scipion manager window) >> or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, >> it could be a versions compatibility issue. >> >> $ scipion3 update >> Scipion v3.0.7 - Eugenius >> The package scipion-pyworkflow is up to date. Your version is 3.0.9 >> The package scipion-em is up to date. Your version is 3.0.7 >> The package scipion-app is up to date. Your version is 3.0.7 >> >> i assume this has something to do with the recently updated workflow package and not with my yet not configured cryosparc configuration, right? >> >> cheers, >> wolfgang >> > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Ana A. A. <ana...@i2...> - 2021-02-23 08:35:23
|
Morning,
When using deep micrograph cleaner/analyse results/: when placing the value 0.97 in the program and clicking on the "eye" nothing happens but in the terminal I get the following error:
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/__init__.py", line 1883, in __call__
return self.func(*args)
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/gui/form.py", line 1281, in _visualizeVar
self.visualizeCallback(self.paramName)
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/viewer.py", line 265, in _visualizeParam
views = self._getVisualizeDict()[paramName](paramName)
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/viewers/viewer_deep_micrograph_cleaner.py", line 83, in _visualizeCoordinates
newOutput = SetOfCoordinates(filename=coordsViewerFn)
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pwem/objects/data.py", line 1437, in __init__
EMSet.__init__(self, **kwargs)
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/object.py", line 1096, in __init__
self.load()
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/object.py", line 1196, in load
self._mapper = self._MapperClass(fn, self._loadClassesDict(), prefix, self._indexes)
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/mapper/sqlite.py", line 751, in __init__
raise SqliteFlatMapperException('Error creating SqliteFlatMapper, '
pyworkflow.mapper.sqlite.SqliteFlatMapperException: Error creating SqliteFlatMapper, dbName: Runs/001218_XmippProtDeepMicrographScreen/tmp/coordsViewer.sqlite, tablePrefix:
error: unable to open database file
How I can fix this?
My kind regards,
ana arteni.
|
|
From: Pablo C. <pc...@cn...> - 2021-02-23 08:04:21
|
Hi, Wolfgang....rest, do not update cryosparc plugin yet. We released a buggy version easy to solve. In the next hour we'll probably fix this. I'll send an email when ready. Apologies! On 22/2/21 13:01, Lugmayr, Wolfgang wrote: > hi, > > i tried to combine scipion and cryosparc today on a local workstation and run into the error message below. > > $ scipion3 last > Scipion v3.0.7 - Eugenius > > error when importing from cryosparc2.protocols: cannot import name 'BETA' from 'pyworkflow' (/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/__init__.py) > File "/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 33, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager window) > or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, > it could be a versions compatibility issue. > > $ scipion3 update > Scipion v3.0.7 - Eugenius > The package scipion-pyworkflow is up to date. Your version is 3.0.9 > The package scipion-em is up to date. Your version is 3.0.7 > The package scipion-app is up to date. Your version is 3.0.7 > > i assume this has something to do with the recently updated workflow package and not with my yet not configured cryosparc configuration, right? > > cheers, > wolfgang > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Lugmayr, W. <w.l...@uk...> - 2021-02-22 12:20:14
|
hi, i tried to combine scipion and cryosparc today on a local workstation and run into the error message below. $ scipion3 last Scipion v3.0.7 - Eugenius > error when importing from cryosparc2.protocols: cannot import name 'BETA' from 'pyworkflow' (/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/__init__.py) File "/cssbsw/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 33, in <module> Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue. $ scipion3 update Scipion v3.0.7 - Eugenius The package scipion-pyworkflow is up to date. Your version is 3.0.9 The package scipion-em is up to date. Your version is 3.0.7 The package scipion-app is up to date. Your version is 3.0.7 i assume this has something to do with the recently updated workflow package and not with my yet not configured cryosparc configuration, right? cheers, wolfgang -- Multi-User Cryo-EM Facility @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 22607 Hamburg, Germany Tel.: +49 40 8998-87706 Email: wol...@cs... http://www.cssb-hamburg.de/ |
|
From: Hoover, D. (NIH/C. [E] <hoo...@hp...> - 2021-02-19 16:22:37
|
Was it compiled with 1.8.x API compatibility macros? I am seeing errors unless I compile HDF5 with --with-default-api-version=v18 option. https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html David On 2/19/2021 9:43 AM, Pablo Conesa wrote: > Mine is linked to : > > libhdf5_serial.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f354a368000) > libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f354a2eb000) > > I think is 1.10.4 > > On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via scipion-users wrote: >> One more question: what version of HDF5 does xmipp require? >> >> David >> >> On 2/19/2021 2:26 AM, Pablo Conesa wrote: >>> Thanks Jason. >>> >>> There is a detailed "custom xmipp installation" page <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> where you can adapt xmipp to your system, providing default installation does not work. >>> >>> >>> On 19/2/21 1:13, Jason Key wrote: >>>> Hi David, >>>> >>>> On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via >>>> scipion-users<sci...@li...> wrote: >>>>> Is there any way of making HDF5 headers and libraries available for compiling xmipp? >>>>> That is, must I install HDF5 with yum or apt-get into /usr/lib and /usr/include, or is there an environment variable or configuration setting that can be set to force the compile to look elsewhere for the header and library files? >>>> I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables >>>> to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". >>>> >>>> Best, >>>> Jason >>>> >>> -- >>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>> >>> >>> _______________________________________________ >>> 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 > -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hoo...@hp... |
|
From: Pablo C. <pc...@cn...> - 2021-02-19 14:43:53
|
Mine is linked to : libhdf5_serial.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f354a368000) libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f354a2eb000) I think is 1.10.4 On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via scipion-users wrote: > One more question: what version of HDF5 does xmipp require? > > David > > On 2/19/2021 2:26 AM, Pablo Conesa wrote: >> Thanks Jason. >> >> There is a detailed "custom xmipp installation" page >> <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> >> where you can adapt xmipp to your system, providing default >> installation does not work. >> >> >> On 19/2/21 1:13, Jason Key wrote: >>> Hi David, >>> >>> On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via >>> scipion-users<sci...@li...> wrote: >>>> Is there any way of making HDF5 headers and libraries available for >>>> compiling xmipp? >>>> That is, must I install HDF5 with yum or apt-get into /usr/lib and >>>> /usr/include, or is there an environment variable or configuration >>>> setting that can be set to force the compile to look elsewhere for >>>> the header and library files? >>> I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables >>> to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". >>> >>> Best, >>> Jason >>> >> -- >> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Hoover, D. (NIH/C. [E] <hoo...@hp...> - 2021-02-19 13:48:17
|
One more question: what version of HDF5 does xmipp require? David On 2/19/2021 2:26 AM, Pablo Conesa wrote: > Thanks Jason. > > There is a detailed "custom xmipp installation" page <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> where you can adapt xmipp to your system, providing default installation does not work. > > > On 19/2/21 1:13, Jason Key wrote: >> Hi David, >> >> On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via >> scipion-users<sci...@li...> wrote: >>> Is there any way of making HDF5 headers and libraries available for compiling xmipp? >>> That is, must I install HDF5 with yum or apt-get into /usr/lib and /usr/include, or is there an environment variable or configuration setting that can be set to force the compile to look elsewhere for the header and library files? >> I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables >> to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". >> >> Best, >> Jason >> > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hoo...@hp... |
|
From: Pablo C. <pc...@cn...> - 2021-02-19 08:18:37
|
Just FYI -------- Forwarded Message -------- Subject: Re: [scipion-users] Online SCIPION tools Date: Thu, 18 Feb 2021 14:23:09 +0100 From: Pablo Conesa <pc...@cn...> To: Dmitry Semchonok <Sem...@gm...> Nope, they are not available anymore, since we had to migrate then on any release and didn't have time for that. This are good news, you teaching Scipion. Is there anyway we can help. I can make some presentations available to you. On 18/2/21 14:02, Dmitry Semchonok wrote: > Dear colleagues, > > > > I am very honoured to distribute knowledge about the Scipion framework > in our lab during the students' teaching. > > I would like to ask if there still an option to use SCIPION tools online? > > > I have noticed that currently, the online tool available online are > not accessible. > > https://instruct-eric.eu/compute/support/electron-microscopy/scipion-web-tools > > > Thank you! > > > Sincerely, > Dmitry > > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2021-02-19 07:27:04
|
Thanks Jason. There is a detailed "custom xmipp installation" page <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> where you can adapt xmipp to your system, providing default installation does not work. On 19/2/21 1:13, Jason Key wrote: > Hi David, > > On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via > scipion-users <sci...@li...> wrote: >> Is there any way of making HDF5 headers and libraries available for compiling xmipp? >> That is, must I install HDF5 with yum or apt-get into /usr/lib and /usr/include, or is there an environment variable or configuration setting that can be set to force the compile to look elsewhere for the header and library files? > I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables > to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". > > Best, > Jason > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Jason K. <ke...@hk...> - 2021-02-19 00:37:23
|
Hi David, On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via scipion-users <sci...@li...> wrote: > Is there any way of making HDF5 headers and libraries available for compiling xmipp? > That is, must I install HDF5 with yum or apt-get into /usr/lib and /usr/include, or is there an environment variable or configuration setting that can be set to force the compile to look elsewhere for the header and library files? I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". Best, Jason -- Jason Key, PhD SBGrid Consortium, Harvard Medical School |
|
From: Dieter B. <die...@me...> - 2021-02-18 18:38:14
|
Hi, I am trying to make a kind of mean volume from many aligned pdb files. I appended all the pdbs and removed everything that is not a coordinate record. This file I feed into xmipp like so: xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian". I am using an old version of this script but I believe that it has not have changed over the years. I get this: ############################################ PDB file: all_atoms.pdb Sampling rate: 1 High sampling rate: 0.0833333 Size: -1 Center PDB: 0 Do not Hetatm: 0 Use blobs: 1 Use poor Gaussian: 0 Use fixed Gaussian: 1 Intensity Col: occupancy Sigma: -1 Bus error (core dumped) Traceback (most recent call last): File "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", line 8, in <module> sys.exit(main()) File "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", line 43, in main runProgram(program, params) File "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", line 64, in runProgram pwutils.runJob(None, program, params, env=env) File "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 51, in runJob return runCommand(command, env, cwd) File "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 66, in runCommand check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, File "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"' returned non-zero exit status 135. ############################################### What is wrong? What would be the best way for doing so? I want to use this volume to finally make a soft mask in relion.... Thanks a lot, best, Dieter ################################################### ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: die...@me... ------------------------------------------------------------------------ |
|
From: Hoover, D. (NIH/C. [E] <hoo...@hp...> - 2021-02-18 17:42:00
|
Is there any way of making HDF5 headers and libraries available for compiling xmipp? That is, must I install HDF5 with yum or apt-get into /usr/lib and /usr/include, or is there an environment variable or configuration setting that can be set to force the compile to look elsewhere for the header and library files? David -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hoo...@hp... |
|
From: Dmitry S. <Sem...@gm...> - 2021-02-18 13:03:11
|
Dear colleagues, I am very honoured to distribute knowledge about the Scipion framework in our lab during the students' teaching. I would like to ask if there still an option to use SCIPION tools online? I have noticed that currently, the online tool available online are not accessible. https://instruct-eric.eu/compute/support/electron-microscopy/scipion-web-tools <https://instruct-eric.eu/compute/support/electron-microscopy/scipion-web-tools> Thank you! Sincerely, Dmitry |
|
From: Dmitry A. S. <sem...@gm...> - 2021-02-16 20:25:18
|
<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><div><p class=MsoNormal>Dear Yunior and all,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I want to run the <b>Local refinement New</b> in cryoSPARC as a continuation of the SCIPION analysis.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>When I try to do that I got the following error:</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='color:red'>[CPU: 6.57 GB] Traceback (most recent call last):<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'> File "cryosparc_worker/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'> File "cryosparc_worker/cryosparc_compute/jobs/local_refine/newrun.py", line 116, in cryosparc_compute.jobs.local_refine.newrun.run_local_refine<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'> File "/home/panos/software/cryosparc/cryosparc2_worker/cryosparc_compute/particles.py", line 77, in read_blobs with open(abs_path, 'rb') as mrc_file: FileNotFoundError: [Errno 2] No such file or directory: '/home/panos/software/cryosparc/scipion_projects/20200823_ApoF_ph9-panos/P9/J63/imported/mic_000001.mrcs'<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Could you please prompt how to tackle this issue?</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I worry that the file required was temporarily created by SCIPION and can not be traced back. </p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you!</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</p></div><p class=MsoNormal>Dmitry</p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
|
From: Xiaochu L. <Xia...@UT...> - 2021-02-12 21:05:05
|
Hi Carlos, Thanks a lot for your help. I have been able to compile xmipp now, seems by installing hdf5 in the scipion conda env. Best, Xiaochu Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 From: Carlos Oscar Sorzano<mailto:co...@cn...> Sent: Thursday, February 11, 2021 1:29 AM To: Mailing list for Scipion users<mailto:sci...@li...>; Xiaochu Lou<mailto:Xia...@UT...> Subject: Re: [scipion-users] error occurred during the compilation of 'xmipp' EXTERNAL MAIL Dear Xiaochu, it seems as if the headers of the hdf5 library are visible, but the binary lib file is not. Can that be? Kind regards, Carlos Oscar El 11/02/2021 a las 1:07, Xiaochu Lou escribió: Dear The Scipion Team, I am trying to install Scipion V3.0 with Miniconda (python 3.8), and I can install successfully on my Centos7 virtual machine following the official instruction of “CentOS with conda”. However, I met some errors when I try to install it on a RHEL server (without admin permit). On the RHEL server, instead of “sudo yum -y install libzstd-devel hdf5-devel gcc gcc-c++ openmpi-devel”, I load the modules such as “ hdf5/gcc/1.12.0, cuda80/toolkit/8.0.61, java/oracle/jdk1.8.0_231, openmpi/gcc/64/4.0.3, gcc/5.4.0” and export their /bin path to The $PATH. I tried different cuda version and/or gcc version (eg: cuda10.1 and gcc/8.3). Could you please have a look at the error message below and let me know what package and/or lib I missed? Or if there any config I can modify? Please let me know if you need more information about my installation process. Thank you ahead for your help! Best, Xiaochu ============================================ lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' /home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' collect2: error: ld returned 1 exit status g++ -o bin/xmipp_angular_commonline applications/programs/angular_commonline/angular_commonline_main.o -L/home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib -Llib -Llib -L/home2/s******/miniconda3/envs/scipion3/lib -L/cm/shared/apps/gcc/5.4.0/lib -L/cm/shared/apps/gcc/5.4.0/lib64 -L/cm/shared/apps/cuda80/toolkit/8.0.61/extras/CUPTI/lib64 -L/cm/local/apps/cuda/libs/current/lib64 -L/cm/shared/apps/cuda80/toolkit/8.0.61/lib64 -L/cm/shared/apps/openmpi/gcc/64/4.0.3/lib -L/cm/shared/apps/hdf5/gcc/1.12.0/lib -L/cm/shared/apps/java/oracle/jdk1.8.0_231/lib -L/cm/shared/apps/slurm/16.05.8/lib64/slurm -L/cm/shared/apps/slurm/16.05.8/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore scons: *** [bin/xmipp_angular_break_symmetry] Error 1 lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' /home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_commonline] Error 1 scons: building terminated because of errors. Some error occurred during the compilation of 'xmipp' ('bin/xmipp_angular_commonline'). Traceback (most recent call last): File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home2/s******/installs/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home2/s******/installs/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') Error at main: target '/home2/s******/installs/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home2/s******/installs/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') _______________________________________________________________________________________ | | | Installation failed | _______________________________________________________________________________________ Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 UT Southwestern Medical Center The future of medicine, today. _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. |
|
From: Carlos O. S. <co...@cn...> - 2021-02-11 07:29:07
|
Dear Xiaochu,
it seems as if the headers of the hdf5 library are visible, but the
binary lib file is not. Can that be?
Kind regards, Carlos Oscar
El 11/02/2021 a las 1:07, Xiaochu Lou escribió:
>
> Dear The Scipion Team,
>
> I am trying to install Scipion V3.0 with Miniconda (python 3.8), and I
> can install successfully on my Centos7 virtual machine following the
> official instruction of “CentOS with conda”. However, I met some
> errors when I try to install it on a RHEL server (without admin
> permit). On the RHEL server, instead of “sudo yum -y install
> libzstd-devel hdf5-devel gcc gcc-c++ openmpi-devel”, I load the
> modules such as “ hdf5/gcc/1.12.0, cuda80/toolkit/8.0.61,
> java/oracle/jdk1.8.0_231, openmpi/gcc/64/4.0.3, gcc/5.4.0” and export
> their /bin path to The $PATH. I tried different cuda version and/or
> gcc version (eg: cuda10.1 and gcc/8.3). Could you please have a look
> at the error message below and let me know what package and/or lib I
> missed? Or if there any config I can modify? Please let me know if you
> need more information about my installation process. Thank you ahead
> for your help!
>
> Best,
>
> Xiaochu
>
> ============================================
>
> lib/libXmipp.so: undefined reference to `non-virtual thunk to
> H5::H5File::throwException(std::string const&, std::string const&) const'
>
> lib/libXmipp.so: undefined reference to
> `H5::H5File::throwException(std::string const&, std::string const&) const'
>
> /home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib/libXmippCore.so:
> undefined reference to `H5::H5Location::getFileName() const'
>
> collect2: error: ld returned 1 exit status
>
> g++ -o bin/xmipp_angular_commonline
> applications/programs/angular_commonline/angular_commonline_main.o
> -L/home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib
> -Llib -Llib -L/home2/s******/miniconda3/envs/scipion3/lib
> -L/cm/shared/apps/gcc/5.4.0/lib -L/cm/shared/apps/gcc/5.4.0/lib64
> -L/cm/shared/apps/cuda80/toolkit/8.0.61/extras/CUPTI/lib64
> -L/cm/local/apps/cuda/libs/current/lib64
> -L/cm/shared/apps/cuda80/toolkit/8.0.61/lib64
> -L/cm/shared/apps/openmpi/gcc/64/4.0.3/lib
> -L/cm/shared/apps/hdf5/gcc/1.12.0/lib
> -L/cm/shared/apps/java/oracle/jdk1.8.0_231/lib
> -L/cm/shared/apps/slurm/16.05.8/lib64/slurm
> -L/cm/shared/apps/slurm/16.05.8/lib64 -lXmipp -lhdf5 -lhdf5_cpp
> -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads
> -lpthread -lpython3.8 -lXmippCore
>
> scons: *** [bin/xmipp_angular_break_symmetry] Error 1
>
> lib/libXmipp.so: undefined reference to `non-virtual thunk to
> H5::H5File::throwException(std::string const&, std::string const&) const'
>
> lib/libXmipp.so: undefined reference to
> `H5::H5File::throwException(std::string const&, std::string const&) const'
>
> /home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib/libXmippCore.so:
> undefined reference to `H5::H5Location::getFileName() const'
>
> collect2: error: ld returned 1 exit status
>
> scons: *** [bin/xmipp_angular_commonline] Error 1
>
> scons: building terminated because of errors.
>
> Some error occurred during the compilation of 'xmipp'
> ('bin/xmipp_angular_commonline').
>
> Traceback (most recent call last):
>
> File
> "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
> line 457, in <module>
>
> main()
>
> File
> "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
> line 297, in main
>
> installPluginMethods()
>
> File
> "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py",
> line 232, in installPluginMethods
>
> plugin.installBin({'args': ['-j', numberProcessor]})
>
> File
> "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
> line 166, in installBin
>
> environment.execute()
>
> File
> "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 748, in execute
>
> self._executeTargets(targetList)
>
> File
> "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 690, in _executeTargets
>
> tgt.execute()
>
> File
> "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 221, in execute
>
> command.execute()
>
> File
> "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 161, in execute
>
> assert glob(t), ("target '%s' not built (after "
>
> AssertionError: target
> '/home2/s******/installs/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant'
> not built (after running 'cd . && ./xmipp config noAsk && ./xmipp
> check_config && ./xmipp compileAndInstall N=8 && ln -srfn build
> /home2/s******/installs/scipion/software/em/xmipp && cd - && touch
> installation_finished && rm bindings_linked 2> /dev/null')
>
> Error at main: target
> '/home2/s******/installs/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant'
> not built (after running 'cd . && ./xmipp config noAsk && ./xmipp
> check_config && ./xmipp compileAndInstall N=8 && ln -srfn build
> /home2/s******/installs/scipion/software/em/xmipp && cd - && touch
> installation_finished && rm bindings_linked 2> /dev/null')
>
> _______________________________________________________________________________________
>
> | |
>
> | Installation failed |
>
> _______________________________________________________________________________________
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986>for
> Windows 10
>
>
> ------------------------------------------------------------------------
>
> UTSouthwestern
>
> Medical Center
>
>
> The future of medicine, today.
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Xiaochu L. <Xia...@UT...> - 2021-02-11 00:25:20
|
Dear The Scipion Team,
I am trying to install Scipion V3.0 with Miniconda (python 3.8), and I can install successfully on my Centos7 virtual machine following the official instruction of "CentOS with conda". However, I met some errors when I try to install it on a RHEL server (without admin permit). On the RHEL server, instead of "sudo yum -y install libzstd-devel hdf5-devel gcc gcc-c++ openmpi-devel", I load the modules such as " hdf5/gcc/1.12.0, cuda80/toolkit/8.0.61, java/oracle/jdk1.8.0_231, openmpi/gcc/64/4.0.3, gcc/5.4.0" and export their /bin path to The $PATH. I tried different cuda version and/or gcc version (eg: cuda10.1 and gcc/8.3). Could you please have a look at the error message below and let me know what package and/or lib I missed? Or if there any config I can modify? Please let me know if you need more information about my installation process. Thank you ahead for your help!
Best,
Xiaochu
============================================
lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const'
lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const'
/home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const'
collect2: error: ld returned 1 exit status
g++ -o bin/xmipp_angular_commonline applications/programs/angular_commonline/angular_commonline_main.o -L/home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib -Llib -Llib -L/home2/s******/miniconda3/envs/scipion3/lib -L/cm/shared/apps/gcc/5.4.0/lib -L/cm/shared/apps/gcc/5.4.0/lib64 -L/cm/shared/apps/cuda80/toolkit/8.0.61/extras/CUPTI/lib64 -L/cm/local/apps/cuda/libs/current/lib64 -L/cm/shared/apps/cuda80/toolkit/8.0.61/lib64 -L/cm/shared/apps/openmpi/gcc/64/4.0.3/lib -L/cm/shared/apps/hdf5/gcc/1.12.0/lib -L/cm/shared/apps/java/oracle/jdk1.8.0_231/lib -L/cm/shared/apps/slurm/16.05.8/lib64/slurm -L/cm/shared/apps/slurm/16.05.8/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore
scons: *** [bin/xmipp_angular_break_symmetry] Error 1
lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const'
lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const'
/home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const'
collect2: error: ld returned 1 exit status
scons: *** [bin/xmipp_angular_commonline] Error 1
scons: building terminated because of errors.
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_angular_commonline').
Traceback (most recent call last):
File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module>
main()
File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main
installPluginMethods()
File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
command.execute()
File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/home2/s******/installs/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home2/s******/installs/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Error at main: target '/home2/s******/installs/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home2/s******/installs/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
_______________________________________________________________________________________
| |
| Installation failed |
_______________________________________________________________________________________
Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
|
1 message has been excluded from this view by a project administrator.
