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From: Yangyang Yi <yy...@si...> - 2020-11-23 08:33:42
|
Sorry for the late reply. Here’s the log from the job begin to the job end.
run.stdout:
00001: RUNNING PROTOCOL -----------------
00002: HostName: headnode.cm.cluster
00003: PID: 209177
00004: Scipion: v2.0 (2019-04-23) Diocletian
00005: currentDir: /ddn/users/spadm/ScipionUserData/projects/relion_benchmark
00006: workingDir: Runs/000347_ProtRelionClassify3D
00007: runMode: Continue
00008: MPI: 5
00009: threads: 2
00010: len(steps) 3 len(prevSteps) 0
00011: Starting at step: 1
00012: Running steps
00013: STARTED: convertInputStep, step 1
00014: 2020-11-12 13:46:13.708639
00015: Converting set from 'Runs/000002_ProtImportParticles/particles.sqlite' into 'Runs/000347_ProtRelionClassify3D/input_particles.star'
00016: convertBinaryFiles: creating soft links.
00017: Root: Runs/000347_ProtRelionClassify3D/extra/input -> Runs/000002_ProtImportParticles/extra
00018: FINISHED: convertInputStep, step 1
00019: 2020-11-12 13:46:48.416238
00020: STARTED: runRelionStep, step 2
00021: 2020-11-12 13:46:48.438416
00022: ** Submiting to queue: 'sbatch /ddn/users/spadm/ScipionUserData/projects/relion_benchmark/Runs/000347_ProtRelionClassify3D/logs/347-0-1.job'
00023: launched job with id 2552
00024: FINISHED: runRelionStep, step 2
00025: 2020-11-12 13:46:48.524619
00026: STARTED: createOutputStep, step 3
00027: 2020-11-12 13:46:48.973668
00028: Traceback (most recent call last):
00029: File "/cm/shared/apps/scipion/2.0/pyworkflow/protocol/executor.py", line 151, in run
00030: self.step._run() # not self.step.run() , to avoid race conditions
00031: File "/cm/shared/apps/scipion/2.0/pyworkflow/protocol/protocol.py", line 237, in _run
00032: resultFiles = self._runFunc()
00033: File "/cm/shared/apps/scipion/2.0/pyworkflow/protocol/protocol.py", line 233, in _runFunc
00034: return self._func(*self._args)
00035: File "/cm/shared/apps/scipion/2.0/software/lib/python2.7/site-packages/relion/protocols/protocol_classify3d.py", line 77, in createOutputStep
00036: self._fillClassesFromIter(classes3D, self._lastIter())
00037: File "/cm/shared/apps/scipion/2.0/software/lib/python2.7/site-packages/relion/protocols/protocol_classify3d.py", line 176, in _fillClassesFromIter
00038: self._loadClassesInfo(iteration)
00039: File "/cm/shared/apps/scipion/2.0/software/lib/python2.7/site-packages/relion/protocols/protocol_classify3d.py", line 166, in _loadClassesInfo
00040: self._getFileName('model', iter=iteration))
00041: File "/cm/shared/apps/scipion/2.0/pyworkflow/protocol/protocol.py", line 841, in _getFileName
00042: return self.__filenamesDict[key] % kwargs
00043: TypeError: %d format: a number is required, not NoneType
00044: Protocol failed: %d format: a number is required, not NoneType
00045: FAILED: createOutputStep, step 3
00046: 2020-11-12 13:46:48.991279
00047: *** Last status is failed
00048: ------------------- PROTOCOL FAILED (DONE 3/3)
run.log:
2020-11-12 13:46:48.438416
00020: 2020-11-12 13:46:48,972 INFO: FINISHED: runRelionStep, step 2
00021: 2020-11-12 13:46:48,973 INFO: 2020-11-12 13:46:48.524619
00022: 2020-11-12 13:46:48,973 INFO: STARTED: createOutputStep, step 3
00023: 2020-11-12 13:46:48,973 INFO: 2020-11-12 13:46:48.973668
00024: 2020-11-12 13:46:49,485 ERROR: Protocol failed: %d format: a number is required, not NoneType
00025: 2020-11-12 13:46:49,508 INFO: FAILED: createOutputStep, step 3
00026: 2020-11-12 13:46:49,508 INFO: 2020-11-12 13:46:48.991279
00027: 2020-11-12 13:46:49,570 INFO: ------------------- PROTOCOL FAILED (DONE 3/3)
> 2020年11月12日 上午2:19，Grigory Sharov <sha...@gm...> 写道：
>
> Hi Yangyang,
>
> I've tried your config with Scipion2 and it seems to work fine. The only problem I found was using curly quotes (“) instead of straight ones (") in the queues dictionary. Did you get the error message after the job was submitted and started to run or before?
>
> Best regards,
> Grigory
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
>
> On Wed, Nov 11, 2020 at 9:20 AM Yangyang Yi <yy...@si... <mailto:yy...@si...>> wrote:
> Dear Scipion users & devs,
>
> I am kindly asking for your advice.
>
> Now we are trying to set Scipion-2.0 on a slurm cluster. It could run on single machine but failed to submit the jobs to queue. Slurm cluster works well and running scipion on single node works.
>
> Here’s our settings for host.conf:
>
> host.conf:
> [localhost]
> PARALLEL_COMMAND = mpirun -np %_(JOB_NODES)d -bynode %_(COMMAND)s
> NAME = SLURM
> MANDATORY = 0
> SUBMIT_COMMAND = sbatch %_(JOB_SCRIPT)s
> CANCEL_COMMAND = scancel %_(JOB_ID)s
> CHECK_COMMAND = squeue -j %_(JOB_ID)s
> SUBMIT_TEMPLATE = #!/bin/bash
> ####SBATCH --export=ALL
> #SBATCH -p %_(JOB_QUEUE)s
> #SBATCH -J %_(JOB_NAME)s
> #SBATCH -o %_(JOB_SCRIPT)s.out
> #SBATCH -e %_(JOB_SCRIPT)s.err
> #SBATCH --time=%_(JOB_TIME)s:00:00
> #SBATCH --nodes=1
> #SBATCH --ntasks=%_(JOB_NODES)d
> #SBATCH --cpus-per-task=%_(JOB_THREADS)d
> WORKDIR=$SLURM_JOB_SUBMIT_DIR
> export XMIPP_IN_QUEUE=1
> cd $WORKDIR
> # Make a copy of node file
> echo $SLURM_JOB_NODELIST > %_(JOB_NODEFILE)s
> ### Display the job context
> echo Running on host `hostname`
> echo Time is `date`
> echo Working directory is `pwd`
> echo $SLURM_JOB_NODELIST
> echo CUDA_VISIBLE_DEVICES: $CUDA_VISIBLE_DEVICES
> #################################
> %_(JOB_COMMAND)s
> find "$SLURM_SUBMIT_DIR" -type f -user $USER -perm 644 -exec chmod 664 {} +
> QUEUES = {
> “a": [["JOB_TIME", "48", "Time (hours)", "Select the time expected (in hours) for this job"],
> ["NODES","1", "Nodes", "How many nodes required for all the nodes"],
> ["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual jobs to queue"]],
> “b": [["JOB_TIME", "48", "Time (hours)", "Select the time expected (in hours) for this job"],
> ["NODES","1", "Nodes", "How many nodes required for all the nodes"],
> ["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual jobs to queue"]],
> “c": [["JOB_MEMORY", "8192", "Memory (MB)", "Select amount of memory (in megabytes) for this job"],
> ["JOB_TIME", "48", "Time (hours)", "Select the time expected (in hours) for this job"],
> ["NODES","1", "Nodes", "How many nodes required for all the nodes"],
> ["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual jobs to queue"]]
> }
> JOB_DONE_REGEX =
>
> And the Scipion reports:
> typeerror: %d format: a number is required, not nonetype
>
> And suggestions about how to solve the problem? Thanks!
> _______________________________________________
> scipion-users mailing list
> sci...@li... <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Pablo C. <pc...@cn...> - 2020-11-23 07:48:09
|
Hi Juha, I haven't seen this before.
Hope Xmipp guys can help here.
On 22/11/20 23:34, Juha Huiskonen wrote:
> Hi all,
>
> I have an issue running Xmipp protocol_align_volume_and_particles.py
> from Scipion.
>
> RuntimeError: FATAL: module compiled as little endian, but detected
> different endianness at runtime
>
> It seems there's an issue with the installation. Any tips how to fix
> it? The full error is below
>
> Best wishes,
> Juha
>
>
> 00054: STARTED: alignVolumeStep, step 2, time 2020-11-23 00:26:33.446121
> 00055: xmipp_volume_align --i1
> Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2
> Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol
> --apply
> Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
> --frm --copyGeo
> Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt
> 00056: RuntimeError: FATAL: module compiled as little endian, but
> detected different endianness at runtime
> 00057:
> /projappl/project_2000637/apps/scipion/3.0/software/em/xmipp/bin/xmipp_volume_align:
> line 3: 39299 Segmentation fault
> $XMIPP_HOME/bin/xmipp_volume_align_prog "$@"
> 00058: Traceback (most recent call last):
> 00059: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 188, in run
> 00060: self._run()
> 00061: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 239, in _run
> 00062: resultFiles = self._runFunc()
> 00063: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 235, in _runFunc
> 00064: return self._func(*self._args)
> 00065: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_align_volume_and_particles.py",
> line 153, in alignVolumeStep
> 00066: self.runJob("xmipp_volume_align", args)
> 00067: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1339, in runJob
> 00068: self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 00069: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 66, in runJob
> 00070: process.runJob(log, programName, params,
> 00071: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 53, in runJob
> 00072: return runCommand(command, env, cwd)
> 00073: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 68, in runCommand
> 00074: check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
> 00075: File
> "/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/subprocess.py",
> line 364, in check_call
> 00076: raise CalledProcessError(retcode, cmd)
> 00077: subprocess.CalledProcessError: Command 'xmipp_volume_align
> --i1 Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol
> --i2 Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol
> --apply
> Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
> --frm --copyGeo
> Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt'
> returned non-zero exit status 139.
> 00078: Protocol failed: Command 'xmipp_volume_align --i1
> Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2
> Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol
> --apply
> Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
> --frm --copyGeo
> Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt'
> returned non-zero exit status 139.
> 00079: FAILED: alignVolumeStep, step 2, time 2020-11-23 00:26:34.625143
> 00080: ------------------- PROTOCOL FAILED (DONE 2/4)
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Juha H. <juh...@gm...> - 2020-11-22 22:34:57
|
Hi all,
I have an issue running Xmipp protocol_align_volume_and_particles.py from
Scipion.
RuntimeError: FATAL: module compiled as little endian, but detected
different endianness at runtime
It seems there's an issue with the installation. Any tips how to fix it?
The full error is below
Best wishes,
Juha
00054: STARTED: alignVolumeStep, step 2, time 2020-11-23 00:26:33.446121
00055: xmipp_volume_align --i1
Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol --apply
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
--frm --copyGeo
Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt
00056: RuntimeError: FATAL: module compiled as little endian, but
detected different endianness at runtime
00057:
/projappl/project_2000637/apps/scipion/3.0/software/em/xmipp/bin/xmipp_volume_align:
line 3: 39299 Segmentation fault
$XMIPP_HOME/bin/xmipp_volume_align_prog "$@"
00058: Traceback (most recent call last):
00059: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
line 188, in run
00060: self._run()
00061: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
line 239, in _run
00062: resultFiles = self._runFunc()
00063: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
line 235, in _runFunc
00064: return self._func(*self._args)
00065: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_align_volume_and_particles.py",
line 153, in alignVolumeStep
00066: self.runJob("xmipp_volume_align", args)
00067: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
line 1339, in runJob
00068: self._stepsExecutor.runJob(self._log, program, arguments,
**kwargs)
00069: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
line 66, in runJob
00070: process.runJob(log, programName, params,
00071: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
line 53, in runJob
00072: return runCommand(command, env, cwd)
00073: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
line 68, in runCommand
00074: check_call(command, shell=True, stdout=sys.stdout,
stderr=sys.stderr,
00075: File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/subprocess.py",
line 364, in check_call
00076: raise CalledProcessError(retcode, cmd)
00077: subprocess.CalledProcessError: Command 'xmipp_volume_align --i1
Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol --apply
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
--frm --copyGeo
Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt'
returned non-zero exit status 139.
00078: Protocol failed: Command 'xmipp_volume_align --i1
Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol --apply
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
--frm --copyGeo
Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt'
returned non-zero exit status 139.
00079: FAILED: alignVolumeStep, step 2, time 2020-11-23 00:26:34.625143
00080: ------------------- PROTOCOL FAILED (DONE 2/4)
|
|
From: Dmitry A. S. <sem...@gm...> - 2020-11-20 19:50:48
|
Dear Pablo, Thank you! Sincerely, Dmitry ------ Original Message ------ From: "Pablo Conesa" <pc...@cn...> To: "Mailing list for Scipion users" <sci...@li...> Sent: 20-Nov-20 7:35:13 PM Subject: Re: [scipion-users] SCIPION__3___installing plugins/protocols >Hi Dmitry. > >You need to adapt the config file to point to the right Motioncor >binary: > >In scipion3, config file is optional. If you don't have it, type > >scipion3 config > >an you will have <scipion_home>/config/scipion.conf populated with all >the default values. > >For motiocor2, in the plugin manager you will find the url where you >can find useful information about how to configure it: > > >This apply too to gCTF plugin. > > > >On 20/11/20 18:41, Dmitry A. Semchonok wrote: >>/opt/Scipion3/software/em/motioncor2-1.3.2/bin/MotionCor2_1.3.2-Cuda101: >>error while loading shared libraries: libcudart.so.10.1: cannot open >>shared object file: No such file or directory >-- >Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es> team |
|
From: Pablo C. <pc...@cn...> - 2020-11-20 18:35:29
|
Hi Dmitry. You need to adapt the config file to point to the right Motioncor binary: In scipion3, config file is optional. If you don't have it, type scipion3 config an you will have <scipion_home>/config/scipion.conf populated with all the default values. For motiocor2, in the plugin manager you will find the url where you can find useful information about how to configure it: This apply too to gCTF plugin. On 20/11/20 18:41, Dmitry A. Semchonok wrote: > /opt/Scipion3/software/em/motioncor2-1.3.2/bin/MotionCor2_1.3.2-Cuda101: > error while loading shared libraries: libcudart.so.10.1: cannot open > shared object file: No such file or directory -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Dmitry A. S. <sem...@gm...> - 2020-11-20 17:42:16
|
Please see below
[32mRUNNING PROTOCOL -----------------[0m
Hostname: cryoem01
PID: 6073
pyworkflow: 3.0.7
plugin: motioncorr
plugin v: 3.0.11
currentDir: /root/ScipionUserData/projects/TestMotioncor2AlignMovies
workingDir: Runs/000410_ProtMotionCorr
runMode: Continue
MPI: 1
threads: 1
Starting at step: 1
Running steps
[35mSTARTED[0m: _convertInputStep, step 1, time 2020-11-20 18:14:46.299801
[35mFINISHED[0m: _convertInputStep, step 1, time 2020-11-20 18:14:46.308113
[35mSTARTED[0m: processMovieStep, step 2, time 2020-11-20 18:14:46.323599
Processing movie: Runs/000410_ProtMotionCorr/tmp/movie_000001/qbeta.mrc
[32m/opt/Scipion3/software/em/motioncor2-1.3.2/bin/MotionCor2_1.3.2-Cuda101 -InMrc "qbeta.mrc" -OutMrc "../../extra/qbeta_aligned_mic.mrc" -Patch 2 2 -MaskCent 0 0 -MaskSize 1 1 -FtBin 1.0 -Tol 0.5 -Group 1 -FmDose 1.3 -Throw 1 -Trunc 1 -PixSize 1.0 -kV 300.0 -LogFile ../../extra/micrograph_000001_ -InitDose 0.0 -OutStack 0 -Gpu 0 -SumRange 0.0 0.0 [0m
/opt/Scipion3/software/em/motioncor2-1.3.2/bin/MotionCor2_1.3.2-Cuda101: error while loading shared libraries: libcudart.so.10.1: cannot open shared object file: No such file or directory
ERROR: Movie failed
[35mFINISHED[0m: processMovieStep, step 2, time 2020-11-20 18:14:46.350371
[31mERROR: Movie Runs/000002_ProtImportMovies/extra/qbeta.mrc couldn't be added to the output set.
[Errno 2] No such file or directory: 'Runs/000410_ProtMotionCorr/extra/micrograph_000001_0-Patch-Full.log'[0m
[33mWARNING: Micrograph Runs/000410_ProtMotionCorr/extra/qbeta_aligned_mic.mrc was not generated, can't add it to output set.[0m
[33mWARNING: Micrograph Runs/000410_ProtMotionCorr/extra/qbeta_aligned_mic_DW.mrc was not generated, can't add it to output set.[0m
[35mSTARTED[0m: createOutputStep, step 3, time 2020-11-20 18:14:49.416644
Traceback (most recent call last):
File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 187, in run
self._run()
File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run
resultFiles = self._runFunc()
File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc
return self._func(*self._args)
File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py", line 120, in createOutputStep
raise Exception("All movies failed, didn't create outputMicrographs."
Exception: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.
[31mProtocol failed: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.[0m
[35mFAILED[0m: createOutputStep, step 3, time 2020-11-20 18:14:49.424758
[32m------------------- PROTOCOL FAILED (DONE 3/3)[0m
Sincerely,
Dmitry
On November 20, 2020 2:54:01 PM Grigory Sharov <sha...@gm...> wrote:
> Dear Dmitry,
>
> Could you please run scipion tests motioncorr.tests.test_protocols_motioncor2 and post the run.stdout here?
>
>
>
> Best regards,
> Grigory
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
>
> On Fri, Nov 20, 2020 at 1:41 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote:
> <>Dear colleagues,
>
> We have some issues during SCIPION3 plugins installations.
>
> Any suggestions?
>
> Thank you!
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
> Motion cor error:
>
>
>
> 00279: WARNING: Micrograph Runs/000174_ProtMotionCorr/extra/20170629_00049_frameImage_aligned_mic_DW.mrc was not generated, can't add it to output set.
>
> 00280: STARTED: createOutputStep, step 26, time 2020-11-20 14:16:28.063854
>
> 00281: Traceback (most recent call last):
>
> 00282: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 187, in run
>
> 00283: self._run()
>
> 00284: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run
>
> 00285: resultFiles = self._runFunc()
>
> 00286: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc
>
> 00287: return self._func(*self._args)
>
> 00288: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py", line 120, in createOutputStep
>
> 00289: raise Exception("All movies failed, didn't create outputMicrographs."
>
> 00290: Exception: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.
>
> 00291: Protocol failed: All movies failed, didn't create outputMicrographs. Please review movie processing steps above.
>
> 00292: FAILED: createOutputStep, step 26, time 2020-11-20 14:16:28.070889
>
> 00293: ------------------- PROTOCOL FAILED (DONE 26/26)
>
>
> GCTF:
>
>
> 00279: WARNING: Micrograph Runs/000174_ProtMotionCorr/extra/20170629_00049_frameImage_aligned_mic_DW.mrc was not generated, can't add it to output set.
>
> 00280: STARTED: createOutputStep, step 26, time 2020-11-20 14:16:28.063854
>
> 00281: Traceback (most recent call last):
>
> 00282: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 187, in run
>
> 00283: self._run()
>
> 00284: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run
>
> 00285: resultFiles = self._runFunc()
>
> 00286: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc
>
> 00287: return self._func(*self._args)
>
> 00288: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py", line 120, in createOutputStep
>
> 00289: raise Exception("All movies failed, didn't create outputMicrographs."
>
> 00290: Exception: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.
>
> 00291: Protocol failed: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.
>
> 00292: FAILED: createOutputStep, step 26, time 2020-11-20 14:16:28.070889
>
> 00293: ------------------- PROTOCOL FAILED (DONE 26/26)
>
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li... <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>
> _______________________________________________
> scipion-users mailing list
> sci...@li... <mailto:scipion-users%40lists.sourceforge.net>
> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
|
|
From: Grigory S. <sha...@gm...> - 2020-11-20 13:53:47
|
Dear Dmitry,
Could you please run *scipion tests
motioncorr.tests.test_protocols_motioncor2* and post the *run.stdout* here?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...
On Fri, Nov 20, 2020 at 1:41 PM Dmitry Semchonok <Sem...@gm...>
wrote:
> Dear colleagues,
>
> We have some issues during SCIPION3 plugins installations.
>
> Any suggestions?
>
> Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
>
>
> *Motion cor error:*
>
>
> 00279: WARNING: Micrograph
> Runs/000174_ProtMotionCorr/extra/20170629_00049_frameImage_aligned_mic_DW.mrc
> was not generated, can't add it to output set.
>
> 00280: STARTED: createOutputStep, step 26, time 2020-11-20
> 14:16:28.063854
>
> 00281: Traceback (most recent call last):
>
> 00282: File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 187, in run
>
> 00283: self._run()
>
> 00284: File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 238, in _run
>
> 00285: resultFiles = self._runFunc()
>
> 00286: File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 234, in _runFunc
>
> 00287: return self._func(*self._args)
>
> 00288: File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py",
> line 120, in createOutputStep
>
> 00289: raise Exception("All movies failed, didn't create
> outputMicrographs."
>
> 00290: Exception: All movies failed, didn't create
> outputMicrographs.Please review movie processing steps above.
>
> 00291: Protocol failed: All movies failed, didn't create
> outputMicrographs. Please review movie processing steps above.
>
> 00292: FAILED: createOutputStep, step 26, time 2020-11-20 14:16:28.070889
>
> 00293: ------------------- PROTOCOL FAILED (DONE 26/26)
>
>
>
> *GCTF:*
>
>
>
> 00279: WARNING: Micrograph
> Runs/000174_ProtMotionCorr/extra/20170629_00049_frameImage_aligned_mic_DW.mrc
> was not generated, can't add it to output set.
>
> 00280: STARTED: createOutputStep, step 26, time 2020-11-20
> 14:16:28.063854
>
> 00281: Traceback (most recent call last):
>
> 00282: File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 187, in run
>
> 00283: self._run()
>
> 00284: File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 238, in _run
>
> 00285: resultFiles = self._runFunc()
>
> 00286: File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 234, in _runFunc
>
> 00287: return self._func(*self._args)
>
> 00288: File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py",
> line 120, in createOutputStep
>
> 00289: raise Exception("All movies failed, didn't create
> outputMicrographs."
>
> 00290: Exception: All movies failed, didn't create
> outputMicrographs.Please review movie processing steps above.
>
> 00291: Protocol failed: All movies failed, didn't create
> outputMicrographs.Please review movie processing steps above.
>
> 00292: FAILED: createOutputStep, step 26, time 2020-11-20 14:16:28.070889
>
> 00293: ------------------- PROTOCOL FAILED (DONE 26/26)
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Dmitry S. <Sem...@gm...> - 2020-11-20 13:41:26
|
<>Dear colleagues,
We have some issues during SCIPION3 plugins installations.
Any suggestions?
Thank you!
Sincerely,
Dmitry
Motion cor error:
00279: WARNING: Micrograph Runs/000174_ProtMotionCorr/extra/20170629_00049_frameImage_aligned_mic_DW.mrc was not generated, can't add it to output set.
00280: STARTED: createOutputStep, step 26, time 2020-11-20 14:16:28.063854
00281: Traceback (most recent call last):
00282: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 187, in run
00283: self._run()
00284: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run
00285: resultFiles = self._runFunc()
00286: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc
00287: return self._func(*self._args)
00288: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py", line 120, in createOutputStep
00289: raise Exception("All movies failed, didn't create outputMicrographs."
00290: Exception: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.
00291: Protocol failed: All movies failed, didn't create outputMicrographs. Please review movie processing steps above.
00292: FAILED: createOutputStep, step 26, time 2020-11-20 14:16:28.070889
00293: ------------------- PROTOCOL FAILED (DONE 26/26)
GCTF:
00279: WARNING: Micrograph Runs/000174_ProtMotionCorr/extra/20170629_00049_frameImage_aligned_mic_DW.mrc was not generated, can't add it to output set.
00280: STARTED: createOutputStep, step 26, time 2020-11-20 14:16:28.063854
00281: Traceback (most recent call last):
00282: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 187, in run
00283: self._run()
00284: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run
00285: resultFiles = self._runFunc()
00286: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc
00287: return self._func(*self._args)
00288: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py", line 120, in createOutputStep
00289: raise Exception("All movies failed, didn't create outputMicrographs."
00290: Exception: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.
00291: Protocol failed: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.
00292: FAILED: createOutputStep, step 26, time 2020-11-20 14:16:28.070889
00293: ------------------- PROTOCOL FAILED (DONE 26/26)
|
|
From: Anne-Pascale J. <ann...@i2...> - 2020-11-19 15:29:46
|
Thank you very much for your answer. the test is ok. Best regards, Anne-Pascale ---------------------------------------------------------------------- Anne-Pascale Jaudier SICS – I2BC Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 01 69 82 34 74 De: "Grigory Sharov" <sha...@gm...> À: "scipion-users" <sci...@li...> Envoyé: Jeudi 19 Novembre 2020 11:18:19 Objet: Re: [scipion-users] error with tests Scipion3 Hi, looks like a mistake on our part. The tests page in the documentation needs updating. The correct test is: scipion tests pyworkflowtests.tests.test_object.TestObject Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Thu, Nov 19, 2020 at 10:13 AM Anne-Pascale JAUDIER < [ mailto:ann...@i2... | ann...@i2... ] > wrote: Hi, I have installed scipion 3 on debian 10 with conda No error and Every things seem ok except installation of pluggins :atomstructils,cryoassess,cryodrqn,tomoj When I run different small an medium tests , I have an error with all tests with "Pyworkflow.*". For example : scipion test pyworkflow.tests.model.test_object i have the following error : ModuleNotFoundError: No module named 'pyworkflow.tests.model' Thanks for your help, Anne-Pascale ---------------------------------------------------------------------- Anne-Pascale Jaudier SICS – I2BC Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 01 69 82 34 74 _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Pablo C. <pc...@cn...> - 2020-11-19 12:25:14
|
Thanks wolfgang! Nice piece for xmipp documentation. On 19/11/20 12:05, Lugmayr, Wolfgang wrote: > dear all, > > just for documentation of the scipion 3.0.6 official release. > > i changed in xmipp.conf the line: > CXXFLAGS= -mtune=native -march=native -std=c++11 -O3 > to > CXXFLAGS= -mfma -mavx2 -m3dnow -fomit-frame-pointer -std=c++11 -O3 > and rebuild xmipp. > now the exes run fine on intel and amd epyc processors. > > the flags come from recommended for gcc: > https://prace-ri.eu/wp-content/uploads/Best-Practice-Guide_AMD.pdf > > cheers and thanks for the help, > wolfgang > > > ------------------------------------------------------------------------ > *From: *"Carlos Oscar Sorzano" <co...@cn...> > *To: *"Pablo Conesa" <pc...@cn...>, "David" > <dst...@cn...>, dma...@cn..., "w lugmayr" > <w.l...@uk...>, "Mailing list for Scipion users" > <sci...@li...> > *Sent: *Thursday, 29 October, 2020 16:11:16 > *Subject: *Re: Fwd: [scipion-users] scipion-installer - how do i > change compiler optimization flags? > > Dear Wolfgang, > > in the compilation of Xmipp, you can set the environment variable > CXXFLAGS before calling the xmipp script. From the Scipion > installation I am not sure how to pass it to the xmipp script. It may > be that setting it in the shell before calling scipion suffices. But I > have never tried. > > Kind regards, Carlos Oscar > > El 29/10/2020 a las 11:13, Pablo Conesa escribió: > > ? > > > > -------- Forwarded Message -------- > Subject: [scipion-users] scipion-installer - how do i change > compiler optimization flags? > Date: Wed, 28 Oct 2020 14:19:29 +0100 (CET) > From: Lugmayr, Wolfgang <w.l...@uk...> <mailto:w.l...@uk...> > Reply-To: Mailing list for Scipion users > <sci...@li...> > <mailto:sci...@li...> > To: Mailing list for Scipion users > <sci...@li...> > <mailto:sci...@li...> > > > > hi, > > i installed and compiled scipion 3.0.5-devel on a system with > intel cpus. > > when i run now scipion on new nodes with "AMD EPYC 7402" > processors the executable fails with: > $ scipion3 last Scipion v3.0.5 () devel > sh: line 1: 45875 Illegal instruction python -m scipion last > > so i do not want to have 2 versions of scipion3 but maybe compile > it with intel and amd compatibility flags. > how do i set these flags? > > cheers, > wolfgang > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Deutsches Elektronen-Synchrotron (DESY) > Notkestrasse 85 Gebäude 15 > 22607 Hamburg, Germany > Tel.: +49 40 8998-87652 > Email:wol...@cs... <mailto:wol...@cs...> > http://www.cssb-hamburg.de/ > > > _______________________________________________ > 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: David M. <dma...@cn...> - 2020-11-19 12:14:53
|
Thank you very much Wolfgang, We are including this information to our documentation. Thanks for reporting and enhancing Scipion/Xmipp. Do not hesitate if any other issue is found. Cheers, <http://ucm.es/> *_____Dr. David Maluenda Niubó* dma...@ub... - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> BioComputing Unit <http://biocomputingunit.es/> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Thu, Nov 19, 2020 at 12:06 PM Lugmayr, Wolfgang <w.l...@uk...> wrote: > dear all, > > just for documentation of the scipion 3.0.6 official release. > > i changed in xmipp.conf the line: > CXXFLAGS= -mtune=native -march=native -std=c++11 -O3 > to > CXXFLAGS= -mfma -mavx2 -m3dnow -fomit-frame-pointer -std=c++11 -O3 > and rebuild xmipp. > now the exes run fine on intel and amd epyc processors. > > the flags come from recommended for gcc: > https://prace-ri.eu/wp-content/uploads/Best-Practice-Guide_AMD.pdf > > cheers and thanks for the help, > wolfgang > > > ------------------------------ > *From: *"Carlos Oscar Sorzano" <co...@cn...> > *To: *"Pablo Conesa" <pc...@cn...>, "David" <dst...@cn...>, > dma...@cn..., "w lugmayr" <w.l...@uk...>, "Mailing list for > Scipion users" <sci...@li...> > *Sent: *Thursday, 29 October, 2020 16:11:16 > *Subject: *Re: Fwd: [scipion-users] scipion-installer - how do i change > compiler optimization flags? > > Dear Wolfgang, > > in the compilation of Xmipp, you can set the environment variable CXXFLAGS > before calling the xmipp script. From the Scipion installation I am not > sure how to pass it to the xmipp script. It may be that setting it in the > shell before calling scipion suffices. But I have never tried. > > Kind regards, Carlos Oscar > El 29/10/2020 a las 11:13, Pablo Conesa escribió: > > ? > > > -------- Forwarded Message -------- > Subject: [scipion-users] scipion-installer - how do i change compiler > optimization flags? > Date: Wed, 28 Oct 2020 14:19:29 +0100 (CET) > From: Lugmayr, Wolfgang <w.l...@uk...> <w.l...@uk...> > Reply-To: Mailing list for Scipion users > <sci...@li...> > <sci...@li...> > To: Mailing list for Scipion users <sci...@li...> > <sci...@li...> > > > hi, > > i installed and compiled scipion 3.0.5-devel on a system with intel cpus. > > when i run now scipion on new nodes with "AMD EPYC 7402" processors the > executable fails with: > $ scipion3 last Scipion v3.0.5 () devel > sh: line 1: 45875 Illegal instruction python -m scipion last > > so i do not want to have 2 versions of scipion3 but maybe compile it with > intel and amd compatibility flags. > how do i set these flags? > > cheers, > wolfgang > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Deutsches Elektronen-Synchrotron (DESY) > Notkestrasse 85 Gebäude 15 > 22607 Hamburg, Germany > Tel.: +49 40 8998-87652 > Email: wol...@cs...http://www.cssb-hamburg.de/ > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir > informació confidencial o protegida legalment i s’adreça exclusivament a la > persona o entitat destinatària. Si no consteu com a destinatari final o no > teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, > modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si > l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant > el missatge com els fitxers adjunts que hi pugui haver. > > Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener > información confidencial o legalmente protegida y está exclusivamente > dirigido a la persona o entidad destinataria. Si usted no consta como > destinatario final ni es la persona encargada de recibirlo, no está > autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a > revelar su contenido. Si lo ha recibido por error, informe de ello al > remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos > que pueda contener. > > This email message and any attachments it carries may contain confidential > or legally protected material and are intended solely for the individual or > organization to whom they are addressed. If you are not the intended > recipient of this message or the person responsible for processing it, then > you are not authorized to read, save, modify, send, copy or disclose any > part of it. If you have received the message by mistake, please inform the > sender of this and eliminate the message and any attachments it carries > from your account. > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Lugmayr, W. <w.l...@uk...> - 2020-11-19 11:05:36
|
dear all, just for documentation of the scipion 3.0.6 official release. i changed in xmipp.conf the line: CXXFLAGS= -mtune=native -march=native -std=c++11 -O3 to CXXFLAGS= -mfma -mavx2 -m3dnow -fomit-frame-pointer -std=c++11 -O3 and rebuild xmipp. now the exes run fine on intel and amd epyc processors. the flags come from recommended for gcc: https://prace-ri.eu/wp-content/uploads/Best-Practice-Guide_AMD.pdf cheers and thanks for the help, wolfgang From: "Carlos Oscar Sorzano" <co...@cn...> To: "Pablo Conesa" <pc...@cn...>, "David" <dst...@cn...>, dma...@cn..., "w lugmayr" <w.l...@uk...>, "Mailing list for Scipion users" <sci...@li...> Sent: Thursday, 29 October, 2020 16:11:16 Subject: Re: Fwd: [scipion-users] scipion-installer - how do i change compiler optimization flags? Dear Wolfgang, in the compilation of Xmipp, you can set the environment variable CXXFLAGS before calling the xmipp script. From the Scipion installation I am not sure how to pass it to the xmipp script. It may be that setting it in the shell before calling scipion suffices. But I have never tried. Kind regards, Carlos Oscar El 29/10/2020 a las 11:13, Pablo Conesa escribió: ? -------- Forwarded Message -------- Subject: [scipion-users] scipion-installer - how do i change compiler optimization flags? Date: Wed, 28 Oct 2020 14:19:29 +0100 (CET) From: Lugmayr, Wolfgang [ mailto:w.l...@uk... | <w.l...@uk...> ] Reply-To: Mailing list for Scipion users [ mailto:sci...@li... | <sci...@li...> ] To: Mailing list for Scipion users [ mailto:sci...@li... | <sci...@li...> ] hi, i installed and compiled scipion 3.0.5-devel on a system with intel cpus. when i run now scipion on new nodes with "AMD EPYC 7402" processors the executable fails with: $ scipion3 last Scipion v3.0.5 () devel sh: line 1: 45875 Illegal instruction python -m scipion last so i do not want to have 2 versions of scipion3 but maybe compile it with intel and amd compatibility flags. how do i set these flags? cheers, wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 22607 Hamburg, Germany Tel.: +49 40 8998-87652 Email: [ mailto:wol...@cs... | wol...@cs... ] [ http://www.cssb-hamburg.de/ | http://www.cssb-hamburg.de/ ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] |
|
From: Grigory S. <sha...@gm...> - 2020-11-19 10:18:51
|
Hi, looks like a mistake on our part. The tests page in the documentation needs updating. The correct test is: scipion tests pyworkflowtests.tests.test_object.TestObject Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Nov 19, 2020 at 10:13 AM Anne-Pascale JAUDIER < ann...@i2...> wrote: > Hi, > > I have installed scipion 3 on debian 10 with conda > No error and Every things seem ok except installation of pluggins > :atomstructils,cryoassess,cryodrqn,tomoj > When I run different small an medium tests , I have an error with all > tests with "Pyworkflow.*". > For example : > scipion test pyworkflow.tests.model.test_object > i have the following error : > ModuleNotFoundError: No module named 'pyworkflow.tests.model' > > Thanks for your help, > Anne-Pascale > > > ---------------------------------------------------------------------- > Anne-Pascale Jaudier > SICS – I2BC > Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette > 01 69 82 34 74 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Anne-Pascale J. <ann...@i2...> - 2020-11-19 10:13:34
|
Hi, I have installed scipion 3 on debian 10 with conda No error and Every things seem ok except installation of pluggins :atomstructils,cryoassess,cryodrqn,tomoj When I run different small an medium tests , I have an error with all tests with "Pyworkflow.*". For example : scipion test pyworkflow.tests.model.test_object i have the following error : ModuleNotFoundError: No module named 'pyworkflow.tests.model' Thanks for your help, Anne-Pascale ---------------------------------------------------------------------- Anne-Pascale Jaudier SICS – I2BC Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 01 69 82 34 74 |
|
From: Tetter S. <tet...@or...> - 2020-11-19 07:34:05
|
Awesome, it worked.
Thanks a lot!
Stephan
________________________________
Von: Grigory Sharov <sha...@gm...>
Gesendet: Mittwoch, 18. November 2020 17:30:45
An: Mailing list for Scipion users
Betreff: Re: [scipion-users] Can't import particles from relion
Hi Stephan,
It looks like a problem with the plugin installation. Can you try:
scipion3 uninstallp -p scipion-em-relion
scipion3 installp -p scipion-em-relion --noBin
and then re-run import particles?
PS. The plugin version (3.0.0.b7) is independent from the Relion binaries version (3.1.0).
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228<tel:+44%201223%20267228>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Wed, Nov 18, 2020 at 4:03 PM Tetter Stephan <tet...@or...<mailto:tet...@or...>> wrote:
Dear all,
I have freshly installed Scipion3. When I wanted to import particles from a refinement done in relion3.0, I got an error message. I didn't have Relion installed on the same computer as the Scipion installation, so that sounded reasonable. Thus, I've installed Relion 3.1 manually. Still couldn't import the particles. I've tried to install Relion via the Scipion plugin manager, and everything went well. I've installed relion without the GUI, but I assume that shouldn't be an issue. The installation should be fine:
$ relion_image_handler --version
RELION version: 3.1.1-commit-9f3bf1
Precision: BASE=double
Again, I've tried to import the particles in Scipion, but it still doesn't work:
########################
Protocol validation failed. It usually happens because there are some input missing. Please check if the error message gives you any hint:
Error: Exception
Description:
> error when importing from relion: No module named 'relion.convert'. Relion is needed to import .star files
File "<frozen importlib._bootstrap>", line 991, in findand_load
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.
Traceback:
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1878, in validate
childErrors = self._validate()
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_import/particles.py", line 245, in validate
ci = self.getImportClass()
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocolimport/particles.py", line 176, in getImportClass
RelionImport = Domain.importFromPlugin('relion.convert', 'RelionImport',
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 294, in importFromPlugin
output = _tryImportFromPlugin(objects)
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 291, in tryImportFromPlugin
Domain._pluginNotFound(plugName, errMsg, doRaise)
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 437, in __pluginNotFound
raise Exception("\n\n" + raiseMsg)
##############################
Checking for updates as instructed in the error messages gives the following. Curiously, this points to a Relion3.0 installation.
##############################
$ ./scipion3 installp --help --checkUpdates
Scipion v3.0.6 - Eugenius
WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
Warning: Couldn't get remote plugin data for scipion-em-deepfinder
Warning: Couldn't get remote plugin data for scipion-em-tomoj
WARNING: scipion-ed-dials's release 3.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed-dials's release 3.0.1a3 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.0 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.0a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.1 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 3.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
usage: scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]
optional arguments:
-h, --help show help
--noBin Optional flag to install plugins only as a python module,
without installing the plugin binaries. This will affect
all plugins specified in the command.
--checkUpdates Optional flag to check which plugins have new releases.
-p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...]
- pluginName: the name of the plugin to install from the list
of available plugins shown below.
- pluginVersion: (optional) pip version to install. If not specified,
will install the latest compatible with current Scipion.
--devel Optional flag to indicate that we will pass install sources instead
of pip names. Sources might be local paths or git urls. With local
paths, will do pip install -e (editable mode). It is expected to find
the plugin name in the basename of the path or in the repo name.
(i.e. it needs to match the one specified in setup.py). E.g:
scipion installp -p path/to/pluginName --devel
scipion installp -p https://github.com/someOrg/pluginName.git --devel
-j j Number of CPUs to use for compilation
Example: scipion installp -p scipion-em-motioncorr 1.0.6 -p scipion-em-relion -p scipion-em-eman2
Available plugins: ([ ] not installed, [X] seems already installed)
scipion-em 3.0.6 [X]
scipion-em-appion [ ]
scipion-em-atomstructutils [ ]
scipion-em-atsas [ ]
scipion-em-bamfordlab [ ]
scipion-em-bsoft [ ]
scipion-em-ccp4 [ ]
scipion-em-chimera [ ]
scipion-em-cistem [ ]
scipion-em-continuousflex [ ]
scipion-em-cryoassess [ ]
scipion-em-cryodrgn [ ]
scipion-em-cryoef [ ]
scipion-em-cryosparc2 [ ]
scipion-em-deepfinder [ ]
scipion-em-dynamo [ ]
scipion-em-eman2 3.1.1 [X]
scipion-em-empiar [ ]
scipion-em-emxlib [ ]
scipion-em-facilities [ ]
scipion-em-fsc3d [ ]
scipion-em-gautomatch [ ]
scipion-em-gctf [ ]
scipion-em-imagic [ ]
scipion-em-imod [ ]
scipion-em-localrec [ ]
scipion-em-locscale [ ]
scipion-em-motioncorr 1.0.6 [X]
scipion-em-novactf [ ]
scipion-em-phenix [ ]
scipion-em-pyseg [ ]
scipion-em-relion 3.0.0b7 [X]
scipion-em-reliontomo [ ]
scipion-em-resmap [ ]
scipion-em-sidesplitter [ ]
scipion-em-sphire [ ]
scipion-em-spider [ ]
scipion-em-tomo 3.0.6 [X]
scipion-em-tomoj [ ]
scipion-em-topaz [ ]
scipion-em-xmipp 20.7.2 [X]
scipion-em-xmipp2 [ ]
scipion-em-xmipptomo [ ]
###########################################
I am further confused as to why this would point to relion 3.0, even though the final lines in the Scipion plugin manager-based installation seemed to point to the 3.1 version.
###########################################
04565: Building scipion-em-relion ...
04566: /home/hilvertg/anaconda3/envs/.scipion3env/bin/python -m pip install scipion-em-relion==3.0.0b7
04567: Done (1.36 seconds)
04568: Building relion-3.1.0 ...
04569: wget -nv -c -O /home/hilvertg/software/em/relion-3.1.0.tgz.part https://github.com/3dem/relion/archive/3.1.0.tar.gz
04570: mv -v /home/hilvertg/software/em/relion-3.1.0.tgz.part /home/hilvertg/software/em/relion-3.1.0.tgz
04571: cd /home/hilvertg/software/em
04572: tar -xf relion-3.1.0.tgz
04573: cd /home/hilvertg/software/em/relion-3.1.0
04574: cmake -DGUI=OFF -DCMAKE_INSTALL_PREFIX=./ .
04575: cd /home/hilvertg/software/em/relion-3.1.0
04576: make -j 4
04577: Skipping command: Link 'relion-3.1.0 -> relion-3.1.0'
04578: All targets exist.
04579: Done (3 m 57 s)
############################################
Any idea what I need to do to import my particles?
Thanks,
Stephan
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Grigory S. <sha...@gm...> - 2020-11-18 16:31:18
|
Hi Stephan,
It looks like a problem with the plugin installation. Can you try:
scipion3 uninstallp -p scipion-em-relion
scipion3 installp -p scipion-em-relion --noBin
and then re-run import particles?
PS. The plugin version (3.0.0.b7) is independent from the Relion binaries
version (3.1.0).
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...
On Wed, Nov 18, 2020 at 4:03 PM Tetter Stephan <tet...@or...>
wrote:
> Dear all,
>
>
> I have freshly installed Scipion3. When I wanted to import particles from
> a refinement done in relion3.0, I got an error message. I didn't have
> Relion installed on the same computer as the Scipion installation, so that
> sounded reasonable. Thus, I've installed Relion 3.1 manually. Still
> couldn't import the particles. I've tried to install Relion via the Scipion
> plugin manager, and everything went well. I've installed relion without the
> GUI, but I assume that shouldn't be an issue. The installation should be
> fine:
>
>
> $ relion_image_handler --version
> RELION version: 3.1.1-commit-9f3bf1
> Precision: BASE=double
>
> Again, I've tried to import the particles in Scipion, but it still doesn't
> work:
>
> ########################
>
> Protocol validation failed. It usually happens because there are some
> input missing. Please check if the error message gives you any hint:
> Error: Exception
> Description:
>
> > error when importing from relion: No module named 'relion.convert'.
> Relion is needed to import .star files
> File "<frozen importlib._bootstrap>", line 991, in findand_load
> 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.
>
> Traceback:
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1878, in validate
> childErrors = self._validate()
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_import/particles.py",
> line 245, in validate
> ci = self.getImportClass()
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocolimport/particles.py",
> line 176, in getImportClass
> RelionImport = Domain.importFromPlugin('relion.convert',
> 'RelionImport',
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py",
> line 294, in importFromPlugin
> output = _tryImportFromPlugin(objects)
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py",
> line 291, in tryImportFromPlugin
> Domain._pluginNotFound(plugName, errMsg, doRaise)
>
> File
> "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py",
> line 437, in __pluginNotFound
> raise Exception("\n\n" + raiseMsg)
>
> ##############################
>
> Checking for updates as instructed in the error messages gives the
> following. Curiously, this points to a Relion3.0 installation.
>
> ##############################
>
> $ ./scipion3 installp --help --checkUpdates
> Scipion v3.0.6 - Eugenius
> WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined.
> Relying on conda being in the PATH
> Warning: Couldn't get remote plugin data for scipion-em-deepfinder
> Warning: Couldn't get remote plugin data for scipion-em-tomoj
> WARNING: scipion-ed-dials's release 3.0.1a2 did not specify a compatible
> Scipion version. Please, remove this release from pypi
> WARNING: scipion-ed-dials's release 3.0.1a3 did not specify a compatible
> Scipion version. Please, remove this release from pypi
> WARNING: scipion-ed's release 0.0.0 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> WARNING: scipion-ed's release 0.0.0a2 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> WARNING: scipion-ed's release 0.0.1 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> WARNING: scipion-ed's release 0.0.1a2 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> WARNING: scipion-ed's release 3.0.1a2 did not specify a compatible Scipion
> version. Please, remove this release from pypi
> usage: scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]
>
> optional arguments:
> -h, --help show help
> --noBin Optional flag to install plugins only as a python
> module,
> without installing the plugin binaries. This will
> affect
> all plugins specified in the command.
> --checkUpdates Optional flag to check which plugins have new
> releases.
> -p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion
> ...]
> - pluginName: the name of the plugin to
> install from the list
> of available plugins shown below.
> - pluginVersion: (optional) pip version to
> install. If not specified,
> will install the latest
> compatible with current Scipion.
> --devel Optional flag to indicate that we will pass
> install sources instead
> of pip names. Sources might be local paths or git
> urls. With local
> paths, will do pip install -e (editable mode). It
> is expected to find
> the plugin name in the basename of the path or in
> the repo name.
> (i.e. it needs to match the one specified in
> setup.py). E.g:
> scipion installp -p path/to/pluginName --devel
> scipion installp -p
> https://github.com/someOrg/pluginName.git --devel
> -j j Number of CPUs to use for compilation
>
> Example: scipion installp -p scipion-em-motioncorr 1.0.6 -p
> scipion-em-relion -p scipion-em-eman2
>
> Available plugins: ([ ] not installed, [X] seems already installed)
>
> scipion-em 3.0.6 [X]
> scipion-em-appion [ ]
> scipion-em-atomstructutils [ ]
> scipion-em-atsas [ ]
> scipion-em-bamfordlab [ ]
> scipion-em-bsoft [ ]
> scipion-em-ccp4 [ ]
> scipion-em-chimera [ ]
> scipion-em-cistem [ ]
> scipion-em-continuousflex [ ]
> scipion-em-cryoassess [ ]
> scipion-em-cryodrgn [ ]
> scipion-em-cryoef [ ]
> scipion-em-cryosparc2 [ ]
> scipion-em-deepfinder [ ]
> scipion-em-dynamo [ ]
> scipion-em-eman2 3.1.1 [X]
> scipion-em-empiar [ ]
> scipion-em-emxlib [ ]
> scipion-em-facilities [ ]
> scipion-em-fsc3d [ ]
> scipion-em-gautomatch [ ]
> scipion-em-gctf [ ]
> scipion-em-imagic [ ]
> scipion-em-imod [ ]
> scipion-em-localrec [ ]
> scipion-em-locscale [ ]
> scipion-em-motioncorr 1.0.6 [X]
> scipion-em-novactf [ ]
> scipion-em-phenix [ ]
> scipion-em-pyseg [ ]
> scipion-em-relion 3.0.0b7 [X]
> scipion-em-reliontomo [ ]
> scipion-em-resmap [ ]
> scipion-em-sidesplitter [ ]
> scipion-em-sphire [ ]
> scipion-em-spider [ ]
> scipion-em-tomo 3.0.6 [X]
> scipion-em-tomoj [ ]
> scipion-em-topaz [ ]
> scipion-em-xmipp 20.7.2 [X]
> scipion-em-xmipp2 [ ]
> scipion-em-xmipptomo [ ]
>
> ###########################################
>
> I am further confused as to why this would point to relion 3.0, even
> though the final lines in the Scipion plugin manager-based installation
> seemed to point to the 3.1 version.
>
> ###########################################
>
> 04565: Building scipion-em-relion ...
> 04566: /home/hilvertg/anaconda3/envs/.scipion3env/bin/python -m pip
> install scipion-em-relion==3.0.0b7
> 04567: Done (1.36 seconds)
> 04568: Building relion-3.1.0 ...
> 04569: wget -nv -c -O /home/hilvertg/software/em/relion-3.1.0.tgz.part
> https://github.com/3dem/relion/archive/3.1.0.tar.gz
> 04570: mv -v /home/hilvertg/software/em/relion-3.1.0.tgz.part
> /home/hilvertg/software/em/relion-3.1.0.tgz
> 04571: cd /home/hilvertg/software/em
> 04572: tar -xf relion-3.1.0.tgz
> 04573: cd /home/hilvertg/software/em/relion-3.1.0
> 04574: cmake -DGUI=OFF -DCMAKE_INSTALL_PREFIX=./ .
> 04575: cd /home/hilvertg/software/em/relion-3.1.0
> 04576: make -j 4
> 04577: Skipping command: Link 'relion-3.1.0 -> relion-3.1.0'
> 04578: All targets exist.
> 04579: Done (3 m 57 s)
>
> ############################################
>
> Any idea what I need to do to import my particles?
>
> Thanks,
>
> Stephan
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Tetter S. <tet...@or...> - 2020-11-18 16:02:27
|
Dear all,
I have freshly installed Scipion3. When I wanted to import particles from a refinement done in relion3.0, I got an error message. I didn't have Relion installed on the same computer as the Scipion installation, so that sounded reasonable. Thus, I've installed Relion 3.1 manually. Still couldn't import the particles. I've tried to install Relion via the Scipion plugin manager, and everything went well. I've installed relion without the GUI, but I assume that shouldn't be an issue. The installation should be fine:
$ relion_image_handler --version
RELION version: 3.1.1-commit-9f3bf1
Precision: BASE=double
Again, I've tried to import the particles in Scipion, but it still doesn't work:
########################
Protocol validation failed. It usually happens because there are some input missing. Please check if the error message gives you any hint:
Error: Exception
Description:
> error when importing from relion: No module named 'relion.convert'. Relion is needed to import .star files
File "<frozen importlib._bootstrap>", line 991, in findand_load
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.
Traceback:
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1878, in validate
childErrors = self._validate()
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_import/particles.py", line 245, in validate
ci = self.getImportClass()
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocolimport/particles.py", line 176, in getImportClass
RelionImport = Domain.importFromPlugin('relion.convert', 'RelionImport',
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 294, in importFromPlugin
output = _tryImportFromPlugin(objects)
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 291, in tryImportFromPlugin
Domain._pluginNotFound(plugName, errMsg, doRaise)
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 437, in __pluginNotFound
raise Exception("\n\n" + raiseMsg)
##############################
Checking for updates as instructed in the error messages gives the following. Curiously, this points to a Relion3.0 installation.
##############################
$ ./scipion3 installp --help --checkUpdates
Scipion v3.0.6 - Eugenius
WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
Warning: Couldn't get remote plugin data for scipion-em-deepfinder
Warning: Couldn't get remote plugin data for scipion-em-tomoj
WARNING: scipion-ed-dials's release 3.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed-dials's release 3.0.1a3 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.0 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.0a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.1 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 3.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
usage: scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]
optional arguments:
-h, --help show help
--noBin Optional flag to install plugins only as a python module,
without installing the plugin binaries. This will affect
all plugins specified in the command.
--checkUpdates Optional flag to check which plugins have new releases.
-p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...]
- pluginName: the name of the plugin to install from the list
of available plugins shown below.
- pluginVersion: (optional) pip version to install. If not specified,
will install the latest compatible with current Scipion.
--devel Optional flag to indicate that we will pass install sources instead
of pip names. Sources might be local paths or git urls. With local
paths, will do pip install -e (editable mode). It is expected to find
the plugin name in the basename of the path or in the repo name.
(i.e. it needs to match the one specified in setup.py). E.g:
scipion installp -p path/to/pluginName --devel
scipion installp -p https://github.com/someOrg/pluginName.git --devel
-j j Number of CPUs to use for compilation
Example: scipion installp -p scipion-em-motioncorr 1.0.6 -p scipion-em-relion -p scipion-em-eman2
Available plugins: ([ ] not installed, [X] seems already installed)
scipion-em 3.0.6 [X]
scipion-em-appion [ ]
scipion-em-atomstructutils [ ]
scipion-em-atsas [ ]
scipion-em-bamfordlab [ ]
scipion-em-bsoft [ ]
scipion-em-ccp4 [ ]
scipion-em-chimera [ ]
scipion-em-cistem [ ]
scipion-em-continuousflex [ ]
scipion-em-cryoassess [ ]
scipion-em-cryodrgn [ ]
scipion-em-cryoef [ ]
scipion-em-cryosparc2 [ ]
scipion-em-deepfinder [ ]
scipion-em-dynamo [ ]
scipion-em-eman2 3.1.1 [X]
scipion-em-empiar [ ]
scipion-em-emxlib [ ]
scipion-em-facilities [ ]
scipion-em-fsc3d [ ]
scipion-em-gautomatch [ ]
scipion-em-gctf [ ]
scipion-em-imagic [ ]
scipion-em-imod [ ]
scipion-em-localrec [ ]
scipion-em-locscale [ ]
scipion-em-motioncorr 1.0.6 [X]
scipion-em-novactf [ ]
scipion-em-phenix [ ]
scipion-em-pyseg [ ]
scipion-em-relion 3.0.0b7 [X]
scipion-em-reliontomo [ ]
scipion-em-resmap [ ]
scipion-em-sidesplitter [ ]
scipion-em-sphire [ ]
scipion-em-spider [ ]
scipion-em-tomo 3.0.6 [X]
scipion-em-tomoj [ ]
scipion-em-topaz [ ]
scipion-em-xmipp 20.7.2 [X]
scipion-em-xmipp2 [ ]
scipion-em-xmipptomo [ ]
###########################################
I am further confused as to why this would point to relion 3.0, even though the final lines in the Scipion plugin manager-based installation seemed to point to the 3.1 version.
###########################################
04565: Building scipion-em-relion ...
04566: /home/hilvertg/anaconda3/envs/.scipion3env/bin/python -m pip install scipion-em-relion==3.0.0b7
04567: Done (1.36 seconds)
04568: Building relion-3.1.0 ...
04569: wget -nv -c -O /home/hilvertg/software/em/relion-3.1.0.tgz.part https://github.com/3dem/relion/archive/3.1.0.tar.gz
04570: mv -v /home/hilvertg/software/em/relion-3.1.0.tgz.part /home/hilvertg/software/em/relion-3.1.0.tgz
04571: cd /home/hilvertg/software/em
04572: tar -xf relion-3.1.0.tgz
04573: cd /home/hilvertg/software/em/relion-3.1.0
04574: cmake -DGUI=OFF -DCMAKE_INSTALL_PREFIX=./ .
04575: cd /home/hilvertg/software/em/relion-3.1.0
04576: make -j 4
04577: Skipping command: Link 'relion-3.1.0 -> relion-3.1.0'
04578: All targets exist.
04579: Done (3 m 57 s)
############################################
Any idea what I need to do to import my particles?
Thanks,
Stephan
|
|
From: Pablo C. <pc...@cn...> - 2020-11-13 08:53:52
|
Hi Georg, eventhough scipion can be installed both "environment styles" (conda or virtualenv), same is not true for the software it integrates. Actually, so far none of them uses virtualenv. "Merging" scipionEnv and deepLeraningToolkit will not work since xmipp code expects to activate an environment. Closest approach would be to manage to have a virtualenv equivalent of the conda ones, but you'll need to do it yourself. I've heard this is tricky when dealing with keras and cuda and tensorflow,....thus the conda ones (easier). Once that environment is ready, then the last issue would be to work on the CONDA_ACTIVATION_CMD to "divert" conda activation to virtualenv activation. As I see it is possible but, tricky and you are the first one to explore this, with my "non verified idea". You count with our assistance if you want to go down that route. All the best, Pablo On 12/11/20 22:40, Kempf, Georg wrote: > > Hello, > > I have installed scipion3 with virtualenv. When installing the > deepLearningToolkit with “scipion3 installb” it was only possible > using conda. Is there a way to install it in the .scipion3env or copy > the files over to the .scipion3env to get independent from conda? > > Thank’s for any help. > > Best, > > Georg Kempf > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Kempf, G. <Geo...@fm...> - 2020-11-12 21:54:39
|
Hello, I have installed scipion3 with virtualenv. When installing the deepLearningToolkit with “scipion3 installb” it was only possible using conda. Is there a way to install it in the .scipion3env or copy the files over to the .scipion3env to get independent from conda? Thank’s for any help. Best, Georg Kempf |
|
From: Grigory S. <sha...@gm...> - 2020-11-11 18:20:21
|
Hi Yangyang,
I've tried your config with Scipion2 and it seems to work fine. The only
problem I found was using curly quotes (“) instead of straight ones (") in
the queues dictionary. Did you get the error message after the job was
submitted and started to run or before?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...
On Wed, Nov 11, 2020 at 9:20 AM Yangyang Yi <yy...@si...> wrote:
> Dear Scipion users & devs,
>
> I am kindly asking for your advice.
>
> Now we are trying to set Scipion-2.0 on a slurm cluster. It could run on
> single machine but failed to submit the jobs to queue. Slurm cluster works
> well and running scipion on single node works.
>
> Here’s our settings for host.conf:
>
> host.conf:
> [localhost]
> PARALLEL_COMMAND = mpirun -np %_(JOB_NODES)d -bynode %_(COMMAND)s
> NAME = SLURM
> MANDATORY = 0
> SUBMIT_COMMAND = sbatch %_(JOB_SCRIPT)s
> CANCEL_COMMAND = scancel %_(JOB_ID)s
> CHECK_COMMAND = squeue -j %_(JOB_ID)s
> SUBMIT_TEMPLATE = #!/bin/bash
> ####SBATCH --export=ALL
> #SBATCH -p %_(JOB_QUEUE)s
> #SBATCH -J %_(JOB_NAME)s
> #SBATCH -o %_(JOB_SCRIPT)s.out
> #SBATCH -e %_(JOB_SCRIPT)s.err
> #SBATCH --time=%_(JOB_TIME)s:00:00
> #SBATCH --nodes=1
> #SBATCH --ntasks=%_(JOB_NODES)d
> #SBATCH --cpus-per-task=%_(JOB_THREADS)d
> WORKDIR=$SLURM_JOB_SUBMIT_DIR
> export XMIPP_IN_QUEUE=1
> cd $WORKDIR
> # Make a copy of node file
> echo $SLURM_JOB_NODELIST > %_(JOB_NODEFILE)s
> ### Display the job context
> echo Running on host `hostname`
> echo Time is `date`
> echo Working directory is `pwd`
> echo $SLURM_JOB_NODELIST
> echo CUDA_VISIBLE_DEVICES: $CUDA_VISIBLE_DEVICES
> #################################
> %_(JOB_COMMAND)s
> find "$SLURM_SUBMIT_DIR" -type f -user $USER -perm 644 -exec chmod
> 664 {} +
> QUEUES = {
> “a": [["JOB_TIME", "48", "Time (hours)", "Select the time expected
> (in hours) for this job"],
> ["NODES","1", "Nodes", "How many nodes required for all the
> nodes"],
> ["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual
> jobs to queue"]],
> “b": [["JOB_TIME", "48", "Time (hours)", "Select the time expected
> (in hours) for this job"],
> ["NODES","1", "Nodes", "How many nodes required for all the
> nodes"],
> ["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual
> jobs to queue"]],
> “c": [["JOB_MEMORY", "8192", "Memory (MB)", "Select amount of
> memory (in megabytes) for this job"],
> ["JOB_TIME", "48", "Time (hours)", "Select the time expected (in
> hours) for this job"],
> ["NODES","1", "Nodes", "How many nodes required for all the
> nodes"],
> ["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual
> jobs to queue"]]
> }
> JOB_DONE_REGEX =
>
> And the Scipion reports:
> typeerror: %d format: a number is required, not nonetype
>
> And suggestions about how to solve the problem? Thanks!
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Grigory S. <sha...@gm...> - 2020-11-11 17:57:52
|
Hello Nicholas, It took me a while to figure it out, but the problem is now fixed in the latest version of relion plugin. Grigory On Wed, Oct 7, 2020, 02:24 Nicholas Prokhorov <pro...@gm...> wrote: > Dear all, > > I’m trying to use Localized Reconstruction plugin in Scipion 3. I imported > particles from Relion 3.1, defined subparticles, filtered them and > extracted with a new box size. Everything worked seemingly okay. But when I > try and do 2D or 3D classification or 3D auto-refine the subparticles are > treated as if they have the size of the original imported particles - 972 > px instead of 168 px. For instance, in 3D auto-refine I have "ERROR The > reference box size is 168 A, but the box size of the first optics group of > the data is 972 A!” (which is btw not correct as the reference box size is > 168 px and the pixel size is 1.1 A) Particles in particles.mrcs have > correct dimensions and the problem seems to be in metadata. I opened > particles.sqlite from the extraction job and it looks like every particle > has its own relion optics group header. I changed rlnImageSize from 972 to > 168 in all entries but still have the same error from 3D auto-refine when I > try using corrected particles.sqlite. What would be the simplest way to > overcome the bug? > > Thank you, > > Nikolai > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Yangyang Yi <yy...@si...> - 2020-11-11 09:19:56
|
Dear Scipion users & devs,
I am kindly asking for your advice.
Now we are trying to set Scipion-2.0 on a slurm cluster. It could run on single machine but failed to submit the jobs to queue. Slurm cluster works well and running scipion on single node works.
Here’s our settings for host.conf:
host.conf:
[localhost]
PARALLEL_COMMAND = mpirun -np %_(JOB_NODES)d -bynode %_(COMMAND)s
NAME = SLURM
MANDATORY = 0
SUBMIT_COMMAND = sbatch %_(JOB_SCRIPT)s
CANCEL_COMMAND = scancel %_(JOB_ID)s
CHECK_COMMAND = squeue -j %_(JOB_ID)s
SUBMIT_TEMPLATE = #!/bin/bash
####SBATCH --export=ALL
#SBATCH -p %_(JOB_QUEUE)s
#SBATCH -J %_(JOB_NAME)s
#SBATCH -o %_(JOB_SCRIPT)s.out
#SBATCH -e %_(JOB_SCRIPT)s.err
#SBATCH --time=%_(JOB_TIME)s:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=%_(JOB_NODES)d
#SBATCH --cpus-per-task=%_(JOB_THREADS)d
WORKDIR=$SLURM_JOB_SUBMIT_DIR
export XMIPP_IN_QUEUE=1
cd $WORKDIR
# Make a copy of node file
echo $SLURM_JOB_NODELIST > %_(JOB_NODEFILE)s
### Display the job context
echo Running on host `hostname`
echo Time is `date`
echo Working directory is `pwd`
echo $SLURM_JOB_NODELIST
echo CUDA_VISIBLE_DEVICES: $CUDA_VISIBLE_DEVICES
#################################
%_(JOB_COMMAND)s
find "$SLURM_SUBMIT_DIR" -type f -user $USER -perm 644 -exec chmod 664 {} +
QUEUES = {
“a": [["JOB_TIME", "48", "Time (hours)", "Select the time expected (in hours) for this job"],
["NODES","1", "Nodes", "How many nodes required for all the nodes"],
["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual jobs to queue"]],
“b": [["JOB_TIME", "48", "Time (hours)", "Select the time expected (in hours) for this job"],
["NODES","1", "Nodes", "How many nodes required for all the nodes"],
["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual jobs to queue"]],
“c": [["JOB_MEMORY", "8192", "Memory (MB)", "Select amount of memory (in megabytes) for this job"],
["JOB_TIME", "48", "Time (hours)", "Select the time expected (in hours) for this job"],
["NODES","1", "Nodes", "How many nodes required for all the nodes"],
["QUEUE_FOR_JOBS", "N", "Use queue for jobs", "Send individual jobs to queue"]]
}
JOB_DONE_REGEX =
And the Scipion reports:
typeerror: %d format: a number is required, not nonetype
And suggestions about how to solve the problem? Thanks! |
|
From: Colin D. <ckd...@gm...> - 2020-11-09 20:43:45
|
To Grigory, Found it, thank you! On Mon, Nov 9, 2020 at 12:04 PM Grigory Sharov <sha...@gm...> wrote: > Hi Colin, > > you can press Ctrl+F to search for "extract coordinates". > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Mon, Nov 9, 2020 at 7:57 PM Colin Deniston <ckd...@gm...> wrote: > >> Hi Juha, >> >> I'm not sure I have. Where is that? Is it in the viewer when you select >> the 2D classes? Or is it a method you run from the table on the left? >> Thanks! >> >> On Mon, Nov 9, 2020 at 11:46 AM Juha Huiskonen < >> juh...@he...> wrote: >> >>> Hi Colin, >>> >>> Have you tried the 'extract coordinates' protocol? >>> >>> Best wishes, >>> Juha >>> >>> On Mon, Nov 9, 2020 at 9:40 PM Colin Deniston <ckd...@gm...> >>> wrote: >>> >>>> Hi, >>>> >>>> I'm processing some data and would like to re-extract a subset of >>>> particles I've picked out after 2D classification. I can't find a way to do >>>> this as Scipion seems to consider this subset as only particles, not >>>> coordinates. Can you not re-extract in Scipion currently? Is the coordinate >>>> info not held onto for each particle? Thanks. >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Grigory S. <sha...@gm...> - 2020-11-09 20:03:53
|
Hi Colin, you can press Ctrl+F to search for "extract coordinates". Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Nov 9, 2020 at 7:57 PM Colin Deniston <ckd...@gm...> wrote: > Hi Juha, > > I'm not sure I have. Where is that? Is it in the viewer when you select > the 2D classes? Or is it a method you run from the table on the left? > Thanks! > > On Mon, Nov 9, 2020 at 11:46 AM Juha Huiskonen <juh...@he...> > wrote: > >> Hi Colin, >> >> Have you tried the 'extract coordinates' protocol? >> >> Best wishes, >> Juha >> >> On Mon, Nov 9, 2020 at 9:40 PM Colin Deniston <ckd...@gm...> wrote: >> >>> Hi, >>> >>> I'm processing some data and would like to re-extract a subset of >>> particles I've picked out after 2D classification. I can't find a way to do >>> this as Scipion seems to consider this subset as only particles, not >>> coordinates. Can you not re-extract in Scipion currently? Is the coordinate >>> info not held onto for each particle? Thanks. >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Colin D. <ckd...@gm...> - 2020-11-09 19:57:47
|
Hi Juha, I'm not sure I have. Where is that? Is it in the viewer when you select the 2D classes? Or is it a method you run from the table on the left? Thanks! On Mon, Nov 9, 2020 at 11:46 AM Juha Huiskonen <juh...@he...> wrote: > Hi Colin, > > Have you tried the 'extract coordinates' protocol? > > Best wishes, > Juha > > On Mon, Nov 9, 2020 at 9:40 PM Colin Deniston <ckd...@gm...> wrote: > >> Hi, >> >> I'm processing some data and would like to re-extract a subset of >> particles I've picked out after 2D classification. I can't find a way to do >> this as Scipion seems to consider this subset as only particles, not >> coordinates. Can you not re-extract in Scipion currently? Is the coordinate >> info not held onto for each particle? Thanks. >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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