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Re: [scipion-users] Bayesian polishing
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From: Grigory S. <sha...@gm...> - 2021-06-10 19:36:31
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I see, thanks for the clarification. Have you tried to run with all frames (default) but with a smaller particle subset, e.g. 3000-5000 particles? You can monitor RAM usage when the protocol starts to see if that is an issue. 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, Jun 10, 2021 at 8:32 PM Dmitry A. Semchonok <sem...@gm...> wrote: > Sorry Grigory, > > > > I would have explained that abbreviation. > > This means a) 1 movie frame and b) 5 movie frames. > > > > a) > > > > And even with Threads 1 MPI 1 the 5 movie frames fail > > > > > > Thanks again > > > > > > > > Sincerely, > > Dmitry > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Grigory Sharov <sha...@gm...> > *Sent: *Thursday, June 10, 2021 8:27 PM > *To: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] Bayesian polishing > > > > I have no idea what 1e or 5e means, I see you are using 14 threads.. > > > 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, Jun 10, 2021 at 7:25 PM Dmitry A. Semchonok <sem...@gm...> > wrote: > > Thank you Grigory, > > > > The interesting point is that if the one uses 1e - the process finishes > without error. > > But 5e seems too be too much. > > > > Sincerely, > > Dmitry > > > > On June 10, 2021 5:20:06 PM Grigory Sharov <sha...@gm...> > wrote: > > Hi Dmitry, > > > > I think you posted a similar error before. You are using too many > particles for training and running out of RAM, hence your process is > killed by Linux kernel. > > > 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, Jun 10, 2021 at 4:02 PM Dmitry Semchonok <Sem...@gm...> > wrote: > > Dear colleagues, > > After running Bayesian polishing script with 5e I got the following error > > > > 2232: > GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc > 02591: 1914: > GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc > 02592: 1985: > GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc > 02593: 2253: > GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc > 02594: 1404: > GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc > 02595: 361: > GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc > 02596: > 02597: - Warning: this dataset does not contain 217187 particles > (--min_p) in micrographs with at least 2 particles > 02598: + preparing alignment data... > 02599: Traceback (most recent call last): > 02600: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 197, in run > 02601: self._run() > 02602: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _run > 02603: resultFiles = self._runFunc() > 02604: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 244, in _runFunc > 02605: return self._func(*self._args) > 02606: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", > line 351, in trainOrPolishStep > 02607: self.runJob(self._getProgram('relion_motion_refine'), args) > 02608: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1388, in runJob > 02609: self._stepsExecutor.runJob(self._log, program, arguments, > **kwargs) > 02610: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > 02611: process.runJob(log, programName, params, > 02612: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 52, in runJob > 02613: return runCommand(command, env, cwd) > 02614: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 67, in runCommand > 02615: check_call(command, shell=True, stdout=sys.stdout, > stderr=sys.stderr, > 02616: File > "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, > in check_call > 02617: raise CalledProcessError(retcode, cmd) > 02618: subprocess.CalledProcessError: Command ' relion_motion_refine --i > Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o > Runs/004833_ProtRelionBayesianPolishing/extra --f > Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref > 0.59200 --corr_mic > Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star > --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 > --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>. > 02619: Protocol failed: Command ' relion_motion_refine --i > Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o > Runs/004833_ProtRelionBayesianPolishing/extra --f > Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref > 0.59200 --corr_mic > Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star > --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 > --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>. > 02620: FAILED: trainOrPolishStep, step 2, time 2021-06-09 11:27:00.176491 > 02621: *** Last status is failed > 02622: ------------------- PROTOCOL FAILED (DONE 2/2) > > Do you know how to fix that? > > > Thank you > > Sincerely, > Dmitry > > > > > _______________________________________________ > 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 > > > > > > > |
