[scipion-users] Bayesian polishing error

[Dmitry S. <Sem...@gm...>]

Dear colleagues,

Could you please advice - 

I am receiving an error during bayesian polishing: 

First I got this error:

1.44/7.13 hrs ............~~(,_,">--------------------------------------------------------------------------
mpirun noticed that process rank 6 with PID 114780 on node dataanalysisserver1 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run
    self._run()
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run
    resultFiles = self._runFunc()
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc
    return self._func(*self._args)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 351, in trainOrPolishStep
    self.runJob(self._getProgram('relion_motion_refine'), args)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob
    self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
    process.runJob(log, programName, params,
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
    return runCommand(command, env, cwd)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
    check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' mpirun -np 8  `which relion_motion_refine_mpi` --i Runs/064772_ProtRelionBayesianPolishing/input_particles.star --o Runs/064772_ProtRelionBayesianPolishing/extra --f Runs/064668_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/064772_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 4 --last_frame 33 --s_vel 0.096 --s_div 1830.000 --s_acc 2.500 --bfac_minfreq 20.000 --bfac_maxfreq -1.000 --combine_frames --j 6 ' returned non-zero exit status 139.
Protocol failed: Command ' mpirun -np 8  `which relion_motion_refine_mpi` --i Runs/064772_ProtRelionBayesianPolishing/input_particles.star --o Runs/064772_ProtRelionBayesianPolishing/extra --f Runs/064668_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/064772_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 4 --last_frame 33 --s_vel 0.096 --s_div 1830.000 --s_acc 2.500 --bfac_minfreq 20.000 --bfac_maxfreq -1.000 --combine_frames --j 6 ' returned non-zero exit status 139.
FAILED: trainOrPolishStep, step 2, time 2021-07-07 19:03:26.495010
*** Last status is failed 



================================================================================

After resubmission - this one - 

0.02/7.27 hrs ~~(,_,">
0.03/6.81 hrs ~~(,_,">
0.04/6.70 hrs ~~(,_,">
0.05/6.38 hrs ~~(,_,">--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 173927 on node dataanalysisserver1 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run
    self._run()
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run
    resultFiles = self._runFunc()
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc
    return self._func(*self._args)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 351, in trainOrPolishStep
    self.runJob(self._getProgram('relion_motion_refine'), args)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob
    self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
    process.runJob(log, programName, params,
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
    return runCommand(command, env, cwd)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
    check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' mpirun -np 6  `which relion_motion_refine_mpi` --i Runs/064772_ProtRelionBayesianPolishing/input_particles.star --o Runs/064772_ProtRelionBayesianPolishing/extra --f Runs/064668_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/064772_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 4 --last_frame 33 --s_vel 0.096 --s_div 1830.000 --s_acc 2.500 --bfac_minfreq 20.000 --bfac_maxfreq -1.000 --combine_frames --j 4 ' returned non-zero exit status 139.
Protocol failed: Command ' mpirun -np 6  `which relion_motion_refine_mpi` --i Runs/064772_ProtRelionBayesianPolishing/input_particles.star --o Runs/064772_ProtRelionBayesianPolishing/extra --f Runs/064668_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/064772_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 4 --last_frame 33 --s_vel 0.096 --s_div 1830.000 --s_acc 2.500 --bfac_minfreq 20.000 --bfac_maxfreq -1.000 --combine_frames --j 4 ' returned non-zero exit status 139.
FAILED: trainOrPolishStep, step 2, time 2021-07-08 06:47:13.642052
*** Last status is failed 
------------------- PROTOCOL FAILED (DONE 2/3)



Thanks in advance

Sincerely,
Dmitry