FMRIPREP - An unknown Error occuring during the preprocessing

oesteban · September 17, 2018, 11:06am

This is likely a memory error. Please check:

and

github.com/nipreps/fmriprep

Broken process pool

opened 05:07PM - 23 Aug 18 UTC

closed 05:47PM - 15 Feb 19 UTC

danielkimmel

memory

Hello, Since issue #1231, I've updated fmriprep-docker to 1.1.4 and am runnin…g on a single participant. However, the program crashed citing: `exception calling callback for <Future at 0x7fefd5eecac8 state=finished raised BrokenProcessPool>` Partial log is attached. (I couldn't find the saved logs in the output or work directories, so I just copied what was available in the terminal buffer) Also note that at the very beginning of the terminal output (not shown in the attached file, but pasted below), there were some numpy exceptions I haven't seen before. Finally, note that near the end of the attached terminal output, just before the crash, were some machine precision warnings I haven't seen before. Thanks so much for your help! Daniel INITIAL TERMINAL OUTPUT: ``` bash-4.2$ ./mnt/staging/daniel/fmriprep/fmriprep_job1.sh RUNNING: docker run --rm -it -v /home/dlk2148/mnt/staging/daniel/fmriprep/freesurfer_license.txt:/opt/freesurfer/license.txt:ro -v /home/dlk2148/mnt/labshare/daniel/BIDS:/data:ro -v /home/dlk2148/data/fmriprep/out:/out -v /home/dlk2148/data/fmriprep/work:/scratch poldracklab/fmriprep:1.1.4 /data /out participant --no-submm-recon --ignore slicetiming --participant_label 18070901 -w /scratch /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 return f(*args, **kwds) /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 return f(*args, **kwds) 180823-15:23:27,212 nipype.workflow IMPORTANT: Running fMRIPREP version 1.1.4: * BIDS dataset path: /data. * Participant list: ['18070901']. * Run identifier: 20180823-152327_d381008d-3c3c-4d4e-8d69-f3ea13a360b9. ``` [terminal_output_2018_08_22.txt](https://github.com/poldracklab/fmriprep/files/2315463/terminal_output_2018_08_22.txt)

first.

Also, it would be nice to have the title of your post edited to include “FMRIPrep” somewhere, and that you tagged the post with “fmriprep” as well.

Please let us know any outcome of your troubleshooting (hopefully those threads will give you the solution).

Cheers,
Oscar