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MemoryError raised by ParcThal when run on CircleCI #30

sebastientourbier opened this issue Mar 18, 2020 · 1 comment

MemoryError raised by ParcThal when run on CircleCI #30

sebastientourbier opened this issue Mar 18, 2020 · 1 comment


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@sebastientourbier sebastientourbier commented Mar 18, 2020

Continuous integration testing with CIrcleCI failed when parcellating the thalamic nuclei with a Memory error message (see execution log on circleCI page more details). Seems 7.5GB RAM is not enough to handle ind = np.where(Ispams < Thresh). See error message below:

200317-16:44:09,131 nipype.interface INFO:
	 Correcting the volumes after the interpolation 
Save output image to /output_dir/nipype/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcThal/T1_class-thalamus_dtissue_after_ants.nii.gz
200317-16:45:11,524 nipype.workflow WARNING:
	 [Node] Error on "anatomical_pipeline.parcellation_stage.parcThal" (/output_dir/nipype/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcThal)
200317-16:45:11,545 nipype.workflow ERROR:
	 Node parcThal failed to run on host 3be4adbaba2e.
200317-16:45:11,690 nipype.workflow ERROR:
	 Saving crash info to /tmp/crash-20200317-164511-root-parcThal-2682b8cb-8991-437c-977c-d15ba5964b8e.txt
Traceback (most recent call last):
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/pipeline/plugins/", line 48, in run
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/pipeline/engine/", line 473, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/pipeline/engine/", line 557, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/pipeline/engine/", line 637, in _run_command
    result =
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/interfaces/base/", line 369, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/cmtklib/", line 1364, in _run_interface
    ind = np.where(Ispams < Thresh)

System configuration on CircleCI
Machine Linux Medium
2 CPU / 7.5 GB RAM


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@sebastientourbier sebastientourbier commented Mar 20, 2020

Fixed by Commit dbae66d in pull request #28

sebastientourbier added a commit that referenced this issue Mar 26, 2020
Beta release 20200320 of CMP3 which includes:

* A major revision of continuous integration testing and deployment with CircleCI which integrates an in-house dataset published and available on Zenodo @
* Multiple bug fixes and enhancements incl. close #30 , update mrtrix3 to RC3 version, bids-app run command generated by the GUI, location of the configuration and log files to be more BIDS compliant
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