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poldracklab / tacc-openneuro

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ds001942-mriqc: Out of Memory #12

Closed jbwexler closed 1 year ago

jbwexler commented 2 years ago

Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface self.raise_exception(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception raise RuntimeError( RuntimeError: Command: fast -t 1 -o segment -g -S 1 /scratch1/03201/jbwexler/work_dir/mriqc/ds001942_sub-S01/mriqc_wf/anatMRIQC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds001942-mriqc..sourcedata..raw..sub-S01..ses-SES01..anat..sub-S01_ses-SES01_acq-ShortInv_run-02_T1w.nii.gz/segmentation/sub-S01_ses-SES01_acq-ShortInv_run-02_T1w_conformed_calc.nii.gz Standard output:

Standard error: Image Exception : #99 :: Out of memory terminate called after throwing an instance of 'RBD_COMMON::BaseException' Aborted Return code: 134

jbwexler commented 1 year ago

Resolved by running one subject per node.