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FCP-INDI / C-PAC

Configurable Pipeline for the Analysis of Connectomes
https://fcp-indi.github.io/
GNU Lesser General Public License v3.0
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SLURM not working after v1.4.0 #1051

Open kvnpnguyen opened 4 years ago

kvnpnguyen commented 4 years ago

Hello developers,

I updated from v1.3.0, which I had been using for some time, to v1.4.3 and encountered an issue running the pipeline on a SLURM cluster. Looking at the SLURM *.out log files we have this:

ImportError: cannot import name run

Looking at the cpac_submit*.slurm file that is automatically generated, there is this line which calls CPAC.pipeline.cpac_pipeline.run:

python -c "from CPAC.pipeline.cpac_pipeline import run; run('/project/bioinformatics/DLLab/s169685/PPMI_Project/data/PPMIcpac/pipeline_config.yml', '/project/bioinformatics/DLLab/s169685/PPMI_Project/data/PPMIcpac/data_config_ppmi_fmri.yml', $SLURM_ARRAY_TASK_ID, 'cpac_default', plugin='MultiProc', plugin_args={'memory_gb': 16, 'n_procs': 16})"

I dug through the version history of CPAC.pipeline.cpac_pipeline and noticed that the run() function was removed at commit 11a0b3d.

It looks like the SLURM script needs to be updated since run() is no longer available?

Thanks, Kevin

sgiavasis commented 4 years ago

Hello @kvnpnguyen,

This needs a big update. Putting this back on the radar.