Xcp_d permission error with singularity on HPC

Hello everyone,

We are trying to use the latest version of xcp_d (v0.3.2) after preprocessing my data with fMRIPrep. However, I’m stuck on a persmission error that I cannot figure out.

Command used:

singularity run --cleanenv \
-B $fprep_dir:/data:ro \
-B $xcp_dir:/out \
-B $temp_dir:/work \
$SINGMAGE /data /out \
participant --participant-label ${subi} \
-p 36P -w /work


xcp_d v0.3.2



Relevant log outputs (up to 20 lines):

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8n6ux0j6 because the default path (/home/xcp_d/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/xcp_d", line 8, in <module>
  File "/usr/local/miniconda/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1890, in get_metadata
    with io.open(self.path, encoding='utf-8', errors="replace") as f:
PermissionError: [Errno 13] Permission denied: '/usr/local/miniconda/lib/python3.8/site-packages/.wh.pip-20.2.4-py3.8.egg-info'

Screenshots / relevant information:

A screen shot of the entire error message

Thank you for your help.

Kind regards

It is solved!
The problem came from using an old version of singularity.
See xcp_d cannot access miniconda with singularity · Issue #793 · PennLINC/xcp_d · GitHub for the entire debugging process.


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