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List:       gpfsug-discuss
Subject:    [gpfsug-discuss] python package installs fail due to attribute copy error (GPFS 5.0.2)
From:       mark.bergman () uphs ! upenn ! edu
Date:       2019-11-26 23:58:02
Message-ID: 32070-1574812682.257155 () ttRP ! UhP3 ! tHtF
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We're running GPFS 5.0.2 (DSS-G 2.2a, in the process of upgrading to
2.4b/GPFS 5.0.3.2) with NFSv4 ACLs and no explicit ACLs on the root or
dependent filesets.

While installing python packages within a python virtual env stored under
GPFS, we get failures with "permission denied" on the destination while
trying to copy attributes. The problem happens to root & end-users,
and is not related to the directory permissions, ownership, or group,
and is consistent and repeatable.

For example, trying to use 'conda' to create a virtual environment results in the \
following message (severely trimmed):

	# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
	
	    Traceback (most recent call last):
	
	      in clone_env
	        shutil.copystat(src, dst)
	      in copystat
	        _copyxattr(src, dst, follow_symlinks=follow)
	      in _copyxattr
	        os.setxattr(dst, name, value, follow_symlinks=follow_symlinks)
	    PermissionError: [Errno 13] Permission denied: \
'/gpfs/fs1/rootdir/external/python/anaconda/3/envs/py3.5.6/lib/python3.5/site-packages/dm/neuralnet/__pycache__/__init__.cpython-35.pyc'
  
	`$ python/anaconda/3/bin/conda create --prefix \
/gpfs/fs1/rootdir/external/python/anaconda/3/envs/py3.5.6 --clone \
/gpfs/fs1/rootdir/external/python/anaconda/3/envs/py3.5.6`


Note that the destination directory path is created, and the destination file \
(__init__.cython-35.pyc) is created...the exception is thrown when python tries to \
apply the ACLs from the source to the destination.

The problem seems to be simiar to this:
        https://github.com/conda/conda/issues/5251
but our version of create.py is newer and already has the suggested fix.
       
or similar to this:
	https://bugs.python.org/issue24538
that's affecting panfs.

We've got a work-around using symlinks, but it's not something for average users.

Has anyone seen this issue?

Thanks,

Mark "about to post to various python fora" Bergman
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