[gpfsug-discuss] python package installs fail due to attribute copy error (GPFS 5.0.2)

[IBM Spectrum Scale]

Hi Diane,

Can you please help customer with the below issue. Or else can you point me
to the right folks who can help here.


Regards, The Spectrum Scale (GPFS) team

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From:	mark.bergman at uphs.upenn.edu
To:	gpfsug main discussion list <gpfsug-discuss at spectrumscale.org>
Date:	27-11-2019 05:47
Subject:	[EXTERNAL] [gpfsug-discuss] python package installs fail due to
            attribute copy	error (GPFS 5.0.2)
Sent by:	gpfsug-discuss-bounces at spectrumscale.org



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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_conda_conda_issues_5251&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=IbxtjdkPAM2Sbon4Lbbi4w&m=kHkKLF_E6f-HbrmIODOa1m064mJD_5IUa4winUqTQOE&s=8cqECGE7aQzVZwSOUDWjUbgMiyWLzpVqThnCrhMXwGc&e=

but our version of create.py is newer and already has the suggested fix.

or similar to this:

https://urldefense.proofpoint.com/v2/url?u=https-3A__bugs.python.org_issue24538&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=IbxtjdkPAM2Sbon4Lbbi4w&m=kHkKLF_E6f-HbrmIODOa1m064mJD_5IUa4winUqTQOE&s=Zyfy_KMaSuhXSmm5sUTBMiRqEiaIfD4BLSyRfpNjQkY&e=

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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