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enhanced extension filter for Python packages causes trouble for netcdf4-python sanity check #2265

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boegel opened this issue Dec 3, 2020 · 4 comments · Fixed by #2267
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@boegel
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boegel commented Dec 3, 2020

The enhanced extension filter for Python packages made in #2224 causes trouble for netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb:

== 2020-12-03 20:44:05,145 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): Sanity check failed: command "mpirun -n 1 PYTHONNOUSERSITE=1 python -c "import netCDF4"" failed; output:
[proxy:0:[email protected]] HYD_spawn (../../../../../src/pm/i_hydra/libhydra/spawn/intel/hydra_spawn.c:128):
execvp error on file PYTHONNOUSERSITE=1 (No such file or directory)

We should set $PYTHONNOUSERSITE to 1 some other way, and make sure its set again after the environment is reset in the sanity check step...

cc @Flamefire

@boegel boegel added this to the 4.3.2 (next release) milestone Dec 3, 2020
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The problem here is that we must make sure it is set for all sanity checks and for the skip check. I don't know where a good place for that would be.

boegel added a commit to boegel/easybuild-easyblocks that referenced this issue Dec 4, 2020
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boegel commented Dec 4, 2020

I'm rolling back the change from #2224 in #2267, I don't want this to block the release of EasyBuild v4.3.2...

@Flamefire
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@boegel Could you then look into a proper implementation of that? Because now we have a possible bug in at least --skip in that it considers user packages while the installed version and the pip check does not and hence might fail. At least an issue should be opened to not forget it.

@boegel
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boegel commented Dec 7, 2020

We should definitely follow up on this, yes. Please open an issue to keep track of why we should set $PYTHONNOUSERSITE (and refer to the initial attempt to do so which was rolled back)

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