jobEnvironment dropping content after = in value

[cancan101]

I am running this script:

   with drmaa.Session() as s:
       jt = s.createJobTemplate()
       jt.remoteCommand = "python"
       jt.args = ['env.py']
       jt.jobEnvironment = {'ALEX':'alex=2'}
       jt.joinFiles=True
       jobid = s.runJob(jt)
       s.deleteJobTemplate(jt)

with this script env.py:

import os
print os.environ

When I look at my environment, I see:

'ALEX': 'alex', 

[cancan101]

For reference, this works fine: $ qsub -v ALEX=alex=2 -b y -j y python env.py.

[dan-blanchard]

That's very strange. From looking at where we handle setting DictAttribute values, I don't see anything that jumps out as wrong.

Could you try changing {'ALEX': 'alex=2'} to {'ALEX': '"alex=2"'} (with extra inner double-quotes around the value)? I'm wondering if the DRMAA C implementation you're using is doing something stupid on its end.

[cancan101]

I believe I was able to get this bug reproduced using your travis setup: https://github.com/pygridtools/drmaa-python/commit/c8a9c5e42425760421dff1611ecd89718a435e7d results: https://travis-ci.org/cancan101/drmaa-python/jobs/72308774

[cancan101]

Wrapping with " still leads to the same truncation after the =: '"alex

[nicoulaj]

FYI, this bug is in the C implementation of DRMAA, see http://gridengine.org/pipermail/users/2016-April/009042.html

[jakirkham]

It's worth noting that users may be able to hack around this by using nativeSpecification. In any event, this is an issue with the particular DRMAA implementation itself and not drmaa-python. As such, this probably should be closed. Possibly could add a note in the docs about this issue and the (proposed) workaround.