[Debian-med-packaging] Usage of python-drmaa

[Olivier Sallou]

On 02/04/2015 11:55 AM, Andreas Tille wrote:
> Hi NeuroDebian people,
>
> I intend to package python-ruffus (packaging is in Git[1]) as a
> precondition for sga (also in Git[2]).  I tried to run the python-ruffus
> test suite and stumbled upon one strange issue which boils down to
>
> $ python
> Python 2.7.8 (default, Oct 18 2014, 12:50:18) 
> [GCC 4.9.1] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import drmaa
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/lib/python2.7/dist-packages/drmaa/__init__.py", line 41, in <module>
>     import drmaa.wrappers as _w
>   File "/usr/lib/python2.7/dist-packages/drmaa/wrappers.py", line 43, in <module>
>     raise RuntimeError(errmsg)
> RuntimeError: could not find drmaa library. Please specify its full path using the environment variable DRMAA_LIBRARY_PATH
it searches for a drmaa.so file (from a lib provided by a drmaa
compliant cluster). It could be from gridengine, torque, ....
Path to the so file is provided with the env variable DRMAA_LIBRARY_PATH.

If you install gridengine, you will get it certainly in
/var/lib/gridengine/...  but this is not a runtime dependency on
gridengine as it could be provided by an other one.
>
>
> I tried to find a clue in
>
>    /usr/share/doc/python-drmaa/README.Debian
>
> which says
>
>   To be able to use this module with libdrmaa from Debian's package of Sun
>   GridEngine, one needs to set the SGE_ROOT environment variable to point to
>   /var/lib/gridengine
>
> but this is not enlightening at all to me since it does not refer to the
> problem thrown above nor do I know what an SGE_ROOT is and what the
> relation to GridEngine might be (and why it is not in the set of
> Dependencies of python-drmaa).
drmaa is a standard library to communicate with cluster software like
gridengine (which will be removed soon from Jessie as discussed at the
sprint).
There are different language bindings.

Anyway, even if you set the SGE_ROOT (path where sge stuff is
installed), it will fail to communicate if you do not have a full
cluster (gridengone, torque,...) with drmaa lib installed.
>
> Any suggestion how I can sensibly run the python-ruffus test suite
> without running into an error?
All drmaa related tests should be disabled, you can't test it
automatically without a cluster.

Am I clear enough ?

Olivier
>
> Kind regards
>
>        Andreas.
>
> [1] git://anonscm.debian.org/debian-med/python-ruffus.git
> [2] git://anonscm.debian.org/debian-med/sga.git
>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

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