[galaxy-dev] SLURM queue

Marina Gourtovaia mg8 at sanger.ac.uk
Wed Feb 9 10:06:52 EST 2011


Try adding

export SGE_ROOT=/directory where drmaa sits or one-two higher

I had a similar problem compiling a perl wrapper for drmaa (LSF). I 
found this SGE_ROOT used in the makefile for generating a SWIG perl 
wrapper for the drmaa.h header. And also there were some assumptions 
about the directory structure below SGE_ROOT which was not what we have 
for LSF. So I edited the makefile and got rid of  SGE_ROOT altogether. 
The upshot of this is that to generate a python binding for your queuing 
system you might have to go deeper than just scrambling

Marina
> Hi,
>
> is there anyone here who has any experience running galaxy with the 
> queuing system SLURM? I've tried to install SLURM and a DRMAA module 
> (http://apps.man.poznan.pl/trac/slurm-drmaa). I use the line:
>
> $ export DRMAA_LIBRARY_PATH=/path/to/drmaa.so; python 
> scripts/scramble.py DRMAA_python
>
> The script compiles the egg nicely. When I try to start galaxy, it 
> seems to be looking for SGE_ROOT though. Any thoughts?
>
>
> Best regards,
> Oscar Eriksson
>
>
> Log file:
> galaxy.datatypes.registry DEBUG 2011-02-09 15:42:27,127 Loaded 
> external metadata tool: __SET_METADATA__
> galaxy.datatypes.registry DEBUG 2011-02-09 15:42:27,132 Loaded 
> indexer: INDEXER_Coverage_0
> galaxy.datatypes.registry DEBUG 2011-02-09 15:42:27,137 Loaded 
> indexer: INDEXER_Coverage_0
> galaxy.datatypes.registry DEBUG 2011-02-09 15:42:27,142 Loaded 
> indexer: INDEXER_Interval_0
> galaxy.jobs.runners.local INFO 2011-02-09 15:42:27,143 starting workers
> galaxy.jobs.runners.local DEBUG 2011-02-09 15:42:27,144 5 workers ready
> Traceback (most recent call last):
>   File "/usr/ebiokit/galaxy/lib/galaxy/web/buildapp.py", line 82, in 
> app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/usr/ebiokit/galaxy/lib/galaxy/app.py", line 72, in __init__
>     self.job_manager = jobs.JobManager( self )
>   File "/usr/ebiokit/galaxy/lib/galaxy/jobs/__init__.py", line 41, in 
> __init__
>     self.dispatcher = DefaultJobDispatcher( app )
>   File "/usr/ebiokit/galaxy/lib/galaxy/jobs/__init__.py", line 749, in 
> __init__
>     self.job_runners[runner_name] = runners.drmaa.DRMAAJobRunner( app )
>   File "/usr/ebiokit/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 
> 81, in __init__
>     self.ds.initialize()
>   File 
> "/usr/ebiokit/galaxy/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", 
> line 274, in initialize
>     _w.init(contactString)
>   File 
> "/usr/ebiokit/galaxy/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py", 
> line 59, in init
>     return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
>   File 
> "/usr/ebiokit/galaxy/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 
> 90, in error_check
>     raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
> InternalException: code 1: Please set the environment variable SGE_ROOT.
>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev at lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev



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