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.
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.
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participants (2)
-
Marina Gourtovaia -
Oscar Eriksson