Question: Not able to queue jobs via PBS
0
gravatar for balaszone
2.3 years ago by
balaszone60
balaszone60 wrote:

Hello,

I've been trying hard for past week or so to queue jobs via PBS to run our ATAC sequence in galaxy. I'm able successfully run a sequence without modifying the job_conf.xml file. i.e. running the analysis locally on the default server. However if I modify the job_conf.xml to use pbs, I couldnt start galaxy and it gives me bunch of errors.

Here is my modified job_conf.xml file -

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<job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" worker="8"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="batch"> <destination id="local" runner="local"/> <destination id="batch" runner="pbs" &gt;="" <param="" id="Resource_List">-l nodes=1:ppn=8,walltime=72:00:00</param> <param id="-p">128</param> </destination> </destinations> </job_conf>

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and here is my error when I start galaxy(>> sh run.sh) just the last few lines.. .. .. galaxy.jobs DEBUG 2016-06-30 17:47:56,375 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File "/home/lakshmananbm/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 63, in paste_app_factory app = galaxy.app.UniverseApplication( global_conf=global_conf, *kwargs ) File "/home/lakshmananbm/galaxy/lib/galaxy/app.py", line 174, in __init__ self.job_manager = manager.JobManager( self ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/handler.py", line 32, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/handler.py", line 723, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/__init__.py", line 672, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], *runner.get( 'kwds', {} ) ) File "/home/lakshmananbm/galaxy/lib/galaxy/jobs/runners/pbs.py", line 93, in __init__ assert pbs is not None, PBS_IMPORT_MESSAGE AssertionError: The Python pbs-python package is required to use this feature, please install it or correct the following error: ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ~/galaxy/.venv/lib/python2.7/site-packages/pbs/_pbs.so)

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I hope somebody could help me debug this issue.

PS. while going though forum, it mentioned about editing eggs.ini file. But I dont see that file in my galaxy folder, maybe because I'm using newer version? Also I do not have root permission but not sure if that is related to my error.

THanks!! Bala

ADD COMMENTlink modified 2.3 years ago by Devon Ryan1.9k • written 2.3 years ago by balaszone60
0
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

It looks like pbs-python was compiled on a different platform with an incompatible version of glibc, you might be able to:

source ~/galaxy/.venv/bin/activate
pip uninstall -y pbs-python
pip install pbs-python

That will rebuild and should then link in the correct version of glibc. Presuming galaxy isn't installed in root's home directory, you won't need root access to do this.

ADD COMMENTlink written 2.3 years ago by Devon Ryan1.9k
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