Hi Luca,
Could you send your job_conf.xml please? Also, is there any chance that you modified run.sh to set DRMAA_LIBRARY_PATH there (which would override what you set on the command line)?
--nate
On Thu, Apr 3, 2014 at 9:17 AM, Luca Toldo lucatoldo@gmail.com wrote:
Dear All, after having discovered the mess in which I was, and the incomplete PBS client installation, I've done the following:
*1) PBS Pro* a) removed the incomplete pbs installation that I had b) downloaded the latest version from vendor c) installed it in //usr/pbs d) configured e) tested it --> worked well
*2) drma-pbs* a) downloaded version 1.0.17 b) compiled it (./configure --with-pbs=/usr/pbs ) without any problem c) installed it in /usr/local/lib
- modified DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
- sh run.sh --stop
- sh run.sh --daemon
Unfortunately, however when I launch a new job I always get the error message
galaxy.jobs DEBUG 2014-04-03 15:13:44,306 (261) Working directory for job is: /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261 galaxy.jobs.handler DEBUG 2014-04-03 15:13:44,321 (261) Dispatching to drmaa runner galaxy.jobs DEBUG 2014-04-03 15:13:44,434 (261) Persisting job destination (destination id: pbs_default) galaxy.jobs.handler INFO 2014-04-03 15:13:44,474 (261) Job dispatched galaxy.tools.deps DEBUG 2014-04-03 15:13:44,659 Building dependency shell command for dependency 'clustalw2' galaxy.tools.deps WARNING 2014-04-03 15:13:44,660 Failed to resolve dependency on 'clustalw2', ignoring galaxy.jobs.runners.drmaa DEBUG 2014-04-03 15:13:45,050 (261) submitting file /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy_261.sh galaxy.jobs.runners.drmaa DEBUG 2014-04-03 15:13:45,050 (261) command is: python /opt/ngs/bin/galaxy-dist/tools/rgenetics/rgClustalw.py -i "/data/imgt.fasta" -o "/opt/ngs/bin/galaxy-dist/database/files/000/dataset_340.dat" -s "ALIGNED" -l "/opt/ngs/bin/galaxy-dist/database/files/000/dataset_341.dat" -t "Clustal_run" -d "DNA" -f "CLUSTAL"; return_code=$?; cd /opt/ngs/bin/galaxy-dist; /opt/ngs/bin/galaxy-dist/set_metadata.sh ./database/files /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261 . /opt/ngs/bin/galaxy-dist/universe_wsgi.ini /opt/ngs/bin/galaxy-dist/database/tmp/tmpq4Rmdl /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy.json /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_in_HistoryDatasetAssociation_347_GsBRYB,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_kwds_HistoryDatasetAssociation_347_dFD5t0,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_out_HistoryDatasetAssociation_347_k0zCP6,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_results_HistoryDatasetAssociation_347_4LVIFs,,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_override_HistoryDatasetAssociation_347_jKfp0r /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_in_HistoryDatasetAssociation_348_Fyy0tJ,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_kwds_HistoryDatasetAssociation_348_9vWiO3,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_out_HistoryDatasetAssociation_348_HL3EIj,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_results_HistoryDatasetAssociation_348_s1gqxk,,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_override_HistoryDatasetAssociation_348_hyQkDF; sh -c "exit $return_code"
galaxy.jobs.runners ERROR 2014-04-03 15:13:45,051 (261) Unhandled exception calling queue_job Traceback (most recent call last): File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 62, in run_next method(arg) File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 150, in queue_job external_job_id = self.ds.runJob(jt) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py", line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value
If from the commandline I do
qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy_261.sh
then
I get 1695145.servername
...
What can I do now ?