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 <lucato...@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
>
> 3) modified DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
> 4) sh run.sh --stop
> 5) 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 ?
>
>
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