From: Jaysheel B. <bja...@gm...> - 2012-05-22 20:22:27
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Hey Anup, I was looking through Ergatis cgi files to figure out when queue option is set, and looks like in Pipeline.pm if pipeline_submission_queue is set its add to runprefix which is written to pipeline.ID.run.sh file. None of my pipeline.ID.run.sh have -q option. I not sure if I am on track here. Below is the content of pipeline.ID.run.sh file. Thanks Jaysheel #!/bin/bash export SCRIPT_NAME="/cgi/run_pipeline.cgi" export REQUEST_METHOD="POST" export SCRIPT_FILENAME="/projects/bsi/RandD/ngs/ergatis/html/cgi/run_pipeline.cgi" export WF_TEMPLATE="/projects/bsi/RandD/ngs/ergatis/workflow/templates" export QUERY_STRING="" export REMOTE_PORT="56650" export WF_ROOT="/projects/bsi/RandD/ngs/ergatis/workflow" export SGE_CELL="default" export vappio_data_placement="0" export HMMER_NCPU="1" export CONTENT_TYPE="application/x-www-form-urlencoded" export PERL5LIB="/home/m101236/perl5/lib/perl5/x86_64-linux-thread-multi:/home/m101236/perl5/lib/perl5::/usr/local/biotools/perl/5.14.2/lib/site_perl/5.14.2/x86_64-linux-thread-multi:/usr/local/biotools/perl/5.14.2/lib/site_perl/5.14.2:/usr/local/biotools/perl/5.14.2/lib/5.14.2/x86_64-linux-thread-multi:/usr/local/biotools/perl/5.14.2/lib/5.14.2" export PATH="/projects/bsi/RandD/ngs/ergatis/workflow:/projects/bsi/RandD/ngs/ergatis/workflow/bin:/projects/bsi/RandD/ngs/ergatis/workflow/add-ons/bin:/projects/bsi/RandD/ngs/ergatis/workflow:/projects/bsi/RandD/ngs/ergatis/workflow/bin:/projects/bsi/RandD/ngs/ergatis/workflow/add-ons/bin:/home/m101236/perl5/bin:/usr/local/biotools/blast/blast-2.2.13/bin:/usr/local/biotools/hmmer/hmmer-3.0/bin:/usr/local/biotools/perl/5.14.2/bin:/home/biotools/sas/linux_SAS_9.2/bin:/usr/local/biotools/misc/ver1/bin:/usr/java/jdk1.6.0_05/bin:/usr/local/biotools/emboss/EMBOSS-5.0.0/bin:/usr/local/biotools/subversion/1.4.6/bin:/home/sge6_2/bin/lx24-amd64:/home/sge6_2/bin/lx24-amd64:/usr/local/biotools/python/2.7/bin:/usr/local/biotools/washu/ver1/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/biotools/git/1.7.9.2/bin:/home/m101236/bin:/projects/bsi/bictools/apps/alignment/samtools/samtools-0.1.18:/projects/bsi/bictools/apps/alignment/blat/34" export GATEWAY_INTERFACE="CGI/1.1" export DOCUMENT_ROOT="/projects/bsi/RandD/ngs/ergatis/html" export HMM_SCRIPTS="/usr/local/devel/ANNOTATION/hmm/bin" export LD_LIBRARY_PATH="" export CONTENT_LENGTH="708" export REMOTE_ADDR="172.31.194.244" export WISECONFIGDIR="/usr/local/devel/ANNOTATION/EGC_utilities/WISE2/wise2.2.0/wisecfg" export SGE_EXECD_PORT="537" export REQUEST_URI="/cgi/run_pipeline.cgi" export SGE_ARCH="lx26-amd64" export WF_ROOT_INSTALL="/projects/bsi/RandD/ngs/ergatis/workflow" export TMPDIR="/tmp" export SGE_ROOT="/home/sge6_2" export TERMCAP="" export vappio_root="/opt/vappio_scripts" /projects/bsi/RandD/ngs/ergatis/workflow/RunWorkflow -i /projects/bsi/RandD/ngs/ergatis/projects/etest/workflow/runtime/pipeline/22/pipeline.xml -m 1 --init-heap=100m --max-heap=1024m --logconf=/projects/bsi/RandD/ngs/ergatis/workflow/log4j.properties >& /projects/bsi/RandD/ngs/ergatis/projects/etest/workflow/runtime/pipeline/22/pipeline.xml.run.out On May 22, 2012, at 10:59 AM, Mahurkar, Anup wrote: > Can you send me the log file an the shell script? > > Anup > > On May 22, 2012, at 11:54 AM, "Jaysheel Bhavsar" <bja...@gm...> wrote: > >> Hey Anup, >> I don't see any -q option in sge_job.sh script written in mock_server_base. In the log file I see a call to she_job.sh which looks like this >> >> qsub -b n -C '#SGE_DIRECTIVE' /projects/bsi/RandD/ngs/ergatis/mock_server_base/working/0/4521/sge_job.sh >> >> Which come from sge_submitter.sh from what I can tell. >> >> Jaysheel >> >> >> On May 21, 2012, at 8:22 PM, Mahurkar, Anup wrote: >> >>> Jaysheel, >>> >>> The -q will be specified in the sge_job.sh script for each of the jobs. Is >>> it not there? If not could you send me the log file? >>> >>> Anup >>> >>> On 5/21/12 3:52 PM, "Jaysheel Bhavsar" <bja...@gm...> wrote: >>> >>>> Hey Anup, >>>> I got the workflow-3.1.x branch and re-installed workflow. I updated >>>> sge_def_queue and sge_pri_queue in ${WORKFLOW_HOME}/server-conf/htc.conf >>>> file but jobs are still being submitted to default queue. I don't see -q >>>> option in the qsub command in sge_submitter.sh. Is there something I >>>> missed? >>>> >>>> Jaysheel >>>> >>>> >>>> On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote: >>>> >>>>> Jaysheel, >>>>> >>>>> I have added the code to configure the default queue name that workflow >>>>> uses as well as specifying a queue name in the workflow that will be >>>>> honored. You will need to update the HTC and Workflow code. In the >>>>> htc.conf file specify the default queue name to be used for workflow >>>>> jobs. >>>>> If nothing is specified in the command, it will look for the property >>>>> "sge_def_queue" in the config file. >>>>> >>>>> We have made slight changes to epilog, prolog, and sge_submitter scripts >>>>> as well. So your best bet is to reinstall workflow. >>>>> >>>>> Anup >>>>> >>>>> >>>>> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...> >>>>> wrote: >>>>> >>>>>> Jaysheel, >>>>>> >>>>>> I am working on this feature right now. Should have it ready early next >>>>>> week. >>>>>> >>>>>> Anup >>>>>> >>>>>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...> >>>>>> wrote: >>>>>> >>>>>>> Hey guys, >>>>>>> I there a way to dynamically define queue name? Currently queue >>>>>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh. I would like to >>>>>>> pass the queue name based on the pipeline I am executing, along with >>>>>>> h_vmem and h_stack parameters. >>>>>>> >>>>>>> Thanks >>>>>>> Jaysheel >>>>>>> >>>>>>> >>>>>>> ----------------------------------------------------------------------- >>>>>>> -- >>>>>>> ----- >>>>>>> Live Security Virtual Conference >>>>>>> Exclusive live event will cover all the ways today's security and >>>>>>> threat landscape has changed and how IT managers can respond. >>>>>>> Discussions >>>>>>> will include endpoint security, mobile security and the latest in >>>>>>> malware >>>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>>> _______________________________________________ >>>>>>> Ergatis-users mailing list >>>>>>> Erg...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------ >>>>>> -- >>>>>> ---- >>>>>> Live Security Virtual Conference >>>>>> Exclusive live event will cover all the ways today's security and >>>>>> threat landscape has changed and how IT managers can respond. >>>>>> Discussions >>>>>> will include endpoint security, mobile security and the latest in >>>>>> malware >>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>> _______________________________________________ >>>>>> Ergatis-users mailing list >>>>>> Erg...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------- >>>>> ----- >>>>> Live Security Virtual Conference >>>>> Exclusive live event will cover all the ways today's security and >>>>> threat landscape has changed and how IT managers can respond. >>>>> Discussions >>>>> will include endpoint security, mobile security and the latest in >>>>> malware >>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>> _______________________________________________ >>>>> Ergatis-users mailing list >>>>> Erg...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>>> >>>> >>>> -------------------------------------------------------------------------- >>>> ---- >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. Discussions >>>> will include endpoint security, mobile security and the latest in malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> Ergatis-users mailing list >>>> Erg...@li... >>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Ergatis-users mailing list >>> Erg...@li... >>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Ergatis-users mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-users > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > Ergatis-users mailing list > Erg...@li... > https://lists.sourceforge.net/lists/listinfo/ergatis-users |