From: Mariette <jma...@to...> - 2012-05-03 13:16:01
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Joshua, Just so you know, we are running ergatis on a red hat 6 system, have you make it run on it ? I get a litle further. From the pipeline.X.run.sh file, I added the folowing lines: sudo -E -u ng6 echo $LD_LIBRARY_PATH > /work/tmp/tt.ld sudo -E -u ng6 env > /work/tmp/tt.env the /work/tmp/tt.ld file does contain the right path! However the /work/tmp/tt.env does not contain the LD_LIBARY_PATH at all! An other point, within ergatis, a simple component running a 'env' command return a LD_LIBRARY_PATH set to: LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 I tryed to figure out where that path could come from ... any idea ? thanks for your time! Jérôme Le 03/05/2012 10:02, Mariette a écrit : > > Joshua, > > they are pretty close, SGE adds some variables (SGE_BINARY_PATH, > SGE_CWD_PATH ...), but the PATH, the LD_LIBRARY_PATH are the same > within or not a qsub. > > Jerome > > > > > Le 02/05/2012 17:29, Joshua Orvis a écrit : >> Jerome - >> >> I think you should take a step back here. Take Ergatis and Workflow >> Engine completely out of this. What happens if you write a shell >> script that sets an ENV variable and then does the equivalent of a >> qsub to run your script that prints your environment to a file? Is >> the ENV retained? >> >> Joshua >> >> On Wed, May 2, 2012 at 10:05 AM, Mariette <jma...@to... >> <mailto:jma...@to...>> wrote: >> >> >> Hi again, >> >> so I made a component with just a env as execution, and the paths >> are not right ! >> What are the steps after the execution of the script ? >> >> Jerome >> >> >> >> >> >> >> Le 02/05/2012 16:48, Mariette a écrit : >>> >>> Hi everyone, >>> >>> I'm still facing the same probleme ... I moved on by making a >>> sed to all ergatis scripts to add the right PERL5LIB path, but >>> this is just a patch! I need to do the same with the >>> LD_LIBRARY_PATH and the PATH variables ... but it's working with >>> non of them! >>> >>> The script produced (pipeline.*.run.sh) is correctly written >>> down, and the execution with an echo right after display the >>> right path ! >>> >>> What we changed is the full cluster, so we are running the open >>> sge version and no longer the sun sge. >>> >>> any idea on debugging ? >>> thanks, >>> >>> Jerome >>> >>> >>> >>> >>> >>> >>> Le 20/04/2012 17:08, Joshua Orvis a écrit : >>>> Jérôme - >>>> >>>> The script looks right, and that was going to be my next >>>> question. Yes, Ergatis writes that shell script and then >>>> executes it, and within that script RunWorkflow is called. Has >>>> anything else changed in your SGE configuration? You could >>>> replace the RunWorkflow line in the script with your own qsub >>>> test that just prints out the environment once it's placed on a >>>> node. This would allow you to see if it's within the SGE job >>>> submission that your job is being lost. Out of curiosity, do >>>> you have the 'submit_pipelines_as_jobs' option turned on in the >>>> ergatis.ini file? >>>> >>>> Joshua >>>> >>>> >>>> >>>> 2012/4/20 Mariette <jma...@to... >>>> <mailto:jma...@to...>> >>>> >>>> >>>> Joshua, >>>> >>>> there is something I'm missing. I did modified the >>>> Pipeline.pm so the PERL5LIB is settled. When I take a look >>>> at the pipeline.XXX.run.sh <http://pipeline.XXX.run.sh> >>>> script written down, >>>> the variable is correctly set ! Is this script used to >>>> process the workflow ? >>>> >>>> Jérôme >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Le 19/04/2012 10:16, Mariette a écrit : >>>>> >>>>> Joshua, >>>>> the file is in attachement. The error returned is: >>>>> >>>>> Can't locate Config/IniFiles.pm in @INC (@INC contains: >>>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5//x86_64-linux-thread-multi >>>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/ >>>>> /usr/local/lib64/perl5 /usr/local/share/perl5 >>>>> /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl >>>>> /usr/lib64/perl5/5.10.0 /usr/lib64/perl5 /usr/share/perl5 >>>>> . >>>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8/x86_64-linux-thread-multi >>>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8) at >>>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/bin/replace_template_keys.pl >>>>> <http://replace_template_keys.pl> line 17 >>>>> >>>>> Paths I provided to Pipeline.pm are not in @INC. >>>>> >>>>> thanks for your time! >>>>> Jérôme >>>>> >>>>> >>>>> Le 13/04/2012 20:32, Joshua Orvis a écrit : >>>>>> Jerome - >>>>>> >>>>>> Do you mind sending me your modified Pipeline.pm file? I >>>>>> don't see any changes here that would cause the ENV >>>>>> changes you make in the _setup_environment() method of >>>>>> Pipeline.pm to not make it to the execution of the >>>>>> create_template_keys.pl <http://create_template_keys.pl> >>>>>> script. I'd like to test it locally. >>>>>> >>>>>> Joshua >>>>>> >>>>>> >>>>>> On Fri, Apr 13, 2012 at 1:14 PM, Joshua Orvis >>>>>> <jo...@gm... <mailto:jo...@gm...>> wrote: >>>>>> >>>>>> Jérôme - >>>>>> >>>>>> I'm taking a look at this. >>>>>> >>>>>> Joshua >>>>>> >>>>>> On Fri, Apr 13, 2012 at 10:24 AM, Mariette >>>>>> <jma...@to... >>>>>> <mailto:jma...@to...>> wrote: >>>>>> >>>>>> Hi everyone, >>>>>> >>>>>> the environment we are running ergatis on is a >>>>>> bit tricky. The perl libs >>>>>> are not located on the usual perl path. >>>>>> usually when I have this kind of trouble with >>>>>> ergatis, I set the path >>>>>> within the Pipeline.pm file. However it doesn't >>>>>> work with the new version. >>>>>> >>>>>> The script crashing is the create_template_keys, >>>>>> when I add the correct >>>>>> lib path to this wrapper line: >>>>>> export >>>>>> PERL5LIB=/usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/:/path/.... >>>>>> >>>>>> it does work! I would have guessed the >>>>>> Pipeline.pm was adding what I >>>>>> wanted bu this one is not called in the >>>>>> create_template_keys.pl >>>>>> <http://create_template_keys.pl> script ... >>>>>> >>>>>> How can I manage to fix this problem, without >>>>>> adding to all the wrapper >>>>>> my path ? >>>>>> thanks, >>>>>> >>>>>> Jérôme >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> For Developers, A Lot Can Happen In A Second. >>>>>> Boundary is the first to Know...and Tell You. >>>>>> Monitor Your Applications in Ultra-Fine >>>>>> Resolution. Try it FREE! >>>>>> http://p.sf.net/sfu/Boundary-d2dvs2 >>>>>> _______________________________________________ >>>>>> Ergatis-users mailing list >>>>>> Erg...@li... >>>>>> <mailto:Erg...@li...> >>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> For Developers, A Lot Can Happen In A Second. >>>>>> Boundary is the first to Know...and Tell You. >>>>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! >>>>>> http://p.sf.net/sfu/Boundary-d2dvs2 >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Ergatis-users mailing list >>>>>> Erg...@li... <mailto:Erg...@li...> >>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> For Developers, A Lot Can Happen In A Second. >>>>> Boundary is the first to Know...and Tell You. >>>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! >>>>> http://p.sf.net/sfu/Boundary-d2dvs2 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Ergatis-users mailing list >>>>> Erg...@li... <mailto:Erg...@li...> >>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> For Developers, A Lot Can Happen In A Second. >>>> Boundary is the first to Know...and Tell You. >>>> Monitor Your Applications in Ultra-Fine Resolution. Try it >>>> FREE! >>>> http://p.sf.net/sfu/Boundary-d2dvs2 >>>> _______________________________________________ >>>> Ergatis-users mailing list >>>> Erg...@li... >>>> <mailto:Erg...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> For Developers, A Lot Can Happen In A Second. >>>> Boundary is the first to Know...and Tell You. >>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! >>>> http://p.sf.net/sfu/Boundary-d2dvs2 >>>> >>>> >>>> _______________________________________________ >>>> Ergatis-users mailing list >>>> Erg...@li... <mailto: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... <mailto: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... >> <mailto: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 |