Bin/sh Module Line 1 Syntax Error Unexpected End Of File
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running shellscript using qsub up vote 8 down vote favorite 1 I have the following shellscript: #!/bin/sh cd /sw/local/bin/ export LD_LIBRARY_PATH=/sw/local/lib:/usr/local/Trolltech/Qt-4.7.2/lib:$LD_LIBRARY_PATH ./FeatureFinderRaw -in /homes/JG-C1-18.mzML -out /homes/test_remove_after_use.featureXML -threads 20 It works fine when I run it from my own command line, but when I try to do: qsub -q ningal.q -cwd -V -o /homes/queue.out -e /queue.err featureFind_C1-18_20t.sh I get the following error: /bin/sh: module: line 1: syntax error: unexpected end syntax error unexpected end of file bash script of file /bin/sh: error importing function definition for `module' ./FeatureFinderRaw: error while loading shared libraries: libOpenMS.so: cannot open shared object file: No such file or directory /bin/sh: module: line 1: syntax error: unexpected end of file /bin/sh: error importing function definition for `module' ./FeatureFinderRaw: error while loading shared libraries: libQtWebKit.so.4: cannot open shared object file: No such file or directory /bin/sh: module: line 1: syntax error: unexpected end of file /bin/sh: error importing function definition for `module' ./FeatureFinderRaw: error while loading shared libraries: libQtWebKit.so.4: cannot open shared object file: No such file or directory /bin/bash: module: line 1: syntax error: unexpected end of file /bin/bash: error importing function definition for `module' ./FeatureFinderRaw: error while loading shared libraries: libQtWebKit.so.4: cannot open shared object file: No such file or directory /bin/sh: module: line 1: syntax error: unexpected end of file /bin/sh: error importing function definition for `module' ./FeatureFinderRaw: error while loading shared libraries: libQtWebKit.so.4: cannot open shared object file: No such file or directory /bin/sh: module: line 1: syntax error: unexpected end of file /bin/sh: error importing function definition for `module' I don't understand why I get this error when using qsub, but not when running the script directly on the same cluster machine.
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Syntax Error Unexpected End Of File Python
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ad (required): Select a file, or drag & drop file here. ✔ ✘ Please provide the ad click URL, if possible: Home Browse Environment Modules Mailing Lists Environment Modules Manage your shell environment variables and aliases http://stackoverflow.com/questions/10496758/unexpected-end-of-file-and-error-importing-function-definition-error-running Brought to you by: leomania, rkowen, sirdude Summary Files Reviews Support Wiki Mailing Lists Code Tickets ▾ Patches Bugs Feature Requests Discussion Git ▾ Environment Modules - C Environment Modules - Tcl Only modules-interest Re: [Modules] modules error during job submission Re: [Modules] modules error during job submission From: Kevin Van Workum
the fresh install of EBS 12.2 , you may encounter the following error while starting Weblogic admin server. Note that : this error does- not prevent weblogic to http://ermanarslan.blogspot.com/2014/06/ebs-122-adadminsrvctlsh-start-sh-module.html work.. ./adadminsrvctl.sh start sh: module: line 1: syntax error: unexpected end of file sh: error importing function definition for `module' Oracle explains this problem with an internal bug :internal Bug 14259166 , and https://www.open-mpi.org/community/lists/users/2012/01/18138.php suggest the followingrename for the fix: Rename /etc/profile.d/modules.sh to /etc/profile.d/modules.sh.bak. Log out, log back in, and set the application environment. Confirm these environment variables are not set: MODULEPATH, LOADEDMODULES and MODULESHOME. Actually, syntax error it is not required because the problem is caused by the script /usr/share/Modules/init/bash, exactly the following line "export -f module" triggers the error. So commenting this line will fix the error. In this post, I will try to explain the cause of this problem; So when we have modules.sh in our profile.d folder, we have modules related environments set; for example; [root@erpprod profile.d]# su syntax error unexpected - applmgr [applmgr@erpprod ~]$ echo $MODULEPATH /usr/share/Modules/modulefiles:/etc/modulefiles Normally when we havent any modules.sh in our profile.d folder, we dont set any modules environment variables. [root@erpprod profile.d]# su - applmgr [applmgr@erpprod ~]$ echo $MODULEPATH Okay, another important thing in the error message is; it reports an error while importing a function definition but it does not display a function name.. Our error is ; sh: error importing function definition for `module' But it must be something like; sh: error importing function definition for `module '/opt/IBM/InformationServer/Server/DSComponents/lib/libicui18n.so' I mean it should display the function name ,and it is also lacking a ' character... It has module' at the end, but that ' character is not closed.. So this seems to be the problem.. This explains the EOF error, as a ' character should be there not EOF.. As we now that our .bash_profile sources bashrc and bashrc source /etc/profile.d/*.sh scripts; Lets take a look what is written in our modules.sh file; shell=`/bin/basename \`/bin/ps -p $$ -ocomm=\`` if [ -f /usr/share/Modules/init/$shell ] then . /usr/share/Modules/init/$shell else . /usr/share/Modules/init/sh fi So basicall it finds our shell and executes related scripts accordingly.. So assuming our shel
Hardware Locality Network Locality MPI Testing Tool Open MPI User Docs Open Tool for Parameter Optimization PMIx Community Mailing Lists OMPI announce archives OMPI users archives OMPI devel archives hwloc announce archives hwloc users archives hwloc devel archives MTT users archives MTT developers archives Getting Help/Support Contribute Mirrors Contact License This web mail archive is frozen. This page is part of a frozen web archive of this mailing list. You can still navigate around this archive, but know that no new mails have been added to it since July of 2016. Click here to be taken to the new web archives of this list The new archive includes all the mails that are in this frozen archive plus all new mails that have been sent to the list since it was migrated to the new archives. Date view Thread view Subject view Author view Subject: [OMPI users] ompi + bash + GE + modules From: Mark Suhovecky (suhovecky_at_[hidden]) Date: 2012-01-11 12:42:22 Next message: Edmund Sumbar: "Re: [OMPI users] ompi + bash + GE + modules" Previous message: Andrew Senin: "Re: [OMPI users] Status of SLURM integration" Next in thread: Edmund Sumbar: "Re: [OMPI users] ompi + bash + GE + modules" Reply: Edmund Sumbar: "Re: [OMPI users] ompi + bash + GE + modules" Reply: Gustavo Correa: "Re: [OMPI users] ompi + bash + GE + modules" Hi- We run OpenMPI 1.4.3 on RHEL5 in a cluster environment. We use Univa Grid Engine 8.0.1 (an SGE spinoff) for job submission. We've just recently begun supporting the bash shell for submitted jobs, and are seeing a problem with submitted MPI jobs. Our software environment is manged with Modules package (version 3.2.8), so a typical job submission looks something like this #!/bin/bash #$