linuxshellcluster-computingqsub

'Unexpected end of file' and 'error importing function definition' error running shellscript using qsub

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 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. How can I run a script using qsub?

Solution

  • Also have this problem in a wrapper script that uses 

    qsub -shell no -b yes -cwd -V somescript.bash arg1 arg2 etc

    if you use it to submit another bash shell script. It produces the annonying 

    /bin/sh: module: line 1: syntax error: unexpected end of file
/bin/sh: error importing function definition for `BASH_FUNC_module'

    (this is Sun Grid Engine 211.11 running on CentOS 6.6) Turns out things are solved by simply putting the following on top of the wrapper script (not of the wrapped script):

    unset module

    That's all.