[GE users] qsub does not run my bash file

Olesen, Mark Mark.Olesen at arvinmeritor.com
Fri Apr 21 09:08:55 BST 2006


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When you create a queue, SGE unfortunately seems to use 'csh' as the default
shell for the queue. Check the entry 'shell' using qconf -sq <queuename> and
modify it using 'qconf -mq' to be /bin/sh.

While you are at it, you may also wish to add bash as a login_shell using
'qconf -mconf', otherwise you may or may not see your ~/.profile being
sourced.

> I got an error:
> [mex at clusun subfile]$ more ~/prova.sh.e20056
> basepath=/export/home/mex/BoTSched: Command not found.
> basepath: Undefined variable.

To ensure that the standard bourne shell is used, you can *additionally* add
'-S /bin/sh' to $SGE_ROOT/$SGE_CELL/common/sge_request

Perhaps the default for new queues could/should be the standard bourne
shell?

> [mex at clusun subfile]$ more ~/prova.sh.o20056
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.

You may wish to protect certain elements in your ~/.profile, ~/.bashrc, etc.


For example:

/usr/bin/tty -s 2>/dev/null     # interactive shell
if [ $? -eq 0 ]; then
  stty intr "^C"
  for i in $HOME/.aliases $HOME/.aliases.group $HOME/.aliases.user
  do
    [ -r $i ] && . $i
  done
fi


/mark

Dr. Mark Olesen
Principal Engineer Thermofluids Analysis
ArvinMeritor Light Vehicle Systems
ArvinMeritor Emissions Technologies GmbH
Biberbachstr. 9
D-86154 Augsburg, GERMANY

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