[GE users] qsub does not run my bash file

Reuti reuti at staff.uni-marburg.de
Fri Apr 21 09:18:14 BST 2006


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Am 21.04.2006 um 10:08 schrieb Olesen, Mark:

> 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?

Setting "shell_start_mode      unix_behavior" in the queue definition  
may be more flexible as it will honor the first line of the script to  
specify the to be used interpreter, as you would expect it also from  
the command line. This avoids any extra sepcification of -S, and/or  
tuning the script for use inside/outside of SGE.

-- Reuti


>> [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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