[GE users] Question on GridEngine (5.3 and 6.0) execution of user scripts using qsub on linux

Bernard Li bli at bcgsc.ca
Wed Sep 29 00:15:21 BST 2004


Hi Ranga:

You need to write a 'wrapper script' for qsub:

[wrapper.sh]
#!/bin/bash

#$ -S /bin/bash

test1.sh <arguments>

Then you would submit the job by typing the following command:

qsub wrapper.sh

For more information on qsub, check the qsub manpages.

Cheers,

Bernard 

> -----Original Message-----
> From: Ranga Srinivasan [mailto:ranga at bizrate.com] 
> Sent: Tuesday, September 28, 2004 15:12
> To: users at gridengine.sunsource.net
> Cc: Ranga Srinivasan
> Subject: [GE users] Question on GridEngine (5.3 and 6.0) 
> execution of user scripts using qsub on linux 
> 
> 
> Hi
> 
> I am new to Grid Engine and trying to see if we can use it 
> for our daily jobs.
> 
> I wrote a script called test1.sh that and is attached to this 
> email. Also I have attached the errors I am getting. To me it 
> looks like the shell (/bin/bash)is not executed. In this case 
> I have only one machine and is getting executed on the same box.
> 
> Any help would be really appreciated.
> 
> Thanks
> 
> Ranga
> 
> 
> 
> My to be executed script looks like this
> 
> #!/bin/bash -x
> 
> GATHER_ROOT="/grid/schedule/Jobs/av/general"
> JAVA_HOME="/usr/local/bin/java"
> BIN_DIR="=/home/schedule/Jobs/av/bin"
> INVENTORY_ROOT="=/pipeline_ro/merchfiles"
> 
> function usage
> {
>         echo "$1 [ -h -f -H <destination_dir> -t 
> <date_time_stamp>] -m <last_mid_digit>"
>         echo "  h: help"
>         echo "  m: the last digit of the mids to gather 0-9"
>         echo "  t: the timestamp to use in format yymmdd_HHMM"
>         echo "  f: Force override of the indexable filter 
> (all indexed)"
>                 echo "  H: Root directory to store files to"
>         exit 2
> }
> 
> 
> set -- `getopt hfm:t:H:C: $*`
> 
> if [ $? != 0 ]; then
>         usage $0
> fi
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 

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