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

Ranga Srinivasan ranga at bizrate.com
Wed Sep 29 01:03:27 BST 2004



Hi

Thanks you for the response.

I tried doing qsub and the script to execute and it starts. If I look at
qstat it displays status of qw and then it claims it has finished. I don't
get any error messages nor the files (error and output) get created.

If there are any errors where does it put it. Is there a way to debug the
qsub process to see were is either fails or exits without doing anything.

Thanks

Ranga
-----Original Message-----
From: Charu Chaubal [mailto:Charu.Chaubal at Sun.COM]
Sent: Tuesday, September 28, 2004 4:29 PM
To: users at gridengine.sunsource.net
Subject: Re: [GE users] Question on GridEngine (5.3 and 6.0) execution
of user scripts using qsub on linux


You don't need to have a wrapper --- you can simply add this line to
the beginning of "test.sh":
#$ -S /bin/bash

Then, just 'qsub test.sh' and it should use bash to run your job.

Regards,
	Charu


On Sep 28, 2004, at 4:15 PM, Bernard Li wrote:

> 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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>
###############################################################
# Charu V. Chaubal				# Phone: (650) 786-7672 (x87672)
# Grid Computing Technologist	# Fax:   (650) 786-4591
# Sun Microsystems, Inc.			# Email: charu.chaubal at sun.com
###############################################################


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