[GE users] echo "blah" | mail -s "test" me at my.address not working in qsub'd jobs

griznog griznog at gmail.com
Tue Aug 17 17:05:49 BST 2010


Chris,

The -b y was just the most recent variant I tested, it fails with or
without that.

jbh

On Tue, Aug 17, 2010 at 11:12 AM, craffi <dag at sonsorol.org> wrote:
> Not quite sure why you are using the "binary=yes" ("-b y") flag when y
> ou are qsub'ing a shell script. Can you try your qsub without that flag
> and see if it makes a difference?
>
> -Chris
>
>
> griznog wrote:
>> Hi,
>>
>> I have a job script, simplified to:
>>
>>
>> #!/bin/bash
>> set -x
>> echo "Testing mail."
>> echo "Test" | mail -s Testing jbh at broadinstitute.org
>> echo $?
>> echo "Done."
>>
>>
>> When I run that directly on a node, either ssh directly to the node,
>> qrsh (which is configured to ssh), or qlogin, then the script works,
>> mail is sent correctly and /var/log/maillog gets a lot of chatter
>> about it.
>>
>> But, if I qsub this script I do not get any mail and nothing is logged
>> to /var/log/maillog even though the exit status of the mail command is
>> 0 as if it were successful. Does anyone know where that mail is going?
>> Example script run is:
>>
>> jbh at tin ~ $ qsub -b y -l hostname=node290 /home/radon01/jbh/testmail.sh
>> Your job 27 ("testmail.sh") has been submitted
>> jbh at tin ~ $ cat testmail.sh.*27
>> + echo 'Testing mail.'
>> + mail -s Testing jbh at broadinstitute.org
>> + echo Test
>> + echo 0
>> + echo Done.
>> Testing mail.
>> 0
>> Done.
>>
>> Any pointers on how to troubleshoot this would be appreciated. I'm
>> pretty stumped as to why sendmail never sees anything when this runs
>> as a qsub'd job.
>>
>>
>> Thanks,
>>
>> jbh
>>
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