I missed your second email to Txema, but I think a simple, if less
than elegant method is to redirect stdout and stderr of the pipeline
jobs to a directory. Each output file and error file can be
identified by its job id or task id. Then, in your clean up code you
can sweep through each directory and report which jobs succeeded and
which jobs failed based on the size and existence of each file.
So you could submit as
qsub -m e -M <user-email> -hold_jid $(qsub -terse -e
${HOME}/err/$JOB_ID -o ${HOME}/out/$JOB_ID pipeline_job)
completion_job
And then in the completion_job you can do something like
IFS='\n' read -d '' -r -a jobid_arr < <(find ${HOME}/err/ -type f -size 0)
echo "Following jobs failed: ${jobid_arr[@]}"
And mail that.
The directory approach means you don't have to worry about locking
like you would if each job were writing to a file. A socket won't
work across multiple hosts. You'd have to use nc or something more
complex.
John.
On Wed, Jul 16, 2014 at 7:17 AM, John Kloss <john.kl...@gmail.com> wrote:
> You can submit a job that has a hold placed on it based on your
> pipeline, whose only purpose is to email you when your pipeline
> finishes.
>
> qsub -m e -M <user-email> -hold_jid $(qsub -terse pipeline_job) completion_job
>
> or, with an array job, which submits job ids as
> <jobid>.1-<array_size>:?, you can hold on the whole array job
>
> qsub -m e -M <user-email> -hold_jid $(qsub -terse -t 1-<pipeline #>
> pipeline_job | cut -d'.' -f1) completion_job
>
> I often do clean up and check for error files in the completion_job.
>
> John.
>
> On Wed, Jul 16, 2014 at 6:05 AM, Paolo Di Tommaso
> <paolo.ditomm...@gmail.com> wrote:
>> Hi Txema,
>>
>> My point is not to disable them but how to get the notification by using a
>> different "transport" other than email. I would like that information to a
>> file or a socket.
>>
>> p
>>
>>
>> On Wed, Jul 16, 2014 at 11:55 AM, Txema Heredia <txema.llis...@gmail.com>
>> wrote:
>>>
>>> Hi Paolo,
>>>
>>> you can disable mails on all but the very last job of the pipeline by
>>> using -m b|e|a|s|n.
>>>
>>> There has been discussions on the list on mechanisms to send all emails to
>>> the local linux user (not an email address) and send "packages of mails"
>>> every day or so, but I can't remember any definitive way to work this out.
>>>
>>> Txema
>>>
>>> El 16/07/14 11:30, Paolo Di Tommaso escribió:
>>>
>>> Hi,
>>>
>>> SGE can send job notification via email by using the -M command line
>>> option.
>>>
>>> This useful when you are submitting few jobs but not for complex pipeline
>>> crunching thousand of jobs.
>>>
>>> I'm wondering if SGE can send these notifications by using other mechanism
>>> e.g. writing to a file, socket, http, etc.
>>>
>>>
>>> Thanks,
>>> Paolo
>>>
>>>
>>>
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>>
>>
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