Changing wall times...
Hi, I was not the original installer of our Galaxy instance, but have been tasked with changing the wall time that is requested when a job is submitted to the pbs queue. I found the job_walltime option in the universe_wsgi.ini, but we seem to be using round robin submission which then, in turn, submits a job to the pbs queue, so this doesn't work for me. Does anyone know an easy way to change the default time of 1 hr on this? Thanks, Kyle -- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com 740.249.9729 ***************************
Kyle Kurz wrote:
Hi, I was not the original installer of our Galaxy instance, but have been tasked with changing the wall time that is requested when a job is submitted to the pbs queue. I found the job_walltime option in the universe_wsgi.ini, but we seem to be using round robin submission which then, in turn, submits a job to the pbs queue, so this doesn't work for me.
Does anyone know an easy way to change the default time of 1 hr on this?
Hi Kyle, job_walltime does not actually use any features of the scheduler other than the current run time (and for anyone else reading this, it's only implemented for PBS, not SGE or local). This feature was added to allow Galaxy to display a "nice" error message when a job reaches a configured walltime, instead of just using what is provided by the execution control process (e.g. pbs_mom). However, I recently added features that allow you to set job parameters as part of the runner. This can be done with PBS by changing the default or per-tool runner like so: pbs:////-l walltime=24:00:00/ Any option that can be placed on the command line or in the PBS script (a la '#PBS -l ...') can be specified in that field of the URL. This implementation should be considered temporary. I don't know how long it will be around (it'll probably be a long time, and we may try to maintain backwards compatibility), but it won't be removed before there's a suitable replacement. --nate
Thanks, Kyle
-- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com <mailto:kyle.w.kurz@gmail.com> 740.249.9729 ***************************
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Hi Nate, I'm still looking into this issue from a couple weeks ago (other problems took precedence...) and have come to what I think is a better question. Is there a way to stop Galaxy from doing its own cleanup? We are submitting to a pbs queue in an HPC environment and the queue is more than capable of killing the jobs if they run too long. We have been unable to get Galaxy to stop killing jobs after 1 hour, however. Thanks, Kyle On Wed, Feb 10, 2010 at 10:53 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Kyle Kurz wrote:
Hi, I was not the original installer of our Galaxy instance, but have been tasked with changing the wall time that is requested when a job is submitted to the pbs queue. I found the job_walltime option in the universe_wsgi.ini, but we seem to be using round robin submission which then, in turn, submits a job to the pbs queue, so this doesn't work for me. Does anyone know an easy way to change the default time of 1 hr on this?
Hi Kyle,
job_walltime does not actually use any features of the scheduler other than the current run time (and for anyone else reading this, it's only implemented for PBS, not SGE or local). This feature was added to allow Galaxy to display a "nice" error message when a job reaches a configured walltime, instead of just using what is provided by the execution control process (e.g. pbs_mom).
However, I recently added features that allow you to set job parameters as part of the runner. This can be done with PBS by changing the default or per-tool runner like so:
pbs:////-l walltime=24:00:00/
Any option that can be placed on the command line or in the PBS script (a la '#PBS -l ...') can be specified in that field of the URL.
This implementation should be considered temporary. I don't know how long it will be around (it'll probably be a long time, and we may try to maintain backwards compatibility), but it won't be removed before there's a suitable replacement.
--nate
Thanks, Kyle
-- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com <mailto:kyle.w.kurz@gmail.com> 740.249.9729 ***************************
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-- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com 740.249.9729 ***************************
Kyle Kurz wrote:
Hi Nate, I'm still looking into this issue from a couple weeks ago (other problems took precedence...) and have come to what I think is a better question.
Is there a way to stop Galaxy from doing its own cleanup?
We are submitting to a pbs queue in an HPC environment and the queue is more than capable of killing the jobs if they run too long. We have been unable to get Galaxy to stop killing jobs after 1 hour, however.
Hi Kyle, As long as job_walltime is unset in universe_wsgi.ini, Galaxy should never try to stop a running job except at the user's request. Are you sure your queue's default_walltime is not set to 1 hour in PBS? --nate
Thanks, Kyle
On Wed, Feb 10, 2010 at 10:53 AM, Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu>> wrote:
Kyle Kurz wrote:
Hi, I was not the original installer of our Galaxy instance, but have been tasked with changing the wall time that is requested when a job is submitted to the pbs queue. I found the job_walltime option in the universe_wsgi.ini, but we seem to be using round robin submission which then, in turn, submits a job to the pbs queue, so this doesn't work for me. Does anyone know an easy way to change the default time of 1 hr on this?
Hi Kyle,
job_walltime does not actually use any features of the scheduler other than the current run time (and for anyone else reading this, it's only implemented for PBS, not SGE or local). This feature was added to allow Galaxy to display a "nice" error message when a job reaches a configured walltime, instead of just using what is provided by the execution control process (e.g. pbs_mom).
However, I recently added features that allow you to set job parameters as part of the runner. This can be done with PBS by changing the default or per-tool runner like so:
pbs:////-l walltime=24:00:00/
Any option that can be placed on the command line or in the PBS script (a la '#PBS -l ...') can be specified in that field of the URL.
This implementation should be considered temporary. I don't know how long it will be around (it'll probably be a long time, and we may try to maintain backwards compatibility), but it won't be removed before there's a suitable replacement.
--nate
Thanks, Kyle
-- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com <mailto:kyle.w.kurz@gmail.com> <mailto:kyle.w.kurz@gmail.com <mailto:kyle.w.kurz@gmail.com>> 740.249.9729 ***************************
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-- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com <mailto:kyle.w.kurz@gmail.com> 740.249.9729 ***************************
thanks nate, we'll have a look at that tomorrow. i know we've commented out the job_walltime option. i also know that the queue only looks at the requested time for its limits, so there seems to be something else going on that we're missing. i'll try to hunt down the person who actually installed galaxy on the system and see if they have any insight. thanks, kyle On Mon, Mar 8, 2010 at 11:53 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Kyle Kurz wrote:
Hi Nate, I'm still looking into this issue from a couple weeks ago (other problems took precedence...) and have come to what I think is a better question.
Is there a way to stop Galaxy from doing its own cleanup? We are submitting to a pbs queue in an HPC environment and the queue is more than capable of killing the jobs if they run too long. We have been unable to get Galaxy to stop killing jobs after 1 hour, however.
Hi Kyle,
As long as job_walltime is unset in universe_wsgi.ini, Galaxy should never try to stop a running job except at the user's request. Are you sure your queue's default_walltime is not set to 1 hour in PBS?
--nate
Thanks,
Kyle
On Wed, Feb 10, 2010 at 10:53 AM, Nate Coraor <nate@bx.psu.edu <mailto: nate@bx.psu.edu>> wrote:
Kyle Kurz wrote:
Hi, I was not the original installer of our Galaxy instance, but have been tasked with changing the wall time that is requested when a job is submitted to the pbs queue. I found the job_walltime option in the universe_wsgi.ini, but we seem to be using round robin submission which then, in turn, submits a job to the pbs queue, so this doesn't work for me. Does anyone know an easy way to change the default time of 1 hr on this?
Hi Kyle,
job_walltime does not actually use any features of the scheduler other than the current run time (and for anyone else reading this, it's only implemented for PBS, not SGE or local). This feature was added to allow Galaxy to display a "nice" error message when a job reaches a configured walltime, instead of just using what is provided by the execution control process (e.g. pbs_mom).
However, I recently added features that allow you to set job parameters as part of the runner. This can be done with PBS by changing the default or per-tool runner like so:
pbs:////-l walltime=24:00:00/
Any option that can be placed on the command line or in the PBS script (a la '#PBS -l ...') can be specified in that field of the URL.
This implementation should be considered temporary. I don't know how long it will be around (it'll probably be a long time, and we may try to maintain backwards compatibility), but it won't be removed before there's a suitable replacement.
--nate
Thanks, Kyle
-- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com <mailto:kyle.w.kurz@gmail.com> <mailto:kyle.w.kurz@gmail.com <mailto:kyle.w.kurz@gmail.com>>
740.249.9729 ***************************
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http://lists.bx.psu.edu/listinfo/galaxy-dev
-- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com <mailto:kyle.w.kurz@gmail.com> 740.249.9729 ***************************
-- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz@gmail.com 740.249.9729 ***************************
participants (2)
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Kyle Kurz -
Nate Coraor