jobs submitted to a cluster

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jobs submitted to a cluster

Shrum, Donald C
I've setup galaxy to submit jobs to our HPC cluster as the logged in user.  I used the drama python module to submit the jobs to our moab server.  

It appears that the working directory for a submitted job is being removed by galaxy prior to the job completing on the cluster.

I can see a working directory is created in the logs:
galaxy.jobs DEBUG 2014-06-12 08:21:03,786 (15) Working directory for job is: /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15

I've confirmed the directory is created by watching on the file system and within about two seconds of the folder being created it is deleted.
[root@admin 000]# watch -d ls -lR
Every 2.0s: ls -lR                                                                                                                      Thu Jun 12 08:21:06 2014
total 64
drwxrwxrwx 2 dcshrum dcshrum 4096 Jun 12 08:21 15


I see the job sent via DRMAA:
galaxy.jobs.handler DEBUG 2014-06-12 08:21:03,795 (15) Dispatching to drmaa runner
galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566 (15) submitting file /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh
galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566 (15) native specification is: -N galaxyjob -l nodes=1,walltime=2:00 -q genacc_q
galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,892 (15) submitting with credentials: dcshrum [uid: 232706]
galaxy.jobs.runners.drmaa INFO 2014-06-12 08:21:06,196 (15) queued as 7570705.moab.local

The job fails:
galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:06,698 (15/7570705.moab.local) state change: job finished, but failed
galaxy.jobs.runners DEBUG 2014-06-12 08:21:07,124 (15/7570705.moab.local) Unable to cleanup /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh: [Errno 2] No such file or directory: '/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh'


I can see the same error in my moab log:
*** error from copy
/bin/cp: cannot create regular file `/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.o': No such file or directory
*** end error output


Any idea as to why galaxy removes the working directory?  Is there a setting in the job_conf.xml that would resolve this?

Thanks for any pointers.

Donny
FSU Research Computing Center


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Re: jobs submitted to a cluster

Evan Bollig PhD
Hey Donny,

What is the value of keep_completed on your queue (from qmgr -c 'p
s')? Could it be that your spool is flushing completed jobs
immediately? I ran into issues the other day with libdrmaa requiring
at least keep_complete = 60 seconds to properly detect completed jobs
and clean up after itself.

Cheers,

-E


-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
[hidden email]
[hidden email]


On Thu, Jun 12, 2014 at 7:36 AM, Shrum, Donald C <[hidden email]> wrote:

> I've setup galaxy to submit jobs to our HPC cluster as the logged in user.  I used the drama python module to submit the jobs to our moab server.
>
> It appears that the working directory for a submitted job is being removed by galaxy prior to the job completing on the cluster.
>
> I can see a working directory is created in the logs:
> galaxy.jobs DEBUG 2014-06-12 08:21:03,786 (15) Working directory for job is: /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15
>
> I've confirmed the directory is created by watching on the file system and within about two seconds of the folder being created it is deleted.
> [root@admin 000]# watch -d ls -lR
> Every 2.0s: ls -lR                                                                                                                      Thu Jun 12 08:21:06 2014
> total 64
> drwxrwxrwx 2 dcshrum dcshrum 4096 Jun 12 08:21 15
>
>
> I see the job sent via DRMAA:
> galaxy.jobs.handler DEBUG 2014-06-12 08:21:03,795 (15) Dispatching to drmaa runner
> galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566 (15) submitting file /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh
> galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566 (15) native specification is: -N galaxyjob -l nodes=1,walltime=2:00 -q genacc_q
> galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,892 (15) submitting with credentials: dcshrum [uid: 232706]
> galaxy.jobs.runners.drmaa INFO 2014-06-12 08:21:06,196 (15) queued as 7570705.moab.local
>
> The job fails:
> galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:06,698 (15/7570705.moab.local) state change: job finished, but failed
> galaxy.jobs.runners DEBUG 2014-06-12 08:21:07,124 (15/7570705.moab.local) Unable to cleanup /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh: [Errno 2] No such file or directory: '/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh'
>
>
> I can see the same error in my moab log:
> *** error from copy
> /bin/cp: cannot create regular file `/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.o': No such file or directory
> *** end error output
>
>
> Any idea as to why galaxy removes the working directory?  Is there a setting in the job_conf.xml that would resolve this?
>
> Thanks for any pointers.
>
> Donny
> FSU Research Computing Center
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: jobs submitted to a cluster

Shrum, Donald C
It's set to 600 seconds so I don't think that is the issue... Is there some sort of wait time to set in job_conf.xml

-----Original Message-----
From: Evan Bollig [mailto:[hidden email]]
Sent: Thursday, June 12, 2014 9:27 AM
To: Shrum, Donald C
Cc: [hidden email]
Subject: Re: [galaxy-dev] jobs submitted to a cluster

Hey Donny,

What is the value of keep_completed on your queue (from qmgr -c 'p s')? Could it be that your spool is flushing completed jobs immediately? I ran into issues the other day with libdrmaa requiring at least keep_complete = 60 seconds to properly detect completed jobs and clean up after itself.

Cheers,

-E


-Evan Bollig
Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
[hidden email]
[hidden email]


On Thu, Jun 12, 2014 at 7:36 AM, Shrum, Donald C <[hidden email]> wrote:

> I've setup galaxy to submit jobs to our HPC cluster as the logged in user.  I used the drama python module to submit the jobs to our moab server.
>
> It appears that the working directory for a submitted job is being removed by galaxy prior to the job completing on the cluster.
>
> I can see a working directory is created in the logs:
> galaxy.jobs DEBUG 2014-06-12 08:21:03,786 (15) Working directory for
> job is:
> /panfs/storage.local/software/galaxy-dist/database/job_working_directo
> ry/000/15
>
> I've confirmed the directory is created by watching on the file system and within about two seconds of the folder being created it is deleted.
> [root@admin 000]# watch -d ls -lR
> Every 2.0s: ls -lR                                                                                                                      Thu Jun 12 08:21:06 2014
> total 64
> drwxrwxrwx 2 dcshrum dcshrum 4096 Jun 12 08:21 15
>
>
> I see the job sent via DRMAA:
> galaxy.jobs.handler DEBUG 2014-06-12 08:21:03,795 (15) Dispatching to
> drmaa runner galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566
> (15) submitting file
> /panfs/storage.local/software/galaxy-dist/database/job_working_directo
> ry/000/15/galaxy_15.sh galaxy.jobs.runners.drmaa DEBUG 2014-06-12
> 08:21:05,566 (15) native specification is: -N galaxyjob -l
> nodes=1,walltime=2:00 -q genacc_q galaxy.jobs.runners.drmaa DEBUG
> 2014-06-12 08:21:05,892 (15) submitting with credentials: dcshrum
> [uid: 232706] galaxy.jobs.runners.drmaa INFO 2014-06-12 08:21:06,196
> (15) queued as 7570705.moab.local
>
> The job fails:
> galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:06,698
> (15/7570705.moab.local) state change: job finished, but failed galaxy.jobs.runners DEBUG 2014-06-12 08:21:07,124 (15/7570705.moab.local) Unable to cleanup /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh: [Errno 2] No such file or directory: '/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh'
>
>
> I can see the same error in my moab log:
> *** error from copy
> /bin/cp: cannot create regular file
> `/panfs/storage.local/software/galaxy-dist/database/job_working_direct
> ory/000/15/galaxy_15.o': No such file or directory
> *** end error output
>
>
> Any idea as to why galaxy removes the working directory?  Is there a setting in the job_conf.xml that would resolve this?
>
> Thanks for any pointers.
>
> Donny
> FSU Research Computing Center
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: jobs submitted to a cluster

Evan Bollig PhD
job_conf.xml is outside of my knowledge. Better wait to see what the
others can tell us.

-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
[hidden email]
[hidden email]


On Thu, Jun 12, 2014 at 8:31 AM, Shrum, Donald C <[hidden email]> wrote:

> It's set to 600 seconds so I don't think that is the issue... Is there some sort of wait time to set in job_conf.xml
>
> -----Original Message-----
> From: Evan Bollig [mailto:[hidden email]]
> Sent: Thursday, June 12, 2014 9:27 AM
> To: Shrum, Donald C
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] jobs submitted to a cluster
>
> Hey Donny,
>
> What is the value of keep_completed on your queue (from qmgr -c 'p s')? Could it be that your spool is flushing completed jobs immediately? I ran into issues the other day with libdrmaa requiring at least keep_complete = 60 seconds to properly detect completed jobs and clean up after itself.
>
> Cheers,
>
> -E
>
>
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> [hidden email]
> [hidden email]
>
>
> On Thu, Jun 12, 2014 at 7:36 AM, Shrum, Donald C <[hidden email]> wrote:
>> I've setup galaxy to submit jobs to our HPC cluster as the logged in user.  I used the drama python module to submit the jobs to our moab server.
>>
>> It appears that the working directory for a submitted job is being removed by galaxy prior to the job completing on the cluster.
>>
>> I can see a working directory is created in the logs:
>> galaxy.jobs DEBUG 2014-06-12 08:21:03,786 (15) Working directory for
>> job is:
>> /panfs/storage.local/software/galaxy-dist/database/job_working_directo
>> ry/000/15
>>
>> I've confirmed the directory is created by watching on the file system and within about two seconds of the folder being created it is deleted.
>> [root@admin 000]# watch -d ls -lR
>> Every 2.0s: ls -lR                                                                                                                      Thu Jun 12 08:21:06 2014
>> total 64
>> drwxrwxrwx 2 dcshrum dcshrum 4096 Jun 12 08:21 15
>>
>>
>> I see the job sent via DRMAA:
>> galaxy.jobs.handler DEBUG 2014-06-12 08:21:03,795 (15) Dispatching to
>> drmaa runner galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566
>> (15) submitting file
>> /panfs/storage.local/software/galaxy-dist/database/job_working_directo
>> ry/000/15/galaxy_15.sh galaxy.jobs.runners.drmaa DEBUG 2014-06-12
>> 08:21:05,566 (15) native specification is: -N galaxyjob -l
>> nodes=1,walltime=2:00 -q genacc_q galaxy.jobs.runners.drmaa DEBUG
>> 2014-06-12 08:21:05,892 (15) submitting with credentials: dcshrum
>> [uid: 232706] galaxy.jobs.runners.drmaa INFO 2014-06-12 08:21:06,196
>> (15) queued as 7570705.moab.local
>>
>> The job fails:
>> galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:06,698
>> (15/7570705.moab.local) state change: job finished, but failed galaxy.jobs.runners DEBUG 2014-06-12 08:21:07,124 (15/7570705.moab.local) Unable to cleanup /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh: [Errno 2] No such file or directory: '/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh'
>>
>>
>> I can see the same error in my moab log:
>> *** error from copy
>> /bin/cp: cannot create regular file
>> `/panfs/storage.local/software/galaxy-dist/database/job_working_direct
>> ory/000/15/galaxy_15.o': No such file or directory
>> *** end error output
>>
>>
>> Any idea as to why galaxy removes the working directory?  Is there a setting in the job_conf.xml that would resolve this?
>>
>> Thanks for any pointers.
>>
>> Donny
>> FSU Research Computing Center
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this and other
>> Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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Re: jobs submitted to a cluster

John Chilton-4
My guess is Galaxy is deleting the directory because it believe the
job is in error because of some communication problem while polling
your DRM via DRMAA - Galaxy thinks the job has failed before it has
even been run.

You can set

cleanup_job = never

in universe_wsgi.ini's app:main section to instruct Galaxy to not
delete the working directory. I suspect this will allow the DRM to
finish running your job - but Galaxy is still going to fail it since
it cannot properly detect its status.

Can you confirm?

-John






On Thu, Jun 12, 2014 at 8:36 AM, Evan Bollig <[hidden email]> wrote:

> job_conf.xml is outside of my knowledge. Better wait to see what the
> others can tell us.
>
> -E
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant
> Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> [hidden email]
> [hidden email]
>
>
> On Thu, Jun 12, 2014 at 8:31 AM, Shrum, Donald C <[hidden email]> wrote:
>> It's set to 600 seconds so I don't think that is the issue... Is there some sort of wait time to set in job_conf.xml
>>
>> -----Original Message-----
>> From: Evan Bollig [mailto:[hidden email]]
>> Sent: Thursday, June 12, 2014 9:27 AM
>> To: Shrum, Donald C
>> Cc: [hidden email]
>> Subject: Re: [galaxy-dev] jobs submitted to a cluster
>>
>> Hey Donny,
>>
>> What is the value of keep_completed on your queue (from qmgr -c 'p s')? Could it be that your spool is flushing completed jobs immediately? I ran into issues the other day with libdrmaa requiring at least keep_complete = 60 seconds to properly detect completed jobs and clean up after itself.
>>
>> Cheers,
>>
>> -E
>>
>>
>> -Evan Bollig
>> Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute
>> 599 Walter Library
>> 612 624 1447
>> [hidden email]
>> [hidden email]
>>
>>
>> On Thu, Jun 12, 2014 at 7:36 AM, Shrum, Donald C <[hidden email]> wrote:
>>> I've setup galaxy to submit jobs to our HPC cluster as the logged in user.  I used the drama python module to submit the jobs to our moab server.
>>>
>>> It appears that the working directory for a submitted job is being removed by galaxy prior to the job completing on the cluster.
>>>
>>> I can see a working directory is created in the logs:
>>> galaxy.jobs DEBUG 2014-06-12 08:21:03,786 (15) Working directory for
>>> job is:
>>> /panfs/storage.local/software/galaxy-dist/database/job_working_directo
>>> ry/000/15
>>>
>>> I've confirmed the directory is created by watching on the file system and within about two seconds of the folder being created it is deleted.
>>> [root@admin 000]# watch -d ls -lR
>>> Every 2.0s: ls -lR                                                                                                                      Thu Jun 12 08:21:06 2014
>>> total 64
>>> drwxrwxrwx 2 dcshrum dcshrum 4096 Jun 12 08:21 15
>>>
>>>
>>> I see the job sent via DRMAA:
>>> galaxy.jobs.handler DEBUG 2014-06-12 08:21:03,795 (15) Dispatching to
>>> drmaa runner galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566
>>> (15) submitting file
>>> /panfs/storage.local/software/galaxy-dist/database/job_working_directo
>>> ry/000/15/galaxy_15.sh galaxy.jobs.runners.drmaa DEBUG 2014-06-12
>>> 08:21:05,566 (15) native specification is: -N galaxyjob -l
>>> nodes=1,walltime=2:00 -q genacc_q galaxy.jobs.runners.drmaa DEBUG
>>> 2014-06-12 08:21:05,892 (15) submitting with credentials: dcshrum
>>> [uid: 232706] galaxy.jobs.runners.drmaa INFO 2014-06-12 08:21:06,196
>>> (15) queued as 7570705.moab.local
>>>
>>> The job fails:
>>> galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:06,698
>>> (15/7570705.moab.local) state change: job finished, but failed galaxy.jobs.runners DEBUG 2014-06-12 08:21:07,124 (15/7570705.moab.local) Unable to cleanup /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh: [Errno 2] No such file or directory: '/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh'
>>>
>>>
>>> I can see the same error in my moab log:
>>> *** error from copy
>>> /bin/cp: cannot create regular file
>>> `/panfs/storage.local/software/galaxy-dist/database/job_working_direct
>>> ory/000/15/galaxy_15.o': No such file or directory
>>> *** end error output
>>>
>>>
>>> Any idea as to why galaxy removes the working directory?  Is there a setting in the job_conf.xml that would resolve this?
>>>
>>> Thanks for any pointers.
>>>
>>> Donny
>>> FSU Research Computing Center
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this and other
>>> Galaxy lists, please use the interface at:
>>>   http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: jobs submitted to a cluster

Shrum, Donald C
Hi John,

That did the trick.  I have some other problem but I don't think it's galaxy from here.

Thanks again for the reply.

Donny

-----Original Message-----
From: John Chilton [mailto:[hidden email]]
Sent: Thursday, June 12, 2014 10:53 AM
To: Evan Bollig
Cc: Shrum, Donald C; [hidden email]
Subject: Re: [galaxy-dev] jobs submitted to a cluster

My guess is Galaxy is deleting the directory because it believe the job is in error because of some communication problem while polling your DRM via DRMAA - Galaxy thinks the job has failed before it has even been run.

You can set

cleanup_job = never

in universe_wsgi.ini's app:main section to instruct Galaxy to not delete the working directory. I suspect this will allow the DRM to finish running your job - but Galaxy is still going to fail it since it cannot properly detect its status.

Can you confirm?

-John






On Thu, Jun 12, 2014 at 8:36 AM, Evan Bollig <[hidden email]> wrote:

> job_conf.xml is outside of my knowledge. Better wait to see what the
> others can tell us.
>
> -E
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant
> Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> [hidden email]
> [hidden email]
>
>
> On Thu, Jun 12, 2014 at 8:31 AM, Shrum, Donald C <[hidden email]> wrote:
>> It's set to 600 seconds so I don't think that is the issue... Is
>> there some sort of wait time to set in job_conf.xml
>>
>> -----Original Message-----
>> From: Evan Bollig [mailto:[hidden email]]
>> Sent: Thursday, June 12, 2014 9:27 AM
>> To: Shrum, Donald C
>> Cc: [hidden email]
>> Subject: Re: [galaxy-dev] jobs submitted to a cluster
>>
>> Hey Donny,
>>
>> What is the value of keep_completed on your queue (from qmgr -c 'p s')? Could it be that your spool is flushing completed jobs immediately? I ran into issues the other day with libdrmaa requiring at least keep_complete = 60 seconds to properly detect completed jobs and clean up after itself.
>>
>> Cheers,
>>
>> -E
>>
>>
>> -Evan Bollig
>> Research Associate | Application Developer | User Support Consultant
>> Minnesota Supercomputing Institute
>> 599 Walter Library
>> 612 624 1447
>> [hidden email]
>> [hidden email]
>>
>>
>> On Thu, Jun 12, 2014 at 7:36 AM, Shrum, Donald C <[hidden email]> wrote:
>>> I've setup galaxy to submit jobs to our HPC cluster as the logged in user.  I used the drama python module to submit the jobs to our moab server.
>>>
>>> It appears that the working directory for a submitted job is being removed by galaxy prior to the job completing on the cluster.
>>>
>>> I can see a working directory is created in the logs:
>>> galaxy.jobs DEBUG 2014-06-12 08:21:03,786 (15) Working directory for
>>> job is:
>>> /panfs/storage.local/software/galaxy-dist/database/job_working_direc
>>> to
>>> ry/000/15
>>>
>>> I've confirmed the directory is created by watching on the file system and within about two seconds of the folder being created it is deleted.
>>> [root@admin 000]# watch -d ls -lR
>>> Every 2.0s: ls -lR                                                                                                                      Thu Jun 12 08:21:06 2014
>>> total 64
>>> drwxrwxrwx 2 dcshrum dcshrum 4096 Jun 12 08:21 15
>>>
>>>
>>> I see the job sent via DRMAA:
>>> galaxy.jobs.handler DEBUG 2014-06-12 08:21:03,795 (15) Dispatching
>>> to drmaa runner galaxy.jobs.runners.drmaa DEBUG 2014-06-12
>>> 08:21:05,566
>>> (15) submitting file
>>> /panfs/storage.local/software/galaxy-dist/database/job_working_direc
>>> to ry/000/15/galaxy_15.sh galaxy.jobs.runners.drmaa DEBUG 2014-06-12
>>> 08:21:05,566 (15) native specification is: -N galaxyjob -l
>>> nodes=1,walltime=2:00 -q genacc_q galaxy.jobs.runners.drmaa DEBUG
>>> 2014-06-12 08:21:05,892 (15) submitting with credentials: dcshrum
>>> [uid: 232706] galaxy.jobs.runners.drmaa INFO 2014-06-12 08:21:06,196
>>> (15) queued as 7570705.moab.local
>>>
>>> The job fails:
>>> galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:06,698
>>> (15/7570705.moab.local) state change: job finished, but failed galaxy.jobs.runners DEBUG 2014-06-12 08:21:07,124 (15/7570705.moab.local) Unable to cleanup /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh: [Errno 2] No such file or directory: '/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh'
>>>
>>>
>>> I can see the same error in my moab log:
>>> *** error from copy
>>> /bin/cp: cannot create regular file
>>> `/panfs/storage.local/software/galaxy-dist/database/job_working_dire
>>> ct
>>> ory/000/15/galaxy_15.o': No such file or directory
>>> *** end error output
>>>
>>>
>>> Any idea as to why galaxy removes the working directory?  Is there a setting in the job_conf.xml that would resolve this?
>>>
>>> Thanks for any pointers.
>>>
>>> Donny
>>> FSU Research Computing Center
>>>
>>>
>>> ___________________________________________________________
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>>
>>
>> ___________________________________________________________
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>
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