condor compute cluster

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condor compute cluster

Shrum, Donald C
Our galaxy server has an apache front end with ldap authentication.  

I've added a condor destination...
<plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner"/>
<destination id="condor" runner="condor"/>

There are some tools I'd like to point to condor but it appears all the jobs will be sent as the user condor.

Is there an existing fix that will submit jobs to our condor cluster as the logged in user?

If not could someone give me a small pointer for a hack fix?
Something along the lines of:

galaxy-dist/lib/galaxy/jobs/runners/util/condor/__init__.py

line 71:
submit = Popen(('condor_submit', submit_file), stdout=PIPE, stderr=STDOUT)

Could be changed to sudo -u xxx -c condor_submit...

Thanks all,
Don
FSU Research Computing Center


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Re: condor compute cluster

John Chilton-4
Jobs run as the condor user? That is surprising - Galaxy isn't running
as the condor user is it?

Is your intention to have the jobs run as the 'galaxy' user or to run
as the LDAP authenticated end-user submitting the job?

If it is to run as the Galaxy user - I think it would be best to have
condor reconfigured to run jobs as the submitting user (in this case
galaxy) - at most institutions that is the way these things are
usually configured.

If you would like to run the jobs as the actual LDAP authenticated
user - that is going to require a somewhat significant development
effort. In that case I would look at the drmaa runner and what it is
doing to run jobs as the actual user and try to do similar things in
the condor runner - I don't think it would be a couple lines of
hacking.

condor has a DRMAA interface - I have never heard of it being used
with Galaxy but that might be something worth trying as well. If you
can get that to work - you should be able to use the drmaa run as real
user mode.

-John


On Wed, Aug 6, 2014 at 4:40 PM, Shrum, Donald C <[hidden email]> wrote:

> Our galaxy server has an apache front end with ldap authentication.
>
> I've added a condor destination...
> <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner"/>
> <destination id="condor" runner="condor"/>
>
> There are some tools I'd like to point to condor but it appears all the jobs will be sent as the user condor.
>
> Is there an existing fix that will submit jobs to our condor cluster as the logged in user?
>
> If not could someone give me a small pointer for a hack fix?
> Something along the lines of:
>
> galaxy-dist/lib/galaxy/jobs/runners/util/condor/__init__.py
>
> line 71:
> submit = Popen(('condor_submit', submit_file), stdout=PIPE, stderr=STDOUT)
>
> Could be changed to sudo -u xxx -c condor_submit...
>
> Thanks all,
> Don
> 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/