Re: [Opaltoolkit-users] Opal job scheduler benefits

[nadya w. <na...@sd...>]

Hi Guillermo,

there are a few issues here. 
On Feb 28, 2013, at 12:47 AM, Guillermo Marco Puche wrote:

> Hello Luca,
> 
> I currently can't run Opal jobs with Condor job scheduler:
> 
> Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
> I know it has empty parameters but it's for testing purposes at this moment. All parameters and flags are run in a shell script invoked by condor job file.
your xml file is not correct. You are using your condor.submit file  in place of an executable:
<binaryLocation>/opt/web/opal_scripts/bwa/bwa.condor</binaryLocation>
Instead, here you need to use your /opt/web/opal_scripts/bwa/bwa.sh 
and any other parameters from which opal will make condor_submit file.  Opal v 2.5 has condor.expr.file
variable in opal.properties file:
# Enable if there are server-specific condor expressions. Put expressions in the file
#condor.expr.file=/opt/opal/etc/condor.expr

This is a file  (condor submit syntax) that needs to be used to tell opal to add extra parameters  to every submit file that is generated. 
This allows for server-side specific variables to be added.  

> 
> I want opal to execute my bwa.condor file (condor job file) which currently works with condor_submit command but not with Opal.
this is not going to happen using your current xml file. The way condor+opal work is opal generates condor submit file
from the parameters given in xml file. You have a universe that we did not test with condor before. 
Currently, opal+condor is working with  vanila or parallel universe only.  

You can use a workaround:  

I suggest you try to make a wrapper script and use it in <binaryLocation> in xml file. 
In you xml file add properties like
(1)	 condor submit file (untagged parameter for upload of  the submit file) as
          <param>
                <id>submitFile</id>
                <paramType>FILE</paramType>
                <ioType>INPUT</ioType>
                <required>true</required>
                <textDesc>upload a condor submit file </textDesc>
            </param>

(2)  use  Fork Job Manager   as  <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>
(3)  use  <parallel>false</parallel>

please see apbs_parallel_1.3.xml  in the opal distro for an example. 
Your wrapper script need to understand that it supposed to look for a submit file (check for presence) 
 and then  condor submission via "condor_submit yourfile"

This way you will have a flexibility to create "any"  submit file and use any universe  and other specifics of the 
condor submission that we currently don't handle for simple cases. 

Regards,
Nadya


> 
> Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
> And here the bwa.sh invoked by bwa.condor to be executed on remote cluster: http://pastebin.com/dWzQa92E
> 
> Best regards,
> Guillermo.
> 
> 
> On 02/27/2013 11:17 PM, Luca Clementi wrote:
>> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
>> <gui...@si...> wrote:
>>> Hello,
>>> 
>>> I would like to know what are the benefits/extras of using Condor
>>> job.scheduler with Opal.
>> The jobs you submit to Opal will be executed using Condor.
>> Opal simply gives you a web service interface and then it has
>> different back-end to actually execute your jobs (condor, sge, pbs,
>> etc.).
>> 
>>> What's the difference between job scheduler and submitting jobs to Condor
>>> straight with condor_submit?
>> you mean the difference between using Opal vs using condor_submit?
>> If you use Opal you can invoke the lanuchJob operation using
>> web-service standard (we provide python and java client side
>> libraries).
>> If you use condor you have to ssh to a machine (aka have an account)
>> and then you need to create a submission script and execute
>> condor_submit.
>> 
>> 
>> In NBCR We use Opal to submit job from web portal (where you have 1
>> user the web portal which is in charge of running different simulation
>> and opal takes care of creating working directories staging input and
>> outputs etc.).
>> 
>> 
>> Luca
> 
> 
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Nadya Williams                 University of California, San Diego
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