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From Eric Kuyt <eric.ku...@wur.nl>
Subject Re: Adding a SGE resourceJobManagerType
Date Fri, 26 Feb 2016 15:52:25 GMT
Hey All,

I'm almost there! Ran the three steps (Only difference with UGE is -pe in
the xslt file to build the pbs) so I use the UGE parse/config classes. Love
thrift btw!

But now, when I run My newly generated SGE it seems not to find the xslt
file...

error message is.

/home/path/to/apache-airavata-server-0.16-SNAPSHOT/bin/file:/home/path/to/
!/SGETemplate.xslt (No such file or directory)

airavata-gfac-impl-0.16-SNAPSHOT.jar, seems to contain the xslt.

jar -tf lib/airavata-gfac-impl-0.16-SNAPSHOT.jar  |grep Template
SGETemplate.xslt
PBSTemplate.xslt
UGETemplate.xslt
SLURMTemplate.xslt
ForkTemplate.xslt
LSFTemplate.xslt


The path seems to be printed double, Could this be the problem? PBS doesn't
seem to have this problem.

Thanks!

Eric

On 24 February 2016 at 16:17, Shameera Rathnayaka <shameerainfo@gmail.com>
wrote:

> Hi Eric,
>
> There are couple of things you need to do to add a new jobmanager type.
>
> 1. Configure your SGE resource type in gfac yaml config file
> (airavata/modules/configuration/server/src/main/resources/gfac-config.yaml.config).
> As you can see you need to provide an output parser and email parser for
> your SGE, Unless you can't use existing implementations you need to come up
> with your own implementations of these interfaces.
>
> 2. Don't modify thrift generated file, instead add your new
> ResourceJobManagerType to
> airavata/thrift-interface-descriptions/data-models/resource-catalog-models/compute_resource_model.thrift
> file and generate thrift classes.
>
> 3. Come up with SGE JobConfiguration class, and modify
> org.apache.airavata.gfac.impl.Factory#getJobManagerConfiguration method to
> provide it. You should have xslt template for your SGE script file.
>
> let us know if you hit any issue while you following these steps.
>
> Thanks,
> Shameera.
>
> On Wed, Feb 24, 2016 at 9:53 AM Chathuri Wimalasena <kamalasini@gmail.com
> <mailto:kamalasini@gmail.com>> wrote:
> Hi Eric,
>
> To understand what you did, you added a new ResourceJobManagerType in the
> thrift definition as "SGE" ? I assume you generate thrift stubs after
> adding it.  For that, you need to have thrift 0.93 installed in your system.
>
> Thanks..
> Chathuri
>
> On Wed, Feb 24, 2016 at 9:03 AM, Eric Kuyt <eric.kuijt@wur.nl<mailto:
> eric.kuijt@wur.nl>> wrote:
> Hey all, I am playing around with airavata and when I can run jobs on my
> SGE using PBS but the parsing of qsub / qstat fails. So my jobs never leave
> the Executing state.
>
> Now I try to make my own SGEJobConfiguration class.
> Created the class plus outputParser in org.apache.airavata.gfac.impl.job
>
> - add SGE in
> /airavata-gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
>
> - add SGE in
> /airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/ResourceJobManagerType.java
>
> - add SGE to
> airavata-php-gateway/app/libraries/Airavata/Model/Job/Types.php in PGA.
>
> What should the next step be? if I Wanted to create my own SGEOutputparser?
> PGA now gives me a Required field 'resourceJobManagerType' is unset! when
> I select SGE in the list.
>
> Thanks,
>
> Eric
>
>
> --
> Central Veterinary Institute of Wageningen UR (CVI)
> Department of Infection Biology
> PO box 65, 8200 AB Lelystad, NL
> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>
> Tel:  +31-(0)320-293391
> Fax: +31-(0)320-238153
> E-mail: eric.kuijt@wur.nl<mailto:eric.kuijt@wur.nl>
> Web: http://www.cvi.wur.nl
>
> --
> Shameera Rathnayaka
>



-- 
Central Veterinary Institute of Wageningen UR (CVI)
Department of Infection Biology
PO box 65, 8200 AB Lelystad, NL
Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

Tel:  +31-(0)320-293391
Fax: +31-(0)320-238153
E-mail: eric.kuijt@wur.nl
Web: http://www.cvi.wur.nl

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