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From "Pierce, Marlon" <marpi...@iu.edu>
Subject Re: Adding a SGE resourceJobManagerType
Date Wed, 24 Feb 2016 21:15:36 GMT
Hi Eric, did this work for you?

From: Suresh Marru <smarru@apache.org<mailto:smarru@apache.org>>
Reply-To: "dev@airavata.apache.org<mailto:dev@airavata.apache.org>" <dev@airavata.apache.org<mailto:dev@airavata.apache.org>>
Date: Wednesday, February 24, 2016 at 10:30 AM
To: Airavata Dev <dev@airavata.apache.org<mailto:dev@airavata.apache.org>>
Subject: Re: Adding a SGE resourceJobManagerType

SGE - Sun Grid Engine is the old variant of Univa Grid Engine, so you should pick UGE in Airavata
and should be good to go. SGE/UGE implement PBS protocol so parsing should be similar. Lonestar4
used to have UGE, so email parsing should be similar to that.

Suresh


On Feb 24, 2016, at 10:17 AM, Shameera Rathnayaka <shameerainfo@gmail.com<mailto: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


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Central Veterinary Institute of Wageningen UR (CVI)
Department of Infection Biology
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Shameera Rathnayaka

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