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From Chathuri Wimalasena <kamalas...@gmail.com>
Subject Re: Adding a SGE resourceJobManagerType
Date Fri, 26 Feb 2016 16:00:58 GMT
Hi Eric,

You need to add your XSLT file in
airavata/distribution/src/main/assembly/bin-assembly.xml. Otherwise it will
not be added to bin directory.

<fileSet>
<directory>${project.build.directory}/conf</directory>
<outputDirectory>bin</outputDirectory>
<includes>
<include>airavata-server.properties</include>
<include>zoo.cfg</include>
<include>registry.properties</include>
<include>log4j.properties</include>
<include>host.xml</include>
<include>persistence.xml</include>
<include>provenance.sql</include>
<include>gfac-config.yaml</include>
<include>PBSTemplate.xslt</include>
<include>SLURMTemplate.xslt</include>
<include>LSFTemplate.xslt</include>
<include>UGETemplate.xslt</include>
<include>ForkTemplate.xslt</include>
<include>gsissh.properties</include>
<include>airavata.jks</include>
<include>client_truststore.jks</include>
<include>airavata-default-xacml-policy.xml</include>
</includes>
</fileSet>

Thanks..
Chathuri

On Fri, Feb 26, 2016 at 10:56 AM, Pierce, Marlon <marpierc@iu.edu> wrote:

> Hi Eric, is the path "/home/path/to/“ in your message below a verbatim
> error message, or did you change to remove your specific path?
>
> From: Eric Kuyt <eric.kuijt@wur.nl>
> Reply-To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> Date: Friday, February 26, 2016 at 10:52 AM
> To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> Subject: Re: Adding a SGE resourceJobManagerType
>
> 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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