runDistributedCommand into iterable component.

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runDistributedCommand into iterable component.

Celine Noirot
Hi Ergatis team,
I tried to change SGE parameters in an iterable component.
But I found a problem, if I set an runDistributedCommand into an
iterator component, I never get the end of the the runDistributedCommand.
Have you ever seen it ?
Thank
Céline
--

Céline Noirot
Plateforme Bioinfo Genotoul- Unité BIA - INRA Toulouse 31326 Castanet-Tolosan
Tel. 05 61 28 57 24
http://bioinfo.genotoul.fr


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Re: runDistributedCommand into iterable component.

Mahurkar, Anup
Celine,

I am not sure I am following completely what you are trying to do. Could you add a little more detail and maybe even attach samples?

Thanks,
Anup

-----Original Message-----
From: Celine Noirot [mailto:[hidden email]]
Sent: Thursday, March 22, 2012 4:17 AM
To: [hidden email]
Subject: [Ergatis-users] runDistributedCommand into iterable component.

Hi Ergatis team,
I tried to change SGE parameters in an iterable component.
But I found a problem, if I set an runDistributedCommand into an iterator component, I never get the end of the the runDistributedCommand.
Have you ever seen it ?
Thank
Céline
--

Céline Noirot
Plateforme Bioinfo Genotoul- Unité BIA - INRA Toulouse 31326 Castanet-Tolosan Tel. 05 61 28 57 24 http://bioinfo.genotoul.fr


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Re: runDistributedCommand into iterable component.

Celine Noirot
In reply to this post by Celine Noirot
For better understanding, here is an example

<commandSetRoot xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation='commandSet.xsd'>
     <commandSet type="serial">
         <name>iterable_blast_compute</name>
         <command>
             <type>RunDistributedCommand</type>
             <name>blast</name>
             <state>incomplete</state>
             <executable>$;BLASTALL_EXEC$;</executable>
             <arg>  -p $;BLASTALL_PROGRAM$; -i $;I_FILE_PATH$; -d $;LIST_ELT$; -e $;EXPECT$; -F $;FILTER$; -b $;DATABASE_MATCHES$; -v $;DESCRIPTIONS$; $;OTHER_OPTS$;</arg>
             <param>
                 <key>stdout</key>
                 <value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.$;LIST_ELT_NAME$;.blast</value>
                </param>
             <param>
                 <key>stderr</key>
                 <value>$;TMP_DIR$;/$;I_FILE_BASE$;.$;COMPONENT_NAME$;.$;LIST_ELT_NAME$;.blast.stderr</value>
             </param>
         </command>
     </commandSet>
</commandSetRoot>

the blast is launch as a DistributedCommand, when it's finished in the
cluster, the "iterable_blast_compute" component do not see that the
rundistributed command is finished.
Yours sincerely
Céline
Le 22/03/2012 09:16, Celine Noirot a écrit :
> Hi Ergatis team,
> I tried to change SGE parameters in an iterable component.
> But I found a problem, if I set an runDistributedCommand into an
> iterator component, I never get the end of the the runDistributedCommand.
> Have you ever seen it ?
> Thank
> Céline


--

Céline Noirot
Plateforme Bioinfo Genotoul- Unité BIA - INRA Toulouse 31326 Castanet-Tolosan
Tel. 05 61 28 57 24
http://bioinfo.genotoul.fr


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Re: runDistributedCommand into iterable component.

Mahurkar, Anup
Celine,

Try marking your command set as distributed-parallel or
distributed-serial. It should accomplish what you are looking to do. The
command itself should be marked as RunUnixCommand.

Anup

On 3/22/12 9:02 AM, "Celine Noirot" <[hidden email]> wrote:

>For better understanding, here is an example
>
><commandSetRoot xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
>xsi:schemaLocation='commandSet.xsd'>
>     <commandSet type="serial">
>         <name>iterable_blast_compute</name>
>         <command>
>             <type>RunDistributedCommand</type>
>             <name>blast</name>
>             <state>incomplete</state>
>             <executable>$;BLASTALL_EXEC$;</executable>
>             <arg>  -p $;BLASTALL_PROGRAM$; -i $;I_FILE_PATH$; -d
>$;LIST_ELT$; -e $;EXPECT$; -F $;FILTER$; -b $;DATABASE_MATCHES$; -v
>$;DESCRIPTIONS$; $;OTHER_OPTS$;</arg>
>             <param>
>                 <key>stdout</key>
>                
><value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_B
>ASE$;.$;LIST_ELT_NAME$;.blast</value>
> </param>
>             <param>
>                 <key>stderr</key>
>                
><value>$;TMP_DIR$;/$;I_FILE_BASE$;.$;COMPONENT_NAME$;.$;LIST_ELT_NAME$;.bl
>ast.stderr</value>
>             </param>
>         </command>
>     </commandSet>
></commandSetRoot>
>
>the blast is launch as a DistributedCommand, when it's finished in the
>cluster, the "iterable_blast_compute" component do not see that the
>rundistributed command is finished.
>Yours sincerely
>Céline
>Le 22/03/2012 09:16, Celine Noirot a écrit :
>> Hi Ergatis team,
>> I tried to change SGE parameters in an iterable component.
>> But I found a problem, if I set an runDistributedCommand into an
>> iterator component, I never get the end of the the
>>runDistributedCommand.
>> Have you ever seen it ?
>> Thank
>> Céline
>
>
>--
>
>Céline Noirot
>Plateforme Bioinfo Genotoul- Unité BIA - INRA Toulouse 31326
>Castanet-Tolosan
>Tel. 05 61 28 57 24
>http://bioinfo.genotoul.fr
>
>
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>Try Windows Azure free for 90 days Click Here
>http://p.sf.net/sfu/sfd2d-msazure
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