Setting a local instance of Ergatis

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Setting a local instance of Ergatis

Mariette
Hi,
I'm trying to set Ergatis as a local instance, outside our cluster. I
basicly set the option grid_enabled at 0
But all pipelines failed (which used to work on a cluster) with the
following error at the iterator i1 stage :


workflow command id: 4426925
state: failed
start time: Mon Sep 13 18:18:07 2010
end time: Mon Sep 13 18:18:09 2010
duration: 2 sec
grid id: 0
workflow grid id: 4426928
workflow event log: ?
<http://vm-bioinfo-dev.toulouse.inra.fr/ergatis/cgi/view_formatted_log_source.cgi?file=?>

remote wf stderr/sdout
:/mnt/wf-working/RunWorkflow.o0,/mnt/wf-working/RunWorkflow.e0
prolog/epilog stderr/stdout /home/guest/staging.*,home/guest/harvesting.*
xml:
/work/ng6/ergatis_dev/workflow/runtime/config_run/1_default/i1/g1/g1.xml.gz
<http://vm-bioinfo-dev.toulouse.inra.fr/ergatis/cgi/view_formatted_xml_source.cgi?file=/work/ng6/ergatis_dev/workflow/runtime/config_run/1_default/i1/g1/g1.xml.gz>




the event log is not assigned, did I missed something in the
configuration ? Or is ergatis not able to run
iterable componant outside a cluster environment ?

thanks for your reply,
Jerome


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Re: Setting a local instance of Ergatis

Joshua Orvis
Jerome -

Are the links provided in your e-mail meant to be accessible outside of your network?

Ergatis certainly is able to run iterative components without a cluster/grid, and you setting the grid_enabled option to 0 was the correct thing to do.  Normally the steps in an iterative component will be submited as remote jobs and executed in parallel, but when you build a pipeline with grid_enabled=0 it transforms that to a serial set of local jobs instead.

Joshua




On Mon, Sep 13, 2010 at 11:27 AM, Mariette <[hidden email]> wrote:
Hi,
I'm trying to set Ergatis as a local instance, outside our cluster. I
basicly set the option grid_enabled at 0
But all pipelines failed (which used to work on a cluster) with the
following error at the iterator i1 stage :


workflow command id:    4426925
state:  failed
start time:     Mon Sep 13 18:18:07 2010
end time:       Mon Sep 13 18:18:09 2010
duration:       2 sec
grid id:        0
workflow grid id:       4426928
workflow event log:     ?
<http://vm-bioinfo-dev.toulouse.inra.fr/ergatis/cgi/view_formatted_log_source.cgi?file=?>

remote wf stderr/sdout
:/mnt/wf-working/RunWorkflow.o0,/mnt/wf-working/RunWorkflow.e0
prolog/epilog stderr/stdout     /home/guest/staging.*,home/guest/harvesting.*
xml:
/work/ng6/ergatis_dev/workflow/runtime/config_run/1_default/i1/g1/g1.xml.gz
<http://vm-bioinfo-dev.toulouse.inra.fr/ergatis/cgi/view_formatted_xml_source.cgi?file=/work/ng6/ergatis_dev/workflow/runtime/config_run/1_default/i1/g1/g1.xml.gz>




the event log is not assigned, did I missed something in the
configuration ? Or is ergatis not able to run
iterable componant outside a cluster environment ?

thanks for your reply,
Jerome


------------------------------------------------------------------------------
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and start using them to simplify application deployment and
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Re: Setting a local instance of Ergatis

Mariette

No the links are not meant to be accessible ...

The fact is that I have cloned the virtual machine with ergatis  
working using the cluster and I only changed the grid_enabled at 0  
option.

Did you have already seen this problem ?
Is it normal that the event log value is unset ?
workflow event log:     ?

There are specials options to set when working out of a cluster ?

thanks for your reply,
Jerome





Joshua Orvis <[hidden email]> a écrit :

> Jerome -
>
> Are the links provided in your e-mail meant to be accessible outside of your
> network?
>
> Ergatis certainly is able to run iterative components without a
> cluster/grid, and you setting the grid_enabled option to 0 was the correct
> thing to do.  Normally the steps in an iterative component will be submited
> as remote jobs and executed in parallel, but when you build a pipeline with
> grid_enabled=0 it transforms that to a serial set of local jobs instead.
>
> Joshua
>
>
>
>
> On Mon, Sep 13, 2010 at 11:27 AM, Mariette <[hidden email]>wrote:
>
>> Hi,
>> I'm trying to set Ergatis as a local instance, outside our cluster. I
>> basicly set the option grid_enabled at 0
>> But all pipelines failed (which used to work on a cluster) with the
>> following error at the iterator i1 stage :
>>
>>
>> workflow command id:    4426925
>> state:  failed
>> start time:     Mon Sep 13 18:18:07 2010
>> end time:       Mon Sep 13 18:18:09 2010
>> duration:       2 sec
>> grid id:        0
>> workflow grid id:       4426928
>> workflow event log:     ?
>> <
>> http://vm-bioinfo-dev.toulouse.inra.fr/ergatis/cgi/view_formatted_log_source.cgi?file=
>> ?>
>>
>> remote wf stderr/sdout
>> :/mnt/wf-working/RunWorkflow.o0,/mnt/wf-working/RunWorkflow.e0
>> prolog/epilog stderr/stdout
>> /home/guest/staging.*,home/guest/harvesting.*
>> xml:
>> /work/ng6/ergatis_dev/workflow/runtime/config_run/1_default/i1/g1/g1.xml.gz
>> <
>> http://vm-bioinfo-dev.toulouse.inra.fr/ergatis/cgi/view_formatted_xml_source.cgi?file=/work/ng6/ergatis_dev/workflow/runtime/config_run/1_default/i1/g1/g1.xml.gz
>> >
>>
>>
>>
>>
>> the event log is not assigned, did I missed something in the
>> configuration ? Or is ergatis not able to run
>> iterable componant outside a cluster environment ?
>>
>> thanks for your reply,
>> Jerome
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Ergatis-users mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>


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Adding output-download link ergatis interface...

Gowthaman Ramasamy
In reply to this post by Joshua Orvis
Hi All,
Couple custom components we have in our pipeline, makes only one output file. For example, summary file for the pipeline. I would like to display the link for that file in the ergatis interface, so that the user downloads and know about the pipeline right away. Is there a way to do that.

Currently I hijacked "stderr" or "stdout" links to do that. But, is it possible to have a link other than these two?

Thanks,
Gowthaman

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Re: Adding output-download link ergatis interface...

Chris Hemmerich

Gowthaman,

I believe a light way to do this would be to add a variable to the
[output] section of the component.config file for the filepath relative
to the component output dir. You could then add a bit of logic to either
  view_pipeline.cgi or view_component.cgi and if the component (or maybe
pipeline) is finished and the variable exists, you can display a download
link. More work could probably handle tarring directories or
wildcard expressions if needed.

  Chris

On Tue, 14 Sep 2010, Gowthaman Ramasamy wrote:

> Hi All,
> Couple custom components we have in our pipeline, makes only one output file. For example, summary file for the pipeline. I would like to display the link for that file in the ergatis interface, so that the user downloads and know about the pipeline right away. Is there a way to do that.
>
> Currently I hijacked "stderr" or "stdout" links to do that. But, is it possible to have a link other than these two?
>
> Thanks,
> Gowthaman
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>

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and start using them to simplify application deployment and
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