Corra stalling error

samp...@qut.edu.au

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Jun 17, 2011, 2:38:15 AM6/17/11

to Corra

We're getting a strange error through the corra pipeline. It seems to
succesfully complete feature picking (for example), we can see this as
the .dat and .peplist files are produced. The corra.log ends with "job
submited" but never gets updated to reflect that the job is completed.
The feature_picking.status indicates that the job is still running,
how/what updates this. Note that the corra tab will sit on yellow
instead of going to green.

Mi-Youn Brusniak

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Jun 22, 2011, 4:35:53 PM6/22/11

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Dear Dayle,

Is this happening only with SpecArray? Or other modules as well (e.g., SuperHirn)?

For your information, our executor checks the "qstat" to see the job has completed.

When job has the status of "C", look at the below example from our PBS installation.

Job id Name User Time Use S Queue

------------------------- ---------------- --------------- -------- - -----

18157.moog ...niak_PandG_TA corra 00:00:15 C big

18158.moog ...niak_PandG_TA corra 00:00:45 C big

Corra checks whether “expected” output of nonzero size of files are found.

According to your description, there was no reporting for “C” status.

Mi-Youn

Mi-Youn Brusniak, PhD

Computational Biologist/Sr. Software Engineer

p 206.732.1327

Institute for Systems Biology | Seattle Proteome Center | 401 Terry Ave N. Seattle WA 98109

Revolutionizing science. Enhancing life.

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samp...@qut.edu.au

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Jun 24, 2011, 7:03:04 PM6/24/11

to Corra

Thanks Mi-Youn,
The scheduler was getting confused because we attempted to have Corra
run on two servers due to system usage.. These issues have now been
sorted and it seems to be running fine.

Regards,
Dayle

Mi-Youn Brusniak

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Jun 28, 2011, 4:28:13 PM6/28/11

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Great! Thank you for sharing with us how you resolved the issue.

Mi-Youn

Mi-Youn Brusniak, PhD
Computational Biologist/Sr. Software Engineer
p 206.732.1327
Institute for Systems Biology | Seattle Proteome Center | 401 Terry Ave N.
Seattle WA 98109
Revolutionizing science. Enhancing life.

This message (including any attachments) contains confidential information
intended for a specific individual and purpose, and is protected by law. If
you are not the intended recipient, you should delete this message and are
hereby notified that any disclosure, copying, or distribution of this
message, or the taking of any action based on it, is strictly prohibited.

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