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Mizzou-CBMI / COSMOS2

Python Scientific Pipeline Management System
GNU General Public License v3.0
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Error: Internal Server Error on Indel Realigner intermittently #27

Closed Double-O-ren closed 8 years ago

Double-O-ren commented 8 years ago

Job started running until spot instance closed. restarting was manual Resubmitting the job again is not an option through the UI Clicking on Indel Realigner shows Internal server error intermittently Job is not being submitted to the SGD queue

Double-O-ren commented 8 years ago

When running the webserver with genomekey runweb I get the drmaa.errors.AlreadyActiveSessionException error

egafni commented 8 years ago

The UI is for debugging and monitoring, it'd be possible to add a restart option but it'd be significant dev time and not likely to happen

Did you restart the cluster? If so the code updates we made friday evening will be gone which will cause the indel realigner problem. Sorry, I was unable to update GenomeKeyDeploy this weekend with that fix, but can do tonight if you restarted.

Double-O-ren commented 8 years ago

I didn't restart the cluster I added the spot instance. The group gk lost the spot instance in the past day. I also see another group gk2, whats the difference between the two? Is there a way to continuously bid for spot instances in order to keep the cluster at capacity? If the spot instance dies then I get the 'no available queues' error

egafni commented 8 years ago

forgot to tear down the gk2 cluster last night when i was testing the changes, was just emailing you to ask you to terminate it for me :D

you should be good to go if you terminate & restart gk2 with the new version of GenomeKeyDeploy

On Tue, Nov 24, 2015 at 10:42 AM, Oren Schaedel notifications@github.com wrote:

I didn't restart the cluster I added the spot instance. The group gk lost the spot instance in the past day. I also see another group gk2, whats the difference between the two?

— Reply to this email directly or view it on GitHub https://github.com/LPM-HMS/COSMOS-2.0/issues/27#issuecomment-159368131.

egafni commented 8 years ago

sorry, i mean terminate & restart gk

On Tue, Nov 24, 2015 at 10:48 AM, Erik Gafni egafni@gmail.com wrote:

forgot to tear down the gk2 cluster last night when i was testing the changes, was just emailing you to ask you to terminate it for me :D

you should be good to go if you terminate & restart gk2 with the new version of GenomeKeyDeploy

On Tue, Nov 24, 2015 at 10:42 AM, Oren Schaedel notifications@github.com wrote:

I didn't restart the cluster I added the spot instance. The group gk lost the spot instance in the past day. I also see another group gk2, whats the difference between the two?

— Reply to this email directly or view it on GitHub https://github.com/LPM-HMS/COSMOS-2.0/issues/27#issuecomment-159368131.

Double-O-ren commented 8 years ago

Should I be running 0.1.2? Do I need to modify the config file? It points to v 0.1.0 throughout

egafni commented 8 years ago

Use 0.1.2 and its config file. I didn't realize its pointing to anything in the 0.1.1 dir but it should be fine. Feel free to make a backup of it and update if you like.