User: chadmatsalla

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chadmatsalla40
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Posts by chadmatsalla

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Systemd for galaxy-web and handlers
... TL;DR These are systemd units for galaxyweb and the handlers. I came across the most interesting problem and I thought I'd share a solution in case this comes up for someone else. We use LDAP. Specifically LDAPs. This became an issue in specific cases with supervisord. Namely supervisord could no ...
python ldap systemd supervisor written 10 months ago by chadmatsalla40 • updated 10 months ago by Jennifer Hillman Jackson25k
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Answer: A: Configure a tool to request a slurm node with a lot of RAM or "How do I change a
... I read the [Galaxy Tool XML Schema][1] and doesn't seem to support destination="". Hmm. I read the [Galaxy Job Configuration page][2] and found that the collection in job_conf.xml seems to do what I need. Sadly, there was no example anywhere. I put this in there: And I resta ...
written 10 months ago by chadmatsalla40
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Comment: A: Configure a tool to request a slurm node with a lot of RAM
... OK, I added a new runner in job_conf.xml: true --ntasks=1 --share --mem=500000 Then I changed the tool's data in : I restarted Galaxy web. The change didn't take place. I reset the metadata for data_mana ...
written 10 months ago by chadmatsalla40
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SOLVED: Configure a tool to request a slurm node with a lot of RAM or "How do I change a tool's <job> attributes?"
... Hi All, This is a generic question regarding slurm and DRMAA. I have a tool. Let's call it "data_manager_star_index_builder". It needs a lot of ram for this specific dataset. 1. Is there a way to request that for a single job (not a job type, a single job) a slurm node with a lot of ram is used? 2 ...
drmaa slurm config job admin written 10 months ago by chadmatsalla40
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Answer: A: Job was reported by drmaa as terminal but job state in SLURM is: PENDING, return
... Thanks for your help. To fix this I used the well-worn strategy of "turning it off and turning it back on". I restarted the entire slurm apparatus and the entire galaxy apparatus. The messages have stopped but sacct still shows that job as pending. I'm not really sure how to deal with that given t ...
written 10 months ago by chadmatsalla40
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Job was reported by drmaa as terminal but job state in SLURM is: PENDING, returning to monitor queue
... I have a brand new install of slurm with two nodes. I just managed to get slurm working. Galaxy web reports no jobs. Galaxy's main logs are filling with: > galaxy.jobs.runners.slurm WARNING 2017-12-06 15:50:59,820 (91/40) Job was reported by drmaa as terminal but job state in SLURM is: PENDIN ...
drmaa galaxy.jobs.runners.drmaa slurm written 10 months ago by chadmatsalla40

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