Mocat excedes memory limit on a SLURM cluster
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#67 Mocat excedes memory limit on a SLURM cluster
Hallo,
I've installed Mocat on our university cluster. Unfortunately they have only Slurm as queing system.
I'm doing a test run of Mocat with two samples. I don't use the ability of Mocat to use queing systems (as it don't supports Slurm), but ask for one node in the cluster to run my Mocat Pipeline.
The problem is now that Mocat excedes the memory limits and get killed.
Is there a way of limiting the number of threas and the memory Mocat is using, something analog to SGE_mem or LSF_mem?
Is there a bether way to use Mocat with a Slurm queing system?
Kind regards
Silas Kieser
If you download the version from the github under MOCAT2 it support SLURM.
On Mon, Jul 31, 2017 at 07:57 Silas Kieser silask@users.sf.net wrote:
Super.
I'll try this.
You can close the ticket.
From: MOCAT [mailto:mocat-pipeline@users.sf.net]
Sent: Montag, 31. Juli 2017 15:30
To: [mocat:tickets] 67@tickets.mocat.p.re.sf.net
Subject: [mocat:tickets] Re: #67 Mocat excedes memory limit on a SLURM
cluster
If you download the version from the github under MOCAT2 it support SLURM.
On Mon, Jul 31, 2017 at 07:57 Silas Kieser silask@users.sf.net
silask@users.sf.net wrote:
[tickets:#67] https://sourceforge.net/p/mocat/tickets/67/ Mocat excedes
memory limit on a SLURM cluster
Status: New
Labels: memory
Created: Mon Jul 31, 2017 11:57 AM UTC by Silas Kieser
Last Updated: Mon Jul 31, 2017 11:57 AM UTC
Owner: nobody
Hallo,
I've installed Mocat on our university cluster. Unfortunately they have
only Slurm as queing system.
I'm doing a test run of Mocat with two samples. I don't use the ability of
Mocat to use queing systems (as it don't supports Slurm), but ask for one
node in the cluster to run my Mocat Pipeline.
The problem is now that Mocat excedes the memory limits and get killed.
Is there a way of limiting the number of threas and the memory Mocat is
using, something analog to SGE_mem or LSF_mem?
Is there a bether way to use Mocat with a Slurm queing system?
Kind regards
Silas Kieser
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[tickets:#67] https://sourceforge.net/p/mocat/tickets/67/ Mocat excedes
memory limit on a SLURM cluster
Status: New
Labels: memory
Created: Mon Jul 31, 2017 11:57 AM UTC by Silas Kieser
Last Updated: Mon Jul 31, 2017 11:57 AM UTC
Owner: nobody
Hallo,
I've installed Mocat on our university cluster. Unfortunately they have only
Slurm as queing system.
I'm doing a test run of Mocat with two samples. I don't use the ability of
Mocat to use queing systems (as it don't supports Slurm), but ask for one
node in the cluster to run my Mocat Pipeline.
The problem is now that Mocat excedes the memory limits and get killed.
Is there a way of limiting the number of threas and the memory Mocat is
using, something analog to SGE_mem or LSF_mem?
Is there a bether way to use Mocat with a Slurm queing system?
Kind regards
Silas Kieser
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/mocat/tickets/67/
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