ulimit problems after update
Hi, I updated to the latest galaxy distribution (after one year). And now every job fails with: /home/imba/solexa/.profile.sh: line 118: ulimit: virtual memory: cannot modify limit: Operation not permitted The limit is ridiculously high: ulimit -v 60000000 Its just to prevent some badly programmed in house galaxy tools to crash the server. I think the problem happens after the set_metadata stage. Any advice? thank you very much, ido
I simply removed the ulimit and the jobs complete successfully, but I still wonder why it does not work and would like to put the ulimit again in place. It happens also with very simple jobs, like filter tool on a 7k region file for “chr1”. thank you very much, ido On 10 Nov 2014, at 11:34, Ido Tamir <tamir@imp.ac.at> wrote:
Hi, I updated to the latest galaxy distribution (after one year). And now every job fails with: /home/imba/solexa/.profile.sh: line 118: ulimit: virtual memory: cannot modify limit: Operation not permitted
The limit is ridiculously high: ulimit -v 60000000
Its just to prevent some badly programmed in house galaxy tools to crash the server. I think the problem happens after the set_metadata stage.
Any advice?
thank you very much, ido ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Hmm... this is probably a script that works fine on your login node but not on your worker nodes or vise versa? The fact that it is writing to standard error and happens for each new shell is probably what is causing Galaxy jobs to fail - Galaxy is thinking the underlying applications are writing content to standard error and failing the job as a result. You could probably just rework the line to suppress standard error as follows (I think): ulimit -v 60000000000000 2>&1 > /dev/null || true Otherwise - you may want to consider figuring out which nodes this should not be running on - and place an if before the ulimit. The details of that are going to vary wildly based on your architecture however. Hope this helps. -John On Mon, Nov 10, 2014 at 5:44 AM, Ido Tamir <tamir@imp.ac.at> wrote:
I simply removed the ulimit and the jobs complete successfully, but I still wonder why it does not work and would like to put the ulimit again in place.
It happens also with very simple jobs, like filter tool on a 7k region file for “chr1”.
thank you very much, ido
On 10 Nov 2014, at 11:34, Ido Tamir <tamir@imp.ac.at> wrote:
Hi, I updated to the latest galaxy distribution (after one year). And now every job fails with: /home/imba/solexa/.profile.sh: line 118: ulimit: virtual memory: cannot modify limit: Operation not permitted
The limit is ridiculously high: ulimit -v 60000000
Its just to prevent some badly programmed in house galaxy tools to crash the server. I think the problem happens after the set_metadata stage.
Any advice?
thank you very much, ido ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Ido Tamir -
John Chilton