[mira_talk] Re: qsub submission of mira 4.0.2 job - job likely killed while loading data
- From: Rick Westerman <westerman@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 28 Jan 2015 07:28:17 -0500
> On Jan 28, 2015, at 7:17 AM, Nicolas Dauchot <nicolas.dauchot@xxxxxxxxx>
> wrote:
>
> Here is the shell script I use to send the job with " qsub mira.sh". I
> checked with mimamem and i should need much more than 130 Gb of ram. I guess
> that the -l h_vmem=20G and -pe 10 does mean 10 cores with each 20 Gb or ram?
> Should i reduce the number of cores and increase the h_vmem parameter?
>
Yes, you should be getting 200G memory total in your job. miramem is only
approximate. 200G may not be enough. Or there may be something else going on.
Your idea of reducing the number of cores and increasing the h_vmem is a good
idea. Go for the gusto and grab most of that 500 GB you can take!
B’s suggestion of running with a smaller number of reads is also a good one.
I work on a variety of projects and there are some — the big ones — which Mira
simply won’t handle.
--
Rick Westerman
westerman@xxxxxxxxxx
> mira.sh script
>
> $# -s /bin/bash
> $# -l h_vmem=20G
> $# -pe 10
>
> module load mira/x86_64/4.0.2
>
> #! /bin/bash
> echo "job started"
> date
> mira manifest_6_L8001_LH.conf >logout.out
> echo "job finished"
> date
>
>
>
> Le 28/01/2015 13:09, Bastien Chevreux a écrit :
>> On January 28, 2015 at 1:00 PM Nicolas Dauchot <nicolas.dauchot@xxxxxxxxx>
>> <mailto:nicolas.dauchot@xxxxxxxxx>
>> wrote:
>>> [...]
>> You forgot to post that shell script you sent me (with the probable 20 GiB
>> limit). I still think that this is the cause for MIRA being killed by the
>> system.
>>
>> You could try with a smaller test file, say, 100k sequences, and see what
>> happens there.
>>
>> B.
>>
>
> --
> <fjfddhid.png>
> Nicolas DAUCHOT - PhD
> URBV - Plant Biotechnology
>
> T. +32 (0)81 724 368
> nicolas.dauchot@xxxxxxxxx <mailto:nicolas.dauchot@xxxxxxxxx>
> http://www.unamur.be/sciences/biologie/urbv/
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> Université de Namur ASBL
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