Re: [AMOS-help] amosvalidate problem

[Adam P. <aph...@gm...>]

Hi John,
Have you tracked the memory of these jobs? Sounds like it may be exhausting
system memory--that's generally the only way I see my cluster nodes
bricked. If not, that's Mike Schatz's code, he may have more insight.

Best,
-Adam



On Sun, May 18, 2014 at 10:24 PM, John Johnston <jo...@ms...> wrote:

> Hello,
>
> I have a user that is attempting to use the "amosvalidate" utility on a
> HPC cluster, and it appears to be crashing nodes.
>
> The process appears to proceed normally until reaching the "analyzeSNPs"
> step with the command (obtained from the log file):
>
> analyzeSNPs -i -b/ /assembly.bnk -S -cumqv 40 -minsnps 2 -r -H >
> assembly.snps
>
> Searching 223685 contigs
>
> At this point, log output ceases, the job terminates abnormally, and the
> scheduling system on that node registers in a "down" state.  We've seen
> this
> on multiple nodes.
>
> Other users have used other parts of the AMOS package over the last 3
> years on the system without these problems (though *not* specifically
> amosvalidate).
> AMOS is installed on a RHEL 6 system with the torque/PBS resource
> manager and moab scheduler.
>
> The version in use is 3.1.0 released in 2011.
>
> Has anyone seen anything like this or might someone have any insight on
> this issue?
>
> Thanks.
>
>
>
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