RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE

From: Juan Carlos <juan.munioz.iiq.csic.es>
Date: Thu, 15 Apr 2010 11:03:46 +0200

Thank you Tom and Ross,

you were right, it seems its only built the serial version of PMEMD
in the high performance computer Im using, so Im working on solving
this. Meanwhile, Ive run my jobs with PMEMD of amber10, which Ive
checked its compiled in parallel, but another problem has appeared.
When I run my job on 8 processors it goes forward perfectly, but
when I run it on 32 processors the job stops at the
first step and I get the following error :

vlimit exceeded for step 1; vmax = 48.6876
rank 31 in job 1 cn040.null_58505 caused collective abort of all
ranks exit status of rank 31: return code 1

How is it possible that my system keeps stable when usign 8 processors
and unstable when using 32? I guess this has to be a problem of
the compilation or configuration of PMEMD in the HPC Im working on.
Could you give me your opinion about it?


Thank you very much.


/J.C. Muoz
PhD student.
Institute of Chemical Research (Instituto de Investigaciones Qumicas),
Sevilla, Spain.
Carbohydrates Group./


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Received on Thu Apr 15 2010 - 02:30:02 PDT
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