AMBER Archive (2006)

Subject: Re: AMBER: problems for running sander.MPI

From: Christophe Deprez (christophe.deprez_at_bri.nrc.ca)
Date: Thu Oct 12 2006 - 08:54:41 CDT

Ross Walker wrote:

>Hi Qizhi
>
>>enode05:03662] mca_btl_tcp_frag_send: writev failed with errno=104
>>
>>(enode05 is one of the node names of the cluster.)
>>
>>Normmally, there is no problem for minimization and constant
>>NVT steps.
>>The problems often occur during constant NPT and production run.
>>
Hi Ross, and thanks for your reply.
I'm working as sysadmin with Qizhi to troubleshoot this issue.

>This looks like a hardware problem to me. Unfortunately a Google search
>sheds little light. E.g.:
>http://www.open-mpi.org/community/lists/users/2006/02/0684.php
>
>Have you seen this with any other codes? Can you run the openmpi test suite
>successfully?
>
This is my first experience with openmpi. Which openmpi test suite are
you refering to? Where is it documented?

>I would check to see if the error is always from the same node. If you
>unplug that node and use the remaining nodes do you see the problem.
>
Unfortunately, the error is not always from the same node!

>I would also try compiling with g95 instead of gfortran. While it appears
>that gfortran is now mature enough to compile Amber I don't know if it has
>been thoroughly tested. You will probably have to recompile openmpi with g95
>as well.
>
I'll give this a try.

Thanks for your suggestions 

-- 
Christophe Deprez                         christophe.deprez_at_bri.nrc.ca
----------------------------------------------------------------------
Institut de Recherche en Biotechnologies / Biotech. Research Institute
6100 Royalmount, Montréal (QC) H4P 2R2, Canada     Tel: (514) 496-6164 

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