AMBER Archive (2006)

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

From: Christophe Deprez (
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.:
>Have you seen this with any other codes? Can you run the openmpi test suite
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               
Institut de Recherche en Biotechnologies / Biotech. Research Institute
6100 Royalmount, Montréal (QC) H4P 2R2, Canada     Tel: (514) 496-6164 

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