AMBER Archive (2006)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Oct 11 2006 - 17:18:14 CDT

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.
>

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?

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.

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.

All the best
Ross

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|\oss Walker

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| San Diego Supercomputer Center |
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