AMBER Archive (2006)

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

From: Ross Walker (
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.:

Have you seen this with any other codes? Can you run the openmpi test suite

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

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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