Dear Christophe,
This is my first experience with openmpi. Which openmpi test suite are you
refering to? Where is it documented?
I have never used Openmpi myself either. I tend to use mpich2. There should
be some kind of test suite distributed with the source code though. Check
the install docs. Typically you do something like: ./configure; make; make
test; make install
It is the make test bit that you need to lookup.
Unfortunately, the error is not always from the same node!
HHmmm, then it could be the switch but could also be an issue with the
openmpi installation. Try downloading mpich2 and trying that out instead and
see if it works.
You could also try building pmemd in $AMBERHOME/src/pmemd and then testing
this. If you see similar problems then it is definately an issue with the
openmpi installation or the hardware.
All the best
Ross
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Christophe Deprez
Sent: Thursday, October 12, 2006 06:55
To: amber.scripps.edu
Subject: Re: AMBER: problems for running sander.MPI
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.bri.nrc.ca
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Received on Thu Oct 12 2006 - 20:36:15 PDT
