AMBER Archive (2009)

Subject: Re: [AMBER] AMBER on a Mac Mini cluster PoC

From: Abdul Rehman Gani (
Date: Mon Aug 17 2009 - 03:13:38 CDT

Ross Walker wrote:
> Hi Abdul,

Hi Ross,
> This looks to be an issue with your MPI installation rather than a
> with AMBER per se. Have you tested your openMPI installation? Often such
> things come with test suites or you can download them to test things out.

I have not run a test suite, but a command like:-

mpirun -machinefile machinefile -np 4 ls -l

does return expected results, as does using 'env' or 'hostname' as the

> Also I note that the error message, suggests TCP connections which to me
> implies you are using ethernet. Is this correct? If so then you are

Yes I am using gigabit ethernet.

> to see any benefit running in parallel at least for regular MD runs.
> Ensemble runs such as replica exchange might work. Unfortunately
these days
> ethernet is too slow to be of much help in parallel. Thus you could try
> running in parallel with 2 threads on one machine. I.e. just one entry in
> your machine file and -np 2. Then run the tests and see how they do. This
> will at least test your actual parallel installation.

I just did this and it worked fine. Using only the local host's IP in
machinfile and -np 2, the issuing 'make test.parallel' ran to completion
and each test either passed or was skipped (required mpi thread to be a
multiple of 4)

> Then you can try running some simulations yourself (or perhaps using the
> benchmarks here across both
nodes so
> you can compare performance. My guess is that it will probably
actually be
> slower using 2 nodes rather than 1 but you might be lucky. It will
> be easier to debug MPI problems (often caused by flakey interconnect
> hardware) when running a job yourself rather than inside the test
> environment.

Will try that. Ignoring for the moment that I am using Ethernet and the
provisos you highlighted, how would I use Amber over XGrid instead of


> Good luck,
> Ross

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