Anna Marabotti wrote:
Dear GMX-developers (in particular dear Carsten Kutzner),
to overcome problems in making parallel runs with GROMACS on a Linux cluster
with Gigabit Ethernet
interconnection, I downloaded the package gmx_all-to-all to speed up the
processes. In the
instructions, however, this package is indicated for GROMACS version 3.3.1,
whereas in our cluster
we installed the 3.3.2 version. Is gmx_alltoall compatible also with this
version?
Hi Anna,
in principle the patch should also work with 3.3.2. I have just applied
the patch to 3.3.2, and then taken a quick look at the patched code
which looks good, so no apparent problems here.
Another question: if we will upgrade to GROMACS 4 when it will be
released, are you expecting that
(nearly) all problems in parallelizazion will be solved or this package will be
still
useful/required/necessary?
The CVS version still uses the MPI_Alltoall routine for the parallel FFT
within PME, so you could run into the same problems on Ethernet.
What you could do is to move over to a recent version of OpenMPI which
comes with optimized collectives. They provide an MPI_Alltoall routine
which switches between several algorithms depending on message size and
number of processors. I think this is turned on by default, so all you
need to do is install OpenMPI, recompile Gromacs on top of that and you
should not have problems with all-to-all congestion any more.
Carsten
Many thanks in advance and best regards
Anna Marabotti
______________________________________________
Anna Marabotti, Ph.D.
Laboratorio di Bioinformatica e Biologia Computazionale
Istituto di Scienze dell'Alimentazione, CNR
Via Roma 52 A/C
83100 Avellino (Italy)
Tel: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: [EMAIL PROTECTED]
Web page: http://bioinformatica.isa.cnr.it/anna.htm
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne
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