David Konerding wrote:
Hi
I was happy to see the 'Speeding up Parallel GROMACS' paper. I'd like
to try
the GROMACS patch for better all-to-all, as well as the all-to-all test
program referred
to on the paper. I can't find it on the GROMACS site.
Hi David,
you can download both at
www.gromacs.org -> download -> user contributions -> contributed software
If you sort by name, it's on page 2, called gmx_alltoall. The all-to-all
test program is also included in the tarfile. Packet drops during all-to-all
communication will lead to very different individual all-to-all timings,
which is easily seen in the output.
We've got a Cisco 6500 and when I run tcpdump during MPI runs I see a
huge amount
of TCP lost packets with retransmits, and tcptrace confirms there are a
large number of restransmits.
I am trying to get our network admins to test the flow control setting
option on our 16-processor cluster.
From my experience I can say that on 16 CPUs you will need either flow
control or an ordered all-to-all to avoid packet loss. If you can enable
flow control, you should definitely do that, because in principle there
can be congestion in many parts of a program, the (lam-) all-to-all just
turned out to be the No. 1 candidate.
Carsten
--
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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