[AMBER] issue running AMBER on double sockets hexa cores

From: Pascal Bonnet <pascal.bonnet.univ-orleans.fr>
Date: Mon, 16 Sep 2013 20:42:12 +0200

Dear amber users,

We have PowerEdge R410 Dell computers, each with double sockets hexa
cores running Linux Centos6.4, 64 bits. Processors are Intel Xeon X5650.

When executing the collection of AMBER benchmarks designed by Ross
Walker, we obtain a good speed increase from single socket single core
to single socket hexa cores (almost 6X faster).
However when we try to use double sockets hexa cores there is no speed
increase, we obtain the same speed as single socket hexa cores.
I wonder if someone already observed this behavior or if someone has a

Here is the command line:
mpirun -np X $AMBERHOME/bin/sander.MPI -O -i ../mdin -o mdout -p
../prmtop -c ../inpcrd (with X=1 to 12)

We use AMBER12, and OpenMPI: 1.6.4.
Best regards,

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Received on Mon Sep 16 2013 - 12:00:02 PDT
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