[AMBER] Running Amber on a SGI cluster

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 24 Sep 2013 16:32:25 -0300

Hi everybody,

I'm trying to run Amber on a cluster of the following specs

SGI Specs SGI ICE X
OS - SUSE Linux Enterprise Server 11 SP2
Kernel Version: 3.0.38-0.5
2x6-Core Intel Xeon

16 blades 12 cores each

Environment
export AMBERHOME=/bio/georgios/MD/amber12
export LD_LIBRARY_PATH=/opt/rpm_share/lib/lib64:/bio/george/amber12/lib:/bio/george/MD/amber12/AmberTools/lib

Command line
mpirun -np 48 pmemd.MPI -O -i prod.in -o prod_12ns.out -p 2erb_bis_solv.prmtop -c prod_10ns.rst -r prod_12ns.rst -x prod_12ns.mdcrd

Question

No advantage in increasing the number of nodes beyond -np 24. The performance is reduced the more cores engaged. In fact it is similar or worse to that on a OSX 2 x 3.06 GHz 6-Core Intel Xeon

I'd be very grateful for any suggestions on what may be wrong

Best regards

George



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Received on Tue Sep 24 2013 - 13:00:04 PDT
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