[gmx-users] GROMACS on double processor nodes

Pietro Lopriore p.lopriore at it.ibm.com
Thu Feb 3 15:48:42 CET 2005

Our Environment:
JS20 BladeCenter Power970 with Linux Suse 9 kernel 2.6.5-7.97-pseries64
(2CPUs per node)
Myrinet, GM 2.0.16-2,
FFTW 2.1.5
gcc 3.3.3-43.24

Our GROMACS installation seems to be unable to perform well when our MPI
machine file includes all the processors in each node (node001:2,
node002:2, node003:2, etc.). We see two mdrun processes on each node, which
seems quite strange.
In fact the performances are very very poor (a 250 steps calculation takes
long time in both double and single precision) if compared to a run with
only 1 processor per node.
Is there somthing we're missing?
Thanks a lot in advance!!



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