[gmx-users] SMP vs Infiniband

Tranchemontagne, Denis dtranche at mc.com
Thu Feb 26 20:11:01 CET 2004

I just got done running the gmxbench mark on a small cluster and am
noticing some odd results. I am currently only running d.villin
I am using a version of mpich provided by our infiniband supplier, not
sure how it was built. fftw is 2.1.5 with --enable-mpi and
--enable-float options.
gromacs 3.2 compiled with --enable-mpi and --program-suffix=_mpi.  
The systems are dual 2.4 GHz Xeons running rh 7.3 linux with
2.4.18-27.7.xsmp as the kernel.
When I run on as 2 processes on the smp machine I see a about 75%
improvement, however if I run as 2 processes each on a different machine
over infiniband I see 85% improvement.  
This seems counter intuitive.
My typical run is grompp -np 2 -v ; mpirun -np -hostfile host mdrun_mpi
I also tried mdrun_mpi -v -shuffle.
Any help or suggestions would be appreciated.
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