[gmx-users] SMP vs Infiniband

[Tranchemontagne, Denis]

Hello
 
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
-v
 
I also tried mdrun_mpi -v -shuffle.
 
Any help or suggestions would be appreciated.
 
Denis
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