[gmx-users] Gromacs on SGI Altix

Mingfeng Yang mfyang at gmail.com
Tue Jan 3 16:08:30 CET 2006

Happy new year to each gromacs user!

I just finished installation of Gromacs 3.3 on our Itanium2 based SGI 
Altix. My configuration option is
|./configure --prefix=/home/myang/usr/local/gromacs_intel --enable-mpi 
CC=icc F77=ifort|
The intel C++ compiler 9.021 and intel fortran compiler 9.021 were used. 
The OS is Red Hat Enterprise WS 3.0.

The parallel efficiency is kind of disappointing. For the benchmark case 
of villin, it took 97 seconds with one CPU, 55 seconds with two CPUs, 
and 35 seconds for 4 CPUs. From the benchmark pages of Gromacs website, 
I saw the parallel efficiency can go beyond 100% under 8 CPUs. Is there 
anything I missed? What supposed to be the best options when install 
gromacs on Itanium2 based machine?

Thank you for any input!


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