[gmx-users] low CPU load percentages on 16 core box with CentOS4.4

[Mark Abraham]

Makoto Yoneya wrote:
> Dear GROMACS-users
> 
> We're in trouble with a new 16 core (8 dual core opteron) box with
> CentOS4.4.
> After the instillation of fftw-3.1.2 (fftw-3.0.1 had failed to compile on
> this system
> with sse and sse2) and gromacs-3.3.1 with pre-installed lam-7.0.6 and
> compiler
> environments on CentOS4.4, we had found the CPU load percentages were
> unexpectedly low with gromacs runs.
> With "-np 16" running option, the CPU load percentages (with top) were
> around 25% and the mpi process frequently went to sleep state.
> Total load also around not 16 but 4.
> Situation was similar with "-np 8" with slightly more load.
> With "-np 4", we'd got around 99% CPU load percentages for each
> mpi process.
> I had tried newer lam-7.1.2, but the situation was same.
> Only with the mipch2-1.0.5, the 16 core load percentages became
> what we expected (keep running state around 99% CPU load and total 16 load
> with top).

Well this looks like a classic problem of incompatibility of your
hardware and these lam versions that is not arising for MPICH. You
should look for help there, since the problem is not arising because of
gromacs - unless you can demonstrate lam works correctly on your
hardware for other parallel software.

> However, the test simulation results looked different (e.g. densities of the
> system) with lam and mpich2 (I should check more).
> How can I solve this situation?

It sounds like gromacs+MPICH is working fine...

Mark