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

Makoto Yoneya yoneya at nanolc.jst.go.jp
Fri Feb 2 04:08:52 CET 2007

Dear GROMACS-users

We're in trouble with a new 16 core (8 dual core opteron) box with
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
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).
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?
Any information and comments will be welcome.

Makoto Yoneya, Dr.
National Inst. of Advanced Industrial Science and Technology (AIST),

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