[gmx-users] Gromacs on Gigabit Ethernet Dual Opteron Cluster

[Ghermes Chilov]

Dear gmx-users,

I've got preliminary results of Gromacs's performance on Dual Opteron
cluster (Gigabit Ethernet, LAM-MPI 7.0). The scalability is good (>80%)
with up to 3 nodes used, but than it drops (44% for 8 nodes) and this
decrease seems to correlate with CPU load (which also drops from
100-95% for 1 node to 60% for 8 nodes).

Should I play with LAM compilation options or go fishing somewhere
else? Probably parameters --with-tcp-short and --with-shm-short for
Gigabit Ethernet may be increased? (with respect to 500 kb for Fast
Ethernet).

Ghermes Chilov
Moscow State University