Curious performance when using OpenMPI 1.2 to run Amber 9 on my Xserve Xeon 5100 cluster. Each cluster node is a dual socket, dual-core system. The cluster is also running with Myrinet 2000 with MX. I'm just running some tests with one of Amber's benchmarks.
It seems that my hostfiles effect the performance of the application. I tried variations of the hostfile to see what would happen. I did a straight mpirun with no mca options set using: "mpirun -np 32"
variation 1: hostname
variation 2: hostname slots=4
variation 3: hostname slots=2
It seems that the best performance I achieve is when I use variation 1 with only the hostname and execute the command:
"mpirun --hostfile hostfile -np 32 <my_application>" . Its shockingly about 13% better performance than if I use the hostfile with a syntax of "hostname slots=4".
I also tried variations of in my mpirun command, here are the times:
straight mpirun with not mca options
"-mca mpi_yield_when_idle 0"
"-mca mtl mx -mca pml cm"
Scientific Computing Consultant