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 
real    0m35.391s

variation 2: hostname slots=4
real    0m45.698s

variation 3: hostname slots=2
real    0m38.761s

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
real    0m45.698s


"-mca mpi_yield_when_idle 0"
real    0m44.912s


 "-mca mtl mx -mca pml cm"
real    0m45.002s

Warner Yuen

Scientific Computing Consultant

Apple Computer


Tel: 408.718.2859

Fax: 408.715.0133