[gmx-users] Performance in ia64 and x86_64

Ignacio Fernández Galván jellby at yahoo.com
Fri Feb 25 10:25:42 CET 2011

I wrote:

> It seems the x86_64 processor has 4 cores and 8 threads support 
> (<http://ark.intel.com/Product.aspx?id=37104>), so the machine has probably two 
> physical processors. I thought MPI was only needed if there was network 
> communication involved, as in a cluster, but not in SMP, which is what both 
> machines are (single memory, single OS), I guess I was wrong. I'll try 
> with MPI.

Well, I've compiled mdrun with MPI (with fortran kernels in the ia64), and run 
my test system in both machines, with a single processor. The results are still 
worrying (to me). This is a 500000 time step (0.5 ns) simulation with 1500 water 
molecules, not a big system, but it still takes some hours:

x86_64: 3.147 ns/day
ia64: 0.507 ns/day

Is this difference normal? Am I doing anything wrong? what further data should I 
provide? The compilation in both machines was quite straightforward (once I had 
solved the library and path issues).



More information about the gromacs.org_gmx-users mailing list