[gmx-users] Performance in ia64 and x86_64

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 25 11:51:15 CET 2011

On 25/02/2011 8:25 PM, Ignacio Fernández Galván wrote:
> 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
>> compiling
>> 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).

You should inspect the first few hundred lines of the .log files and 
observe what kernels GROMACS is using at run time.


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