[gmx-users] Performance in ia64 and x86_64

Carsten Kutzner ckutzne at gwdg.de
Fri Feb 11 15:05:38 CET 2011

Hi Ignacio,

On Feb 11, 2011, at 1:33 PM, Ignacio Fernández Galván wrote:

> Hi all,
> I'm compiling and testing gromacs 4.5.3 in different machines, and I'm wondering 
> if it's normal that the ia64 is much slower than the x86_64
> I don't know full details of the machines, because I'm not the administrator or 
> owner, but /proc/cpuinfo says:
> ia64 (128 cores): Dual-Core Intel(R) Itanium(R) Processor 9140N
> x86_64 (16 cores): Intel(R) Xeon(R) CPU           E5540  @ 2.53GHz
> Just looking at the GHz, one is 2.5 and the other is 1.4, so I'd expect some 
> difference, but not a tenfold one: with 8 threads (mdrun -nt 8) I get 0.727 
> hours/ns on the x86_64, but 7.607 hours/ns on the ia64. (With 4 threads, it's 
> 1.3 and 13.7).
> I compiled both cases with gcc, although different versions, and default 
> options. I had read assembly or fortran kernels could help with ia64, but 
> fortran is apparently incompatible with threads, and when I tried with assembly 
> the mdrun seemed stuck (no timestep output was written). Is this normal? Is 
Yes, there is a problem with the ia64 assembly loops and this is exactly
how it manifests. I did run into that problem several times. What you can
do is to use the fortran kernels and compile with MPI. The performance
of the threaded and MPI versions should be the same, and the fortran 
kernels are nearly as fast as the ia64 assembly. Probably you can speed
things up a few percent by using the Intel compiler.


> there something else I'm missing?
> Also, in the x86_64 system I get much lower performance with 12 or 16 threads, I 
> guess that could be because of the cores/processors, but I don't know what's the 
> exact configuration of the machine. Again: is this normal?
> Thanks,
> Ignacio
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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