[gmx-users] Performance in ia64 and x86_64

Ignacio Fernández Galván jellby at yahoo.com
Fri Feb 11 13:33:28 CET 2011

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 
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?



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