On 11/02/2011 11:33 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
there something else I'm missing?
GROMACS assembly kernels for IA64 have been known to have problems (see
mailing list archives), but IIRC usually in compilation, not execution.
You will need to inspect the first few hundred lines of the .log files
where GROMACS reports what kernels are being used for the execution.
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?
We can't say with the information given. For best performance, the
number of threads cannot exceed the number of physical cores available
to one processor. To go higher, you need to compile and use GROMACS with
MPI, not threading. If the IA64 is "dual core" then you are not
measuring anything useful. You also need to be sure you're measuring for
a decent length of time - a few minutes at least.
Mark
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