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. Cheers, Carsten > 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 > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists