[gmx-users] Gromacs on SGI Altix
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jan 3 17:17:56 CET 2006
Florian Haberl wrote:
>On Tuesday 03 January 2006 16:08, Mingfeng Yang wrote:
>>Happy new year to each gromacs user!
>>I just finished installation of Gromacs 3.3 on our Itanium2 based SGI
>>Altix. My configuration option is
>>|./configure --prefix=/home/myang/usr/local/gromacs_intel --enable-mpi
>>The intel C++ compiler 9.021 and intel fortran compiler 9.021 were used.
>>The OS is Red Hat Enterprise WS 3.0.
>>The parallel efficiency is kind of disappointing. For the benchmark case
>>of villin, it took 97 seconds with one CPU, 55 seconds with two CPUs,
>>and 35 seconds for 4 CPUs. From the benchmark pages of Gromacs website,
>>I saw the parallel efficiency can go beyond 100% under 8 CPUs. Is there
>>anything I missed? What supposed to be the best options when install
>>gromacs on Itanium2 based machine?
>I think that d.villin is not the right benchmark for more cpus and measering
>I would prefer here d.dppc as shown on gromacs webpage. Reason for this bad
>scalling is is small system size.
Apart from that, what interconnect are you using? And which MPI library?
I presume the Altix has some kind of nice interconnect, but do you use it?
>>Thank you for any input!
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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