[gmx-users] Multiprocessor problems
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 17 10:26:01 CEST 2003
On Tue, 2003-06-17 at 09:38, Sampo Karkola wrote:
> > Please supply more information on gromacs version, machine type number
> > of processors and simulation system.
> > If you haven't got the latest gmx version (3.1.4) that would a good
> > start...
> > --
> I'm using gromacs3.0.3. and updating it is out of my hands. The machine is
> an IBM eServer Cluster 1600 with 16 IBM p690 nodes, each equipped with 32
> Power4 processors. The simulation consists of a 500 aa protein with a heme
> group with/without a substrate and water or oxygen in the active site. There
> are about 10000 water molecules and around 70 ions. The first mdrun was made
> with the backbones of the SCRs fixed and the second would be made with a
> free backbone.
I asked about the version because I vaguely recall that problem similar
to the ones you are describing were fixed at some stage. I may be wrong
Nevertheless, it is quite straightforward to install gromacs even if you
are not the system administrator (in your own directory). Alternatively
you can ask the sysadmin to upgrade it for you.
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
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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