[gmx-users] Re: MPICH on Gbit with > 4 CPUs?
spoel at xray.bmc.uu.se
Fri Oct 14 20:51:16 CEST 2005
On Fri, 2005-10-14 at 12:28 -0600, Justin MacCallum wrote:
> > has anybody ever managed to run gromacs in parallel on more than 4
> > CPUs
> > when using MPICH on Gigabit Ethernet? I have just searched the mailing
> > lists, where this problem was also reported (but no solution!).
> > We have dual-CPU Xeons, Linux 2.4. With up to 4 CPUs, gromacs 3.3 and
> > 3.2.1 work. With 5+ CPUs, mdrun initializes properly but never
> > finishes the first
> > time step. An MPI test program (that does an all-to-all communication)
> > works happily on up to 40 CPUs with MPICH. With LAM, mdrun works fine
> > on any number of CPUs as well. Why not with MPICH?
> Hi Carsten,
> I have experienced the same problem you mention. I haven't been able
> to resolve it yet. I've noticed some very strange behavior regarding
> the distribution of processes. Some of the nodes seem to have too
> many mdrun process while other nodes only have one (when they should
> have two). Also, some of the nodes have 100% CPU usage, while others
> are sitting completely idle. Unfortunately its been quite a while
> since I tested this so I don't exactly remember the specifics.
Are there different MPICH versions out there? It might be good to check.
E.g. the Infiniband installation that Pim mentioned could be a later
version than the one Carsten has, also the Linux kernel could play a
role. (BTW Carsten, you are welcome to test it on our Opteron cluster
running the 2.6 kernel but Gbit).
> Justin MacCallum
> PhD Student
> Departement of Biological Sciences
> University of Calgary
> email: jlmaccal at ucalgary.ca
> web: moose.bio.ucalgary.ca
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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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