[gmx-users] seriell but parallel ???
David van der Spoel
spoel at xray.bmc.uu.se
Fri May 18 22:41:11 CEST 2007
Nicolas Schmidt wrote:
> Dear gromacs-users,
> First of all thanks to all contributers of the answers considering my first issue, actually this was my first simulation on gromacs, so maybe this explains my kind of unnecessary questions ;-)
> Anyway, again a probably easy to solve problem:
> I only got the possibility to run all the gromacs programs on a single processor engine, in addition to that I have access to a unix cluster (206 x 2 Intel Xeon 3.2 GHz), where ONLY mdrun_mpi was installed. It's in heavy use, so I can't just try if something works, I have to wait a day or two, till I can find out, if a simulation worked or not.
> I read in the manual, that I would have to use the same amount of nodes (option -np of mdrun_mpi) as I typed in at grompp, but this option doesn't exist in my version of grompp installed on an serial computer.
> So my question is:
> Is this a problem?
> In the case of an existing problem, is there any possibility to solve it, without installing anything on the cluster?
> Thanks in advance to everyone contributing. and just to everybody:
> Have a nice weekend.
You can run gromacs in parallel on a single computer to test things.
Just enable mpi when compiling. It will be slightly slower (running two
processes on one CPU compared to one on one CPU), but fine for testing.
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://folding.bmc.uu.se
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