[gmx-users] GROMACS Parallel Runs
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 2 16:37:36 CEST 2006
> Hi David,
>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] GROMACS Parallel Runs
>> Date: Mon, 02 Oct 2006 16:04:45 +0200
>> Sunny wrote:
>>> Hi all,
>>> Thanks for your proposed solutions. I will try to set fourier_nx to
>>> 64 first.
>>> Do I also need to set fourier_nx to a bigger number, e.g. 256, when I
>>> want to run on 128 CPUs?
>> at least twice the number of CPUs.
> Sorry, I mean I will set fourier_nx to 128 first to see if it can work
> on 64 CPUs.
>>> As I am using a regional supercomputing system, it might be not easy
>>> to have gmx updated to the CVS version in short time. I will contact
>>> the system support to see if they would do the update.
>> You can easily do it yourself.
> Do you mean I can install gmx in my user space instead of updating the
> version under the root directory?
Of course, it is quite straightforward. Check instruction on the website
for downloading and installingthe CVS version. We do in general
discourage people to use CVS versions for production, because of the
problem of reproducibility. It is however very useful to be able to
install it yourself.
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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