Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time.
Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey <kgp.a...@gmail.com> wrote: > Hi Mark, > > Yes thats one way to go about it. But it would have been great if i could > get a rough estimation. > > Thank you. > > amit > > > On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham <mark.abra...@anu.edu.au> > wrote: >> >> On 3/03/2010 12:53 PM, Amit Choubey wrote: >>> >>> Hi Mark, >>> >>> I quoted the memory usage requirements from a presentation by Berk >>> Hess, Following is the link to it >>> >>> >>> >>> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf >>> >>> l. In that presentation on pg 27,28 Berk does talk about memory >>> usage but then I am not sure if he referred to any other specific >>> thing. >>> >>> My system only contains SPC water. I want Berendsen T coupling and >>> Coulomb interaction with Reaction Field. >>> >>> I just want a rough estimate of how big of a system of water can be >>> simulated on our super computers. >> >> Try increasingly large systems until it runs out of memory. There's your >> answer. >> >> Mark >> >>> On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham <mark.abra...@anu.edu.au >>> <mailto:mark.abra...@anu.edu.au>> wrote: >>> >>> ----- Original Message ----- >>> From: Amit Choubey <kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>> >>> Date: Saturday, February 27, 2010 10:17 >>> Subject: Re: [gmx-users] gromacs memory usage >>> To: Discussion list for GROMACS users <gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org>> >>> >>> > Hi Mark, >>> > We have few nodes with 64 GB memory and many other with 16 GB of >>> memory. I am attempting a simulation of around 100 M atoms.> >>> >>> Well, try some smaller systems and work upwards to see if you have a >>> limit in practice. 50K atoms can be run in less than 32GB over 64 >>> processors. You didn't say whether your simulation system can run on >>> 1 processor... if it does, then you can be sure the problem really >>> is related to parallelism. >>> >>> > I did find some document which says one need (50bytes)*NATOMS on >>> master node, also one needs >>> > (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute >>> nodes. Is this true?> >>> >>> In general, no. It will vary with the simulation algorithm you're >>> using. Quoting such without attributing the source or describing the >>> context is next to useless. You also dropped a parenthesis. >>> >>> Mark >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
