Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB).
I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > 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-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 > > > > > > -- > > 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 > > > > > > -- > 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 >
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