Hi, last time I checked (summer) I got 40bytes per atom and 294byes per atom/core (RF with 12Å cut-off)
100M atoms works with that cut-off on 128 16GB nodes with 8 cores. I haven't tried on less than 128 nodes. (See http://cmb.ornl.gov/research/petascale-md ) We could relatively easy fix the 40bytes per atom (no one had time so far to work on it) but I don't think there is much which can be done about the 294bytes per atom/core. On how many nodes do you want to simulate? Thus are you limited by the 40bytes per atom or the 294bytes per atom/core? Roland On Tue, Mar 2, 2010 at 11:31 PM, 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 > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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