> > 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. > > Thank you, > > Amit > On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > ----- Original Message ----- > From: Amit Choubey <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> > > > 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 > 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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