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 >
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