Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped
If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey <kgp.a...@gmail.com> wrote: > 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 >> > > > -- > 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
-- 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
