Amit, try the full line (with the "file")
Roland On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey <kgp.a...@gmail.com> wrote: > Hi Roland > > I tried 'which mdrun' but it only gives the path name of installation. Is > there any other way to know if the installation is 64 bit ot not? > > Thank you, > Amit > > > On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz <rol...@utk.edu> wrote: > >> 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/searchbefore >>>> >>> 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 >> > > > -- > 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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