Hi Roland, It says
gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz <rol...@utk.edu> wrote: > 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 > > -- > 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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