[gmx-users] gromacs memory usage

Roland Schulz roland at utk.edu
Wed Mar 3 16:34:44 CET 2010 

Hi,

ok then it is compiled in 64bit.

You didn't say how many cores each node has and on how many nodes you want
to run.

Roland

On Wed, Mar 3, 2010 at 4:32 AM, Amit Choubey <kgp.amit at gmail.com> wrote:

> 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 <roland at utk.edu> wrote:
>
>> Amit,
>>
>> try the full line (with the "file")
>>
>> Roland
>>
>> On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey <kgp.amit at 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 <roland at 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.amit at 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 <tsjerkw at 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.amit at 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.Abraham at 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.abraham at anu.edu.au
>>>>>> >>> <mailto:mark.abraham at anu.edu.au>> wrote:
>>>>>> >>>
>>>>>> >>>    ----- Original Message -----
>>>>>> >>>    From: Amit Choubey <kgp.amit at gmail.com <mailto:
>>>>>> kgp.amit at gmail.com>>
>>>>>> >>>    Date: Saturday, February 27, 2010 10:17
>>>>>> >>>    Subject: Re: [gmx-users] gromacs memory usage
>>>>>> >>>    To: Discussion list for GROMACS users <gmx-users at gromacs.org
>>>>>> >>>    <mailto:gmx-users at 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 at gromacs.org
>>>>>> >>>    <mailto:gmx-users at 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-request at gromacs.org
>>>>>> >>>    <mailto:gmx-users-request at gromacs.org>.
>>>>>> >>>    Can't post? Read
>>>>>> http://www.gromacs.org/mailing_lists/users.php
>>>>>> >>>
>>>>>> >>>
>>>>>> >> --
>>>>>> >> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>>>>>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>> >
>>>>>> >
>>>>>> > --
>>>>>> > gmx-users mailing list    gmx-users at 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-request at 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 at 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-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> gmx-users mailing list    gmx-users at 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-request at 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 at 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-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>
>>>
>>> --
>>> gmx-users mailing list    gmx-users at 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-request at 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 at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
> --
> gmx-users mailing list    gmx-users at 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-request at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100303/a0a8834f/attachment.html>

More information about the gromacs.org_gmx-users mailing list