[gmx-users] gromacs memory usage

Roland Schulz roland at utk.edu
Wed Mar 3 07:03:05 CET 2010 

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
>> >>>    --
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>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
>> --
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>
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