[gmx-users] gromacs memory usage

Amit Choubey kgp.amit at gmail.com
Wed Mar 3 10:32:44 CET 2010 

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