[gmx-users] gromacs memory usage

Roland Schulz roland at utk.edu
Wed Mar 3 07:34:48 CET 2010 

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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>>>>
>>>>
>>>> --
>>>> 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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865-241-1537, ORNL PO BOX 2008 MS6309
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