[gmx-users] gromacs memory usage
kgp.amit at gmail.com
Wed Mar 3 05:31:34 CET 2010
Yes thats one way to go about it. But it would have been great if i could
get a rough estimation.
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
>> 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
>> 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
> 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.
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