Hi Mark,<div><br></div><div>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.</div><div><br></div><div>I did find some document which says one need (50bytes)*NATOMS on master node, also one needs</div>
<div> (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true?</div><div><br></div><div><br></div><div>Thank you,</div><div>amit <br><br><div class="gmail_quote">On Fri, Feb 26, 2010 at 2:57 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:)<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5">----- Original Message -----<br>
From: Amit Choubey <<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>><br>
Date: Friday, February 26, 2010 20:05<br>
Subject: [gmx-users] gromacs memory usage<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<br>
> Hi,<br>
> I am having trouble with running gromacs with a large system. I am trying to use several processors for the md. The error is a memory allocation error and it might be due to low RAM or large no of particles. I want to know the detailed memory usage of mdrun ie say for N atoms how much memory does the master node need and then also whats the memory requirement for the other nodes. By master node i mean the node that does the domain decomposition calculation etc during the start of mdrun. A webpage which describes the memory requirement at various stages during mdrun will be very helpful. <br>
<br>
</div></div>The master node does not have a significantly larger memory footprint than any other, during setup or the run... For example, a 50K-atom system runs fine on 64 BlueGene/L processors with a hard limit of 500MB per processor for OS+code+data+MPI.<br>
<br>
Does your system run on 1 processor, with and without MPI? How much (physical) memory do you have for how large a system?<br>
<br>
Mark<br>
<font color="#888888">--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</font></blockquote></div><br></div>