<div>Hi Mark,</div><div><br></div>I am not using PME calculation.<div><br></div><div>I was hoping mdrun will do the cell allocation itself.</div><div><br></div><div>Thanks,<br>Amit</div><div><br></div><div><br><div class="gmail_quote">
On Fri, Feb 19, 2010 at 2:27 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 class="im">----- Original Message -----<br>
From: Amit Choubey <<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>><br>
Date: Saturday, February 20, 2010 8:51<br>
Subject: [gmx-users] domain decomposition and load balancing<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<br>
> Hi Everyone,<br>
> I am trying to run a simulation with the option "pbc=xy" turned on. I am using 64 processors for the simulation. The mdrun_mpi evokes the following error message before starting the md steps<br>
><br>
> There is no domain decomposition for 64 nodes that is compatible with the given box and a minimum cell size of 0.889862 nm> Change the number of nodes or mdrun option -rdd or -dds><br>
Look in the log file for details on the domain decomposition><br>
> This has to do with the load balancing in the domain decomposition version of mdrun. Can anyone suggest me how to set the option -rdd or -dds?<br>
<br>
</div>Those options are not normally the problem - but see the log file for info and mdrun -h for instructions.<br>
<br>
You should read up in the manual about domain decomposition, and see about choosing npme such that 64-npme is a number that is suitably composite that you can make a reasonably compact 3D grid so that the minimum cell size is not a constraint. Cells have to be large enough that all nonbonded interactions can be resolved in consultation with at most nearest-neighbour cells (and some other constraints).<br>
<br>
I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45 gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the cells to have the smallest diameter possible. Of course if your simulation box is so small that the 2D DD for pbc=xy will always lead to slabs that are too small in one dimension then you can't solve this problem with DD.<br>
<br>
If pbc=xy permits a 3D DD, then the same considerations apply. npme=19 gives 5x3x3 but npme=28 allows 4x3x3<br>
<div class="im"><br>
> Also the simulation runs fine on one node (with domain decomposition) and with particle decomposition but both of them extremely slow.><br>
<br>
</div>Well, that's normal...<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>