[gmx-users] Error while scaling mdrun for more number of nodes.

[vivek sharma]

Hi Berk,
Thanks for your suggestion, It is working well now, Can you explain Why it
didn't worked for prime number?


Thanks & Regards,
Vivek
2009/9/25 Berk Hess <gmx3 at hotmail.com>

>  Hi,
>
> Why do you want to run on exactly 57 nodes?
> That is a nasty prime number.
> I guess 56 or 60 nodes would work fine.
>
> Berk
>
> ------------------------------
> Date: Fri, 25 Sep 2009 14:39:27 +0530
> From: viveksharma.iitb at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Error while scaling mdrun for more number of nodes.
>
>
> Hi There,
> I was trying to rum mdrun on large number of nodes. When I tried the run on
> 57 nodes, I got an error which is pasted below.
> -------------------------------------------------------
> Program mpi_mdrun_d, VERSION 4.0.3
> Source code file: domdec_setup.c, line: 147
>
> Fatal error:
> Could not find an appropriate number of separate PME nodes. i.e. >=
> 0.409991*#nodes (44) and <= #nodes/2 (57) and reasonable performance wise
> (grid_x=63, grid_y=63).
> Use the -npme option of mdrun or change the number of processors or the PME
> grid dimensions, see the manual for details.
> -------------------------------------------------------
> then I tried with -npme option as "-npme 20", this time it failed with the
> following error.
> -------------------------------------------------------
> Program mpi_mdrun_d, VERSION 4.0.3
> Source code file: domdec.c, line: 5858
>
> Fatal error:
> There is no domain decomposition for 94 nodes that is compatible with the
> given box and a minimum cell size of 1.025 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS
> settings
> Look in the log file for details on the domain decomposition
> -------------------------------------------------------
> Same system was running fine when I tried it on 4 nodes.
> I havn't used gromacs4.0 very well, so i don't understand these errors.
> Please suggest me a way to get out of these errors, It will be really
> helpful if anybody can explain me these errors.
>
> With thanks in advance.
>
> Thanks & Regards,
> Vivek
>
> ------------------------------
> What can you do with the new Windows Live? Find out<http://www.microsoft.com/windows/windowslive/default.aspx>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090925/2e09e801/attachment.html>