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: [email protected]
To: [email protected]
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
