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

[Berk Hess]

You should read the manual, look in the index for domain decomposition.
For domain decomposition the unit-cell is divided into n sub-cells n=nx*ny*nz.
If n is a prime, you can only decompose in one dimension and 57 cells in one
dimension is often not possible due to certain restrictions.
Also 57 is inconvenient for PME, whether you use separate PME nodes or not.

Berk

Date: Fri, 25 Sep 2009 15:16:40 +0530
Subject: Re: [gmx-users] Error while scaling mdrun for more number of nodes.
From: viveksharma.iitb at gmail.com
To: gmx-users at gromacs.org

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
 		 	   		  
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