On 8/29/13 2:24 AM, Jernej Zidar wrote:
Hi,
I ran some MD simulations (NPT ensemble) and a series of simulations
to determine the free energy of water solvation of a not to big
molecule.
I noticed that while I was able to run the MD simulations using all
the CPUs (or threads) in my workstation (12 CPUs or 24 threads,
respectively), whereas during free energy I can use 2 CPUs at most. If
I try to use more, the simulations would crash stating:
Program mdrun, VERSION 4.6.3
Source code file: /home/zidar/utils/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 4.52667 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
- - - -
I can use more CPUs only if I switch from domain decomposition to
particle decomposition scheme. The size of the systems evaluated is
11.92513nm x 5.44212nm x 5.35234nm with ~30.000 atoms, so I assume
the size of the system is not an issue.
Big question: Why is that so? Why can I use more CPUs for 'regular'
MD but only two for free energy simulations?
This issue is discussed very frequently, particularly in the context of free
energy calculations. Please refer to the list archive and consider the effect
that couple_intramol setting has on the DD setup.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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