On 4/14/13 11:23 PM, Stephanie Teich-McGoldrick wrote:
Dear all,
I am running a NPT simulation of 33,534 tip4P waters, and I am using domain
decomposition as the parallelization scheme. Previously, I had been using
Gromacs version 4.5.5 but have recently installed and switched to Gromacs
version 4.6.1. Using Gromacs 4.5.5 I can successfully run my water box
using domain decomposition over many different processor numbers. However
the same simulation returns the following error when I try Gromacs 4.6.1
"The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell size is: X 2.48 nm Y 2.48 nm Z 1.46 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.000 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.40 Y 0.40 Z 0.68
"
The above error occurred running over 16 nodes / 128 processors. The system
runs for version 4.6.1 for 1,8, and 16 processors but not for 32,64, or 128
processors.
I have tried other systems (including NVT, Berendsen/PR barostats,
anisotropic/isotropic ) at the higher number of processors using both
version 4.5.5 and 4.6.1 and get the same result - v4.5.5 runs fine while
v4.6.1 returns the error type listed above.
Is anyone else having a similar issue? Is there something I am not
considering? Any help would be greatly appreciated! The details I have used
to compile each code are below. My log files indicate that I am indeed
calling the correct executable at run time.
Based on what you've posted, I don't see any error. All of the above is normal
output.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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