[gmx-users] Large Periodic Molecule
rogan at ks.uiuc.edu
Tue Nov 30 21:16:28 CET 2010
I am having a problem, where my simulation fails when I run on
multiple nodes. On an 8-core machine, my job runs fine, but when I
run on 240 processors (20 12-core nodes), I get the errors
"U-B of 59312 missing 1"
"Software inconsistency error:
Some interactions seem to be assigned multiple times"
I can use the .tpr file from the supercomputer (the 240 core job) and
it runs fine on my 8-core machine as well.
I believe the problem is that I am simulating a system containing an
"infinite" slab of amorphous silica, which is one large molecule,
bonded to itself across the periodic boundaries. I am using the
charmm-compatible parameters developed by Cruz-Chu, Aksimentiev and
Schulten (http://www.ks.uiuc.edu/Research/silica/SiO2ff.html), so I
have each atom as its own charge group, and each atom is harmonically
restrained to its initial coordinates (I also added in angle terms
with small force constants so that I could use the GBSA solver, which
requires all bonded triplets to have an angle defined).
From my discussions with others, I have heard that it is common to
have such problems with "infinite" molecules, where not all
information about bonded interactions are shared between nodes. One
solution might be to use the old "particle decomposition"
parallelization, but I would like to use domain decomposition for its
Has anyone had any experience with this?
More information about the gromacs.org_gmx-users