You are right. With MARTINI you often need an rdd bigger than default.
1.4 is reasonable.
On Jun 29, 2009, at 19:33, Michael Lerner <[email protected]>
wrote:
Hi,
I have a 72-lipid DPPC (MARTINI) system that I ran for 400ns in
GROMACS 3.3.3. I picked a snapshot from the middle (~100ns), so I
know it should be equilibrated and be able to run for several
hundred nanoseconds. If I use GROMACS 4.0.3 (or 4.0.5) and 1, 2, or
4 processors, everything is great. However, if I use more than 4
processors (either on a single node or on two nodes), I get errors
like this:
------------- begin error -------------
vol 0.87 imb F 2% step 350900, will finish Sat Jun 27 23:16:51 2009
vol 0.84 imb F 4% step 351000, will finish Sat Jun 27 23:16:49 2009
A list of missing interactions:
G96Angle of 576 missing 1
Molecule type 'DPP'
the first 10 missing interactions, except for exclusions:
G96Angle atoms 2 3 5 global 254 255
257
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.5
Source code file: domdec_top.c, line: 341
Fatal error:
1 of the 1368 bonded interactions could not be calculated because
some atoms involved moved further apart than the multi-body cut-off
distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see
option -rdd, for pairs and tabulated bonds also see option -ddcheck
-------------------------------------------------------
"Pump Up the Volume Along With the Tempo" (Jazzy Jeff)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
gcq#177: "Pump Up the Volume Along With the Tempo" (Jazzy Jeff)
h199:0.MPID_Abort: h199:0.MPI Abort by user Aborting program !
h199:0.MPID_CH_Abort: h199:0.Aborting program!
Abort on node h199 due to MPI_Abort (type 2)
-------------- end error --------------
This error happens on a different step depending on how many
processors I use, whether I use gfortran or ifort, etc.
Am I understanding correctly that I have a triplet of particles A-B-
C where the bond-angle term cannot be calculated because the
distance between A and C is greater than 1.2 nm?
Is dynamic load balancing causing the error to happen at different
steps for different numbers of processors?
It appears that I can fix the problem by setting -rdd=1.4 on the
command line, but I'd like to make sure I'm not just sweeping
something else under the rug.
For what it's worth, the equilibrium bond lengths in MARTINI's DPPC
model are all either .47 or .37 nm. In the -rdd=1.4 run, the maximum
bond lengths range from .68 to .71 nm depending on the particular
bond and the A-C distances from the A-B-C triplets range from 1.09
to 1.21.
Also, is there any chance that the default settings will get this
right for my system in the future?
Thanks,
-michael
--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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