Hello,
I have a run that was working fine under parallel mdrun -pd and when I
then switched to domain decomposition I got:
Fatal error:
The size of the domain decomposition grid (1) does not match the
number of nodes (8). The total number of nodes is 8
while running like this:
/scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -mca
btl_sm_num_fifos 7 -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -mca
btl self,sm -machinefile $PBS_NODEFILE
/scratch/cneale/GPC/exe/intel/gromacs-4.0.5_berkpdfix/exec/bin/mdrun_openmpi
-deffnm md1 -dlb yes -npme -1 -cpt 1 -maxh 47.5 -cpi md1.cpt -px
coord.xvg -pf force.xvg -rdd 2.5
If I then add -dd 2 2 2 to the mdrun command line it runs fine.
I found a couple of things about this on the mailing list but nothing
that seemed entirely related to this case, e.g.:
http://oldwww.gromacs.org/pipermail/gmx-developers/2008-September/002721.html
I'm not sure there's a question here beyond the standard does it seem
as if I forgot to do something?.
Here's the log file:
Log file opened on Sat Jan 16 23:33:54 2010
Host: gpc-f105n032 pid: 24876 nodeid: 0 nnodes: 8
The Gromacs distribution was built Fri Jan 8 20:42:07 EST 2010 by
cne...@gpc-f101n084 (Linux 2.6.18-128.7.1.el5 x86_64)
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-)
/scratch/cneale/GPC/exe/intel/gromacs-4.0.5_berkpdfix/exec/bin/mdrun_openmpi
(-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
parameters of the run:
integrator = sd
nsteps = 875
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 0
nstxout = 875
nstvout = 875
nstfout = 875
nstenergy= 250
nstxtcout= 250
init_t = 0
delta_t = 0.004
xtcprec = 1000
nkx = 54
nky = 56
nkz = 96
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = No
epc = Berendsen
epctype = Semiisotropic
tau_p= 4
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi
