Hi all
My apologies for the lack of detail in my previous e-mail. I am trying
to run gromacs-4.0.7 for a system that I am studying. I have ran several
simulations on serial on my own computer that have to date worked fine.
I am now however trying to run the simulations on our local cluster in
parallel using mpich-1.2.7 and experiencing some difficulty. Please note
that the version of gromacs mentioned above is installed in parallel.
Right when I run a short simulation of 500 steps in one two or three nodes the
simulations
runs fine (takes about 10 seconds) and all the data is written to the
log file. However when I increase the nodes to 4 there is no stepwise
info written and the simulation does not progress. For clarity I have
attached the log file that iam getting for the 4 node simulation. I realise that
this maybe a cluster problem, but if anyone has experienced similar
issues I would be grateful of some feedback.
Here is the script I use:
#!/bin/bash
#PBS -N hex
#PBS -r n
#PBS -q longterm
#PBS -l walltime=00:30:00
#PBS -l nodes=4
cd $PBS_O_WORKDIR
export P4_GLOBMEMSIZE=100000000
/usr/local/bin/mpiexec mdrun -s
Also here is my path:
# Gromacs
export GMXLIB=/k/gavin/gromacs-4.0.7-parallel/share/gromacs/top
export PATH="$PATH:/k/gavin/gromacs-4.0.7-parallel/bin"
Cheers
Gavin
Log file opened on Wed Mar 3 14:46:51 2010
Host: kari57 pid: 32586 nodeid: 0 nnodes: 4
The Gromacs distribution was built Wed Jan 20 10:02:46 GMT 2010 by
ga...@kari (Linux 2.6.17asc64 x86_64)
:-) G R O M A C S (-:
GROningen MAchine for Chemical Simulation
:-) VERSION 4.0.7 (-:
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.
:-) mdrun (-:
++++ 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 = md
nsteps = 500
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 25
nstxout = 25
nstvout = 25
nstfout = 25
nstenergy = 25
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 35
nky = 35
nkz = 35
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Nose-Hoover
epc = Parrinello-Rahman
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 1.01325e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.01325e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01325e+00}
compress (3x3):
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 1.5
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.5
vdwtype = Switch
rvdw_switch = 1.2
rvdw = 1.4
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 13821
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Initializing Domain Decomposition on 4 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.867 nm, Bond, atoms 535 536
multi-body bonded interactions: 0.867 nm, Fourier Dih., atoms 508 515
Minimum cell size due to bonded interactions: 0.953 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 4 cells with a minimum initial size of 1.191 nm
The maximum allowed number of cells is: X 8 Y 8 Z 8
Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0
Using two step summing over 2 groups of on average 2.0 processes
Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.480244 nm for Ewald
Using shifted Lennard-Jones, switch between 1.2 and 1.4 nm
Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.4
System total charge: -0.000
Generated table with 1250 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1250 data points for LJ6Switch.
Tabscale = 500 points/nm
Generated table with 1250 data points for LJ12Switch.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Removing pbc first time
Linking all bonded interactions to atoms
There are 11072 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1
The initial domain decomposition cell size is: X 2.50 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.500 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.500 nm
multi-body bonded interactions (-rdd) 1.500 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1
The minimum size for domain decomposition cells is 1.500 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.60
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.500 nm
two-body bonded interactions (-rdd) 1.500 nm
multi-body bonded interactions (-rdd) 1.500 nm
Making 1D domain decomposition grid 4 x 1 x 1, home cell index 0 0 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 4608 Atoms
Charge group distribution at step 0: 35 734 751 16
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