[gmx-users] parallel simulations
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 $PBS_O_WORKDIR
export P4_GLOBMEMSIZE=1
/usr/local/bin/mpiexec mdrun -s
Also here is my path:
# Gromacs
export GMXLIB=/k/gavin/gromacs-4.0.7-parallel/share/gromacs/top
export PATH="$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, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.01325e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.01325e+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+
[gmx-users] parallel simulations
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 $PBS_O_WORKDIR
export P4_GLOBMEMSIZE=1
/usr/local/bin/mpiexec mdrun -s
Also here is my path:
# Gromacs
export GMXLIB=/k/gavin/gromacs-4.0.7-parallel/share/gromacs/top
export PATH="$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, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.01325e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.01325e+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+
