Re: [gmx-users] How to tune number of CPUs for a run?
Hi Pablo,
the tool g_tune_pme helps to find the optimum setting on a given
number of
processors. If you do not want to use the newest git version of
gromacs, there is also a version for gromacs 4.0.5 available here:
http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/
If grompp reports a lower PME/PP ratio than 0.25, it will be helpful
for the
scaling on large numbers of cores. On the other hand, having much more
than a third of all processors doing PME will very likely be very bad
if you want
to scale to a large number of processors.
Typical PME setups, like cutoffs at 1 nm, fourier grid spacing about
0.135 nm,
will result in PME/PP ratios of 0.25-0.33 though.
If you want to tune the number of CPUs for a run you need to think about
whether you want the highest performance possible or a decent
performance
without wasting CPU time due to bad scaling. For both settings it
helps a
lot to derive the performance numbers as a function of the number of
processors.
Carsten
On Nov 4, 2009, at 3:52 PM, Pablo Englebienne wrote:
Hi all,
I'm having some trouble running simulations with increasing number
of CPUs. What parameters should I modify to make sure that the
simulation would run with a specific number of processors? Or,
having access to a large number of processors, how to select the
number of CPUs to request?
Besides this, should the PP/PME reported by grompp always fall in
the range 0.25-0.33? What if it is lower (e.g., 0.16)?
I'm attaching an mdrun logfile of a failed run.
Thanks for suggestions,
Pablo
--
Pablo Englebienne, PhD
Institute of Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349
Log file opened on Mon Nov 2 18:23:16 2009
Host: node052 pid: 22760 nodeid: 0 nnodes: 16
The Gromacs distribution was built Thu Oct 29 14:19:59 CET 2009 by
pengle...@st-hpc-main (Linux 2.6.18-128.7.1.el5 x86_64)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) 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.
:-) /home/penglebie/software/bin/mdrun_openmpi (double
precision) (-:
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 = 5
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstenergy= 1000
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 40
nky = 40
nkz = 40
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= TRUE
bShakeSOR= FALSE
etc = V-rescale
epc = Parrinello-Rahman
epctype = Isotropic
tau_p= 5
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e
[gmx-users] How to tune number of CPUs for a run?
Hi all,
I'm having some trouble running simulations with increasing number of
CPUs. What parameters should I modify to make sure that the simulation
would run with a specific number of processors? Or, having access to a
large number of processors, how to select the number of CPUs to request?
Besides this, should the PP/PME reported by grompp always fall in the
range 0.25-0.33? What if it is lower (e.g., 0.16)?
I'm attaching an mdrun logfile of a failed run.
Thanks for suggestions,
Pablo
--
Pablo Englebienne, PhD
Institute of Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349
Log file opened on Mon Nov 2 18:23:16 2009
Host: node052 pid: 22760 nodeid: 0 nnodes: 16
The Gromacs distribution was built Thu Oct 29 14:19:59 CET 2009 by
pengle...@st-hpc-main (Linux 2.6.18-128.7.1.el5 x86_64)
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) 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.
:-) /home/penglebie/software/bin/mdrun_openmpi (double precision) (-:
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 = 5
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstenergy= 1000
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 40
nky = 40
nkz = 40
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= TRUE
bShakeSOR= FALSE
etc = V-rescale
epc = Parrinello-Rahman
epctype = Isotropic
tau_p= 5
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]={ 1.0e-04, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 1.0e-04, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 1.0e-04}
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= 1.4
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.4
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solv
