For example, Run 1
Started mdrun on node 0 Fri May 22 22:53:51 2009
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
1.95406e+02 1.04746e+02 4.97704e+01 4.13260e+01
1.40158e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.60139e+03 -2.64656e+04 -2.20714e+04 4.03780e+03
-1.80336e+04
Temperature Pressure (bar) Cons. rmsd ()
3.03142e+02 -8.46977e+02 1.92470e-05
DD step 9 load imb.: force 29.9%
At step 10 the performance loss due to force load imbalance is 8.6 %
NOTE: Turning on dynamic load balancing
DD step 99 vol min/aver 0.731 load imb.: force 6.9%
Step Time Lambda
100 0.20000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.05310e+02 1.30129e+02 5.63474e+01 1.81814e+01
1.44270e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.69491e+03 -2.69624e+04 -2.24148e+04 4.19456e+03
-1.82203e+04
Temperature Pressure (bar) Cons. rmsd ()
3.14910e+02 -5.19031e+02 1.76248e-05
DD load balancing is limited by minimum cell size in dimension Y
DD step 199 vol min/aver 0.766! load imb.: force 10.7%
Step Time Lambda
200 0.40000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.20550e+02 1.09068e+02 6.93319e+01 5.32511e+01
1.43458e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.78241e+03 -2.70319e+04 -2.23627e+04 4.13455e+03
-1.82281e+04
Temperature Pressure (bar) Cons. rmsd ()
3.10405e+02 -5.01205e+02 1.70105e-05
DD load balancing is limited by minimum cell size in dimension Y
DD step 299 vol min/aver 0.750! load imb.: force 3.3%
Step Time Lambda
300 0.60000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.17474e+02 8.65489e+01 5.24995e+01 4.72592e+01
1.44419e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
3.17643e+03 -2.72841e+04 -2.22597e+04 3.95024e+03
-1.83095e+04
Temperature Pressure (bar) Cons. rmsd ()
2.96568e+02 1.40098e+03 1.55861e-05
DD step 399 vol min/aver 0.700 load imb.: force 5.9%
Step Time Lambda
400 0.80000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.43143e+02 9.93116e+01 7.16796e+01 4.63666e+01
1.46722e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.84150e+03 -2.70065e+04 -2.22372e+04 4.05976e+03
-1.81775e+04
Temperature Pressure (bar) Cons. rmsd ()
3.04791e+02 2.48551e+02 1.61141e-05
DD step 499 vol min/aver 0.678 load imb.: force 6.6%
Step Time Lambda
500 1.00000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.19638e+02 8.98359e+01 8.99946e+01 5.16612e+01
1.46338e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.80267e+03 -2.68507e+04 -2.21335e+04 4.14195e+03
-1.79916e+04
Temperature Pressure (bar) Cons. rmsd ()
3.10961e+02 -1.17210e+02 1.71420e-05
DD step 599 vol min/aver 0.678 load imb.: force 6.7%
Step Time Lambda
600 1.20000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.32938e+02 1.04322e+02 7.11343e+01 2.16046e+01
1.45770e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
3.07425e+03 -2.71320e+04 -2.21700e+04 4.17285e+03
-1.79972e+04
Temperature Pressure (bar) Cons. rmsd ()
3.13281e+02 5.60002e+01 1.97532e-05
DD step 699 vol min/aver 0.664 load imb.: force 13.1%
----------------------------------------------------------------------------
-------------------------------------
Run 2
Step 0 is the same, but then the results start to differ more and
more:
Started mdrun on node 0 Sat Jun 6 14:38:03 2009
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
1.95406e+02 1.04746e+02 4.97704e+01 4.13260e+01
1.40158e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.60139e+03 -2.64656e+04 -2.20714e+04 4.03780e+03
-1.80336e+04
Temperature Pressure (bar) Cons. rmsd ()
3.03142e+02 -8.46977e+02 1.92470e-05
DD step 9 load imb.: force 32.9%
At step 10 the performance loss due to force load imbalance is 8.8 %
NOTE: Turning on dynamic load balancing
DD load balancing is limited by minimum cell size in dimension Y
DD step 99 vol min/aver 0.711! load imb.: force 13.3%
Step Time Lambda
100 0.20000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.05314e+02 1.30130e+02 5.63508e+01 1.81808e+01
1.44270e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.69491e+03 -2.69627e+04 -2.24151e+04 4.19468e+03
-1.82204e+04
Temperature Pressure (bar) Cons. rmsd ()
3.14919e+02 -5.13520e+02 1.76037e-05
DD load balancing is limited by minimum cell size in dimension Y Z
DD step 199 vol min/aver 0.760! load imb.: force 12.7%
Step Time Lambda
200 0.40000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.20600e+02 1.09011e+02 6.92931e+01 5.32915e+01
1.43453e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.78045e+03 -2.70297e+04 -2.23626e+04 4.13378e+03
-1.82288e+04
Temperature Pressure (bar) Cons. rmsd ()
3.10348e+02 -5.07193e+02 1.69736e-05
DD load balancing is limited by minimum cell size in dimension Y
DD step 299 vol min/aver 0.757! load imb.: force 12.1%
Step Time Lambda
300 0.60000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.18647e+02 8.76939e+01 5.26630e+01 4.67556e+01
1.44438e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
3.15118e+03 -2.72121e+04 -2.22108e+04 3.91294e+03
-1.82978e+04
Temperature Pressure (bar) Cons. rmsd ()
2.93768e+02 1.36397e+03 1.56756e-05
DD load balancing is limited by minimum cell size in dimension Y Z
DD step 399 vol min/aver 0.688! load imb.: force 12.6%
Step Time Lambda
400 0.80000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.37290e+02 9.91231e+01 6.10010e+01 3.87031e+01
1.46621e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.68805e+03 -2.68308e+04 -2.22404e+04 4.05083e+03
-1.81896e+04
Temperature Pressure (bar) Cons. rmsd ()
3.04120e+02 -2.55369e+02 1.63518e-05
DD load balancing is limited by minimum cell size in dimension Z
DD step 499 vol min/aver 0.677! load imb.: force 10.1%
Step Time Lambda
500 1.00000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.30361e+02 8.47035e+01 8.84842e+01 4.44614e+01
1.44045e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.91452e+03 -2.70665e+04 -2.22635e+04 4.18886e+03
-1.80746e+04
Temperature Pressure (bar) Cons. rmsd ()
3.14483e+02 1.47268e+02 1.75008e-05
DD load balancing is limited by minimum cell size in dimension Z
DD step 599 vol min/aver 0.692! load imb.: force 7.7%
Step Time Lambda
600 1.20000 0.00000
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14
Coulomb-14
2.19896e+02 9.93832e+01 6.10071e+01 2.95745e+01
1.45874e+03
LJ (SR) Coulomb (SR) Potential Kinetic En. Total
Energy
2.81555e+03 -2.71300e+04 -2.24458e+04 4.17303e+03
-1.82728e+04
Temperature Pressure (bar) Cons. rmsd ()
3.13294e+02 -3.05949e+02 1.64990e-05
DD load balancing is limited by minimum cell size in dimension Z
DD step 699 vol min/aver 0.719! load imb.: force 4.9%
----------------------------------------------------------------------------
--------------------
Any ideas why I am seeing this?
Here is the initial mdrun printed input info:
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) 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.
:-) mdrun_mpi (-:
++++ 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 = 5000000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 50
nstvout = 0
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
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 = Berendsen
epc = No
epctype = Isotropic
tau_p = 0.5
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
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 = 0.0001
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: 284.733 2919.27
ref_t: 300 300
tau_t: 0.1 0.1
anneal: No No
ann_npoints: 0 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 12 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: 0.597 nm, LJ-14, atoms 5 18
multi-body bonded interactions: 0.597 nm, Proper Dih., atoms 5 18
Minimum
cell size due to bonded interactions: 0.657 nm Maximum distance for 5
constraints, at 120 deg. angles, all-trans: 0.820 nm Estimated
maximum
distance required for P-LINCS: 0.820 nm This distance will limit
the DD cell
size, you can override this with -rcon Scaling the initial minimum
size with
1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 12 cells with a
minimum initial size of 1.025 nm The maximum allowed number of
cells is: X 2
Y 3 Z 2 Domain decomposition grid 2 x 3 x 2, separate PME nodes 0
Domain
decomposition nodeid 0, coordinates 0 0 0
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: 1.000
Generated table with 1000 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 487 molecules.
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Removing pbc first time
Initializing Parallel LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular
simulation J.
Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------
The number of constraints is 144
There are inter charge-group constraints, will communicate selected
coordinates each lincs iteration
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms
for Rigid
Water Models J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Linking all bonded interactions to atoms
The initial number of communication pulses is: X 1 Y 1 Z 1 The
initial
domain decomposition cell size is: X 1.21 nm Y 1.05 nm Z 1.11 nm
The maximum allowed distance for charge groups involved in
interactions is:
non-bonded interactions 1.000 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
atoms separated by up to 5 constraints (-rcon) 1.054 nm
When dynamic load balancing gets turned on, these settings will
change to:
The maximum number of communication pulses is: X 1 Y 2 Z 1 The
minimum size
for domain decomposition cells is 0.826 nm The requested allowed
shrink of
DD cells (option -dds) is: 0.80 The allowed shrink of domain
decomposition
cells is: X 0.82 Y 0.78 Z 0.90 The maximum allowed distance for
charge
groups involved in interactions is:
non-bonded interactions 1.000 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 0.826 nm
atoms separated by up to 5 constraints (-rcon) 0.826 nm
Making 3D domain decomposition grid 2 x 3 x 2, 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
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular
dynamics with coupling to an external bath J. Chem. Phys. 81 (1984)
pp.
3684-3690
-------- -------- --- Thank You --- -------- --------
There are: 1604 Atoms
Charge group distribution at step 0: 45 50 45 42 46 41 44 45 41 47
51 47
Grid: 4 x 4 x 4 cells
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0) RMS relative
constraint
deviation after constraining: 2.38e-05 Initial temperature: 299.151 K
Which is, of course, identical between the runs.
Thanks for any comments/ advice.
Jim
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