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Log file opened on Tue May 24 13:19:05 2016
Host: tcbs14 pid: 16842 rank ID: 0 number of ranks: 1
:-) GROMACS - gmx mdrun, 2016-beta1-dev-20160524-3a9e67d (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2016-beta1-dev-20160524-3a9e67d
Executable: /nethome/lindahl/Code/gmx/git/development/builds/reference/bin/gmx
Data prefix: /nethome/lindahl/Code/gmx/git/development/gromacs (source tree)
Command line:
gmx mdrun -notunepme
GROMACS version: 2016-beta1-dev-20160524-3a9e67d
GIT SHA1 hash: 3a9e67dd55949e7daaa666e5bc4de95bcfece2c4
Branched from: f8a709034c4726936df1817d071899065f5d31f7 (21 newer local commits)
Precision: single
Memory model: 64 bit
MPI library: none
OpenMP support: disabled
GPU support: disabled
SIMD instructions: NONE
FFT library: fftpack (built-in)
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-1.9.0
Tracing support: disabled
Built on: Tue May 24 10:20:55 CEST 2016
Built by: lindahl@tcbs14 [CMAKE]
Build OS/arch: Linux 3.13.0-86-generic x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
Build CPU family: 6 Model: 63 Stepping: 2
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/gcc-4.7 GNU 4.7.3
C compiler flags: -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wno-unknown-pragmas -O0 -g
C++ compiler: /usr/bin/g++-4.7 GNU 4.7.3
C++ compiler flags: -std=c++0x -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -Wno-unknown-pragmas -O0 -g
Running on 1 node with total 8 cores, 16 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
Family: 6 Model: 63 Stepping: 2
Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: None
Hardware topology: Full, with devices
Sockets, cores, and logical processors:
Socket 0: [ 0 8] [ 1 9] [ 2 10] [ 3 11] [ 4 12] [ 5 13] [ 6 14] [ 7 15]
Numa nodes:
Node 0 (16717836288 bytes mem): 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Latency:
0
0 1.00
Caches:
L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
L3: 20971520 bytes, linesize 64 bytes, assoc. 20, shared 16 ways
PCI devices:
0000:02:00.0 Id: 10de:17c2 Class: 0x0300 Numa: 0
0000:03:00.0 Id: 10de:17f0 Class: 0x0300 Numa: 0
0000:00:19.0 Id: 8086:15a1 Class: 0x0200 Numa: 0
0000:00:1f.2 Id: 8086:8d02 Class: 0x0106 Numa: 0
Binary not matching hardware - you might be losing performance.
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: None
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------
++++ 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 --- -------- --------
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 20
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 10
bd-fric = 0
ld-seed = 1993
emtol = 0.001
emstep = 0.1
niter = 1
fcstep = 0
nstcgsteep = 200
nbfgscorr = 10
rtpi = 0.05
nstxout = 20
nstvout = 1
nstfout = 1
nstlog = 0
nstcalcenergy = 1
nstenergy = 1
nstxout-compressed = 0
compressed-x-precision = 200
cutoff-scheme = Verlet
nstlist = 10
ns-type = Grid
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 0.871
coulombtype = Reaction-Field
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 0.8
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 0.8
DispCorr = No
table-extension = 1
fourierspacing = 0.12
fourier-nx = 32
fourier-ny = 32
fourier-nz = 32
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
implicit-solvent = No
gb-algorithm = Still
nstgbradii = 1
rgbradii = 1
gb-epsilon-solvent = 80
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
tcoupl = V-rescale
nsttcouple = 10
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = No
pcoupltype = Isotropic
nstpcouple = -1
tau-p = 1
compressibility (3x3):
compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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}
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
QMMM = false
QMconstraints = 0
QMMMscheme = 0
MMChargeScaleFactor = 1
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = false
Shake-SOR = false
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = true
pull-cylinder-r = 1.5
pull-constr-tol = 1e-06
pull-print-COM = false
pull-print-ref-value = false
pull-print-components = false
pull-nstxout = 0
pull-nstfout = 0
pull-ngroups = 4
pull-group 0:
atom: not available
weight: not available
pbcatom = -1
pull-group 1:
atom (3):
atom[0,...,2] = {0,...,2}
weight: not available
pbcatom = 1
pull-group 2:
atom (3):
atom[0,...,2] = {3,...,5}
weight: not available
pbcatom = 4
pull-group 3:
atom (3):
atom[0,...,2] = {6,...,8}
weight: not available
pbcatom = 7
pull-ncoords = 2
pull-coord 0:
type = constraint
geometry = distance
group[0] = 1
group[1] = 2
dim (3):
dim[0]=1
dim[1]=1
dim[2]=1
origin (3):
origin[0]= 0.00000e+00
origin[1]= 0.00000e+00
origin[2]= 0.00000e+00
vec (3):
vec[0]= 0.00000e+00
vec[1]= 0.00000e+00
vec[2]= 0.00000e+00
start = false
init = 0.5
rate = 0
k = 0
kB = 0
pull-coord 1:
type = flat-bottom
geometry = distance
group[0] = 1
group[1] = 3
dim (3):
dim[0]=1
dim[1]=1
dim[2]=1
origin (3):
origin[0]= 0.00000e+00
origin[1]= 0.00000e+00
origin[2]= 0.00000e+00
vec (3):
vec[0]= 0.00000e+00
vec[1]= 0.00000e+00
vec[2]= 0.00000e+00
start = false
init = 0.4
rate = 0
k = 100
kB = 100
rotation = false
interactiveMD = false
disre = No
disre-weighting = Conservative
disre-mixed = false
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = no
cos-acceleration = 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}
simulated-tempering = false
E-x:
n = 0
E-xt:
n = 0
E-y:
n = 0
E-yt:
n = 0
E-z:
n = 0
E-zt:
n = 0
swapcoords = no
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 1292
ref-t: 298.15
tau-t: 0.5
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
NOTE: GROMACS was compiled without OpenMP and (thread-)MPI support, can only use a single CPU core
Cut-off's: NS: 0.871 Coulomb: 0.8 LJ: 0.8
Reaction-Field:
epsRF = 0, rc = 0.8, krf = 0.976562, crf = 1.875, epsfac = 138.935
The electrostatics potential has its minimum at r = 0.8
System total charge: 0.000
Potential shift: LJ r^-12: -1.455e+01 r^-6: -3.815e+00
Using plain C 4x4 non-bonded kernels
WARNING: Using the slow plain C kernels. This should
not happen during routine usage on supported platforms.
Using geometric Lennard-Jones combination rule
Removing pbc first time
NOTE: Thread affinity setting failed. This can cause performance degradation.
If you think your settings are correct, ask on the gmx-users list.
Will apply potential COM pulling
Will apply constraint COM pulling
with 2 pull coordinates and 4 groups
Pull group 1: 3 atoms, mass 18.015
Pull group 2: 3 atoms, mass 18.015
Pull group 3: 3 atoms, mass 18.015
++++ 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 --- -------- --------
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 ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
There are: 648 Atoms
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 278.251 K
Started mdrun on rank 0 Tue May 24 13:19:05 2016
Step Time
0 0.00000
Energies (kJ/mol)
LJ (SR) Coulomb (SR) COM Pull En. Potential Kinetic En.
1.63591e+03 -1.05821e+04 5.30006e+00 -8.94085e+03 1.49087e+03
Total Energy Conserved En. Temperature Pressure (bar)
-7.44997e+03 -7.44997e+03 2.77571e+02 5.49961e+02
Step Time
20 0.04000
Writing checkpoint, step 20 at Tue May 24 13:19:05 2016
Energies (kJ/mol)
LJ (SR) Coulomb (SR) COM Pull En. Potential Kinetic En.
1.54810e+03 -1.05128e+04 4.75037e+00 -8.96000e+03 1.52109e+03
Total Energy Conserved En. Temperature Pressure (bar)
-7.43891e+03 -7.45020e+03 2.83197e+02 -2.29797e+02
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 21 steps using 21 frames
Energies (kJ/mol)
LJ (SR) Coulomb (SR) COM Pull En. Potential Kinetic En.
1.56079e+03 -1.05602e+04 5.02706e+00 -8.99436e+03 1.55471e+03
Total Energy Conserved En. Temperature Pressure (bar)
-7.43964e+03 -7.45075e+03 2.89457e+02 -1.65579e+02
Total Virial (kJ/mol)
7.71047e+02 5.93857e+01 -1.29222e+02
5.94431e+01 2.20101e+02 1.55891e+02
-1.29190e+02 1.55898e+02 6.60133e+02
Pressure (bar)
-1.30463e+03 3.90070e+01 7.50825e+02
3.87120e+01 1.56147e+03 -8.86655e+02
7.50660e+02 -8.86687e+02 -7.53571e+02
M E G A - F L O P S A C C O U N T I N G
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
W3=SPC/TIP3p W4=TIP4p (single or pairs)
V&F=Potential and force V=Potential only F=Force only
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
Pair Search distance check 0.452638 4.074 2.3
NxN RF Elec. + LJ [V&F] 1.911824 103.238 57.8
NxN RF Electrostatics [V&F] 1.904944 68.578 38.4
Shift-X 0.001944 0.012 0.0
Virial 0.014553 0.262 0.1
Stop-CM 0.002592 0.026 0.0
Calc-Ekin 0.014256 0.385 0.2
Constraint-V 0.014256 0.114 0.1
Constraint-Vir 0.013608 0.327 0.2
Settle 0.004968 1.605 0.9
-----------------------------------------------------------------------------
Total 178.620 100.0
-----------------------------------------------------------------------------
R E A L C Y C L E A N D T I M E A C C O U N T I N G
On 1 MPI rank
Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
-----------------------------------------------------------------------------
Neighbor search 1 1 3 0.018 0.055 4.1
Force 1 1 21 0.347 1.053 78.9
NB X/F buffer ops. 1 1 39 0.000 0.001 0.1
COM pull force 1 1 21 0.000 0.000 0.0
Write traj. 1 1 21 0.064 0.193 14.5
Update 1 1 21 0.001 0.002 0.1
Constraints 1 1 21 0.004 0.012 0.9
Rest 0.006 0.019 1.4
-----------------------------------------------------------------------------
Total 0.440 1.335 100.0
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 0.389 0.440 88.4
(ns/day) (hour/ns)
Performance: 8.240 2.913
Finished mdrun on rank 0 Tue May 24 13:19:05 2016
|
