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md_0_1_Version5.1.1.log
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md_0_1_Version5.1.1.log
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Log file opened on Thu Jan 16 13:41:21 2020
Host: node-h00a-022.myriad.ucl.ac.uk pid: 275502 rank ID: 0 number of ranks: 1
:-) GROMACS - gmx mdrun, VERSION 5.1.1 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
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 5.1.1
Executable: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx
Data prefix: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2
Command line:
gmx mdrun -deffnm md_0_1 -cpi -append
GROMACS version: VERSION 5.1.1
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support: disabled
OpenCL support: disabled
invsqrt routine: gmx_software_invsqrt(x)
SIMD instructions: SSE4.1
FFT library: Intel MKL
RDTSCP usage: enabled
C++11 compilation: enabled
TNG support: enabled
Tracing support: disabled
Built on: Tue 10 Nov 16:40:14 GMT 2015
Built by: ccspapp@node-y00a-002 [CMAKE]
Build OS/arch: Linux 3.10.0-123.20.1.el7.x86_64 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
Build CPU family: 6 Model: 44 Stepping: 2
Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
C compiler: /shared/ucl/apps/intel/2015/composer_xe_2015.2.164/bin/intel64/icc Intel 15.0.0.20150121
C compiler flags: -msse4.1 -mkl=sequential -std=gnu99 -w3 -wd177 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
C++ compiler: /shared/ucl/apps/intel/2015/composer_xe_2015.2.164/bin/intel64/icpc Intel 15.0.0.20150121
C++ compiler flags: -msse4.1 -std=c++0x -w3 -wd177 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd1782 -wd2282 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
Boost version: 1.55.0 (internal)
Number of logical cores detected (36) does not match the number reported by OpenMP (12).
Consider setting the launch configuration manually!
Running on 1 node with total 36 logical cores
Hardware detected:
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz
Family: 6 model: 85 stepping: 4
CPU features: aes apic avx avx2 avx512f avx512cd clfsh cmov cx8 cx16 f16c fma htt lahf_lm 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: SSE4.1
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: SSE4.1
++++ 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 --- -------- --------
Changing nstlist from 10 to 20, rlist from 1 to 1.035
Non-default thread affinity set, disabling internal thread affinity
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 1000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 2947599496
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 50000
nstvout = 0
nstfout = 0
nstlog = 50000
nstcalcenergy = 100
nstenergy = 50000
nstxout-compressed = 50000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 20
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 1.035
rlistlong = 1.035
nstcalclr = 10
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.16
fourier-nx = 72
fourier-ny = 72
fourier-nz = 72
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 = Parrinello-Rahman
pcoupltype = Isotropic
nstpcouple = 10
tau-p = 2
compressibility (3x3):
compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
ref-p (3x3):
ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+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 = TRUE
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 = FALSE
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
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 13150.8 242679
ref-t: 335 335
tau-t: 0.1 0.1
annealing: No No
annealing-npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Initializing Domain Decomposition on 36 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.456 nm, LJ-14, atoms 321 1321
multi-body bonded interactions: 0.456 nm, Ryckaert-Bell., atoms 321 1321
Minimum cell size due to bonded interactions: 0.501 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.872 nm
Estimated maximum distance required for P-LINCS: 0.872 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.15
Will use 30 particle-particle and 6 PME only ranks
This is a guess, check the performance at the end of the log file
Using 6 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 30 cells with a minimum initial size of 1.089 nm
The maximum allowed number of cells is: X 10 Y 10 Z 10
Domain decomposition grid 6 x 5 x 1, separate PME ranks 6
PME domain decomposition: 6 x 1 x 1
Interleaving PP and PME ranks
This rank does only particle-particle work.
Domain decomposition rank 0, coordinates 0 0 0
Using 36 MPI threads
Using 1 OpenMP thread per tMPI thread
Will do PME sum in reciprocal space for electrostatic interactions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, 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 --- -------- --------
Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1.035 Coulomb: 1 LJ: 1
Long Range LJ corr.: <C6> 3.1973e-04
System total charge: -0.000
Generated table with 1017 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1017 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1017 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1017 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1017 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1017 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
Using SSE4.1 4x4 non-bonded kernels
Using geometric Lennard-Jones combination rule
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 6700
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
The initial domain decomposition cell size is: X 1.82 nm Y 2.18 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.035 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.035 nm
multi-body bonded interactions (-rdd) 1.035 nm
atoms separated by up to 5 constraints (-rcon) 1.819 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1
The minimum size for domain decomposition cells is 1.035 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.57 Y 0.47
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.035 nm
two-body bonded interactions (-rdd) 1.035 nm
multi-body bonded interactions (-rdd) 1.035 nm
atoms separated by up to 5 constraints (-rcon) 1.035 nm
Making 2D domain decomposition grid 6 x 5 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
++++ 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: 127790 Atoms
Atom distribution over 30 domains: av 4259 stddev 90 min 4193 max 4370
Initial temperature: 334.497 K
Started mdrun on rank 0 Thu Jan 16 13:41:22 2020
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
1.43311e+04 8.04885e+02 5.97989e+03 9.93770e+03 5.15922e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
3.30000e+05 -1.67997e+04 -2.40102e+06 1.37285e+04 -1.99144e+06
Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar)
3.55717e+05 -1.63573e+06 3.34464e+02 -2.14805e+02 -1.95361e+01
Constr. rmsd
2.79905e-05
DD step 19 load imb.: force 22.6% pme mesh/force 0.982
DD step 999 load imb.: force 19.2% pme mesh/force 1.221
Step Time Lambda
1000 2.00000 0.00000
Writing checkpoint, step 1000 at Thu Jan 16 13:42:07 2020
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
1.48769e+04 8.89160e+02 5.87628e+03 9.78533e+03 5.16002e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
3.30589e+05 -1.67808e+04 -2.40215e+06 1.38574e+04 -1.99145e+06
Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar)
3.56207e+05 -1.63525e+06 3.34925e+02 -2.14321e+02 -7.01544e+01
Constr. rmsd
2.93548e-05
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 1001 steps using 11 frames
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
1.45443e+04 8.13691e+02 6.08673e+03 9.84082e+03 5.16848e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
3.32030e+05 -1.68036e+04 -2.40460e+06 1.37083e+04 -1.99269e+06
Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar)
3.56343e+05 -1.63635e+06 3.35052e+02 -2.14905e+02 -1.63619e+00
Constr. rmsd
0.00000e+00
Box-X Box-Y Box-Z
1.09139e+01 1.09139e+01 1.09139e+01
Total Virial (kJ/mol)
1.16720e+05 6.03393e+02 -3.86433e+02
5.90612e+02 1.20193e+05 -1.15953e+03
-3.98859e+02 -1.14725e+03 1.19632e+05
Pressure (bar)
5.13804e+01 -1.68338e+01 1.26919e+01
-1.65069e+01 -3.22849e+01 3.22965e+01
1.30097e+01 3.19828e+01 -2.40040e+01
T-Protein T-non-Protein
3.36029e+02 3.34999e+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
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Pair Search distance check 2520.143912 22681.295 1.0
NxN QSTab Elec. + LJ [F] 27689.515136 1135270.121 50.7
NxN QSTab Elec. + LJ [V&F] 307.769152 18158.380 0.8
NxN QSTab Elec. [F] 24541.562240 834413.116 37.3
NxN QSTab Elec. [V&F] 272.914432 11189.492 0.5
1,4 nonbonded interactions 17.496479 1574.683 0.1
Calc Weights 383.753370 13815.121 0.6
Spread Q Bspline 8186.738560 16373.477 0.7
Gather F Bspline 8186.738560 49120.431 2.2
3D-FFT 13831.289472 110650.316 4.9
Solve PME 5.189184 332.108 0.0
Reset In Box 6.389500 19.169 0.0
CG-CoM 6.517290 19.552 0.0
Angles 12.088076 2030.797 0.1
Propers 1.323322 303.041 0.0
RB-Dihedrals 13.633620 3367.504 0.2
Virial 13.043140 234.777 0.0
Stop-CM 1.405690 14.057 0.0
Calc-Ekin 25.813580 696.967 0.0
Lincs 10.419267 625.156 0.0
Lincs-Mat 222.729660 890.919 0.0
Constraint-V 152.804754 1222.438 0.1
Constraint-Vir 14.366427 344.794 0.0
Settle 43.988740 14208.363 0.6
-----------------------------------------------------------------------------
Total 2237556.072 100.0
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D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
av. #atoms communicated per step for force: 2 x 160345.9
av. #atoms communicated per step for LINCS: 2 x 14925.7
Average load imbalance: 21.2 %
Part of the total run time spent waiting due to load imbalance: 7.3 %
Average PME mesh/force load: 1.071
Part of the total run time spent waiting due to PP/PME imbalance: 4.0 %
NOTE: 7.3 % of the available CPU time was lost due to load imbalance
in the domain decomposition.
You might want to use dynamic load balancing (option -dlb.)
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 30 MPI ranks doing PP, and
on 6 MPI ranks doing PME
Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
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Domain decomp. 30 1 50 0.861 59.247 1.6
DD comm. load 30 1 2 0.002 0.108 0.0
Send X to PME 30 1 1001 0.700 48.163 1.3
Neighbor search 30 1 51 2.048 140.963 3.7
Comm. coord. 30 1 950 4.295 295.660 7.8
Force 30 1 1001 16.361 1126.233 29.7
Wait + Comm. F 30 1 1001 8.631 594.169 15.7
PME mesh * 6 1 1001 37.997 523.127 13.8
PME wait for PP * 7.851 108.084 2.9
Wait + Recv. PME F 30 1 1001 3.200 220.273 5.8
NB X/F buffer ops. 30 1 2901 5.720 393.740 10.4
Write traj. 30 1 2 0.086 5.912 0.2
Update 30 1 1001 0.452 31.091 0.8
Constraints 30 1 1001 3.167 217.985 5.8
Comm. energies 30 1 101 0.271 18.641 0.5
Rest 0.058 3.975 0.1
-----------------------------------------------------------------------------
Total 45.849 3787.396 100.0
-----------------------------------------------------------------------------
(*) Note that with separate PME ranks, the walltime column actually sums to
twice the total reported, but the cycle count total and % are correct.
-----------------------------------------------------------------------------
Breakdown of PME mesh computation
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PME redist. X/F 6 1 2002 13.199 181.722 4.8
PME spread/gather 6 1 2002 18.602 256.110 6.8
PME 3D-FFT 6 1 2002 0.859 11.831 0.3
PME 3D-FFT Comm. 6 1 2002 1.788 24.615 0.6
PME solve Elec 6 1 1001 0.230 3.164 0.1
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 547.708 45.849 1194.6
(ns/day) (hour/ns)
Performance: 3.773 6.362
Finished mdrun on rank 0 Thu Jan 16 13:42:08 2020