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0519-gromacs-2018_3.log

Stefan Becuwe, 04/29/2019 01:31 PM

 
1
Log file opened on Fri Mar 22 09:18:11 2019
2
Host: r2c01cn3.leibniz  pid: 11618  rank ID: 0  number of ranks:  112
3
                      :-) GROMACS - gmx mdrun, 2018.3 (-:
4

    
5
                            GROMACS is written by:
6
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
7
    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
8
  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
9
 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    
10
  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  
11
  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   
12
    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  
13
   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen 
14
 Christian Wennberg    Maarten Wolf   
15
                           and the project leaders:
16
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
17

    
18
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
19
Copyright (c) 2001-2017, The GROMACS development team at
20
Uppsala University, Stockholm University and
21
the Royal Institute of Technology, Sweden.
22
check out http://www.gromacs.org for more information.
23

    
24
GROMACS is free software; you can redistribute it and/or modify it
25
under the terms of the GNU Lesser General Public License
26
as published by the Free Software Foundation; either version 2.1
27
of the License, or (at your option) any later version.
28

    
29
GROMACS:      gmx mdrun, version 2018.3
30
Executable:   /apps/broadwell/centos7/GROMACS/2018.3-intel-2018b-UArecipe/bin/gmx_mpi
31
Data prefix:  /apps/broadwell/centos7/GROMACS/2018.3-intel-2018b-UArecipe
32
Working dir:  /scratch/gromacs-2019/test2018
33
Command line:
34
  gmx_mpi mdrun -ntomp 1 -s 0519.tpr -o /scratch/gromacs-2019/test2018/0519.trr -x /scratch/gromacs-2019/test2018/0519.xtc -cpo /scratch/gromacs-2019/test2018/0519.cpt -c /scratch/gromacs-2019/test2018/0519.gro -e /scratch/gromacs-2019/test2018/0519.edr -dhdl /scratch/gromacs-2019/test2018/0519.xvg -g /scratch/gromacs-2019/test2018/0519.log -px /scratch/gromacs-2019/test2018/0519.x.xvg -pf /scratch/gromacs-2019/test2018/0519.f.xvg -noconfout -rcon 0.7 -pin on -dds 0.9 -dlb auto -maxh 1
35

    
36
GROMACS version:    2018.3
37
Precision:          single
38
Memory model:       64 bit
39
MPI library:        MPI
40
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
41
GPU support:        disabled
42
SIMD instructions:  AVX2_256
43
FFT library:        Intel MKL
44
RDTSCP usage:       enabled
45
TNG support:        enabled
46
Hwloc support:      hwloc-1.11.2
47
Tracing support:    disabled
48
Built on:           2018-09-03 09:39:43
49
Built by:           ...@r2c10cn3.leibniz [CMAKE]
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Build OS/arch:      Linux 3.10.0-693.17.1.el7.x86_64 x86_64
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Build CPU vendor:   Intel
52
Build CPU brand:    Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
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Build CPU family:   6   Model: 79   Stepping: 1
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Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
55
C compiler:         /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicc Intel 18.0.3.20180410
56
C compiler flags:    -march=core-avx2   -mkl=sequential  -std=gnu99  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits  
57
C++ compiler:       /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicpc Intel 18.0.3.20180410
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C++ compiler flags:  -march=core-avx2   -mkl=sequential  -std=c++11   -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits  
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Running on 4 nodes with total 112 cores, 112 logical cores
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  Cores per node:           28
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  Logical cores per node:   28
64
Hardware detected on host r2c01cn3.leibniz (the node of MPI rank 0):
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
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    Family: 6   Model: 79   Stepping: 1
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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  Hardware topology: Full, with devices
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    Sockets, cores, and logical processors:
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      Socket  0: [   0] [   1] [   2] [   3] [   4] [   5] [   6] [   7] [   8] [   9] [  10] [  11] [  12] [  13]
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      Socket  1: [  14] [  15] [  16] [  17] [  18] [  19] [  20] [  21] [  22] [  23] [  24] [  25] [  26] [  27]
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    Numa nodes:
75
      Node  0 (68600541184 bytes mem):   0   1   2   3   4   5   6   7   8   9  10  11  12  13
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      Node  1 (68719476736 bytes mem):  14  15  16  17  18  19  20  21  22  23  24  25  26  27
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      Latency:
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               0     1
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         0  1.00  2.10
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         1  2.10  1.00
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    Caches:
82
      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
83
      L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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      L3: 36700160 bytes, linesize 64 bytes, assoc. 20, shared 14 ways
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    PCI devices:
86
      0000:01:00.0  Id: 8086:1521  Class: 0x0200  Numa: 0
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      0000:01:00.1  Id: 8086:1521  Class: 0x0200  Numa: 0
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      0000:02:00.0  Id: 15b3:1013  Class: 0x0207  Numa: 0
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      0000:00:11.4  Id: 8086:8d62  Class: 0x0106  Numa: 0
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      0000:07:00.0  Id: 1a03:2000  Class: 0x0300  Numa: 0
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      0000:00:1f.2  Id: 8086:8d02  Class: 0x0106  Numa: 0
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93

    
94
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
95
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
96
Lindahl
97
GROMACS: High performance molecular simulations through multi-level
98
parallelism from laptops to supercomputers
99
SoftwareX 1 (2015) pp. 19-25
100
-------- -------- --- Thank You --- -------- --------
101

    
102

    
103
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
104
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
105
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
106
GROMACS
107
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
108
-------- -------- --- Thank You --- -------- --------
109

    
110

    
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
112
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
113
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
114
GROMACS 4.5: a high-throughput and highly parallel open source molecular
115
simulation toolkit
116
Bioinformatics 29 (2013) pp. 845-54
117
-------- -------- --- Thank You --- -------- --------
118

    
119

    
120
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
121
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
122
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
123
molecular simulation
124
J. Chem. Theory Comput. 4 (2008) pp. 435-447
125
-------- -------- --- Thank You --- -------- --------
126

    
127

    
128
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
129
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
130
Berendsen
131
GROMACS: Fast, Flexible and Free
132
J. Comp. Chem. 26 (2005) pp. 1701-1719
133
-------- -------- --- Thank You --- -------- --------
134

    
135

    
136
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
137
E. Lindahl and B. Hess and D. van der Spoel
138
GROMACS 3.0: A package for molecular simulation and trajectory analysis
139
J. Mol. Mod. 7 (2001) pp. 306-317
140
-------- -------- --- Thank You --- -------- --------
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142

    
143
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
144
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
145
GROMACS: A message-passing parallel molecular dynamics implementation
146
Comp. Phys. Comm. 91 (1995) pp. 43-56
147
-------- -------- --- Thank You --- -------- --------
148

    
149
Input Parameters:
150
   integrator                     = md
151
   tinit                          = 0
152
   dt                             = 0.002
153
   nsteps                         = 500000
154
   init-step                      = 0
155
   simulation-part                = 1
156
   comm-mode                      = Linear
157
   nstcomm                        = 100
158
   bd-fric                        = 0
159
   ld-seed                        = -350048814
160
   emtol                          = 10
161
   emstep                         = 0.01
162
   niter                          = 20
163
   fcstep                         = 0
164
   nstcgsteep                     = 1000
165
   nbfgscorr                      = 10
166
   rtpi                           = 0.05
167
   nstxout                        = 0
168
   nstvout                        = 0
169
   nstfout                        = 0
170
   nstlog                         = 50000
171
   nstcalcenergy                  = 100
172
   nstenergy                      = 50000
173
   nstxout-compressed             = 50000
174
   compressed-x-precision         = 1000
175
   cutoff-scheme                  = Verlet
176
   nstlist                        = 20
177
   ns-type                        = Grid
178
   pbc                            = xyz
179
   periodic-molecules             = false
180
   verlet-buffer-tolerance        = 0.005
181
   rlist                          = 1.223
182
   coulombtype                    = PME
183
   coulomb-modifier               = Potential-shift
184
   rcoulomb-switch                = 0
185
   rcoulomb                       = 1.2
186
   epsilon-r                      = 1
187
   epsilon-rf                     = inf
188
   vdw-type                       = Cut-off
189
   vdw-modifier                   = Potential-shift
190
   rvdw-switch                    = 1
191
   rvdw                           = 1.2
192
   DispCorr                       = EnerPres
193
   table-extension                = 1
194
   fourierspacing                 = 0.16
195
   fourier-nx                     = 96
196
   fourier-ny                     = 84
197
   fourier-nz                     = 80
198
   pme-order                      = 4
199
   ewald-rtol                     = 1e-05
200
   ewald-rtol-lj                  = 0.001
201
   lj-pme-comb-rule               = Geometric
202
   ewald-geometry                 = 0
203
   epsilon-surface                = 0
204
   implicit-solvent               = No
205
   gb-algorithm                   = Still
206
   nstgbradii                     = 1
207
   rgbradii                       = 1
208
   gb-epsilon-solvent             = 80
209
   gb-saltconc                    = 0
210
   gb-obc-alpha                   = 1
211
   gb-obc-beta                    = 0.8
212
   gb-obc-gamma                   = 4.85
213
   gb-dielectric-offset           = 0.009
214
   sa-algorithm                   = Ace-approximation
215
   sa-surface-tension             = 2.05016
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   tcoupl                         = V-rescale
217
   nsttcouple                     = 20
218
   nh-chain-length                = 0
219
   print-nose-hoover-chain-variables = false
220
   pcoupl                         = Berendsen
221
   pcoupltype                     = Isotropic
222
   nstpcouple                     = 20
223
   tau-p                          = 2
224
   compressibility (3x3):
225
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
226
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
227
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
228
   ref-p (3x3):
229
      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
230
      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
231
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
232
   refcoord-scaling               = COM
233
   posres-com (3):
234
      posres-com[0]= 0.00000e+00
235
      posres-com[1]= 0.00000e+00
236
      posres-com[2]= 0.00000e+00
237
   posres-comB (3):
238
      posres-comB[0]= 0.00000e+00
239
      posres-comB[1]= 0.00000e+00
240
      posres-comB[2]= 0.00000e+00
241
   QMMM                           = false
242
   QMconstraints                  = 0
243
   QMMMscheme                     = 0
244
   MMChargeScaleFactor            = 1
245
qm-opts:
246
   ngQM                           = 0
247
   constraint-algorithm           = Lincs
248
   continuation                   = true
249
   Shake-SOR                      = false
250
   shake-tol                      = 0.0001
251
   lincs-order                    = 4
252
   lincs-iter                     = 1
253
   lincs-warnangle                = 30
254
   nwall                          = 0
255
   wall-type                      = 9-3
256
   wall-r-linpot                  = -1
257
   wall-atomtype[0]               = -1
258
   wall-atomtype[1]               = -1
259
   wall-density[0]                = 0
260
   wall-density[1]                = 0
261
   wall-ewald-zfac                = 3
262
   pull                           = true
263
   pull-cylinder-r                = 1.5
264
   pull-constr-tol                = 1e-06
265
   pull-print-COM                 = true
266
   pull-print-ref-value           = true
267
   pull-print-components          = true
268
   pull-nstxout                   = 50000
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   pull-nstfout                   = 50000
270
   pull-ngroups                   = 3
271
   pull-group 0:
272
     atom: not available
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     weight: not available
274
     pbcatom                        = -1
275
   pull-group 1:
276
     atom (1):
277
        atom[0]=1442
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     weight: not available
279
     pbcatom                        = -1
280
   pull-group 2:
281
     atom (2):
282
        atom[0]=4641
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        atom[1]=4643
284
     weight: not available
285
     pbcatom                        = 4641
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   pull-ncoords                   = 1
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   pull-coord 0:
288
   type                           = umbrella
289
   geometry                       = distance
290
   group[0]                       = 1
291
   group[1]                       = 2
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   dim (3):
293
      dim[0]=1
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      dim[1]=1
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      dim[2]=1
296
   origin (3):
297
      origin[0]= 0.00000e+00
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      origin[1]= 0.00000e+00
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      origin[2]= 0.00000e+00
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   vec (3):
301
      vec[0]= 0.00000e+00
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      vec[1]= 0.00000e+00
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      vec[2]= 0.00000e+00
304
   start                          = true
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   init                           = 0.518654
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   rate                           = 0
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   k                              = 1000
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   kB                             = 1000
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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = No
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   disre-weighting                = Conservative
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   disre-mixed                    = false
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   dr-fc                          = 1000
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   dr-tau                         = 0
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   nstdisreout                    = 100
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 100
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   free-energy                    = no
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   cos-acceleration               = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
325
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   simulated-tempering            = false
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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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   applied-forces:
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     electric-field:
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       x:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
343
         sigma                    = 0
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       y:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       z:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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grpopts:
355
   nrdf:     12909.9      439152
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   ref-t:         300         300
357
   tau-t:         0.1         0.1
358
annealing:          No          No
359
annealing-npoints:           0           0
360
   acc:	           0           0           0
361
   nfreeze:           N           N           N
362
   energygrp-flags[  0]: 0
363

    
364
Changing nstlist from 20 to 80, rlist from 1.223 to 1.326
365

    
366

    
367
Initializing Domain Decomposition on 112 ranks
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Dynamic load balancing: locked
369
Minimum cell size due to atom displacement: 0.625 nm
370
Initial maximum inter charge-group distances:
371
    two-body bonded interactions: 0.443 nm, LJ-14, atoms 1990 2780
372
  multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1990 2780
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Minimum cell size due to bonded interactions: 0.487 nm
374
User supplied maximum distance required for P-LINCS: 0.700 nm
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Guess for relative PME load: 0.13
376
Will use 96 particle-particle and 16 PME only ranks
377
This is a guess, check the performance at the end of the log file
378
Using 16 separate PME ranks, as guessed by mdrun
379
Scaling the initial minimum size with 1/0.9 (option -dds) = 1.11111
380
Optimizing the DD grid for 96 cells with a minimum initial size of 0.778 nm
381
The maximum allowed number of cells is: X 18 Y 17 Z 15
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Domain decomposition grid 4 x 4 x 6, separate PME ranks 16
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PME domain decomposition: 4 x 4 x 1
384
Interleaving PP and PME ranks
385
This rank does only particle-particle work.
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Domain decomposition rank 0, coordinates 0 0 0
388

    
389
The initial number of communication pulses is: X 1 Y 1 Z 1
390
The initial domain decomposition cell size is: X 3.63 nm Y 3.31 nm Z 2.00 nm
391

    
392
The maximum allowed distance for charge groups involved in interactions is:
393
                 non-bonded interactions           1.326 nm
394
(the following are initial values, they could change due to box deformation)
395
            two-body bonded interactions  (-rdd)   1.326 nm
396
          multi-body bonded interactions  (-rdd)   1.326 nm
397
  atoms separated by up to 5 constraints  (-rcon)  2.003 nm
398

    
399
When dynamic load balancing gets turned on, these settings will change to:
400
The maximum number of communication pulses is: X 1 Y 1 Z 1
401
The minimum size for domain decomposition cells is 1.326 nm
402
The requested allowed shrink of DD cells (option -dds) is: 0.90
403
The allowed shrink of domain decomposition cells is: X 0.37 Y 0.40 Z 0.66
404
The maximum allowed distance for charge groups involved in interactions is:
405
                 non-bonded interactions           1.326 nm
406
            two-body bonded interactions  (-rdd)   1.326 nm
407
          multi-body bonded interactions  (-rdd)   1.326 nm
408
  atoms separated by up to 5 constraints  (-rcon)  1.326 nm
409

    
410
Using two step summing over 4 groups of on average 24.0 ranks
411

    
412
Using 112 MPI processes
413
Using 1 OpenMP thread per MPI process
414

    
415

    
416
Overriding thread affinity set outside gmx mdrun
417

    
418
Pinning threads with an auto-selected logical core stride of 1
419
System total charge: -0.000
420
Will do PME sum in reciprocal space for electrostatic interactions.
421

    
422
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
423
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
424
A smooth particle mesh Ewald method
425
J. Chem. Phys. 103 (1995) pp. 8577-8592
426
-------- -------- --- Thank You --- -------- --------
427

    
428
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
429
Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06
430
Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
431

    
432
Long Range LJ corr.: <C6> 3.1361e-04
433
Generated table with 1163 data points for Ewald.
434
Tabscale = 500 points/nm
435
Generated table with 1163 data points for LJ6.
436
Tabscale = 500 points/nm
437
Generated table with 1163 data points for LJ12.
438
Tabscale = 500 points/nm
439
Generated table with 1163 data points for 1-4 COUL.
440
Tabscale = 500 points/nm
441
Generated table with 1163 data points for 1-4 LJ6.
442
Tabscale = 500 points/nm
443
Generated table with 1163 data points for 1-4 LJ12.
444
Tabscale = 500 points/nm
445

    
446
Using SIMD 4x8 nonbonded short-range kernels
447

    
448
Using a dual 4x8 pair-list setup updated with dynamic pruning:
449
  outer list: updated every 80 steps, buffer 0.126 nm, rlist 1.326 nm
450
  inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm
451
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
452
  outer list: updated every 80 steps, buffer 0.275 nm, rlist 1.475 nm
453
  inner list: updated every 13 steps, buffer 0.052 nm, rlist 1.252 nm
454

    
455
Using full Lennard-Jones parameter combination matrix
456

    
457

    
458
Will apply potential COM pulling
459
with 1 pull coordinate and 2 groups
460
Pull group 1:     1 atoms, mass    13.019
461
Pull group 2:     2 atoms, mass    26.018
462
Will use a sub-communicator for pull communication
463

    
464
Initializing Parallel LINear Constraint Solver
465

    
466
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
467
B. Hess
468
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
469
J. Chem. Theory Comput. 4 (2008) pp. 116-122
470
-------- -------- --- Thank You --- -------- --------
471

    
472
The number of constraints is 1073
473
There are inter charge-group constraints,
474
will communicate selected coordinates each lincs iteration
475

    
476
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
477
S. Miyamoto and P. A. Kollman
478
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
479
Water Models
480
J. Comp. Chem. 13 (1992) pp. 952-962
481
-------- -------- --- Thank You --- -------- --------
482

    
483

    
484
Linking all bonded interactions to atoms
485

    
486

    
487
The -noconfout functionality is deprecated, and may be removed in a future version.
488

    
489
Intra-simulation communication will occur every 20 steps.
490
Center of mass motion removal mode is Linear
491
We have the following groups for center of mass motion removal:
492
  0:  rest
493

    
494
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
495
G. Bussi, D. Donadio and M. Parrinello
496
Canonical sampling through velocity rescaling
497
J. Chem. Phys. 126 (2007) pp. 014101
498
-------- -------- --- Thank You --- -------- --------
499

    
500
There are: 224238 Atoms
501
Atom distribution over 96 domains: av 2335 stddev 86 min 2090 max 2430
502

    
503
Started mdrun on rank 0 Fri Mar 22 09:18:14 2019
504
           Step           Time
505
              0        0.00000
506

    
507
   Energies (kJ/mol)
508
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
509
    5.09960e+03    7.77425e+03    4.85656e+03    2.47900e+03   -1.61705e+02
510
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
511
    6.64263e+04    5.11422e+05   -1.65591e+04   -3.68724e+06    1.05264e+04
512
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
513
    6.82855e-14   -3.09538e+06    9.65238e+03   -3.08573e+06   -3.08550e+06
514
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
515
    5.13609e+00   -1.19286e+02   -1.38954e+03    2.44671e-06
516

    
517
DD  step 79 load imb.: force  4.9%  pme mesh/force 0.852
518

    
519

    
520
step 240 Turning on dynamic load balancing, because the performance loss due to load imbalance is 3.8 %.
521

    
522

    
523
step 8000 Turning off dynamic load balancing, because it is degrading performance.
524

    
525
Atom distribution over 96 domains: av 2335 stddev 86 min 2110 max 2401
526

    
527
step 24000 Turning on dynamic load balancing, because the performance loss due to load imbalance is 6.7 %.
528

    
529

    
530
step 25600 Turning off dynamic load balancing, because it is degrading performance.
531

    
532
Atom distribution over 96 domains: av 2335 stddev 89 min 2078 max 2408
533

    
534
step 32000 Turning on dynamic load balancing, because the performance loss due to load imbalance is 6.0 %.
535

    
536

    
537
step 35200 Turning off dynamic load balancing, because it is degrading performance.
538

    
539
Atom distribution over 96 domains: av 2335 stddev 87 min 2092 max 2408
540

    
541
step 40000 Will no longer try dynamic load balancing, as it degraded performance.
542

    
543
DD  step 49999 load imb.: force  5.3%  pme mesh/force 0.644
544

    
545
           Step           Time
546
          50000      100.00000
547

    
548
   Energies (kJ/mol)
549
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
550
    4.83032e+03    7.91144e+03    4.75862e+03    2.58501e+03   -1.28384e+02
551
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
552
    6.65623e+04    5.12972e+05   -1.65428e+04   -3.69199e+06    1.06877e+04
553
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
554
    3.75102e+00   -3.09835e+06    5.63326e+05   -2.53502e+06   -3.10342e+06
555
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
556
    2.99749e+02   -1.19052e+02   -1.98544e+00    2.95643e-06
557

    
558
DD  step 99999 load imb.: force  5.7%  pme mesh/force 0.647
559

    
560
           Step           Time
561
         100000      200.00000
562

    
563
   Energies (kJ/mol)
564
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
565
    4.75345e+03    7.58282e+03    4.85553e+03    2.57402e+03   -1.79248e+02
566
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
567
    6.64540e+04    5.11097e+05   -1.65655e+04   -3.68951e+06    1.06834e+04
568
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
569
    3.31456e+00   -3.09825e+06    5.64329e+05   -2.53392e+06   -3.10198e+06
570
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
571
    3.00283e+02   -1.19378e+02   -2.32919e+01    2.76256e-06
572

    
573
DD  step 149999 load imb.: force  5.5%  pme mesh/force 0.641
574

    
575
           Step           Time
576
         150000      300.00000
577

    
578
   Energies (kJ/mol)
579
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
580
    5.04330e+03    7.84732e+03    4.76267e+03    2.59187e+03   -1.62709e+02
581
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
582
    6.63614e+04    5.11111e+05   -1.65646e+04   -3.68670e+06    1.05392e+04
583
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
584
    6.31904e+00   -3.09516e+06    5.63786e+05   -2.53138e+06   -3.10055e+06
585
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
586
    2.99994e+02   -1.19365e+02    1.36845e+01    2.96967e-06
587

    
588
Writing checkpoint, step 188880 at Fri Mar 22 09:33:14 2019
589

    
590

    
591
DD  step 199999 load imb.: force  3.8%  pme mesh/force 0.657
592

    
593
           Step           Time
594
         200000      400.00000
595

    
596
   Energies (kJ/mol)
597
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
598
    4.94785e+03    7.55779e+03    4.90840e+03    2.40698e+03   -7.60589e+01
599
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
600
    6.66943e+04    5.10013e+05   -1.65563e+04   -3.68945e+06    1.06891e+04
601
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
602
    1.73298e+01   -3.09885e+06    5.65413e+05   -2.53344e+06   -3.09905e+06
603
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
604
    3.00859e+02   -1.19246e+02   -6.90249e+01    2.82245e-06
605

    
606
DD  step 249999 load imb.: force  5.9%  pme mesh/force 0.640
607

    
608
           Step           Time
609
         250000      500.00000
610

    
611
   Energies (kJ/mol)
612
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
613
    5.04615e+03    7.56546e+03    4.92053e+03    2.49466e+03   -1.13046e+02
614
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
615
    6.66422e+04    5.12506e+05   -1.65587e+04   -3.69014e+06    1.06123e+04
616
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
617
    1.24707e+01   -3.09701e+06    5.64644e+05   -2.53237e+06   -3.09746e+06
618
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
619
    3.00450e+02   -1.19281e+02    1.69750e+01    3.14922e-06
620

    
621
DD  step 299999 load imb.: force  5.1%  pme mesh/force 0.645
622

    
623
           Step           Time
624
         300000      600.00000
625

    
626
   Energies (kJ/mol)
627
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
628
    4.87397e+03    7.61933e+03    4.95450e+03    2.49306e+03   -1.36325e+02
629
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
630
    6.64239e+04    5.13536e+05   -1.65692e+04   -3.69342e+06    1.05761e+04
631
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
632
    1.48148e+01   -3.09963e+06    5.64550e+05   -2.53508e+06   -3.09601e+06
633
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
634
    3.00400e+02   -1.19431e+02    3.83472e+01    3.14445e-06
635

    
636
DD  step 349999 load imb.: force  6.2%  pme mesh/force 0.638
637

    
638
           Step           Time
639
         350000      700.00000
640

    
641
   Energies (kJ/mol)
642
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
643
    5.08991e+03    7.69764e+03    4.89299e+03    2.53503e+03   -1.66483e+02
644
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
645
    6.63619e+04    5.11430e+05   -1.65514e+04   -3.68938e+06    1.05755e+04
646
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
647
    9.36988e+00   -3.09751e+06    5.63559e+05   -2.53395e+06   -3.09443e+06
648
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
649
    2.99873e+02   -1.19176e+02   -4.38299e+01    2.81165e-06
650

    
651
Writing checkpoint, step 377760 at Fri Mar 22 09:48:14 2019
652

    
653

    
654
DD  step 399999 load imb.: force  5.4%  pme mesh/force 0.640
655

    
656
           Step           Time
657
         400000      800.00000
658

    
659
   Energies (kJ/mol)
660
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
661
    4.83583e+03    7.86137e+03    4.79819e+03    2.54585e+03   -1.37643e+02
662
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
663
    6.65807e+04    5.13211e+05   -1.65584e+04   -3.69136e+06    1.06535e+04
664
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
665
    1.91043e+01   -3.09755e+06    5.63681e+05   -2.53387e+06   -3.09296e+06
666
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
667
    2.99938e+02   -1.19276e+02    7.98090e+00    3.10775e-06
668

    
669
DD  step 449999 load imb.: force  3.9%  pme mesh/force 0.623
670

    
671
           Step           Time
672
         450000      900.00000
673

    
674
   Energies (kJ/mol)
675
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
676
    5.03504e+03    7.58068e+03    4.95366e+03    2.55010e+03   -7.27573e+01
677
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
678
    6.67311e+04    5.10533e+05   -1.65552e+04   -3.68593e+06    1.06144e+04
679
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
680
    9.14612e+00   -3.09455e+06    5.63459e+05   -2.53109e+06   -3.09145e+06
681
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
682
    2.99820e+02   -1.19230e+02    2.88342e+00    2.83940e-06
683

    
684
DD  step 499999 load imb.: force  5.3%  pme mesh/force 0.629
685

    
686
           Step           Time
687
         500000     1000.00000
688

    
689
   Energies (kJ/mol)
690
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
691
    4.86851e+03    7.78448e+03    5.02171e+03    2.57295e+03   -1.99886e+02
692
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
693
    6.65664e+04    5.11263e+05   -1.65511e+04   -3.69094e+06    1.05802e+04
694
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
695
    5.72201e+00   -3.09903e+06    5.61760e+05   -2.53727e+06   -3.08991e+06
696
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
697
    2.98916e+02   -1.19172e+02   -8.74913e+01    2.84239e-06
698

    
699
	<======  ###############  ==>
700
	<====  A V E R A G E S  ====>
701
	<==  ###############  ======>
702

    
703
	Statistics over 500001 steps using 5001 frames
704

    
705
   Energies (kJ/mol)
706
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
707
    4.91060e+03    7.67629e+03    4.91081e+03    2.55615e+03   -1.84510e+02
708
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
709
    6.65040e+04    5.12981e+05   -1.65579e+04   -3.69164e+06    1.05927e+04
710
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
711
    8.79495e+00   -3.09824e+06    5.63645e+05   -2.53459e+06   -3.09749e+06
712
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
713
    2.99919e+02   -1.19269e+02    1.04596e+00    0.00000e+00
714

    
715
          Box-X          Box-Y          Box-Z
716
    1.45132e+01    1.32261e+01    1.20182e+01
717

    
718
   Total Virial (kJ/mol)
719
    1.87733e+05    1.80507e+01   -5.28405e+01
720
    1.99566e+01    1.87843e+05    1.49384e+01
721
   -5.10672e+01    1.46297e+01    1.87851e+05
722

    
723
   Pressure (bar)
724
    2.00325e+00   -4.36769e-01    8.11049e-01
725
   -4.64232e-01    5.17693e-01   -1.78615e-01
726
    7.85505e-01   -1.74166e-01    6.16928e-01
727

    
728
T-protein_and_gpfT-water_and_ions
729
    2.99993e+02    2.99916e+02
730

    
731

    
732
	M E G A - F L O P S   A C C O U N T I N G
733

    
734
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
735
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
736
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
737
 V&F=Potential and force  V=Potential only  F=Force only
738

    
739
 Computing:                               M-Number         M-Flops  % Flops
740
-----------------------------------------------------------------------------
741
 Pair Search distance check          845339.861640     7608058.755     0.1
742
 NxN Ewald Elec. + LJ [F]          53531920.679536  3533106764.849    51.0
743
 NxN Ewald Elec. + LJ [V&F]          540836.388816    57869493.603     0.8
744
 NxN LJ [F]                           77728.720608     2565047.780     0.0
745
 NxN LJ [V&F]                           785.026592       33756.143     0.0
746
 NxN Ewald Elec. [F]               50759238.604624  3096313554.882    44.7
747
 NxN Ewald Elec. [V&F]               512821.787472    43077030.148     0.6
748
 1,4 nonbonded interactions            3669.507339      330255.661     0.0
749
 Calc Weights                        336357.672714    12108876.218     0.2
750
 Spread Q Bspline                   7175630.351232    14351260.702     0.2
751
 Gather F Bspline                   7175630.351232    43053782.107     0.6
752
 3D-FFT                            12450329.900610    99602639.205     1.4
753
 Solve PME                            16128.032256     1032194.064     0.0
754
 Reset In Box                          1400.814786        4202.444     0.0
755
 CG-CoM                                1401.711738        4205.135     0.0
756
 Bonds                                 1849.003698      109091.218     0.0
757
 Angles                                3514.507029      590437.181     0.0
758
 Propers                               1640.503281      375675.251     0.0
759
 Impropers                             1287.002574      267696.535     0.0
760
 Virial                                5714.178558      102855.214     0.0
761
 Stop-CM                               1121.414238       11214.142     0.0
762
 P-Coupling                            5606.174238       33637.045     0.0
763
 Calc-Ekin                            11212.348476      302733.409     0.0
764
 Lincs                                  566.014829       33960.890     0.0
765
 Lincs-Mat                              954.342888        3817.372     0.0
766
 Constraint-V                        121602.252436      972818.019     0.0
767
 Constraint-Vir                        6052.042015      145249.008     0.0
768
 Settle                               40156.740926    12970627.319     0.2
769
-----------------------------------------------------------------------------
770
 Total                                              6926980934.302   100.0
771
-----------------------------------------------------------------------------
772

    
773

    
774
    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
775

    
776
 av. #atoms communicated per step for force:  2 x 447044.7
777
 av. #atoms communicated per step for LINCS:  2 x 21812.1
778

    
779

    
780
 Dynamic load balancing report:
781
 DLB got disabled because it was unsuitable to use.
782
 Average load imbalance: 7.8%.
783
 The balanceable part of the MD step is 87%, load imbalance is computed from this.
784
 Part of the total run time spent waiting due to load imbalance: 6.7%.
785
 Average PME mesh/force load: 0.628
786
 Part of the total run time spent waiting due to PP/PME imbalance: 5.0 %
787

    
788
NOTE: 6.7 % of the available CPU time was lost due to load imbalance
789
      in the domain decomposition.
790
      You might want to use dynamic load balancing (option -dlb.)
791

    
792

    
793
     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
794

    
795
On 96 MPI ranks doing PP, and
796
on 16 MPI ranks doing PME
797

    
798
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
799
                     Ranks Threads  Count      (s)         total sum    %
800
-----------------------------------------------------------------------------
801
 Domain decomp.        96    1       6250      17.190       3960.630   0.6
802
 DD comm. load         96    1        173       0.004          0.867   0.0
803
 DD comm. bounds       96    1        157       0.007          1.726   0.0
804
 Send X to PME         96    1     500001       1.973        454.537   0.1
805
 Neighbor search       96    1       6251      33.463       7709.991   1.2
806
 Comm. coord.          96    1     493750      38.782       8935.419   1.4
807
 Force                 96    1     500001    2026.176     466836.010  73.0
808
 Wait + Comm. F        96    1     500001     103.307      23802.143   3.7
809
 PME mesh *            16    1     500001    1402.994      53875.529   8.4
810
 PME wait for PP *                            976.796      37509.361   5.9
811
 Wait + Recv. PME F    96    1     500001       5.720       1317.844   0.2
812
 NB X/F buffer ops.    96    1    1487501      21.655       4989.357   0.8
813
 COM pull force        96    1     500001       6.986       1609.659   0.3
814
 Write traj.           96    1         13       0.036          8.262   0.0
815
 Update                96    1     500001       5.806       1337.611   0.2
816
 Constraints           96    1     500001     112.219      25855.418   4.0
817
 Comm. energies        96    1      25001       3.201        737.606   0.1
818
 Rest                                           3.280        755.727   0.1
819
-----------------------------------------------------------------------------
820
 Total                                       2379.805     639698.273 100.0
821
-----------------------------------------------------------------------------
822
(*) Note that with separate PME ranks, the walltime column actually sums to
823
    twice the total reported, but the cycle count total and % are correct.
824
-----------------------------------------------------------------------------
825
 Breakdown of PME mesh computation
826
-----------------------------------------------------------------------------
827
 PME redist. X/F       16    1    1000002     198.588       7625.860   1.2
828
 PME spread            16    1     500001     460.457      17681.751   2.8
829
 PME gather            16    1     500001     289.656      11122.896   1.7
830
 PME 3D-FFT            16    1    1000002     317.011      12173.346   1.9
831
 PME 3D-FFT Comm.      16    1    2000004     107.426       4125.187   0.6
832
 PME solve Elec        16    1     500001      28.890       1109.375   0.2
833
-----------------------------------------------------------------------------
834

    
835
               Core t (s)   Wall t (s)        (%)
836
       Time:   266538.111     2379.805    11200.0
837
                         39:39
838
                 (ns/day)    (hour/ns)
839
Performance:       36.306        0.661
840
Finished mdrun on rank 0 Fri Mar 22 09:57:54 2019