Project

General

Profile

md.log

Paul Bauer, 05/15/2019 11:28 AM

 
1
Log file opened on Tue May 14 10:37:10 2019
2
Host: dev-purley01  pid: 13834  rank ID: 0  number of ranks:  1
3
                      :-) GROMACS - gmx mdrun, 2018.6 (-:
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 2018.6
30
Executable:   /nethome/pbauer/data/bugs/2762/testruns/2018-ntmpi1/../../gromacs-2018/gromacs-2018.6/build-ubuntu-gcc-7.3-ubuntu-glibc-2.27-avx512/bin/gmx
31
Data prefix:  /nethome/pbauer/data/bugs/2762/gromacs-2018/gromacs-2018.6 (source tree)
32
Working dir:  /nethome/pbauer/data/bugs/2762/testruns/2018-ntmpi1/omp-threads-20
33
Command line:
34
  gmx mdrun -s quick.tpr -ntmpi 1 -ntomp 20
35

    
36
GROMACS version:    2018.6
37
Precision:          single
38
Memory model:       64 bit
39
MPI library:        thread_mpi
40
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
41
GPU support:        disabled
42
SIMD instructions:  AVX_512
43
FFT library:        fftw-3.3.7-sse2-avx
44
RDTSCP usage:       enabled
45
TNG support:        enabled
46
Hwloc support:      hwloc-1.11.9
47
Tracing support:    disabled
48
Built on:           2019-05-13 14:12:49
49
Built by:           pbauer@dev-purley01 [CMAKE]
50
Build OS/arch:      Linux 4.18.0-17-generic x86_64
51
Build CPU vendor:   Intel
52
Build CPU brand:    Unknown
53
Build CPU family:   6   Model: 85   Stepping: 2
54
Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl 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:         /usr/bin/gcc-7 GNU 7.3.0
56
C compiler flags:    -mavx512f -mfma    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3  -funroll-all-loops -fexcess-precision=fast  
57
C++ compiler:       /usr/bin/g++-7 GNU 7.3.0
58
C++ compiler flags:  -mavx512f -mfma    -std=c++11  -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wall  -O3  -funroll-all-loops -fexcess-precision=fast  
59

    
60

    
61
Running on 1 node with total 48 cores, 96 logical cores
62
Hardware detected:
63
  CPU info:
64
    Vendor: Intel
65
    Brand:  
66
    Family: 6   Model: 85   Stepping: 2
67
    Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl 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
68
    Number of AVX-512 FMA units: 2
69
  Hardware topology: Full, with devices
70
    Sockets, cores, and logical processors:
71
      Socket  0: [   0  48] [   1  49] [   2  50] [   3  51] [   4  52] [   5  53] [   6  54] [   7  55] [   8  56] [   9  57] [  10  58] [  11  59] [  12  60] [  13  61] [  14  62] [  15  63] [  16  64] [  17  65] [  18  66] [  19  67] [  20  68] [  21  69] [  22  70] [  23  71]
72
      Socket  1: [  24  72] [  25  73] [  26  74] [  27  75] [  28  76] [  29  77] [  30  78] [  31  79] [  32  80] [  33  81] [  34  82] [  35  83] [  36  84] [  37  85] [  38  86] [  39  87] [  40  88] [  41  89] [  42  90] [  43  91] [  44  92] [  45  93] [  46  94] [  47  95]
73
    Numa nodes:
74
      Node  0 (67229851648 bytes mem):   0  48   1  49   2  50   3  51   4  52   5  53   6  54   7  55   8  56   9  57  10  58  11  59  12  60  13  61  14  62  15  63  16  64  17  65  18  66  19  67  20  68  21  69  22  70  23  71
75
      Node  1 (67634958336 bytes mem):  24  72  25  73  26  74  27  75  28  76  29  77  30  78  31  79  32  80  33  81  34  82  35  83  36  84  37  85  38  86  39  87  40  88  41  89  42  90  43  91  44  92  45  93  46  94  47  95
76
      Latency:
77
               0     1
78
         0  1.00  2.10
79
         1  2.10  1.00
80
    Caches:
81
      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
82
      L2: 1048576 bytes, linesize 64 bytes, assoc. 16, shared 2 ways
83
      L3: 34603008 bytes, linesize 64 bytes, assoc. 11, shared 48 ways
84
    PCI devices:
85
      0000:00:11.5  Id: 8086:a252  Class: 0x0106  Numa: 0
86
      0000:00:17.0  Id: 8086:a202  Class: 0x0106  Numa: 0
87
      0000:02:00.0  Id: 1a03:2000  Class: 0x0300  Numa: 0
88
      0000:3d:00.0  Id: 8086:37d2  Class: 0x0200  Numa: 0
89
      0000:3d:00.1  Id: 8086:37d2  Class: 0x0200  Numa: 0
90

    
91

    
92
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
93
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
94
Lindahl
95
GROMACS: High performance molecular simulations through multi-level
96
parallelism from laptops to supercomputers
97
SoftwareX 1 (2015) pp. 19-25
98
-------- -------- --- Thank You --- -------- --------
99

    
100

    
101
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
102
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
103
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
104
GROMACS
105
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
106
-------- -------- --- Thank You --- -------- --------
107

    
108

    
109
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
110
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
111
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
112
GROMACS 4.5: a high-throughput and highly parallel open source molecular
113
simulation toolkit
114
Bioinformatics 29 (2013) pp. 845-54
115
-------- -------- --- Thank You --- -------- --------
116

    
117

    
118
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
119
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
120
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
121
molecular simulation
122
J. Chem. Theory Comput. 4 (2008) pp. 435-447
123
-------- -------- --- Thank You --- -------- --------
124

    
125

    
126
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
127
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
128
Berendsen
129
GROMACS: Fast, Flexible and Free
130
J. Comp. Chem. 26 (2005) pp. 1701-1719
131
-------- -------- --- Thank You --- -------- --------
132

    
133

    
134
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
135
E. Lindahl and B. Hess and D. van der Spoel
136
GROMACS 3.0: A package for molecular simulation and trajectory analysis
137
J. Mol. Mod. 7 (2001) pp. 306-317
138
-------- -------- --- Thank You --- -------- --------
139

    
140

    
141
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
142
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
143
GROMACS: A message-passing parallel molecular dynamics implementation
144
Comp. Phys. Comm. 91 (1995) pp. 43-56
145
-------- -------- --- Thank You --- -------- --------
146

    
147
Input Parameters:
148
   integrator                     = md
149
   tinit                          = 0
150
   dt                             = 0.002
151
   nsteps                         = 10000
152
   init-step                      = 0
153
   simulation-part                = 1
154
   comm-mode                      = Linear
155
   nstcomm                        = 100
156
   bd-fric                        = 0
157
   ld-seed                        = 718849372
158
   emtol                          = 10
159
   emstep                         = 0.01
160
   niter                          = 20
161
   fcstep                         = 0
162
   nstcgsteep                     = 1000
163
   nbfgscorr                      = 10
164
   rtpi                           = 0.05
165
   nstxout                        = 0
166
   nstvout                        = 0
167
   nstfout                        = 0
168
   nstlog                         = 1000
169
   nstcalcenergy                  = 100
170
   nstenergy                      = 5000
171
   nstxout-compressed             = 5000
172
   compressed-x-precision         = 1000
173
   cutoff-scheme                  = Verlet
174
   nstlist                        = 20
175
   ns-type                        = Grid
176
   pbc                            = xyz
177
   periodic-molecules             = false
178
   verlet-buffer-tolerance        = 0.005
179
   rlist                          = 0.931
180
   coulombtype                    = PME
181
   coulomb-modifier               = Potential-shift
182
   rcoulomb-switch                = 0
183
   rcoulomb                       = 0.9
184
   epsilon-r                      = 1
185
   epsilon-rf                     = inf
186
   vdw-type                       = Cut-off
187
   vdw-modifier                   = Potential-shift
188
   rvdw-switch                    = 0
189
   rvdw                           = 0.9
190
   DispCorr                       = EnerPres
191
   table-extension                = 1
192
   fourierspacing                 = 0.16
193
   fourier-nx                     = 52
194
   fourier-ny                     = 60
195
   fourier-nz                     = 72
196
   pme-order                      = 4
197
   ewald-rtol                     = 1e-05
198
   ewald-rtol-lj                  = 0.001
199
   lj-pme-comb-rule               = Geometric
200
   ewald-geometry                 = 0
201
   epsilon-surface                = 0
202
   implicit-solvent               = No
203
   gb-algorithm                   = Still
204
   nstgbradii                     = 1
205
   rgbradii                       = 1
206
   gb-epsilon-solvent             = 80
207
   gb-saltconc                    = 0
208
   gb-obc-alpha                   = 1
209
   gb-obc-beta                    = 0.8
210
   gb-obc-gamma                   = 4.85
211
   gb-dielectric-offset           = 0.009
212
   sa-algorithm                   = Ace-approximation
213
   sa-surface-tension             = 2.05016
214
   tcoupl                         = V-rescale
215
   nsttcouple                     = 20
216
   nh-chain-length                = 0
217
   print-nose-hoover-chain-variables = false
218
   pcoupl                         = Parrinello-Rahman
219
   pcoupltype                     = Isotropic
220
   nstpcouple                     = 20
221
   tau-p                          = 2
222
   compressibility (3x3):
223
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
224
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
225
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
226
   ref-p (3x3):
227
      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
228
      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
229
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
230
   refcoord-scaling               = No
231
   posres-com (3):
232
      posres-com[0]= 0.00000e+00
233
      posres-com[1]= 0.00000e+00
234
      posres-com[2]= 0.00000e+00
235
   posres-comB (3):
236
      posres-comB[0]= 0.00000e+00
237
      posres-comB[1]= 0.00000e+00
238
      posres-comB[2]= 0.00000e+00
239
   QMMM                           = false
240
   QMconstraints                  = 0
241
   QMMMscheme                     = 0
242
   MMChargeScaleFactor            = 1
243
qm-opts:
244
   ngQM                           = 0
245
   constraint-algorithm           = Lincs
246
   continuation                   = true
247
   Shake-SOR                      = false
248
   shake-tol                      = 0.0001
249
   lincs-order                    = 4
250
   lincs-iter                     = 1
251
   lincs-warnangle                = 30
252
   nwall                          = 0
253
   wall-type                      = 9-3
254
   wall-r-linpot                  = -1
255
   wall-atomtype[0]               = -1
256
   wall-atomtype[1]               = -1
257
   wall-density[0]                = 0
258
   wall-density[1]                = 0
259
   wall-ewald-zfac                = 3
260
   pull                           = false
261
   awh                            = false
262
   rotation                       = false
263
   interactiveMD                  = false
264
   disre                          = No
265
   disre-weighting                = Conservative
266
   disre-mixed                    = false
267
   dr-fc                          = 1000
268
   dr-tau                         = 0
269
   nstdisreout                    = 100
270
   orire-fc                       = 0
271
   orire-tau                      = 0
272
   nstorireout                    = 100
273
   free-energy                    = no
274
   cos-acceleration               = 0
275
   deform (3x3):
276
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
277
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
278
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
279
   simulated-tempering            = false
280
   swapcoords                     = no
281
   userint1                       = 0
282
   userint2                       = 0
283
   userint3                       = 0
284
   userint4                       = 0
285
   userreal1                      = 0
286
   userreal2                      = 0
287
   userreal3                      = 0
288
   userreal4                      = 0
289
   applied-forces:
290
     electric-field:
291
       x:
292
         E0                       = 0
293
         omega                    = 0
294
         t0                       = 0
295
         sigma                    = 0
296
       y:
297
         E0                       = 0
298
         omega                    = 0
299
         t0                       = 0
300
         sigma                    = 0
301
       z:
302
         E0                       = 0
303
         omega                    = 0
304
         t0                       = 0
305
         sigma                    = 0
306
grpopts:
307
   nrdf:     16011.7      141396
308
   ref-t:         300         300
309
   tau-t:         0.1         0.1
310
annealing:          No          No
311
annealing-npoints:           0           0
312
   acc:	           0           0           0
313
   nfreeze:           N           N           N
314
   energygrp-flags[  0]: 0
315

    
316
Changing nstlist from 20 to 40, rlist from 0.931 to 0.999
317

    
318
Using 1 MPI thread
319
Using 20 OpenMP threads 
320

    
321

    
322
NOTE: The number of threads is not equal to the number of (logical) cores
323
      and the -pin option is set to auto: will not pin threads to cores.
324
      This can lead to significant performance degradation.
325
      Consider using -pin on (and -pinoffset in case you run multiple jobs).
326
System total charge: -0.000
327
Will do PME sum in reciprocal space for electrostatic interactions.
328

    
329
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
330
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
331
A smooth particle mesh Ewald method
332
J. Chem. Phys. 103 (1995) pp. 8577-8592
333
-------- -------- --- Thank You --- -------- --------
334

    
335
Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
336
Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-05
337
Initialized non-bonded Ewald correction tables, spacing: 8.85e-04 size: 1018
338

    
339
Long Range LJ corr.: <C6> 3.3851e-04
340
Generated table with 999 data points for Ewald.
341
Tabscale = 500 points/nm
342
Generated table with 999 data points for LJ6.
343
Tabscale = 500 points/nm
344
Generated table with 999 data points for LJ12.
345
Tabscale = 500 points/nm
346
Generated table with 999 data points for 1-4 COUL.
347
Tabscale = 500 points/nm
348
Generated table with 999 data points for 1-4 LJ6.
349
Tabscale = 500 points/nm
350
Generated table with 999 data points for 1-4 LJ12.
351
Tabscale = 500 points/nm
352

    
353
Using SIMD 4x8 nonbonded short-range kernels
354

    
355
Using a dual 4x8 pair-list setup updated with dynamic pruning:
356
  outer list: updated every 40 steps, buffer 0.099 nm, rlist 0.999 nm
357
  inner list: updated every 11 steps, buffer 0.001 nm, rlist 0.901 nm
358
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
359
  outer list: updated every 40 steps, buffer 0.213 nm, rlist 1.113 nm
360
  inner list: updated every 11 steps, buffer 0.041 nm, rlist 0.941 nm
361

    
362
Using Lorentz-Berthelot Lennard-Jones combination rule
363

    
364

    
365
Initializing LINear Constraint Solver
366

    
367
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
368
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
369
LINCS: A Linear Constraint Solver for molecular simulations
370
J. Comp. Chem. 18 (1997) pp. 1463-1472
371
-------- -------- --- Thank You --- -------- --------
372

    
373
The number of constraints is 8054
374

    
375
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
376
S. Miyamoto and P. A. Kollman
377
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
378
Water Models
379
J. Comp. Chem. 13 (1992) pp. 952-962
380
-------- -------- --- Thank You --- -------- --------
381

    
382

    
383
Intra-simulation communication will occur every 20 steps.
384
Center of mass motion removal mode is Linear
385
We have the following groups for center of mass motion removal:
386
  0:  rest
387

    
388
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
389
G. Bussi, D. Donadio and M. Parrinello
390
Canonical sampling through velocity rescaling
391
J. Chem. Phys. 126 (2007) pp. 014101
392
-------- -------- --- Thank You --- -------- --------
393

    
394
There are: 78646 Atoms
395

    
396
Started mdrun on rank 0 Tue May 14 10:37:13 2019
397
           Step           Time
398
              0        0.00000
399