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  1. Log file opened on Wed Apr 29 20:27:57 2015
  2. Host: nid18122 pid: 16863 rank ID: 0 number of ranks: 1024
  3. GROMACS: gmx mdrun, VERSION 5.0.2
  4.  
  5. GROMACS is written by:
  6. Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
  7. Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
  8. Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
  9. Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
  10. Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
  11. Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
  12. Peter Tieleman Christian Wennberg Maarten Wolf
  13. and the project leaders:
  14. Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
  15.  
  16. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  17. Copyright (c) 2001-2014, The GROMACS development team at
  18. Uppsala University, Stockholm University and
  19. the Royal Institute of Technology, Sweden.
  20. check out http://www.gromacs.org for more information.
  21.  
  22. GROMACS is free software; you can redistribute it and/or modify it
  23. under the terms of the GNU Lesser General Public License
  24. as published by the Free Software Foundation; either version 2.1
  25. of the License, or (at your option) any later version.
  26.  
  27. GROMACS: gmx mdrun, VERSION 5.0.2
  28. Executable: mdrun_mpi
  29. Library dir: /sw/xk6/gromacs/5.0.2/cle5.2_gnu4.8.2/share/gromacs/top
  30. Command line:
  31. mdrun_mpi -gpu_id 000000 -npme 256 -dlb yes -pin on -resethway -noconfout -v -s ../size.tpr -deffnm test
  32.  
  33. Gromacs version: VERSION 5.0.2
  34. Precision: single
  35. Memory model: 64 bit
  36. MPI library: MPI
  37. OpenMP support: enabled
  38. GPU support: enabled
  39. invsqrt routine: gmx_software_invsqrt(x)
  40. SIMD instructions: AVX_128_FMA
  41. FFT library: commercial-fftw-3.3.4-fma-sse2-avx
  42. RDTSCP usage: disabled
  43. C++11 compilation: disabled
  44. TNG support: enabled
  45. Tracing support: disabled
  46. Built on: Thu Mar 12 18:27:12 EDT 2015
  47. Built by: ff1@titan-ext8 [CMAKE]
  48. Build OS/arch: Linux 3.0.101-0.46-default x86_64
  49. Build CPU vendor: AuthenticAMD
  50. Build CPU brand: AMD Opteron(tm) Processor 6140
  51. Build CPU family: 16 Model: 9 Stepping: 1
  52. Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm misalignsse mmx msr nonstop_tsc pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a
  53. C compiler: /opt/cray/craype/2.2.1/bin/cc GNU 4.8.2
  54. C compiler flags: -mavx -mfma4 -mxop -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
  55. C++ compiler: /opt/cray/craype/2.2.1/bin/CC GNU 4.8.2
  56. C++ compiler flags: -mavx -mfma4 -mxop -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
  57. Boost version: 1.55.0 (internal)
  58. CUDA compiler: /opt/nvidia/cudatoolkit/5.5.51-1.0502.9594.3.1/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2013 NVIDIA Corporation;Built on Thu_Mar__6_02:21:19_PST_2014;Cuda compilation tools, release 5.5, V5.5.0
  59. CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35;-use_fast_math;; ;-mavx;-mfma4;-mxop;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-fomit-frame-pointer;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
  60. CUDA driver: 5.50
  61. CUDA runtime: 5.50
  62.  
  63.  
  64.  
  65. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  66. B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
  67. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
  68. molecular simulation
  69. J. Chem. Theory Comput. 4 (2008) pp. 435-447
  70. -------- -------- --- Thank You --- -------- --------
  71.  
  72.  
  73. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  74. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
  75. Berendsen
  76. GROMACS: Fast, Flexible and Free
  77. J. Comp. Chem. 26 (2005) pp. 1701-1719
  78. -------- -------- --- Thank You --- -------- --------
  79.  
  80.  
  81. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  82. E. Lindahl and B. Hess and D. van der Spoel
  83. GROMACS 3.0: A package for molecular simulation and trajectory analysis
  84. J. Mol. Mod. 7 (2001) pp. 306-317
  85. -------- -------- --- Thank You --- -------- --------
  86.  
  87.  
  88. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  89. H. J. C. Berendsen, D. van der Spoel and R. van Drunen
  90. GROMACS: A message-passing parallel molecular dynamics implementation
  91. Comp. Phys. Comm. 91 (1995) pp. 43-56
  92. -------- -------- --- Thank You --- -------- --------
  93.  
  94.  
  95. Number of hardware threads detected (16) does not match the number reported by OpenMP (1).
  96. Consider setting the launch configuration manually!
  97. Changing nstlist from 20 to 40, rlist from 1.2 to 1.239
  98.  
  99. Input Parameters:
  100. integrator = md
  101. tinit = 0
  102. dt = 0.002
  103. nsteps = 10000
  104. init-step = 0
  105. simulation-part = 1
  106. comm-mode = Linear
  107. nstcomm = 100
  108. bd-fric = 0
  109. ld-seed = 60975668
  110. emtol = 10
  111. emstep = 0.01
  112. niter = 20
  113. fcstep = 0
  114. nstcgsteep = 1000
  115. nbfgscorr = 10
  116. rtpi = 0.05
  117. nstxout = 5000
  118. nstvout = 5000
  119. nstfout = 5000
  120. nstlog = 1000
  121. nstcalcenergy = 100
  122. nstenergy = 1000
  123. nstxout-compressed = 0
  124. compressed-x-precision = 1000
  125. cutoff-scheme = Verlet
  126. nstlist = 40
  127. ns-type = Grid
  128. pbc = xyz
  129. periodic-molecules = FALSE
  130. verlet-buffer-tolerance = 0.005
  131. rlist = 1.239
  132. rlistlong = 1.239
  133. nstcalclr = 20
  134. coulombtype = PME
  135. coulomb-modifier = Potential-shift
  136. rcoulomb-switch = 0
  137. rcoulomb = 1.2
  138. epsilon-r = 1
  139. epsilon-rf = inf
  140. vdw-type = Cut-off
  141. vdw-modifier = Force-switch
  142. rvdw-switch = 1
  143. rvdw = 1.2
  144. DispCorr = No
  145. table-extension = 1
  146. fourierspacing = 0.12
  147. fourier-nx = 144
  148. fourier-ny = 144
  149. fourier-nz = 64
  150. pme-order = 4
  151. ewald-rtol = 1e-05
  152. ewald-rtol-lj = 0.001
  153. lj-pme-comb-rule = Geometric
  154. ewald-geometry = 0
  155. epsilon-surface = 0
  156. implicit-solvent = No
  157. gb-algorithm = Still
  158. nstgbradii = 1
  159. rgbradii = 1
  160. gb-epsilon-solvent = 80
  161. gb-saltconc = 0
  162. gb-obc-alpha = 1
  163. gb-obc-beta = 0.8
  164. gb-obc-gamma = 4.85
  165. gb-dielectric-offset = 0.009
  166. sa-algorithm = Ace-approximation
  167. sa-surface-tension = 2.05016
  168. tcoupl = Nose-Hoover
  169. nsttcouple = 20
  170. nh-chain-length = 1
  171. print-nose-hoover-chain-variables = FALSE
  172. pcoupl = Parrinello-Rahman
  173. pcoupltype = Semiisotropic
  174. nstpcouple = 20
  175. tau-p = 5
  176. compressibility (3x3):
  177. compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
  178. compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
  179. compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
  180. ref-p (3x3):
  181. ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
  182. ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
  183. ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
  184. refcoord-scaling = COM
  185. posres-com (3):
  186. posres-com[0]= 0.00000e+00
  187. posres-com[1]= 0.00000e+00
  188. posres-com[2]= 0.00000e+00
  189. posres-comB (3):
  190. posres-comB[0]= 0.00000e+00
  191. posres-comB[1]= 0.00000e+00
  192. posres-comB[2]= 0.00000e+00
  193. QMMM = FALSE
  194. QMconstraints = 0
  195. QMMMscheme = 0
  196. MMChargeScaleFactor = 1
  197. qm-opts:
  198. ngQM = 0
  199. constraint-algorithm = Lincs
  200. continuation = TRUE
  201. Shake-SOR = FALSE
  202. shake-tol = 0.0001
  203. lincs-order = 4
  204. lincs-iter = 1
  205. lincs-warnangle = 30
  206. nwall = 0
  207. wall-type = 9-3
  208. wall-r-linpot = -1
  209. wall-atomtype[0] = -1
  210. wall-atomtype[1] = -1
  211. wall-density[0] = 0
  212. wall-density[1] = 0
  213. wall-ewald-zfac = 3
  214. pull = no
  215. rotation = FALSE
  216. interactiveMD = FALSE
  217. disre = No
  218. disre-weighting = Conservative
  219. disre-mixed = FALSE
  220. dr-fc = 1000
  221. dr-tau = 0
  222. nstdisreout = 100
  223. orire-fc = 0
  224. orire-tau = 0
  225. nstorireout = 100
  226. free-energy = no
  227. cos-acceleration = 0
  228. deform (3x3):
  229. deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  230. deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  231. deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  232. simulated-tempering = FALSE
  233. E-x:
  234. n = 0
  235. E-xt:
  236. n = 0
  237. E-y:
  238. n = 0
  239. E-yt:
  240. n = 0
  241. E-z:
  242. n = 0
  243. E-zt:
  244. n = 0
  245. swapcoords = no
  246. adress = FALSE
  247. userint1 = 0
  248. userint2 = 0
  249. userint3 = 0
  250. userint4 = 0
  251. userreal1 = 0
  252. userreal2 = 0
  253. userreal3 = 0
  254. userreal4 = 0
  255. grpopts:
  256. nrdf: 261777 192987
  257. ref-t: 303.15 303.15
  258. tau-t: 1 1
  259. annealing: No No
  260. annealing-npoints: 0 0
  261. acc: 0 0 0
  262. nfreeze: N N N
  263. energygrp-flags[ 0]: 0
  264.  
  265. Initializing Domain Decomposition on 1024 ranks
  266. Dynamic load balancing: yes
  267. Will sort the charge groups at every domain (re)decomposition
  268. Initial maximum inter charge-group distances:
  269. two-body bonded interactions: 0.420 nm, LJ-14, atoms 42821 42830
  270. multi-body bonded interactions: 0.420 nm, Proper Dih., atoms 42821 42830
  271. Minimum cell size due to bonded interactions: 0.462 nm
  272. Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm
  273. Estimated maximum distance required for P-LINCS: 0.222 nm
  274. Using 256 separate PME ranks, per user request
  275. Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
  276. Optimizing the DD grid for 768 cells with a minimum initial size of 0.578 nm
  277. The maximum allowed number of cells is: X 27 Y 27 Z 13
  278. Domain decomposition grid 16 x 16 x 3, separate PME ranks 256
  279. PME domain decomposition: 16 x 16 x 1
  280. Interleaving PP and PME ranks
  281. This rank does only particle-particle work.
  282.  
  283. Domain decomposition rank 0, coordinates 0 0 0
  284.  
  285. Using two step summing over 128 groups of on average 6.0 ranks
  286.  
  287. Using 1024 MPI processes
  288. Using 2 OpenMP threads per MPI process
  289.  
  290. Detecting CPU SIMD instructions.
  291. Present hardware specification:
  292. Vendor: AuthenticAMD
  293. Brand: AMD Opteron(TM) Processor 6274
  294. Family: 21 Model: 1 Stepping: 2
  295. Features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop
  296. SIMD instructions most likely to fit this hardware: AVX_128_FMA
  297. SIMD instructions selected at GROMACS compile time: AVX_128_FMA
  298.  
  299.  
  300. The current CPU can measure timings more accurately than the code in
  301. mdrun_mpi was configured to use. This might affect your simulation
  302. speed as accurate timings are needed for load-balancing.
  303. Please consider rebuilding mdrun_mpi with the GMX_USE_RDTSCP=OFF CMake option.
  304.  
  305.  
  306. 1 GPU detected on host nid18122:
  307. #0: NVIDIA Tesla K20X, compute cap.: 3.5, ECC: yes, stat: compatible
  308.  
  309. 1 GPU user-selected for this run.
  310. Mapping of GPUs to the 6 PP ranks in this node: #0, #0, #0, #0, #0, #0
  311.  
  312. NOTE: You assigned GPUs to multiple MPI processes.
  313. Will do PME sum in reciprocal space for electrostatic interactions.
  314.  
  315. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  316. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
  317. A smooth particle mesh Ewald method
  318. J. Chem. Phys. 103 (1995) pp. 8577-8592
  319. -------- -------- --- Thank You --- -------- --------
  320.  
  321. Will do ordinary reciprocal space Ewald sum.
  322. Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
  323. Cut-off's: NS: 1.239 Coulomb: 1.2 LJ: 1.2
  324. System total charge: 0.000
  325. Generated table with 1119 data points for Ewald.
  326. Tabscale = 500 points/nm
  327. Generated table with 1119 data points for LJ6Shift.
  328. Tabscale = 500 points/nm
  329. Generated table with 1119 data points for LJ12Shift.
  330. Tabscale = 500 points/nm
  331. Generated table with 1119 data points for 1-4 COUL.
  332. Tabscale = 500 points/nm
  333. Generated table with 1119 data points for 1-4 LJ6.
  334. Tabscale = 500 points/nm
  335. Generated table with 1119 data points for 1-4 LJ12.
  336. Tabscale = 500 points/nm
  337.  
  338. Using CUDA 8x8 non-bonded kernels
  339.  
  340. Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -1.000e-05
  341. Initialized non-bonded Ewald correction tables, spacing: 7.82e-04 size: 1536
  342.  
  343.  
  344. Overriding thread affinity set outside mdrun_mpi
  345.  
  346. Pinning threads with an auto-selected logical core stride of 1
  347.  
  348. Initializing Parallel LINear Constraint Solver
  349.  
  350. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  351. B. Hess
  352. P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
  353. J. Chem. Theory Comput. 4 (2008) pp. 116-122
  354. -------- -------- --- Thank You --- -------- --------
  355.  
  356. The number of constraints is 67980
  357. There are inter charge-group constraints,
  358. will communicate selected coordinates each lincs iteration
  359.  
  360. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  361. S. Miyamoto and P. A. Kollman
  362. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
  363. Water Models
  364. J. Comp. Chem. 13 (1992) pp. 952-962
  365. -------- -------- --- Thank You --- -------- --------
  366.  
  367.  
  368. Linking all bonded interactions to atoms
  369. There are 739685 inter charge-group exclusions,
  370. will use an extra communication step for exclusion forces for PME
  371.  
  372. The maximum number of communication pulses is: X 2 Y 2 Z 2
  373. The minimum size for domain decomposition cells is 0.711 nm
  374. The requested allowed shrink of DD cells (option -dds) is: 0.80
  375. The allowed shrink of domain decomposition cells is: X 0.71 Y 0.71 Z 0.28
  376. The maximum allowed distance for charge groups involved in interactions is:
  377. non-bonded interactions 1.239 nm
  378. two-body bonded interactions (-rdd) 1.239 nm
  379. multi-body bonded interactions (-rdd) 0.711 nm
  380. atoms separated by up to 5 constraints (-rcon) 0.711 nm
  381.  
  382.  
  383. Making 3D domain decomposition grid 16 x 16 x 3, home cell index 0 0 0
  384.  
  385. Center of mass motion removal mode is Linear
  386. We have the following groups for center of mass motion removal:
  387. 0: NPROT
  388. 1: SOL_ION
  389. There are: 206415 Atoms
  390. Charge group distribution at step 0: 260 264 256 284 267 281 271 280 244 252 268 272 257 272 273 277 249 272 266 276 277 254 274 274 268 261 250 275 254 277 267 280 278 273 284 275 256 295 258 271 260 268 285 271 270 272 290 248 263 287 287 263 265 262 266 267 264 272 269 260 271 273 276 243 284 244 254 282 277 279 255 288 276 258 264 261 275 258 269 298 280 261 265 259 287 253 260 254 266 282 273 275 258 257 260 262 267 269 266 261 278 270 256 271 275 254 255 254 252 275 273 273 282 270 267 270 267 267 271 265 260 282 286 265 298 266 269 271 269 294 279 271 266 293 264 254 286 264 280 274 277 262 286 274 284 277 277 281 284 253 267 274 269 262 265 277 251 282 285 271 250 271 272 290 253 251 270 248 270 271 267 285 278 279 253 275 249 278 267 268 252 286 268 245 271 262 275 271 268 274 276 270 272 260 276 251 259 272 281 273 268 279 303 265 260 284 263 263 256 262 266 275 251 267 248 256 277 252 256 263 254 266 267 277 247 265 262 258 277 247 269 277 265 247 264 281 260 267 288 280 276 270 267 276 258 283 244 262 262 267 279 260 261 283 248 282 263 286 271 296 280 269 284 276 277 254 258 286 265 263 268 259 261 280 271 274 267 280 266 267 277 271 285 283 256 277 279 264 275 281 271 280 281 266 267 288 256 286 276 243 286 269 276 270 278 257 270 262 261 269 273 284 267 285 278 270 270 257 261 264 241 284 277 269 259 275 258 259 293 263 283 282 270 268 270 286 264 268 272 266 281 260 271 287 274 265 274 262 277 274 260 273 260 257 257 282 267 283 264 277 259 268 263 263 274 258 253 274 267 271 264 262 276 255 270 263 286 277 267 254 274 277 279 259 268 261 267 261 287 264 277 274 269 262 273 278 254 277 255 246 286 270 246 272 266 262 260 264 280 282 273 264 248 276 266 269 269 262 274 260 268 268 272 261 286 253 250 274 282 276 276 266 264 271 256 268 273 262 271 261 277 255 256 265 274 280 272 258 270 266 276 262 284 262 294 258 263 240 269 276 274 283 266 268 256 260 268 273 282 257 258 267 263 271 255 285 264 265 290 270 271 271 276 288 276 267 281 264 278 263 267 264 257 279 264 246 289 267 276 280 274 257 263 259 272 262 268 261 265 286 266 275 284 254 256 265 270 267 253 264 281 261 271 284 256 252 252 261 286 271 270 263 274 267 275 267 266 273 282 259 257 273 269 286 256 264 260 270 265 281 289 252 271 275 273 283 297 269 257 253 267 262 274 258 268 254 280 264 268 271 266 285 255 271 274 262 269 294 267 274 272 266 267 285 260 252 259 268 275 276 248 282 294 278 273 267 268 266 273 272 277 282 268 286 246 272 269 273 265 280 282 275 276 270 252 264 265 253 297 278 267 264 269 275 258 273 251 260 239 271 253 295 271 264 261 274 270 274 272 251 275 263 257 245 259 260 280 266 278 274 263 266 260 268 266 247 263 261 301 275 264 268 256 270 274 256 246 258 263 273 242 280 251 287 257 257 285 261 279 267 272 279 281 248 256 269 280 269 284 257 268 263 283 264 286 276 267 261 273 272 246 274 252 266 255 271 265 268 274 288 261 275 242 262 268 264 268 282 283 281 259 286 274 268 281 272 259 277 277 264 277 256 271 287 251 261 287 252 255 278 257 273 284 279 270 288 269 263 256 271 266 275 280 262 285 259 269 270 269 264 258 262 278 275 242 275 269 270
  391. Initial temperature: 303.008 K
  392.  
  393. Started mdrun on rank 0 Wed Apr 29 20:27:59 2015
  394. Step Time Lambda
  395. 0 0.00000 0.00000
  396.  
  397. Energies (kJ/mol)
  398. Bond U-B Proper Dih. Improper Dih. LJ-14
  399. 5.27858e+04 2.89239e+05 1.51310e+05 1.50125e+03 3.17014e+04
  400. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  401. -4.55645e+05 -3.43455e+04 -1.43186e+06 8.83147e+03 -1.38648e+06
  402. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  403. 5.74416e+05 -8.12065e+05 3.03832e+02 -5.33417e+01 4.19699e-06
  404.  
  405. DD step 39 vol min/aver 1.000 load imb.: force 27.9% pme mesh/force 15.922
  406.  
  407. step 120: timed with pme grid 144 144 64, coulomb cutoff 1.200: 207.9 M-cycles
  408. step 200: timed with pme grid 128 128 60, coulomb cutoff 1.269: 224.6 M-cycles
  409. step 200: the domain decompostion limits the PME load balancing to a coulomb cut-off of 1.359
  410. step 280: timed with pme grid 144 144 64, coulomb cutoff 1.200: 189.4 M-cycles
  411. step 360: timed with pme grid 128 128 64, coulomb cutoff 1.252: 180.9 M-cycles
  412. step 440: timed with pme grid 128 128 60, coulomb cutoff 1.269: 150.0 M-cycles
  413. step 520: timed with pme grid 120 120 60, coulomb cutoff 1.336: 141.0 M-cycles
  414. step 600: timed with pme grid 120 120 56, coulomb cutoff 1.359: 260.2 M-cycles
  415. step 680: timed with pme grid 128 128 60, coulomb cutoff 1.269: 130.3 M-cycles
  416. step 760: timed with pme grid 120 120 60, coulomb cutoff 1.336: 224.4 M-cycles
  417. step 840: timed with pme grid 120 120 56, coulomb cutoff 1.359: 134.1 M-cycles
  418. step 920: timed with pme grid 128 128 60, coulomb cutoff 1.269: 129.6 M-cycles
  419. step 1000: timed with pme grid 120 120 60, coulomb cutoff 1.336: 141.2 M-cycles
  420. DD load balancing is limited by minimum cell size in dimension X Y
  421. DD step 999 vol min/aver 0.363! load imb.: force 17.0% pme mesh/force 2.067
  422.  
  423. Step Time Lambda
  424. 1000 2.00000 0.00000
  425.  
  426. Energies (kJ/mol)
  427. Bond U-B Proper Dih. Improper Dih. LJ-14
  428. 5.25136e+04 2.88848e+05 1.51005e+05 1.38986e+03 3.17244e+04
  429. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  430. -4.55009e+05 -3.44202e+04 -1.42575e+06 5.53129e+03 -1.38416e+06
  431. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  432. 5.73008e+05 -8.11155e+05 3.03087e+02 -1.04824e+02 4.21551e-06
  433.  
  434. step 1080: timed with pme grid 120 120 56, coulomb cutoff 1.359: 150.4 M-cycles
  435. optimal pme grid 128 128 60, coulomb cutoff 1.269
  436. DD load balancing is limited by minimum cell size in dimension X Y
  437. DD step 1999 vol min/aver 0.332! load imb.: force 8.4% pme mesh/force 2.273
  438.  
  439. Step Time Lambda
  440. 2000 4.00000 0.00000
  441.  
  442. Energies (kJ/mol)
  443. Bond U-B Proper Dih. Improper Dih. LJ-14
  444. 5.21692e+04 2.89332e+05 1.50911e+05 1.43851e+03 3.15611e+04
  445. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  446. -4.56371e+05 -3.63099e+04 -1.42387e+06 7.07723e+03 -1.38406e+06
  447. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  448. 5.75015e+05 -8.09047e+05 3.04149e+02 -4.90641e+01 4.18145e-06
  449.  
  450. DD load balancing is limited by minimum cell size in dimension X Y
  451. DD step 2999 vol min/aver 0.317! load imb.: force 13.4% pme mesh/force 2.451
  452.  
  453. Step Time Lambda
  454. 3000 6.00000 0.00000
  455.  
  456. Energies (kJ/mol)
  457. Bond U-B Proper Dih. Improper Dih. LJ-14
  458. 5.19405e+04 2.87606e+05 1.50667e+05 1.40795e+03 3.16478e+04
  459. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  460. -4.56266e+05 -3.58792e+04 -1.42650e+06 7.10623e+03 -1.38827e+06
  461. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  462. 5.73686e+05 -8.14584e+05 3.03446e+02 3.00575e+01 4.20742e-06
  463.  
  464. DD load balancing is limited by minimum cell size in dimension X Y
  465. DD step 3999 vol min/aver 0.282! load imb.: force 8.3% pme mesh/force 2.231
  466.  
  467. Step Time Lambda
  468. 4000 8.00000 0.00000
  469.  
  470. Energies (kJ/mol)
  471. Bond U-B Proper Dih. Improper Dih. LJ-14
  472. 5.24817e+04 2.88629e+05 1.51135e+05 1.52874e+03 3.16850e+04
  473. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  474. -4.56781e+05 -3.60871e+04 -1.42668e+06 7.06199e+03 -1.38702e+06
  475. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  476. 5.72541e+05 -8.14481e+05 3.02841e+02 5.07281e+00 4.19474e-06
  477.  
  478.  
  479. step 5000: resetting all time and cycle counters
  480.  
  481. Restarted time on rank 0 Wed Apr 29 20:28:18 2015
  482. DD load balancing is limited by minimum cell size in dimension X Y
  483. DD step 4999 vol min/aver 0.271! load imb.: force 14.2% pme mesh/force 2.135
  484.  
  485. Step Time Lambda
  486. 5000 10.00000 0.00000
  487.  
  488. Energies (kJ/mol)
  489. Bond U-B Proper Dih. Improper Dih. LJ-14
  490. 5.20484e+04 2.87531e+05 1.50809e+05 1.42815e+03 3.16280e+04
  491. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  492. -4.56035e+05 -3.39488e+04 -1.42817e+06 7.09660e+03 -1.38762e+06
  493. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  494. 5.74374e+05 -8.13241e+05 3.03810e+02 1.13927e+02 4.21019e-06
  495.  
  496. DD load balancing is limited by minimum cell size in dimension X Y
  497. DD step 5999 vol min/aver 0.255! load imb.: force 13.7% pme mesh/force 2.375
  498.  
  499. Step Time Lambda
  500. 6000 12.00000 0.00000
  501.  
  502. Energies (kJ/mol)
  503. Bond U-B Proper Dih. Improper Dih. LJ-14
  504. 5.18091e+04 2.87109e+05 1.50389e+05 1.51299e+03 3.16732e+04
  505. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  506. -4.55916e+05 -3.41533e+04 -1.42927e+06 7.03660e+03 -1.38981e+06
  507. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  508. 5.73307e+05 -8.16504e+05 3.03246e+02 8.89033e+01 4.23258e-06
  509.  
  510. DD load balancing is limited by minimum cell size in dimension X Y
  511. DD step 6999 vol min/aver 0.261! load imb.: force 16.8% pme mesh/force 2.207
  512.  
  513. Step Time Lambda
  514. 7000 14.00000 0.00000
  515.  
  516. Energies (kJ/mol)
  517. Bond U-B Proper Dih. Improper Dih. LJ-14
  518. 5.13918e+04 2.88573e+05 1.50490e+05 1.36152e+03 3.18782e+04
  519. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  520. -4.56167e+05 -3.66293e+04 -1.42518e+06 7.26886e+03 -1.38701e+06
  521. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  522. 5.75096e+05 -8.11913e+05 3.04192e+02 5.89956e+01 4.21537e-06
  523.  
  524. DD load balancing is limited by minimum cell size in dimension X Y
  525. DD step 7999 vol min/aver 0.247! load imb.: force 13.7% pme mesh/force 2.007
  526.  
  527. Step Time Lambda
  528. 8000 16.00000 0.00000
  529.  
  530. Energies (kJ/mol)
  531. Bond U-B Proper Dih. Improper Dih. LJ-14
  532. 5.21922e+04 2.87428e+05 1.50495e+05 1.42444e+03 3.16092e+04
  533. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  534. -4.56859e+05 -3.48592e+04 -1.42958e+06 7.16045e+03 -1.39099e+06
  535. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  536. 5.73582e+05 -8.17409e+05 3.03391e+02 -5.46835e+01 4.22299e-06
  537.  
  538. DD load balancing is limited by minimum cell size in dimension X Y
  539. DD step 8999 vol min/aver 0.232! load imb.: force 9.3% pme mesh/force 1.579
  540.  
  541. Step Time Lambda
  542. 9000 18.00000 0.00000
  543.  
  544. Energies (kJ/mol)
  545. Bond U-B Proper Dih. Improper Dih. LJ-14
  546. 5.16809e+04 2.89415e+05 1.50690e+05 1.41345e+03 3.15696e+04
  547. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  548. -4.56447e+05 -3.70618e+04 -1.42534e+06 7.12735e+03 -1.38695e+06
  549. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  550. 5.74075e+05 -8.12876e+05 3.03652e+02 -1.02713e+02 4.20379e-06
  551.  
  552. DD load balancing is limited by minimum cell size in dimension X Y
  553. DD step 9999 vol min/aver 0.214! load imb.: force 11.3% pme mesh/force 1.541
  554.  
  555. Step Time Lambda
  556. 10000 20.00000 0.00000
  557.  
  558. Energies (kJ/mol)
  559. Bond U-B Proper Dih. Improper Dih. LJ-14
  560. 5.20900e+04 2.89413e+05 1.50257e+05 1.42651e+03 3.18652e+04
  561. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  562. -4.56555e+05 -3.41817e+04 -1.42953e+06 7.09639e+03 -1.38812e+06
  563. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  564. 5.74405e+05 -8.13712e+05 3.03826e+02 1.30671e+02 4.19219e-06
  565.  
  566. <====== ############### ==>
  567. <==== A V E R A G E S ====>
  568. <== ############### ======>
  569.  
  570. Statistics over 10001 steps using 101 frames
  571.  
  572. Energies (kJ/mol)
  573. Bond U-B Proper Dih. Improper Dih. LJ-14
  574. 5.19094e+04 2.87665e+05 1.50765e+05 1.41236e+03 3.16878e+04
  575. Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
  576. -4.56185e+05 -3.56137e+04 -1.42753e+06 7.08582e+03 -1.38880e+06
  577. Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd
  578. 5.73106e+05 -8.15694e+05 3.03139e+02 2.44192e+00 0.00000e+00
  579.  
  580. Box-X Box-Y Box-Z
  581. 1.60031e+01 1.60031e+01 7.63354e+00
  582.  
  583. Total Virial (kJ/mol)
  584. 1.87164e+05 1.30930e+02 3.29879e+02
  585. 1.36231e+02 1.86451e+05 1.20864e+03
  586. 3.34302e+02 1.21286e+03 1.99063e+05
  587.  
  588. Pressure (bar)
  589. -9.84451e+00 -2.25070e+00 -5.69777e+00
  590. -2.34057e+00 8.09534e-02 -1.55724e+01
  591. -5.77266e+00 -1.56440e+01 1.70893e+01
  592.  
  593. T-NPROT T-SOL_ION
  594. 3.03166e+02 3.03104e+02
  595.  
  596.  
  597. P P - P M E L O A D B A L A N C I N G
  598.  
  599. PP/PME load balancing changed the cut-off and PME settings:
  600. particle-particle PME
  601. rcoulomb rlist grid spacing 1/beta
  602. initial 1.200 nm 1.239 nm 144 144 64 0.119 nm 0.384 nm
  603. final 1.269 nm 1.308 nm 128 128 60 0.127 nm 0.406 nm
  604. cost-ratio 1.18 0.74
  605. (note that these numbers concern only part of the total PP and PME load)
  606.  
  607.  
  608. M E G A - F L O P S A C C O U N T I N G
  609.  
  610. NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
  611. RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
  612. W3=SPC/TIP3p W4=TIP4p (single or pairs)
  613. V&F=Potential and force V=Potential only F=Force only
  614.  
  615. Computing: M-Number M-Flops % Flops
  616. -----------------------------------------------------------------------------
  617. NB VdW [V&F] 1088.367630 1088.368 0.0
  618. Pair Search distance check 2867.648848 25808.840 0.0
  619. NxN Ewald Elec. + LJ [F] 1404416.077376 109544454.035 95.7
  620. NxN Ewald Elec. + LJ [V&F] 14469.143808 1866519.551 1.6
  621. 1,4 nonbonded interactions 1575.315000 141778.350 0.1
  622. Calc Weights 3096.844245 111486.393 0.1
  623. Spread Q Bspline 66066.010560 132132.021 0.1
  624. Gather F Bspline 66066.010560 396396.063 0.3
  625. 3D-FFT 195731.828538 1565854.628 1.4
  626. Solve PME 1310.982144 83902.857 0.1
  627. Reset In Box 26.008290 78.025 0.0
  628. CG-CoM 26.008290 78.025 0.0
  629. Bonds 212.942580 12563.612 0.0
  630. Propers 1815.312990 415706.675 0.4
  631. Impropers 5.901180 1227.445 0.0
  632. Virial 60.484725 1088.725 0.0
  633. Stop-CM 10.527165 105.272 0.0
  634. Calc-Ekin 103.413915 2792.176 0.0
  635. Lincs 431.624616 25897.477 0.0
  636. Lincs-Mat 3117.020496 12468.082 0.0
  637. Constraint-V 1438.129074 11505.033 0.0
  638. Constraint-Vir 50.516532 1212.397 0.0
  639. Settle 191.626614 61895.396 0.1
  640. -----------------------------------------------------------------------------
  641. Total 114416039.446 100.0
  642. -----------------------------------------------------------------------------
  643.  
  644.  
  645. 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
  646.  
  647. av. #atoms communicated per step for force: 2 x 1268936.3
  648. av. #atoms communicated per step for LINCS: 2 x 49739.9
  649.  
  650. Average load imbalance: 15.1 %
  651. Part of the total run time spent waiting due to load imbalance: 4.8 %
  652. Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 2 % Y 2 % Z 0 %
  653. Average PME mesh/force load: 2.123
  654. Part of the total run time spent waiting due to PP/PME imbalance: 35.1 %
  655.  
  656. NOTE: 35.1 % performance was lost because the PME ranks
  657. had more work to do than the PP ranks.
  658. You might want to increase the number of PME ranks
  659. or increase the cut-off and the grid spacing.
  660.  
  661.  
  662. 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
  663.  
  664. On 768 MPI ranks doing PP, each using 2 OpenMP threads, and
  665. on 256 MPI ranks doing PME, each using 2 OpenMP threads
  666.  
  667. Computing: Num Num Call Wall time Giga-Cycles
  668. Ranks Threads Count (s) total sum %
  669. -----------------------------------------------------------------------------
  670. Domain decomp. 768 2 126 0.473 1597.946 3.2
  671. DD comm. load 768 2 126 0.003 11.738 0.0
  672. DD comm. bounds 768 2 126 0.023 76.656 0.2
  673. Send X to PME 768 2 5001 0.012 40.607 0.1
  674. Neighbor search 768 2 126 0.100 336.302 0.7
  675. Launch GPU ops. 768 2 10002 0.811 2740.606 5.4
  676. Comm. coord. 768 2 4875 0.694 2345.741 4.7
  677. Force 768 2 5001 0.678 2290.582 4.6
  678. Wait + Comm. F 768 2 5001 1.437 4855.475 9.7
  679. PME mesh * 256 2 5001 9.334 10513.604 20.9
  680. PME wait for PP * 1.828 2059.480 4.1
  681. Wait + Recv. PME F 768 2 5001 4.308 14559.095 28.9
  682. Wait GPU nonlocal 768 2 5001 0.656 2216.981 4.4
  683. Wait GPU local 768 2 5001 0.476 1609.887 3.2
  684. NB X/F buffer ops. 768 2 19752 0.288 973.902 1.9
  685. Write traj. 768 2 2 0.067 225.239 0.4
  686. Update 768 2 5001 0.093 314.724 0.6
  687. Constraints 768 2 5001 0.565 1910.861 3.8
  688. Comm. energies 768 2 251 0.413 1396.729 2.8
  689. Rest 0.064 216.253 0.4
  690. -----------------------------------------------------------------------------
  691. Total 11.162 50292.432 100.0
  692. -----------------------------------------------------------------------------
  693. (*) Note that with separate PME ranks, the walltime column actually sums to
  694. twice the total reported, but the cycle count total and % are correct.
  695. -----------------------------------------------------------------------------
  696. Breakdown of PME mesh computation
  697. -----------------------------------------------------------------------------
  698. PME redist. X/F 256 2 10002 1.820 2049.686 4.1
  699. PME spread/gather 256 2 10002 1.644 1852.208 3.7
  700. PME 3D-FFT 256 2 10002 0.517 581.979 1.2
  701. PME 3D-FFT Comm. 256 2 20004 5.274 5941.029 11.8
  702. PME solve Elec 256 2 5001 0.055 61.938 0.1
  703. -----------------------------------------------------------------------------
  704.  
  705. Core t (s) Wall t (s) (%)
  706. Time: 21737.433 11.162 194742.4
  707. (ns/day) (hour/ns)
  708. Performance: 77.420 0.310
  709. Finished mdrun on rank 0 Wed Apr 29 20:28:29 2015
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