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  1. Log file opened on Fri Jul 25 15:02:23 2014
  2. Host: c4437 pid: 29821 rank ID: 0 number of ranks: 1
  3. GROMACS: gmx mdrun, VERSION 5.0
  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
  28. Executable: /work/gromacs5gpu/bin/gmx_5gpu
  29. Library dir: /work/gromacs5gpu/share/gromacs/top
  30. Command line:
  31. mdrun_5gpu -v
  32.  
  33. Gromacs version: VERSION 5.0
  34. Precision: single
  35. Memory model: 64 bit
  36. MPI library: thread_mpi
  37. OpenMP support: enabled
  38. GPU support: enabled
  39. invsqrt routine: gmx_software_invsqrt(x)
  40. SIMD instructions: AVX_256
  41. FFT library: fftw-3.3.4-sse2
  42. RDTSCP usage: enabled
  43. C++11 compilation: disabled
  44. TNG support: enabled
  45. Tracing support: disabled
  46. Built on: Fri Jul 25 14:35:10 CDT 2014
  47. Built by: mohtadin@c4437 [CMAKE]
  48. Build OS/arch: Linux 2.6.32-431.11.2.el6.x86_64 x86_64
  49. Build CPU vendor: GenuineIntel
  50. Build CPU brand: Intel(R) Xeon(R) CPU E5-2630 0 @ 2.30GHz
  51. Build CPU family: 6 Model: 45 Stepping: 7
  52. Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  53. C compiler: /util/comp/gcc/4.7/bin/gcc GNU 4.7.1
  54. C compiler flags: -mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -I/util/opt/cuda/6.0/include -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG
  55. C++ compiler: /util/comp/gcc/4.7/bin/g++ GNU 4.7.1
  56. C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -m64 -march=bdver1 -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG
  57. Boost version: 1.55.0 (internal)
  58. CUDA compiler: /util/opt/cuda/6.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2013 NVIDIA Corporation;Built on Thu_Mar_13_11:58:58_PDT_2014;Cuda compilation tools, release 6.0, V6.0.1
  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;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-m64;-march=bdver1;-fomit-frame-pointer;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;-O3;-DNDEBUG
  60. CUDA driver: 6.0
  61. CUDA runtime: 6.0
  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 (24) does not match the number reported by OpenMP (12).
  96. Consider setting the launch configuration manually!
  97.  
  98. For optimal performance with a GPU nstlist (now 10) should be larger.
  99. The optimum depends on your CPU and GPU resources.
  100. You might want to try several nstlist values.
  101. Changing nstlist from 10 to 20, rlist from 1.094 to 1.208
  102.  
  103.  
  104. Non-default thread affinity set, disabling internal thread affinity
  105. Input Parameters:
  106. integrator = md
  107. tinit = 0
  108. dt = 0.002
  109. nsteps = 5000
  110. init-step = 0
  111. simulation-part = 1
  112. comm-mode = Linear
  113. nstcomm = 100
  114. bd-fric = 0
  115. ld-seed = 1993
  116. emtol = 10
  117. emstep = 0.01
  118. niter = 20
  119. fcstep = 0
  120. nstcgsteep = 1000
  121. nbfgscorr = 10
  122. rtpi = 0.05
  123. nstxout = 0
  124. nstvout = 0
  125. nstfout = 0
  126. nstlog = 0
  127. nstcalcenergy = 100
  128. nstenergy = 0
  129. nstxout-compressed = 0
  130. compressed-x-precision = 1000
  131. cutoff-scheme = Verlet
  132. nstlist = 20
  133. ns-type = Grid
  134. pbc = xyz
  135. periodic-molecules = FALSE
  136. verlet-buffer-tolerance = 0.005
  137. rlist = 1.208
  138. rlistlong = 1.208
  139. nstcalclr = 10
  140. coulombtype = Cut-off
  141. coulomb-modifier = Potential-shift
  142. rcoulomb-switch = 0
  143. rcoulomb = 1
  144. epsilon-r = 1
  145. epsilon-rf = inf
  146. vdw-type = Cut-off
  147. vdw-modifier = Potential-shift
  148. rvdw-switch = 0
  149. rvdw = 1
  150. DispCorr = No
  151. table-extension = 1
  152. fourierspacing = 0.12
  153. fourier-nx = 0
  154. fourier-ny = 0
  155. fourier-nz = 0
  156. pme-order = 4
  157. ewald-rtol = 1e-05
  158. ewald-rtol-lj = 1e-05
  159. lj-pme-comb-rule = Geometric
  160. ewald-geometry = 0
  161. epsilon-surface = 0
  162. implicit-solvent = No
  163. gb-algorithm = Still
  164. nstgbradii = 1
  165. rgbradii = 1
  166. gb-epsilon-solvent = 80
  167. gb-saltconc = 0
  168. gb-obc-alpha = 1
  169. gb-obc-beta = 0.8
  170. gb-obc-gamma = 4.85
  171. gb-dielectric-offset = 0.009
  172. sa-algorithm = Ace-approximation
  173. sa-surface-tension = 2.05016
  174. tcoupl = Berendsen
  175. nsttcouple = 10
  176. nh-chain-length = 0
  177. print-nose-hoover-chain-variables = FALSE
  178. pcoupl = No
  179. pcoupltype = Isotropic
  180. nstpcouple = -1
  181. tau-p = 1
  182. compressibility (3x3):
  183. compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  184. compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  185. compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  186. ref-p (3x3):
  187. ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  188. ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  189. ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  190. refcoord-scaling = No
  191. posres-com (3):
  192. posres-com[0]= 0.00000e+00
  193. posres-com[1]= 0.00000e+00
  194. posres-com[2]= 0.00000e+00
  195. posres-comB (3):
  196. posres-comB[0]= 0.00000e+00
  197. posres-comB[1]= 0.00000e+00
  198. posres-comB[2]= 0.00000e+00
  199. QMMM = FALSE
  200. QMconstraints = 0
  201. QMMMscheme = 0
  202. MMChargeScaleFactor = 1
  203. qm-opts:
  204. ngQM = 0
  205. constraint-algorithm = Lincs
  206. continuation = FALSE
  207. Shake-SOR = FALSE
  208. shake-tol = 0.0001
  209. lincs-order = 4
  210. lincs-iter = 1
  211. lincs-warnangle = 30
  212. nwall = 0
  213. wall-type = 9-3
  214. wall-r-linpot = -1
  215. wall-atomtype[0] = -1
  216. wall-atomtype[1] = -1
  217. wall-density[0] = 0
  218. wall-density[1] = 0
  219. wall-ewald-zfac = 3
  220. pull = no
  221. rotation = FALSE
  222. interactiveMD = FALSE
  223. disre = No
  224. disre-weighting = Conservative
  225. disre-mixed = FALSE
  226. dr-fc = 1000
  227. dr-tau = 0
  228. nstdisreout = 100
  229. orire-fc = 0
  230. orire-tau = 0
  231. nstorireout = 100
  232. free-energy = no
  233. cos-acceleration = 0
  234. deform (3x3):
  235. deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  236. deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  237. deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  238. simulated-tempering = FALSE
  239. E-x:
  240. n = 0
  241. E-xt:
  242. n = 0
  243. E-y:
  244. n = 0
  245. E-yt:
  246. n = 0
  247. E-z:
  248. n = 0
  249. E-zt:
  250. n = 0
  251. swapcoords = no
  252. adress = FALSE
  253. userint1 = 0
  254. userint2 = 0
  255. userint3 = 0
  256. userint4 = 0
  257. userreal1 = 0
  258. userreal2 = 0
  259. userreal3 = 0
  260. userreal4 = 0
  261. grpopts:
  262. nrdf: 103423 141310
  263. ref-t: 323 323
  264. tau-t: 0.1 0.1
  265. annealing: No No
  266. annealing-npoints: 0 0
  267. acc: 0 0 0
  268. nfreeze: N N N
  269. energygrp-flags[ 0]: 0
  270.  
  271. Initializing Domain Decomposition on 3 ranks
  272. Dynamic load balancing: auto
  273. Will sort the charge groups at every domain (re)decomposition
  274. Initial maximum inter charge-group distances:
  275. two-body bonded interactions: 0.410 nm, LJ-14, atoms 19458 19463
  276. multi-body bonded interactions: 0.410 nm, Proper Dih., atoms 19458 19463
  277. Minimum cell size due to bonded interactions: 0.452 nm
  278. Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.771 nm
  279. Estimated maximum distance required for P-LINCS: 0.771 nm
  280. This distance will limit the DD cell size, you can override this with -rcon
  281. Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
  282. Optimizing the DD grid for 3 cells with a minimum initial size of 0.964 nm
  283. The maximum allowed number of cells is: X 18 Y 19 Z 6
  284. Domain decomposition grid 1 x 3 x 1, separate PME ranks 0
  285. Domain decomposition rank 0, coordinates 0 0 0
  286.  
  287. Using 3 MPI threads
  288. Using 8 OpenMP threads per tMPI thread
  289.  
  290. Detecting CPU SIMD instructions.
  291. Present hardware specification:
  292. Vendor: GenuineIntel
  293. Brand: Intel(R) Xeon(R) CPU E5-2630 0 @ 2.30GHz
  294. Family: 6 Model: 45 Stepping: 7
  295. Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  296. SIMD instructions most likely to fit this hardware: AVX_256
  297. SIMD instructions selected at GROMACS compile time: AVX_256
  298.  
  299.  
  300. 3 GPUs detected:
  301. #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
  302. #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
  303. #2: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
  304.  
  305. 3 GPUs auto-selected for this run.
  306. Mapping of GPUs to the 3 PP ranks in this node: #0, #1, #2
  307.  
  308. Cut-off's: NS: 1.208 Coulomb: 1 LJ: 1
  309. System total charge: 0.000
  310. Generated table with 1104 data points for 1-4 COUL.
  311. Tabscale = 500 points/nm
  312. Generated table with 1104 data points for 1-4 LJ6.
  313. Tabscale = 500 points/nm
  314. Generated table with 1104 data points for 1-4 LJ12.
  315. Tabscale = 500 points/nm
  316.  
  317. Using CUDA 8x8 non-bonded kernels
  318.  
  319. Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Coulomb -1e+00
  320. Removing pbc first time
  321.  
  322. Initializing Parallel LINear Constraint Solver
  323.  
  324. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  325. B. Hess
  326. P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
  327. J. Chem. Theory Comput. 4 (2008) pp. 116-122
  328. -------- -------- --- Thank You --- -------- --------
  329.  
  330. The number of constraints is 50176
  331. There are inter charge-group constraints,
  332. will communicate selected coordinates each lincs iteration
  333.  
  334. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  335. S. Miyamoto and P. A. Kollman
  336. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
  337. Water Models
  338. J. Comp. Chem. 13 (1992) pp. 952-962
  339. -------- -------- --- Thank You --- -------- --------
  340.  
  341.  
  342. Linking all bonded interactions to atoms
  343.  
  344. The initial number of communication pulses is: Y 1
  345. The initial domain decomposition cell size is: Y 6.11 nm
  346.  
  347. The maximum allowed distance for charge groups involved in interactions is:
  348. non-bonded interactions 1.208 nm
  349. two-body bonded interactions (-rdd) 1.208 nm
  350. multi-body bonded interactions (-rdd) 1.208 nm
  351. atoms separated by up to 5 constraints (-rcon) 6.113 nm
  352.  
  353. When dynamic load balancing gets turned on, these settings will change to:
  354. The maximum number of communication pulses is: Y 1
  355. The minimum size for domain decomposition cells is 1.208 nm
  356. The requested allowed shrink of DD cells (option -dds) is: 0.80
  357. The allowed shrink of domain decomposition cells is: Y 0.20
  358. The maximum allowed distance for charge groups involved in interactions is:
  359. non-bonded interactions 1.208 nm
  360. two-body bonded interactions (-rdd) 1.208 nm
  361. multi-body bonded interactions (-rdd) 1.208 nm
  362. atoms separated by up to 5 constraints (-rcon) 1.208 nm
  363.  
  364.  
  365. Making 1D domain decomposition grid 1 x 3 x 1, home cell index 0 0 0
  366.  
  367. Center of mass motion removal mode is Linear
  368. We have the following groups for center of mass motion removal:
  369. 0: rest
  370.  
  371. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  372. H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
  373. Molecular dynamics with coupling to an external bath
  374. J. Chem. Phys. 81 (1984) pp. 3684-3690
  375. -------- -------- --- Thank You --- -------- --------
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