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  1. Log file opened on Fri Jul 25 14:10:09 2014
  2. Host: c4437 pid: 6527 nodeid: 0 nnodes: 1
  3. Gromacs version: VERSION 4.6.6
  4. Precision: single
  5. Memory model: 64 bit
  6. MPI library: thread_mpi
  7. OpenMP support: enabled
  8. GPU support: enabled
  9. invsqrt routine: gmx_software_invsqrt(x)
  10. CPU acceleration: AVX_256
  11. FFT library: fftw-3.3.4-sse2
  12. Large file support: enabled
  13. RDTSCP usage: enabled
  14. Built on: Fri Jul 25 13:50:06 CDT 2014
  15. Built by: mohtadin [CMAKE]
  16. Build OS/arch: Linux 2.6.32-431.11.2.el6.x86_64 x86_64
  17. Build CPU vendor: AuthenticAMD
  18. Build CPU brand: AMD Opteron(TM) Processor 6272
  19. Build CPU family: 21 Model: 1 Stepping: 2
  20. Build CPU 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
  21. C compiler: /util/comp/gcc/4.7/bin/gcc GNU gcc (GCC) 4.7.1
  22. C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -I/util/opt/cuda/6.0/include -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
  23. C++ compiler: /util/comp/gcc/4.7/bin/g++ GNU g++ (GCC) 4.7.1
  24. C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -m64 -march=bdver1 -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
  25. 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
  26. 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;-Wno-sign-compare;-Wall;-Wno-unused;-Wunused-value;-m64;-march=bdver1;-fomit-frame-pointer;-funroll-all-loops;-fexcess-precision=fast;-O3;-DNDEBUG
  27. CUDA driver: 6.0
  28. CUDA runtime: 6.0
  29.  
  30.  
  31. :-) G R O M A C S (-:
  32.  
  33. Gravel Rubs Often Many Awfully Cauterized Sores
  34.  
  35. :-) VERSION 4.6.6 (-:
  36.  
  37. Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
  38. Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
  39. Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
  40. Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
  41. Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
  42. Michael Shirts, Alfons Sijbers, Peter Tieleman,
  43.  
  44. Berk Hess, David van der Spoel, and Erik Lindahl.
  45.  
  46. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  47. Copyright (c) 2001-2012,2013, The GROMACS development team at
  48. Uppsala University & The Royal Institute of Technology, Sweden.
  49. check out http://www.gromacs.org for more information.
  50.  
  51. This program is free software; you can redistribute it and/or
  52. modify it under the terms of the GNU Lesser General Public License
  53. as published by the Free Software Foundation; either version 2.1
  54. of the License, or (at your option) any later version.
  55.  
  56. :-) mdrun_4gpu (-:
  57.  
  58.  
  59. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  60. B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
  61. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
  62. molecular simulation
  63. J. Chem. Theory Comput. 4 (2008) pp. 435-447
  64. -------- -------- --- Thank You --- -------- --------
  65.  
  66.  
  67. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  68. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
  69. Berendsen
  70. GROMACS: Fast, Flexible and Free
  71. J. Comp. Chem. 26 (2005) pp. 1701-1719
  72. -------- -------- --- Thank You --- -------- --------
  73.  
  74.  
  75. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  76. E. Lindahl and B. Hess and D. van der Spoel
  77. GROMACS 3.0: A package for molecular simulation and trajectory analysis
  78. J. Mol. Mod. 7 (2001) pp. 306-317
  79. -------- -------- --- Thank You --- -------- --------
  80.  
  81.  
  82. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  83. H. J. C. Berendsen, D. van der Spoel and R. van Drunen
  84. GROMACS: A message-passing parallel molecular dynamics implementation
  85. Comp. Phys. Comm. 91 (1995) pp. 43-56
  86. -------- -------- --- Thank You --- -------- --------
  87.  
  88.  
  89. Number of CPUs detected (24) does not match the number reported by OpenMP (12).
  90. Consider setting the launch configuration manually!
  91.  
  92. For optimal performance with a GPU nstlist (now 10) should be larger.
  93. The optimum depends on your CPU and GPU resources.
  94. You might want to try several nstlist values.
  95. Changing nstlist from 10 to 20, rlist from 1.094 to 1.208
  96.  
  97.  
  98. Non-default thread affinity set, disabling internal thread affinity
  99. Input Parameters:
  100. integrator = md
  101. nsteps = 5000
  102. init-step = 0
  103. cutoff-scheme = Verlet
  104. ns_type = Grid
  105. nstlist = 20
  106. ndelta = 2
  107. nstcomm = 100
  108. comm-mode = Linear
  109. nstlog = 0
  110. nstxout = 0
  111. nstvout = 0
  112. nstfout = 0
  113. nstcalcenergy = 100
  114. nstenergy = 0
  115. nstxtcout = 0
  116. init-t = 0
  117. delta-t = 0.002
  118. xtcprec = 1000
  119. fourierspacing = 0.12
  120. nkx = 0
  121. nky = 0
  122. nkz = 0
  123. pme-order = 4
  124. ewald-rtol = 1e-05
  125. ewald-geometry = 0
  126. epsilon-surface = 0
  127. optimize-fft = FALSE
  128. ePBC = xyz
  129. bPeriodicMols = FALSE
  130. bContinuation = FALSE
  131. bShakeSOR = FALSE
  132. etc = Berendsen
  133. bPrintNHChains = FALSE
  134. nsttcouple = 10
  135. epc = No
  136. epctype = Isotropic
  137. nstpcouple = -1
  138. tau-p = 1
  139. ref-p (3x3):
  140. ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  141. ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  142. ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  143. compress (3x3):
  144. compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  145. compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  146. compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  147. refcoord-scaling = No
  148. posres-com (3):
  149. posres-com[0]= 0.00000e+00
  150. posres-com[1]= 0.00000e+00
  151. posres-com[2]= 0.00000e+00
  152. posres-comB (3):
  153. posres-comB[0]= 0.00000e+00
  154. posres-comB[1]= 0.00000e+00
  155. posres-comB[2]= 0.00000e+00
  156. verlet-buffer-drift = 0.005
  157. rlist = 1.208
  158. rlistlong = 1.208
  159. nstcalclr = 10
  160. rtpi = 0.05
  161. coulombtype = Cut-off
  162. coulomb-modifier = Potential-shift
  163. rcoulomb-switch = 0
  164. rcoulomb = 1
  165. vdwtype = Cut-off
  166. vdw-modifier = Potential-shift
  167. rvdw-switch = 0
  168. rvdw = 1
  169. epsilon-r = 1
  170. epsilon-rf = inf
  171. tabext = 1
  172. implicit-solvent = No
  173. gb-algorithm = Still
  174. gb-epsilon-solvent = 80
  175. nstgbradii = 1
  176. rgbradii = 1
  177. gb-saltconc = 0
  178. gb-obc-alpha = 1
  179. gb-obc-beta = 0.8
  180. gb-obc-gamma = 4.85
  181. gb-dielectric-offset = 0.009
  182. sa-algorithm = Ace-approximation
  183. sa-surface-tension = 2.05016
  184. DispCorr = No
  185. bSimTemp = FALSE
  186. free-energy = no
  187. nwall = 0
  188. wall-type = 9-3
  189. wall-atomtype[0] = -1
  190. wall-atomtype[1] = -1
  191. wall-density[0] = 0
  192. wall-density[1] = 0
  193. wall-ewald-zfac = 3
  194. pull = no
  195. rotation = FALSE
  196. disre = No
  197. disre-weighting = Conservative
  198. disre-mixed = FALSE
  199. dr-fc = 1000
  200. dr-tau = 0
  201. nstdisreout = 100
  202. orires-fc = 0
  203. orires-tau = 0
  204. nstorireout = 100
  205. dihre-fc = 0
  206. em-stepsize = 0.01
  207. em-tol = 10
  208. niter = 20
  209. fc-stepsize = 0
  210. nstcgsteep = 1000
  211. nbfgscorr = 10
  212. ConstAlg = Lincs
  213. shake-tol = 0.0001
  214. lincs-order = 4
  215. lincs-warnangle = 30
  216. lincs-iter = 1
  217. bd-fric = 0
  218. ld-seed = 1993
  219. cos-accel = 0
  220. deform (3x3):
  221. deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  222. deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  223. deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  224. adress = FALSE
  225. userint1 = 0
  226. userint2 = 0
  227. userint3 = 0
  228. userint4 = 0
  229. userreal1 = 0
  230. userreal2 = 0
  231. userreal3 = 0
  232. userreal4 = 0
  233. grpopts:
  234. nrdf: 103423 141310
  235. ref-t: 323 323
  236. tau-t: 0.1 0.1
  237. anneal: No No
  238. ann-npoints: 0 0
  239. acc: 0 0 0
  240. nfreeze: N N N
  241. energygrp-flags[ 0]: 0
  242. efield-x:
  243. n = 0
  244. efield-xt:
  245. n = 0
  246. efield-y:
  247. n = 0
  248. efield-yt:
  249. n = 0
  250. efield-z:
  251. n = 0
  252. efield-zt:
  253. n = 0
  254. bQMMM = FALSE
  255. QMconstraints = 0
  256. QMMMscheme = 0
  257. scalefactor = 1
  258. qm-opts:
  259. ngQM = 0
  260.  
  261. Initializing Domain Decomposition on 3 nodes
  262. Dynamic load balancing: auto
  263. Will sort the charge groups at every domain (re)decomposition
  264. Initial maximum inter charge-group distances:
  265. two-body bonded interactions: 0.410 nm, LJ-14, atoms 19458 19463
  266. multi-body bonded interactions: 0.410 nm, Proper Dih., atoms 19458 19463
  267. Minimum cell size due to bonded interactions: 0.452 nm
  268. Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.771 nm
  269. Estimated maximum distance required for P-LINCS: 0.771 nm
  270. This distance will limit the DD cell size, you can override this with -rcon
  271. Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
  272. Optimizing the DD grid for 3 cells with a minimum initial size of 0.964 nm
  273. The maximum allowed number of cells is: X 18 Y 19 Z 6
  274. Domain decomposition grid 1 x 3 x 1, separate PME nodes 0
  275. Domain decomposition nodeid 0, coordinates 0 0 0
  276.  
  277. Using 3 MPI threads
  278. Using 8 OpenMP threads per tMPI thread
  279.  
  280. Detecting CPU-specific acceleration.
  281. Present hardware specification:
  282. Vendor: GenuineIntel
  283. Brand: Intel(R) Xeon(R) CPU E5-2630 0 @ 2.30GHz
  284. Family: 6 Model: 45 Stepping: 7
  285. 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
  286. Acceleration most likely to fit this hardware: AVX_256
  287. Acceleration selected at GROMACS compile time: AVX_256
  288.  
  289.  
  290. 3 GPUs detected:
  291. #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
  292. #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
  293. #2: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
  294.  
  295. 3 GPUs auto-selected for this run.
  296. Mapping of GPUs to the 3 PP ranks in this node: #0, #1, #2
  297.  
  298. Cut-off's: NS: 1.208 Coulomb: 1 LJ: 1
  299. System total charge: 0.000
  300. Generated table with 1104 data points for 1-4 COUL.
  301. Tabscale = 500 points/nm
  302. Generated table with 1104 data points for 1-4 LJ6.
  303. Tabscale = 500 points/nm
  304. Generated table with 1104 data points for 1-4 LJ12.
  305. Tabscale = 500 points/nm
  306.  
  307. Using CUDA 8x8 non-bonded kernels
  308.  
  309. Potential shift: LJ r^-12: 1.000 r^-6 1.000, Coulomb 1.000
  310. Removing pbc first time
  311.  
  312. Initializing Parallel LINear Constraint Solver
  313.  
  314. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  315. B. Hess
  316. P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
  317. J. Chem. Theory Comput. 4 (2008) pp. 116-122
  318. -------- -------- --- Thank You --- -------- --------
  319.  
  320. The number of constraints is 50176
  321. There are inter charge-group constraints,
  322. will communicate selected coordinates each lincs iteration
  323.  
  324. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  325. S. Miyamoto and P. A. Kollman
  326. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
  327. Water Models
  328. J. Comp. Chem. 13 (1992) pp. 952-962
  329. -------- -------- --- Thank You --- -------- --------
  330.  
  331.  
  332. Linking all bonded interactions to atoms
  333.  
  334. The initial number of communication pulses is: Y 1
  335. The initial domain decomposition cell size is: Y 6.11 nm
  336.  
  337. The maximum allowed distance for charge groups involved in interactions is:
  338. non-bonded interactions 1.208 nm
  339. two-body bonded interactions (-rdd) 1.208 nm
  340. multi-body bonded interactions (-rdd) 1.208 nm
  341. atoms separated by up to 5 constraints (-rcon) 6.113 nm
  342.  
  343. When dynamic load balancing gets turned on, these settings will change to:
  344. The maximum number of communication pulses is: Y 1
  345. The minimum size for domain decomposition cells is 1.208 nm
  346. The requested allowed shrink of DD cells (option -dds) is: 0.80
  347. The allowed shrink of domain decomposition cells is: Y 0.20
  348. The maximum allowed distance for charge groups involved in interactions is:
  349. non-bonded interactions 1.208 nm
  350. two-body bonded interactions (-rdd) 1.208 nm
  351. multi-body bonded interactions (-rdd) 1.208 nm
  352. atoms separated by up to 5 constraints (-rcon) 1.208 nm
  353.  
  354.  
  355. Making 1D domain decomposition grid 1 x 3 x 1, home cell index 0 0 0
  356.  
  357. Center of mass motion removal mode is Linear
  358. We have the following groups for center of mass motion removal:
  359. 0: rest
  360.  
  361. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  362. H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
  363. Molecular dynamics with coupling to an external bath
  364. J. Chem. Phys. 81 (1984) pp. 3684-3690
  365. -------- -------- --- Thank You --- -------- --------
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