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gromacs-nb-gpu-pme-cpu

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  1. Log file opened on Fri Mar 2 16:15:49 2018
  2. Host: orca pid: 14911 rank ID: 0 number of ranks: 1
  3. :-) GROMACS - gmx mdrun, 2018 (-:
  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 Gerrit Groenhof
  8. Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
  9. Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
  10. Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff
  11. Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
  12. Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
  13. Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
  14. and the project leaders:
  15. Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
  16.  
  17. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  18. Copyright (c) 2001-2017, The GROMACS development team at
  19. Uppsala University, Stockholm University and
  20. the Royal Institute of Technology, Sweden.
  21. check out http://www.gromacs.org for more information.
  22.  
  23. GROMACS is free software; you can redistribute it and/or modify it
  24. under the terms of the GNU Lesser General Public License
  25. as published by the Free Software Foundation; either version 2.1
  26. of the License, or (at your option) any later version.
  27.  
  28. GROMACS: gmx mdrun, version 2018
  29. Executable: /usr/local/gromacs/bin/gmx
  30. Data prefix: /usr/local/gromacs
  31. Working dir: /home/mahmood/gromacs-2018/bench/lysozyme
  32. Command line:
  33. gmx mdrun -nobackup -nb gpu -pme cpu -deffnm md_0_1
  34.  
  35. GROMACS version: 2018
  36. Precision: single
  37. Memory model: 64 bit
  38. MPI library: thread_mpi
  39. OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
  40. GPU support: CUDA
  41. SIMD instructions: AVX2_128
  42. FFT library: fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
  43. RDTSCP usage: enabled
  44. TNG support: enabled
  45. Hwloc support: disabled
  46. Tracing support: disabled
  47. Built on: 2018-02-23 17:10:06
  48. Built by: mahmood@orca [CMAKE]
  49. Build OS/arch: Linux 4.10.0-28-generic x86_64
  50. Build CPU vendor: AMD
  51. Build CPU brand: AMD Ryzen 7 1800X Eight-Core Processor
  52. Build CPU family: 23 Model: 1 Stepping: 1
  53. Build CPU features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  54. C compiler: /usr/bin/cc GNU 5.4.0
  55. C compiler flags: -march=core-avx2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
  56. C++ compiler: /usr/bin/c++ GNU 5.4.0
  57. C++ compiler flags: -march=core-avx2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
  58. CUDA compiler: /usr/local/cuda-9.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2017 NVIDIA Corporation;Built on Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0, V9.0.176
  59. CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;-D_FORCE_INLINES;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
  60. CUDA driver: 9.0
  61. CUDA runtime: 9.0
  62.  
  63.  
  64. Running on 1 node with total 16 cores, 16 logical cores, 1 compatible GPU
  65. Hardware detected:
  66. CPU info:
  67. Vendor: AMD
  68. Brand: AMD Ryzen 7 1800X Eight-Core Processor
  69. Family: 23 Model: 1 Stepping: 1
  70. Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  71. Hardware topology: Basic
  72. Sockets, cores, and logical processors:
  73. Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] [ 14] [ 15]
  74. GPU info:
  75. Number of GPUs detected: 1
  76. #0: NVIDIA Quadro M2000, compute cap.: 5.2, ECC: no, stat: compatible
  77.  
  78.  
  79. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  80. M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
  81. Lindahl
  82. GROMACS: High performance molecular simulations through multi-level
  83. parallelism from laptops to supercomputers
  84. SoftwareX 1 (2015) pp. 19-25
  85. -------- -------- --- Thank You --- -------- --------
  86.  
  87.  
  88. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  89. S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
  90. Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
  91. GROMACS
  92. In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
  93. -------- -------- --- Thank You --- -------- --------
  94.  
  95.  
  96. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  97. S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
  98. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
  99. GROMACS 4.5: a high-throughput and highly parallel open source molecular
  100. simulation toolkit
  101. Bioinformatics 29 (2013) pp. 845-54
  102. -------- -------- --- Thank You --- -------- --------
  103.  
  104.  
  105. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  106. B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
  107. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
  108. molecular simulation
  109. J. Chem. Theory Comput. 4 (2008) pp. 435-447
  110. -------- -------- --- Thank You --- -------- --------
  111.  
  112.  
  113. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  114. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
  115. Berendsen
  116. GROMACS: Fast, Flexible and Free
  117. J. Comp. Chem. 26 (2005) pp. 1701-1719
  118. -------- -------- --- Thank You --- -------- --------
  119.  
  120.  
  121. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  122. E. Lindahl and B. Hess and D. van der Spoel
  123. GROMACS 3.0: A package for molecular simulation and trajectory analysis
  124. J. Mol. Mod. 7 (2001) pp. 306-317
  125. -------- -------- --- Thank You --- -------- --------
  126.  
  127.  
  128. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  129. H. J. C. Berendsen, D. van der Spoel and R. van Drunen
  130. GROMACS: A message-passing parallel molecular dynamics implementation
  131. Comp. Phys. Comm. 91 (1995) pp. 43-56
  132. -------- -------- --- Thank You --- -------- --------
  133.  
  134. Input Parameters:
  135. integrator = md
  136. tinit = 0
  137. dt = 0.002
  138. nsteps = 50000
  139. init-step = 0
  140. simulation-part = 1
  141. comm-mode = Linear
  142. nstcomm = 100
  143. bd-fric = 0
  144. ld-seed = 350012245
  145. emtol = 10
  146. emstep = 0.01
  147. niter = 20
  148. fcstep = 0
  149. nstcgsteep = 1000
  150. nbfgscorr = 10
  151. rtpi = 0.05
  152. nstxout = 5000
  153. nstvout = 5000
  154. nstfout = 0
  155. nstlog = 5000
  156. nstcalcenergy = 100
  157. nstenergy = 5000
  158. nstxout-compressed = 5000
  159. compressed-x-precision = 1000
  160. cutoff-scheme = Verlet
  161. nstlist = 10
  162. ns-type = Grid
  163. pbc = xyz
  164. periodic-molecules = false
  165. verlet-buffer-tolerance = 0.005
  166. rlist = 1
  167. coulombtype = PME
  168. coulomb-modifier = Potential-shift
  169. rcoulomb-switch = 0
  170. rcoulomb = 1
  171. epsilon-r = 1
  172. epsilon-rf = inf
  173. vdw-type = Cut-off
  174. vdw-modifier = Potential-shift
  175. rvdw-switch = 0
  176. rvdw = 1
  177. DispCorr = EnerPres
  178. table-extension = 1
  179. fourierspacing = 0.16
  180. fourier-nx = 44
  181. fourier-ny = 44
  182. fourier-nz = 44
  183. pme-order = 4
  184. ewald-rtol = 1e-05
  185. ewald-rtol-lj = 0.001
  186. lj-pme-comb-rule = Geometric
  187. ewald-geometry = 0
  188. epsilon-surface = 0
  189. implicit-solvent = No
  190. gb-algorithm = Still
  191. nstgbradii = 1
  192. rgbradii = 1
  193. gb-epsilon-solvent = 80
  194. gb-saltconc = 0
  195. gb-obc-alpha = 1
  196. gb-obc-beta = 0.8
  197. gb-obc-gamma = 4.85
  198. gb-dielectric-offset = 0.009
  199. sa-algorithm = Ace-approximation
  200. sa-surface-tension = 2.05016
  201. tcoupl = V-rescale
  202. nsttcouple = 10
  203. nh-chain-length = 0
  204. print-nose-hoover-chain-variables = false
  205. pcoupl = Parrinello-Rahman
  206. pcoupltype = Isotropic
  207. nstpcouple = 10
  208. tau-p = 2
  209. compressibility (3x3):
  210. compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
  211. compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
  212. compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
  213. ref-p (3x3):
  214. ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
  215. ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
  216. ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
  217. refcoord-scaling = No
  218. posres-com (3):
  219. posres-com[0]= 0.00000e+00
  220. posres-com[1]= 0.00000e+00
  221. posres-com[2]= 0.00000e+00
  222. posres-comB (3):
  223. posres-comB[0]= 0.00000e+00
  224. posres-comB[1]= 0.00000e+00
  225. posres-comB[2]= 0.00000e+00
  226. QMMM = false
  227. QMconstraints = 0
  228. QMMMscheme = 0
  229. MMChargeScaleFactor = 1
  230. qm-opts:
  231. ngQM = 0
  232. constraint-algorithm = Lincs
  233. continuation = true
  234. Shake-SOR = false
  235. shake-tol = 0.0001
  236. lincs-order = 4
  237. lincs-iter = 1
  238. lincs-warnangle = 30
  239. nwall = 0
  240. wall-type = 9-3
  241. wall-r-linpot = -1
  242. wall-atomtype[0] = -1
  243. wall-atomtype[1] = -1
  244. wall-density[0] = 0
  245. wall-density[1] = 0
  246. wall-ewald-zfac = 3
  247. pull = false
  248. awh = false
  249. rotation = false
  250. interactiveMD = false
  251. disre = No
  252. disre-weighting = Conservative
  253. disre-mixed = false
  254. dr-fc = 1000
  255. dr-tau = 0
  256. nstdisreout = 100
  257. orire-fc = 0
  258. orire-tau = 0
  259. nstorireout = 100
  260. free-energy = no
  261. cos-acceleration = 0
  262. deform (3x3):
  263. deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  264. deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  265. deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  266. simulated-tempering = false
  267. swapcoords = no
  268. userint1 = 0
  269. userint2 = 0
  270. userint3 = 0
  271. userint4 = 0
  272. userreal1 = 0
  273. userreal2 = 0
  274. userreal3 = 0
  275. userreal4 = 0
  276. applied-forces:
  277. electric-field:
  278. x:
  279. E0 = 0
  280. omega = 0
  281. t0 = 0
  282. sigma = 0
  283. y:
  284. E0 = 0
  285. omega = 0
  286. t0 = 0
  287. sigma = 0
  288. z:
  289. E0 = 0
  290. omega = 0
  291. t0 = 0
  292. sigma = 0
  293. grpopts:
  294. nrdf: 3895.83 63837.2
  295. ref-t: 300 300
  296. tau-t: 0.1 0.1
  297. annealing: No No
  298. annealing-npoints: 0 0
  299. acc: 0 0 0
  300. nfreeze: N N N
  301. energygrp-flags[ 0]: 0
  302.  
  303. Changing nstlist from 10 to 100, rlist from 1 to 1.167
  304.  
  305. Using 1 MPI thread
  306. Using 16 OpenMP threads
  307.  
  308. 1 GPU auto-selected for this run.
  309. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
  310. PP:0
  311.  
  312. NOTE: GROMACS was configured without NVML support hence it can not exploit
  313. application clocks of the detected Quadro M2000 GPU to improve performance.
  314. Recompile with the NVML library (compatible with the driver used) or set application clocks manually.
  315.  
  316. Pinning threads with an auto-selected logical core stride of 1
  317. System total charge: -0.000
  318. Will do PME sum in reciprocal space for electrostatic interactions.
  319.  
  320. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  321. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
  322. A smooth particle mesh Ewald method
  323. J. Chem. Phys. 103 (1995) pp. 8577-8592
  324. -------- -------- --- Thank You --- -------- --------
  325.  
  326. Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
  327. Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
  328. Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
  329.  
  330. Long Range LJ corr.: <C6> 3.1923e-04
  331. Generated table with 1083 data points for Ewald.
  332. Tabscale = 500 points/nm
  333. Generated table with 1083 data points for LJ6.
  334. Tabscale = 500 points/nm
  335. Generated table with 1083 data points for LJ12.
  336. Tabscale = 500 points/nm
  337. Generated table with 1083 data points for 1-4 COUL.
  338. Tabscale = 500 points/nm
  339. Generated table with 1083 data points for 1-4 LJ6.
  340. Tabscale = 500 points/nm
  341. Generated table with 1083 data points for 1-4 LJ12.
  342. Tabscale = 500 points/nm
  343.  
  344. Using GPU 8x8 nonbonded short-range kernels
  345.  
  346. Using a dual 8x4 pair-list setup updated with dynamic, rolling pruning:
  347. outer list: updated every 100 steps, buffer 0.167 nm, rlist 1.167 nm
  348. inner list: updated every 10 steps, buffer 0.002 nm, rlist 1.002 nm
  349. At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  350. outer list: updated every 100 steps, buffer 0.319 nm, rlist 1.319 nm
  351. inner list: updated every 10 steps, buffer 0.043 nm, rlist 1.043 nm
  352.  
  353. Using geometric Lennard-Jones combination rule
  354.  
  355.  
  356. Initializing LINear Constraint Solver
  357.  
  358. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  359. B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
  360. LINCS: A Linear Constraint Solver for molecular simulations
  361. J. Comp. Chem. 18 (1997) pp. 1463-1472
  362. -------- -------- --- Thank You --- -------- --------
  363.  
  364. The number of constraints is 1984
  365.  
  366. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  367. S. Miyamoto and P. A. Kollman
  368. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
  369. Water Models
  370. J. Comp. Chem. 13 (1992) pp. 952-962
  371. -------- -------- --- Thank You --- -------- --------
  372.  
  373.  
  374. Intra-simulation communication will occur every 10 steps.
  375. Center of mass motion removal mode is Linear
  376. We have the following groups for center of mass motion removal:
  377. 0: rest
  378.  
  379. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  380. G. Bussi, D. Donadio and M. Parrinello
  381. Canonical sampling through velocity rescaling
  382. J. Chem. Phys. 126 (2007) pp. 014101
  383. -------- -------- --- Thank You --- -------- --------
  384.  
  385. There are: 33876 Atoms
  386.  
  387. Started mdrun on rank 0 Fri Mar 2 16:15:49 2018
  388. Step Time
  389. 0 0.00000
  390.  
  391. Energies (kJ/mol)
  392. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  393. 3.93091e+03 2.23591e+02 1.86111e+03 2.95927e+03 7.96031e+03
  394. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  395. 9.30619e+04 -4.56887e+03 -6.35016e+05 2.98155e+03 -5.26606e+05
  396. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  397. 8.55246e+04 -4.41082e+05 -4.41061e+05 3.03729e+02 -2.26420e+02
  398. Pressure (bar) Constr. rmsd
  399. -1.93678e+02 3.02853e-05
  400.  
  401. step 200: timed with pme grid 44 44 44, coulomb cutoff 1.000: 968.9 M-cycles
  402. step 400: timed with pme grid 40 40 40, coulomb cutoff 1.086: 1244.1 M-cycles
  403. step 600: timed with pme grid 42 42 42, coulomb cutoff 1.034: 880.3 M-cycles
  404. step 800: timed with pme grid 44 44 44, coulomb cutoff 1.000: 779.2 M-cycles
  405. step 1000: timed with pme grid 44 44 44, coulomb cutoff 1.000: 1014.1 M-cycles
  406. optimal pme grid 44 44 44, coulomb cutoff 1.000
  407. Step Time
  408. 5000 10.00000
  409.  
  410. Energies (kJ/mol)
  411. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  412. 3.87008e+03 2.33527e+02 1.81201e+03 2.99284e+03 7.93441e+03
  413. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  414. 9.29761e+04 -4.54701e+03 -6.33631e+05 3.06111e+03 -5.25298e+05
  415. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  416. 8.48157e+04 -4.40483e+05 -4.41192e+05 3.01212e+02 -2.24261e+02
  417. Pressure (bar) Constr. rmsd
  418. -5.59669e+01 2.75525e-05
  419.  
  420. Step Time
  421. 10000 20.00000
  422.  
  423. Energies (kJ/mol)
  424. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  425. 3.90330e+03 2.47066e+02 1.76046e+03 3.02176e+03 7.94808e+03
  426. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  427. 9.30703e+04 -4.58018e+03 -6.35178e+05 2.90633e+03 -5.26901e+05
  428. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  429. 8.43137e+04 -4.42587e+05 -4.41359e+05 2.99429e+02 -2.27541e+02
  430. Pressure (bar) Constr. rmsd
  431. 4.26526e+01 2.57495e-05
  432.  
  433. Step Time
  434. 15000 30.00000
  435.  
  436. Energies (kJ/mol)
  437. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  438. 3.80929e+03 2.58457e+02 1.72996e+03 3.00312e+03 8.01146e+03
  439. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  440. 9.29952e+04 -4.55118e+03 -6.33263e+05 2.97278e+03 -5.25034e+05
  441. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  442. 8.47719e+04 -4.40262e+05 -4.41547e+05 3.01056e+02 -2.24673e+02
  443. Pressure (bar) Constr. rmsd
  444. -5.86684e+01 2.76595e-05
  445.  
  446. Step Time
  447. 20000 40.00000
  448.  
  449. Energies (kJ/mol)
  450. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  451. 3.75138e+03 2.29140e+02 1.71569e+03 2.97685e+03 7.92601e+03
  452. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  453. 9.40864e+04 -4.56277e+03 -6.34478e+05 2.97198e+03 -5.25384e+05
  454. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  455. 8.36602e+04 -4.41723e+05 -4.41704e+05 2.97108e+02 -2.25817e+02
  456. Pressure (bar) Constr. rmsd
  457. 4.01311e+01 2.97819e-05
  458.  
  459. Step Time
  460. 25000 50.00000
  461.  
  462. Energies (kJ/mol)
  463. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  464. 3.79873e+03 2.58745e+02 1.78016e+03 3.02893e+03 8.09707e+03
  465. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  466. 9.40725e+04 -4.57079e+03 -6.36875e+05 2.93178e+03 -5.27478e+05
  467. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  468. 8.39342e+04 -4.43543e+05 -4.41901e+05 2.98081e+02 -2.26610e+02
  469. Pressure (bar) Constr. rmsd
  470. -1.95384e+01 2.86438e-05
  471.  
  472. Step Time
  473. 30000 60.00000
  474.  
  475. Energies (kJ/mol)
  476. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  477. 3.75340e+03 2.52380e+02 1.82113e+03 3.07090e+03 7.99766e+03
  478. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  479. 9.35044e+04 -4.54969e+03 -6.34822e+05 2.93175e+03 -5.26040e+05
  480. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  481. 8.47298e+04 -4.41311e+05 -4.42082e+05 3.00907e+02 -2.24525e+02
  482. Pressure (bar) Constr. rmsd
  483. 4.12881e+01 2.78862e-05
  484.  
  485. Step Time
  486. 35000 70.00000
  487.  
  488. Energies (kJ/mol)
  489. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  490. 3.59816e+03 2.48663e+02 1.84177e+03 2.94768e+03 7.96820e+03
  491. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  492. 9.33685e+04 -4.57011e+03 -6.35742e+05 2.92996e+03 -5.27409e+05
  493. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  494. 8.38523e+04 -4.43556e+05 -4.42265e+05 2.97790e+02 -2.26543e+02
  495. Pressure (bar) Constr. rmsd
  496. -1.04661e+02 2.73537e-05
  497.  
  498. Step Time
  499. 40000 80.00000
  500.  
  501. Energies (kJ/mol)
  502. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  503. 3.81235e+03 2.58038e+02 1.91601e+03 3.14256e+03 8.03990e+03
  504. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  505. 9.30417e+04 -4.55979e+03 -6.34432e+05 2.91625e+03 -5.25865e+05
  506. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  507. 8.51125e+04 -4.40753e+05 -4.42432e+05 3.02266e+02 -2.25522e+02
  508. Pressure (bar) Constr. rmsd
  509. 8.45917e+01 2.74855e-05
  510.  
  511. Step Time
  512. 45000 90.00000
  513.  
  514. Energies (kJ/mol)
  515. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  516. 3.69693e+03 2.57780e+02 1.79566e+03 3.09377e+03 8.03382e+03
  517. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  518. 9.44418e+04 -4.55713e+03 -6.36636e+05 2.93656e+03 -5.26937e+05
  519. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  520. 8.43101e+04 -4.42626e+05 -4.42618e+05 2.99416e+02 -2.25259e+02
  521. Pressure (bar) Constr. rmsd
  522. 1.43569e+02 2.70133e-05
  523.  
  524. Step Time
  525. 50000 100.00000
  526.  
  527. Writing checkpoint, step 50000 at Fri Mar 2 16:18:04 2018
  528.  
  529.  
  530. Energies (kJ/mol)
  531. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  532. 3.81037e+03 2.43539e+02 1.86515e+03 2.99830e+03 8.10404e+03
  533. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  534. 9.27007e+04 -4.56846e+03 -6.34808e+05 2.92378e+03 -5.26731e+05
  535. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  536. 8.42529e+04 -4.42478e+05 -4.42802e+05 2.99213e+02 -2.26379e+02
  537. Pressure (bar) Constr. rmsd
  538. -2.30758e+02 2.83750e-05
  539.  
  540. <====== ############### ==>
  541. <==== A V E R A G E S ====>
  542. <== ############### ======>
  543.  
  544. Statistics over 50001 steps using 501 frames
  545.  
  546. Energies (kJ/mol)
  547. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  548. 3.82297e+03 2.50006e+02 1.82822e+03 3.00558e+03 7.98777e+03
  549. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  550. 9.36129e+04 -4.56181e+03 -6.34887e+05 2.93918e+03 -5.26003e+05
  551. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  552. 8.44279e+04 -4.41575e+05 -4.41900e+05 2.99834e+02 -2.25724e+02
  553. Pressure (bar) Constr. rmsd
  554. -1.06300e+00 0.00000e+00
  555.  
  556. Box-X Box-Y Box-Z
  557. 6.95200e+00 6.95200e+00 6.95200e+00
  558.  
  559. Total Virial (kJ/mol)
  560. 2.82549e+04 9.71236e+01 8.48384e+01
  561. 9.66739e+01 2.81135e+04 -8.33024e+01
  562. 8.46930e+01 -8.27172e+01 2.80961e+04
  563.  
  564. Pressure (bar)
  565. -1.11080e+01 -8.97500e+00 -8.50948e+00
  566. -8.93059e+00 2.92506e+00 7.64583e+00
  567. -8.49501e+00 7.58794e+00 4.99393e+00
  568.  
  569. T-Protein T-non-Protein
  570. 2.99629e+02 2.99847e+02
  571.  
  572.  
  573. M E G A - F L O P S A C C O U N T I N G
  574.  
  575. NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
  576. RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
  577. W3=SPC/TIP3p W4=TIP4p (single or pairs)
  578. V&F=Potential and force V=Potential only F=Force only
  579.  
  580. Computing: M-Number M-Flops % Flops
  581. -----------------------------------------------------------------------------
  582. Pair Search distance check 1628.333072 14654.998 0.0
  583. NxN Ewald Elec. + LJ [F] 1657020.758976 109363370.092 96.2
  584. NxN Ewald Elec. + LJ [V&F] 16771.065984 1794504.060 1.6
  585. 1,4 nonbonded interactions 255.305106 22977.460 0.0
  586. Calc Weights 5081.501628 182934.059 0.2
  587. Spread Q Bspline 108405.368064 216810.736 0.2
  588. Gather F Bspline 108405.368064 650432.208 0.6
  589. 3D-FFT 139291.587136 1114332.697 1.0
  590. Solve PME 96.700336 6188.822 0.0
  591. Shift-X 16.971876 101.831 0.0
  592. Angles 177.353547 29795.396 0.0
  593. Propers 21.300426 4877.798 0.0
  594. RB-Dihedrals 197.503950 48783.476 0.0
  595. Virial 169.638921 3053.501 0.0
  596. Stop-CM 16.971876 169.719 0.0
  597. Calc-Ekin 338.827752 9148.349 0.0
  598. Lincs 99.201984 5952.119 0.0
  599. Lincs-Mat 2128.242564 8512.970 0.0
  600. Constraint-V 1793.835876 14350.687 0.0
  601. Constraint-Vir 169.493892 4067.853 0.0
  602. Settle 531.810636 171774.835 0.2
  603. -----------------------------------------------------------------------------
  604. Total 113666793.666 100.0
  605. -----------------------------------------------------------------------------
  606.  
  607.  
  608. 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
  609.  
  610. On 1 MPI rank, each using 16 OpenMP threads
  611.  
  612. Computing: Num Num Call Wall time Giga-Cycles
  613. Ranks Threads Count (s) total sum %
  614. -----------------------------------------------------------------------------
  615. Neighbor search 1 16 501 1.096 63.150 0.8
  616. Launch GPU ops. 1 16 50001 2.412 138.951 1.8
  617. Force 1 16 50001 5.699 328.256 4.2
  618. PME mesh 1 16 50001 48.261 2779.836 35.8
  619. Wait GPU NB local 1 16 50001 46.450 2675.517 34.4
  620. NB X/F buffer ops. 1 16 99501 11.267 648.989 8.4
  621. Write traj. 1 16 11 0.229 13.183 0.2
  622. Update 1 16 50001 6.287 362.144 4.7
  623. Constraints 1 16 50001 10.044 578.508 7.4
  624. Rest 3.187 183.569 2.4
  625. -----------------------------------------------------------------------------
  626. Total 134.932 7772.104 100.0
  627. -----------------------------------------------------------------------------
  628. Breakdown of PME mesh computation
  629. -----------------------------------------------------------------------------
  630. PME spread 1 16 50001 20.429 1176.726 15.1
  631. PME gather 1 16 50001 14.132 814.001 10.5
  632. PME 3D-FFT 1 16 100002 12.117 697.953 9.0
  633. PME solve Elec 1 16 50001 0.924 53.223 0.7
  634. -----------------------------------------------------------------------------
  635.  
  636. Core t (s) Wall t (s) (%)
  637. Time: 2158.918 134.932 1600.0
  638. (ns/day) (hour/ns)
  639. Performance: 64.033 0.375
  640. Finished mdrun on rank 0 Fri Mar 2 16:18:04 2018
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