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Log file opened on Wed Jan 13 17:36:19 2016
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Host: tcbs14 pid: 4213 rank ID: 0 number of ranks: 1
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:-) GROMACS - gmx mdrun, VERSION 5.1.2-dev-20160113-8b14e14 (-:
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GROMACS is written by:
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Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
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Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
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Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
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Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
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Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
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Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
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Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
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Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
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and the project leaders:
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Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2015, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS: gmx mdrun, VERSION 5.1.2-dev-20160113-8b14e14
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Executable: /nethome/pszilard-projects/gromacs/gromacs-5.1/build_gcc48_hsw_cuda65/bin/gmx
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Data prefix: /nethome/pszilard-projects/gromacs/gromacs-5.1 (source tree)
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Command line:
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gmx mdrun -quiet -v -resethway -noconfout -pin on -ntmpi 1 -ntomp 16 -nsteps 10000 -g test_1x16_tune_5 -tunepme
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GROMACS version: VERSION 5.1.2-dev-20160113-8b14e14
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GIT SHA1 hash: 8b14e14f4a18193eacc86a2da9a4d812df0e03eb
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Precision: single
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Memory model: 64 bit
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MPI library: thread_mpi
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OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
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GPU support: enabled
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OpenCL support: disabled
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invsqrt routine: gmx_software_invsqrt(x)
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SIMD instructions: AVX2_256
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FFT library: fftw-3.3.4-sse2-avx
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RDTSCP usage: enabled
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C++11 compilation: disabled
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TNG support: enabled
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Tracing support: disabled
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Built on: Mon Sep 14 15:56:07 CEST 2015
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Built by: pszilard@tcbs14 [CMAKE]
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Build OS/arch: Linux 3.13.0-63-generic x86_64
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Build CPU vendor: GenuineIntel
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Build CPU brand: Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
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Build CPU family: 6 Model: 63 Stepping: 2
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Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler: /usr/bin/gcc-4.8 GNU 4.8.1
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C compiler flags: -march=core-avx2 -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
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C++ compiler: /usr/bin/g++-4.8 GNU 4.8.1
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C++ compiler flags: -march=core-avx2 -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
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Boost version: 1.55.0 (internal)
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CUDA compiler: /opt/tcbsys/cuda/6.5/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2014 NVIDIA Corporation;Built on Wed_Aug_27_10:36:36_CDT_2014;Cuda compilation tools, release 6.5, V6.5.16
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CUDA compiler flags:-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;-use_fast_math;-Xptxas;-dlcm=ca; ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
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CUDA driver: 7.50
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CUDA runtime: 6.50
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Running on 1 node with total 8 cores, 16 logical cores, 1 compatible GPU
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Hardware detected:
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CPU info:
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Vendor: GenuineIntel
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Brand: Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
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Family: 6 model: 63 stepping: 2
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CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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SIMD instructions most likely to fit this hardware: AVX2_256
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SIMD instructions selected at GROMACS compile time: AVX2_256
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GPU info:
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Number of GPUs detected: 1
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#0: NVIDIA Quadro M6000, compute cap.: 5.2, ECC: no, stat: compatible
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
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GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
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GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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For optimal performance with a GPU nstlist (now 10) should be larger.
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The optimum depends on your CPU and GPU resources.
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You might want to try several nstlist values.
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Changing nstlist from 10 to 40, rlist from 0.9 to 0.996
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Input Parameters:
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integrator = md
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tinit = 0
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dt = 0.002
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nsteps = 10000
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init-step = 0
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simulation-part = 1
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comm-mode = Linear
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nstcomm = 100
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bd-fric = 0
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ld-seed = 4200386634
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emtol = 10
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emstep = 0.01
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niter = 20
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fcstep = 0
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nstcgsteep = 1000
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nbfgscorr = 10
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rtpi = 0.05
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nstxout = 0
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nstvout = 0
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nstfout = 0
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nstlog = 0
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nstcalcenergy = 100
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nstenergy = 500
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nstxout-compressed = 0
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compressed-x-precision = 1000
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cutoff-scheme = Verlet
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nstlist = 40
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ns-type = Grid
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pbc = xyz
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periodic-molecules = FALSE
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verlet-buffer-tolerance = 0.005
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rlist = 0.996
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rlistlong = 0.996
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nstcalclr = 10
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coulombtype = PME
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coulomb-modifier = Potential-shift
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rcoulomb-switch = 0
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rcoulomb = 0.9
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epsilon-r = 1
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epsilon-rf = inf
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vdw-type = Cut-off
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vdw-modifier = Potential-shift
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rvdw-switch = 0
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rvdw = 0.9
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DispCorr = No
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table-extension = 1
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fourierspacing = 0.1125
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fourier-nx = 56
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fourier-ny = 56
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fourier-nz = 56
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pme-order = 4
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ewald-rtol = 1e-05
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ewald-rtol-lj = 0.001
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lj-pme-comb-rule = Geometric
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ewald-geometry = 0
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epsilon-surface = 0
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implicit-solvent = No
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gb-algorithm = Still
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nstgbradii = 1
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rgbradii = 1
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gb-epsilon-solvent = 80
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gb-saltconc = 0
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gb-obc-alpha = 1
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gb-obc-beta = 0.8
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gb-obc-gamma = 4.85
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gb-dielectric-offset = 0.009
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sa-algorithm = Ace-approximation
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sa-surface-tension = 2.05016
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tcoupl = V-rescale
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nsttcouple = 10
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nh-chain-length = 0
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print-nose-hoover-chain-variables = FALSE
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pcoupl = No
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pcoupltype = Isotropic
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nstpcouple = -1
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tau-p = 1
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compressibility (3x3):
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compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p (3x3):
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ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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refcoord-scaling = No
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posres-com (3):
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posres-com[0]= 0.00000e+00
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posres-com[1]= 0.00000e+00
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posres-com[2]= 0.00000e+00
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posres-comB (3):
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posres-comB[0]= 0.00000e+00
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posres-comB[1]= 0.00000e+00
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posres-comB[2]= 0.00000e+00
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QMMM = FALSE
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QMconstraints = 0
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QMMMscheme = 0
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MMChargeScaleFactor = 1
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qm-opts:
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ngQM = 0
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constraint-algorithm = Lincs
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continuation = FALSE
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Shake-SOR = FALSE
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shake-tol = 0.0001
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lincs-order = 4
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lincs-iter = 1
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lincs-warnangle = 30
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nwall = 0
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wall-type = 9-3
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wall-r-linpot = -1
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wall-atomtype[0] = -1
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wall-atomtype[1] = -1
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wall-density[0] = 0
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wall-density[1] = 0
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wall-ewald-zfac = 3
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pull = FALSE
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rotation = FALSE
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interactiveMD = FALSE
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disre = No
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disre-weighting = Conservative
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disre-mixed = FALSE
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dr-fc = 1000
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dr-tau = 0
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nstdisreout = 100
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orire-fc = 0
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orire-tau = 0
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nstorireout = 100
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free-energy = no
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cos-acceleration = 0
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deform (3x3):
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deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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simulated-tempering = FALSE
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E-x:
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n = 0
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E-xt:
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n = 0
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E-y:
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n = 0
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E-yt:
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n = 0
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E-z:
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n = 0
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E-zt:
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n = 0
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swapcoords = no
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adress = FALSE
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userint1 = 0
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userint2 = 0
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userint3 = 0
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userint4 = 0
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userreal1 = 0
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userreal2 = 0
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userreal3 = 0
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userreal4 = 0
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grpopts:
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nrdf: 48056
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ref-t: 300
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tau-t: 0.1
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annealing: No
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annealing-npoints: 0
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acc: 0 0 0
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nfreeze: N N N
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energygrp-flags[ 0]: 0
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Overriding nsteps with value passed on the command line: 10000 steps, 20 ps
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Using 1 MPI thread
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Using 16 OpenMP threads
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1 compatible GPU is present, with ID 0
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1 GPU auto-selected for this run.
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Mapping of GPU ID to the 1 PP rank in this node: 0
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Will do PME sum in reciprocal space for electrostatic interactions.
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
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A smooth particle mesh Ewald method
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J. Chem. Phys. 103 (1995) pp. 8577-8592
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-------- -------- --- Thank You --- -------- --------
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326
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Will do ordinary reciprocal space Ewald sum.
|
|
327
|
Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
|
|
328
|
Cut-off's: NS: 0.996 Coulomb: 0.9 LJ: 0.9
|
|
329
|
System total charge: 0.000
|
|
330
|
Generated table with 998 data points for Ewald.
|
|
331
|
Tabscale = 500 points/nm
|
|
332
|
Generated table with 998 data points for LJ6.
|
|
333
|
Tabscale = 500 points/nm
|
|
334
|
Generated table with 998 data points for LJ12.
|
|
335
|
Tabscale = 500 points/nm
|
|
336
|
Generated table with 998 data points for 1-4 COUL.
|
|
337
|
Tabscale = 500 points/nm
|
|
338
|
Generated table with 998 data points for 1-4 LJ6.
|
|
339
|
Tabscale = 500 points/nm
|
|
340
|
Generated table with 998 data points for 1-4 LJ12.
|
|
341
|
Tabscale = 500 points/nm
|
|
342
|
Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.000e-05
|
|
343
|
Initialized non-bonded Ewald correction tables, spacing: 8.85e-04 size: 1018
|
|
344
|
|
|
345
|
|
|
346
|
NOTE: GROMACS was configured without NVML support hence it can not exploit
|
|
347
|
application clocks of the detected Quadro M6000 GPU to improve performance.
|
|
348
|
Recompile with the NVML library (compatible with the driver used) or set application clocks manually.
|
|
349
|
|
|
350
|
|
|
351
|
Using GPU 8x8 non-bonded kernels
|
|
352
|
|
|
353
|
Removing pbc first time
|
|
354
|
Pinning threads with an auto-selected logical core stride of 1
|
|
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 2053
|
|
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
|
Center of mass motion removal mode is Linear
|
|
374
|
We have the following groups for center of mass motion removal:
|
|
375
|
0: rest
|
|
376
|
|
|
377
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
378
|
G. Bussi, D. Donadio and M. Parrinello
|
|
379
|
Canonical sampling through velocity rescaling
|
|
380
|
J. Chem. Phys. 126 (2007) pp. 014101
|
|
381
|
-------- -------- --- Thank You --- -------- --------
|
|
382
|
|
|
383
|
There are: 24040 Atoms
|
|
384
|
|
|
385
|
Constraining the starting coordinates (step 0)
|
|
386
|
|
|
387
|
Constraining the coordinates at t0-dt (step 0)
|
|
388
|
RMS relative constraint deviation after constraining: 1.20e-05
|
|
389
|
Initial temperature: 297.8 K
|
|
390
|
|
|
391
|
Started mdrun on rank 0 Wed Jan 13 17:36:20 2016
|
|
392
|
Step Time Lambda
|
|
393
|
0 0.00000 0.00000
|
|
394
|
|
|
395
|
Energies (kJ/mol)
|
|
396
|
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
|
|
397
|
4.44103e+03 5.70375e+03 2.50388e+02 2.00472e+03 1.68037e+04
|
|
398
|
LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
|
|
399
|
4.16574e+04 -3.84143e+05 3.38823e+03 -3.09894e+05 5.99548e+04
|
|
400
|
Total Energy Conserved En. Temperature Pressure (bar) Constr. rmsd
|
|
401
|
-2.49939e+05 -2.49939e+05 3.00104e+02 -3.53122e+02 2.74372e-05
|
|
402
|
|
|
403
|
step 80: timed with pme grid 56 56 56, coulomb cutoff 0.900: 123.8 M-cycles
|
|
404
|
step 160: timed with pme grid 48 48 48, coulomb cutoff 1.046: 117.1 M-cycles
|
|
405
|
step 240: timed with pme grid 44 44 44, coulomb cutoff 1.141: 133.1 M-cycles
|
|
406
|
step 320: timed with pme grid 48 48 48, coulomb cutoff 1.046: 118.2 M-cycles
|
|
407
|
step 400: timed with pme grid 52 52 52, coulomb cutoff 0.966: 122.4 M-cycles
|
|
408
|
step 480: timed with pme grid 56 56 56, coulomb cutoff 0.900: 123.7 M-cycles
|
|
409
|
optimal pme grid 48 48 48, coulomb cutoff 1.046
|
|
410
|
|
|
411
|
step 5000: resetting all time and cycle counters
|
|
412
|
|
|
413
|
Restarted time on rank 0 Wed Jan 13 17:36:26 2016
|
|
414
|
Step Time Lambda
|
|
415
|
10000 20.00000 0.00000
|
|
416
|
|
|
417
|
Energies (kJ/mol)
|
|
418
|
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
|
|
419
|
4.64193e+03 5.55978e+03 2.47517e+02 2.05754e+03 1.67330e+04
|
|
420
|
LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
|
|
421
|
4.18313e+04 -3.83297e+05 2.02986e+03 -3.10196e+05 5.97392e+04
|
|
422
|
Total Energy Conserved En. Temperature Pressure (bar) Constr. rmsd
|
|
423
|
-2.50457e+05 -2.50371e+05 2.99025e+02 -4.38195e+02 2.88291e-05
|
|
424
|
|
|
425
|
<====== ############### ==>
|
|
426
|
<==== A V E R A G E S ====>
|
|
427
|
<== ############### ======>
|
|
428
|
|
|
429
|
Statistics over 10001 steps using 101 frames
|
|
430
|
|
|
431
|
Energies (kJ/mol)
|
|
432
|
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
|
|
433
|
4.48499e+03 5.59426e+03 2.63861e+02 2.08071e+03 1.68182e+04
|
|
434
|
LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
|
|
435
|
4.21315e+04 -3.83617e+05 2.00659e+03 -3.10237e+05 5.99538e+04
|
|
436
|
Total Energy Conserved En. Temperature Pressure (bar) Constr. rmsd
|
|
437
|
-2.50284e+05 -2.50146e+05 3.00099e+02 -2.02113e+02 0.00000e+00
|
|
438
|
|
|
439
|
Total Virial (kJ/mol)
|
|
440
|
2.14504e+04 9.68297e+01 -1.62449e+00
|
|
441
|
9.73269e+01 2.14502e+04 -9.18374e+01
|
|
442
|
-3.62943e+00 -9.24507e+01 2.15676e+04
|
|
443
|
|
|
444
|
Pressure (bar)
|
|
445
|
-1.91677e+02 -1.46230e+01 -5.33324e-01
|
|
446
|
-1.46898e+01 -2.05441e+02 9.64885e+00
|
|
447
|
-2.64037e-01 9.73122e+00 -2.09222e+02
|
|
448
|
|
|
449
|
|
|
450
|
P P - P M E L O A D B A L A N C I N G
|
|
451
|
|
|
452
|
PP/PME load balancing changed the cut-off and PME settings:
|
|
453
|
particle-particle PME
|
|
454
|
rcoulomb rlist grid spacing 1/beta
|
|
455
|
initial 0.900 nm 0.996 nm 56 56 56 0.112 nm 0.288 nm
|
|
456
|
final 1.046 nm 1.142 nm 48 48 48 0.131 nm 0.335 nm
|
|
457
|
cost-ratio 1.51 0.63
|
|
458
|
(note that these numbers concern only part of the total PP and PME load)
|
|
459
|
|
|
460
|
|
|
461
|
M E G A - F L O P S A C C O U N T I N G
|
|
462
|
|
|
463
|
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
|
|
464
|
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
|
|
465
|
W3=SPC/TIP3p W4=TIP4p (single or pairs)
|
|
466
|
V&F=Potential and force V=Potential only F=Force only
|
|
467
|
|
|
468
|
Computing: M-Number M-Flops % Flops
|
|
469
|
-----------------------------------------------------------------------------
|
|
470
|
Pair Search distance check 400.637920 3605.741 0.0
|
|
471
|
NxN Ewald Elec. + LJ [F] 109431.129728 7222454.562 95.1
|
|
472
|
NxN Ewald Elec. + LJ [V&F] 1127.540288 120646.811 1.6
|
|
473
|
1,4 nonbonded interactions 26.710341 2403.931 0.0
|
|
474
|
Calc Weights 360.672120 12984.196 0.2
|
|
475
|
Spread Q Bspline 7694.338560 15388.677 0.2
|
|
476
|
Gather F Bspline 7694.338560 46166.031 0.6
|
|
477
|
3D-FFT 18533.265912 148266.127 2.0
|
|
478
|
Solve PME 11.522304 737.427 0.0
|
|
479
|
Shift-X 3.029040 18.174 0.0
|
|
480
|
Angles 18.523704 3111.982 0.0
|
|
481
|
Propers 27.915582 6392.668 0.1
|
|
482
|
Impropers 2.110422 438.968 0.0
|
|
483
|
Virial 1.228335 22.110 0.0
|
|
484
|
Stop-CM 1.226040 12.260 0.0
|
|
485
|
Calc-Ekin 24.064040 649.729 0.0
|
|
486
|
Lincs 10.267053 616.023 0.0
|
|
487
|
Lincs-Mat 222.284448 889.138 0.0
|
|
488
|
Constraint-V 130.596114 1044.769 0.0
|
|
489
|
Constraint-Vir 1.227111 29.451 0.0
|
|
490
|
Settle 36.687336 11850.010 0.2
|
|
491
|
-----------------------------------------------------------------------------
|
|
492
|
Total 7597728.787 100.0
|
|
493
|
-----------------------------------------------------------------------------
|
|
494
|
|
|
495
|
|
|
496
|
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
|
|
497
|
|
|
498
|
On 1 MPI rank, each using 16 OpenMP threads
|
|
499
|
|
|
500
|
Computing: Num Num Call Wall time Giga-Cycles
|
|
501
|
Ranks Threads Count (s) total sum %
|
|
502
|
-----------------------------------------------------------------------------
|
|
503
|
Neighbor search 1 16 126 0.152 7.285 3.2
|
|
504
|
Launch GPU ops. 1 16 5001 0.175 8.384 3.7
|
|
505
|
Force 1 16 5001 0.540 25.926 11.4
|
|
506
|
PME mesh 1 16 5001 2.227 106.993 46.9
|
|
507
|
Wait GPU local 1 16 5001 0.691 33.182 14.5
|
|
508
|
NB X/F buffer ops. 1 16 9876 0.117 5.621 2.5
|
|
509
|
Update 1 16 5001 0.202 9.717 4.3
|
|
510
|
Constraints 1 16 5001 0.587 28.212 12.4
|
|
511
|
Rest 0.063 3.013 1.3
|
|
512
|
-----------------------------------------------------------------------------
|
|
513
|
Total 4.754 228.333 100.0
|
|
514
|
-----------------------------------------------------------------------------
|
|
515
|
Breakdown of PME mesh computation
|
|
516
|
-----------------------------------------------------------------------------
|
|
517
|
PME spread/gather 1 16 10002 1.439 69.106 30.3
|
|
518
|
PME 3D-FFT 1 16 10002 0.704 33.793 14.8
|
|
519
|
PME solve Elec 1 16 5001 0.072 3.466 1.5
|
|
520
|
-----------------------------------------------------------------------------
|
|
521
|
Breakdown of PP computation
|
|
522
|
-----------------------------------------------------------------------------
|
|
523
|
NS grid local 1 16 126 0.029 1.386 0.6
|
|
524
|
NS search local 1 16 126 0.114 5.465 2.4
|
|
525
|
Bonded F 1 16 5001 0.306 14.702 6.4
|
|
526
|
Listed buffer ops. 1 16 5001 0.169 8.129 3.6
|
|
527
|
NB X buffer ops. 1 16 4875 0.056 2.713 1.2
|
|
528
|
NB F buffer ops. 1 16 5001 0.060 2.881 1.3
|
|
529
|
-----------------------------------------------------------------------------
|
|
530
|
|
|
531
|
GPU timings
|
|
532
|
-----------------------------------------------------------------------------
|
|
533
|
Computing: Count Wall t (s) ms/step %
|
|
534
|
-----------------------------------------------------------------------------
|
|
535
|
Pair list H2D 126 0.015 0.120 0.4
|
|
536
|
X / q H2D 5001 0.200 0.040 5.7
|
|
537
|
Nonbonded F kernel 4850 3.021 0.623 85.5
|
|
538
|
Nonbonded F+ene k. 25 0.023 0.935 0.7
|
|
539
|
Nonbonded F+prune k. 100 0.082 0.819 2.3
|
|
540
|
Nonbonded F+ene+prune k. 26 0.029 1.131 0.8
|
|
541
|
F D2H 5001 0.162 0.032 4.6
|
|
542
|
-----------------------------------------------------------------------------
|
|
543
|
Total 3.533 0.706 100.0
|
|
544
|
-----------------------------------------------------------------------------
|
|
545
|
|
|
546
|
Force evaluation time GPU/CPU: 0.706 ms/0.553 ms = 1.277
|
|
547
|
For optimal performance this ratio should be close to 1!
|
|
548
|
|
|
549
|
|
|
550
|
NOTE: The GPU has >20% more load than the CPU. This imbalance causes
|
|
551
|
performance loss, consider using a shorter cut-off and a finer PME grid.
|
|
552
|
|
|
553
|
Core t (s) Wall t (s) (%)
|
|
554
|
Time: 75.955 4.754 1597.8
|
|
555
|
(ns/day) (hour/ns)
|
|
556
|
Performance: 181.791 0.132
|
|
557
|
Finished mdrun on rank 0 Wed Jan 13 17:36:31 2016
|