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Log file opened on Thu Mar  1 16:05:27 2018
Host: gpu-compute-5-8.local  pid: 15547  rank ID: 0  number of ranks:  1
    |   |   |   |   | :-) GROMACS - gmx mdrun, 2016.4 (-:

    |   |   |   |   |   |   GROMACS is written by:
    |Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof
 Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik Marklund
   Teemu Murtola       Szilard Pall       Sander Pronk      Roland Schulz
  Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter Tieleman
  Teemu Virolainen  Christian Wennberg    Maarten Wolf
    |   |   |   |   |   |  and the project leaders:
    |   Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2016.4
Executable:   /home/hoemberg/SOFTWARE/GROMACS/GMX_2016.4_AVX2/bin/gmx_mpi
Data prefix:  /home/hoemberg/SOFTWARE/GROMACS/GMX_2016.4_AVX2
Working dir:  /home/hoemberg/ADK/PRESSURE/EADK/CLOSED/TMD_KAPPA_TEST/GPU/TMD_1000_GPU
Command line:
  gmx_mpi mdrun -pin on -pinoffset 0 -gpu_id 0 -ntomp 8 -v -cpi -s TMD_1000.tpr -o TMD_1000.trr -x TMD_1000.xtc -g TMD_1000.log -c eADK_TMD_1000.gro

GROMACS version:    2016.4
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:        CUDA
SIMD instructions:  SSE4.1
FFT library:        fftw-3.3.5-sse2
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
Built on:           Thu Mar  1 11:37:24 EST 2018
Built by:           hoemberg@gpu-compute-5-8.local [CMAKE]
Build OS/arch:      Linux 2.6.32-573.18.1.el6.x86_64 x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
Build CPU family:   6   Model: 62   Stepping: 4
Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:         /scisoft/local/GCC-4.9.3/GCC-GFORTRAN/bin/gcc GNU 4.9.3
C compiler flags:    -msse4.1 -pthread    -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler:       /scisoft/local/GCC-4.9.3/GCC-GFORTRAN/bin/g++ GNU 4.9.3
C++ compiler flags:  -msse4.1 -pthread   -std=c++0x   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
CUDA compiler:      /scisoft/CUDA-7.5.18/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, release 7.5, V7.5.17
CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-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_52,code=compute_52;-use_fast_math;;;-Xcompiler;,-msse4.1,-pthread,,,,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,;
CUDA driver:        7.50
CUDA runtime:       7.50


Running on 1 node with total 16 cores, 16 logical cores, 4 compatible GPUs
Hardware detected on host gpu-compute-5-8.local (the node of MPI rank 0):
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
    Family: 6   Model: 62   Stepping: 4
    Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
    SIMD instructions most likely to fit this hardware: AVX_256
    SIMD instructions selected at GROMACS compile time: SSE4.1

  Hardware topology: Basic
    Sockets, cores, and logical processors:
    | Socket  0: [   0] [   1] [   2] [   3] [   4] [   5] [   6] [   7]
    | Socket  1: [   8] [   9] [  10] [  11] [  12] [  13] [  14] [  15]
  GPU info:
    Number of GPUs detected: 4
    #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat: compatible
    #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat: compatible
    #2: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat: compatible
    #3: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat: compatible


Binary not matching hardware - you might be losing performance.
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: SSE4.1
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------


For optimal performance with a GPU nstlist (now 10) should be larger.
The optimum depends on your CPU and GPU resources.
You might want to try several nstlist values.
Changing nstlist from 10 to 40, rlist from 1.2 to 1.28

Input Parameters:
   integrator                     = md
   tinit                          = 0
   dt                             = 0.002
   nsteps                         = 26000000
   init-step                      = 0
   simulation-part                = 1
   comm-mode                      = Linear
   nstcomm                        = 10
   bd-fric                        = 0
   ld-seed                        = -297470968
   emtol                          = 10
   emstep                         = 0.01
   niter                          = 20
   fcstep                         = 0
   nstcgsteep                     = 1000
   nbfgscorr                      = 10
   rtpi                           = 0.05
   nstxout                        = 500000
   nstvout                        = 500000
   nstfout                        = 0
   nstlog                         = 2500
   nstcalcenergy                  = 10
   nstenergy                      = 2500
   nstxout-compressed             = 2500
   compressed-x-precision         = 1000
   cutoff-scheme                  = Verlet
   nstlist                        = 40
   ns-type                        = Grid
   pbc                            = xyz
   periodic-molecules             = false
   verlet-buffer-tolerance        = 0.005
   rlist                          = 1.28
   coulombtype                    = PME
   coulomb-modifier               = Potential-shift
   rcoulomb-switch                = 0
   rcoulomb                       = 1.2
   epsilon-r                      = 1
   epsilon-rf                     = inf
   vdw-type                       = Cut-off
   vdw-modifier                   = Force-switch
   rvdw-switch                    = 1
   rvdw                           = 1.2
   DispCorr                       = No
   table-extension                = 1
   fourierspacing                 = 0.12
   fourier-nx                     = 72
   fourier-ny                     = 72
   fourier-nz                     = 72
   pme-order                      = 6
   ewald-rtol                     = 1e-05
   ewald-rtol-lj                  = 0.001
   lj-pme-comb-rule               = Geometric
   ewald-geometry                 = 0
   epsilon-surface                = 0
   implicit-solvent               = No
   gb-algorithm                   = Still
   nstgbradii                     = 1
   rgbradii                       = 1
   gb-epsilon-solvent             = 80
   gb-saltconc                    = 0
   gb-obc-alpha                   = 1
   gb-obc-beta                    = 0.8
   gb-obc-gamma                   = 4.85
   gb-dielectric-offset           = 0.009
   sa-algorithm                   = Ace-approximation
   sa-surface-tension             = 2.05016
   tcoupl                         = Nose-Hoover
   nsttcouple                     = 10
   nh-chain-length                = 1
   print-nose-hoover-chain-variables = false
   pcoupl                         = Parrinello-Rahman
   pcoupltype                     = Isotropic
   nstpcouple                     = 10
   tau-p                          = 1
   compressibility (3x3):
    | compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
    | compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
    | compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   ref-p (3x3):
    | ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
    | ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
    | ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   refcoord-scaling               = COM
   posres-com (3):
    | posres-com[0]= 5.62934e-01
    | posres-com[1]= 4.22365e-01
    | posres-com[2]= 4.54117e-01
   posres-comB (3):
    | posres-comB[0]= 5.62934e-01
  QMMM                           = false
   QMconstraints                  = 0
   QMMMscheme                     = 0
   MMChargeScaleFactor            = 1
qm-opts:
   ngQM                           = 0
   constraint-algorithm           = Lincs
   continuation                   = false
   Shake-SOR                      = false
   shake-tol                      = 0.0001
   lincs-order                    = 4
   lincs-iter                     = 1
   lincs-warnangle                = 30
   nwall                          = 0
   wall-type                      = 9-3
   wall-r-linpot                  = -1
   wall-atomtype[0]               = -1
   wall-atomtype[1]               = -1
   wall-density[0]                = 0
   wall-density[1]                = 0
   wall-ewald-zfac                = 3
   pull                           = false
   rotation                       = false
   interactiveMD                  = false
   disre                          = No
   disre-weighting                = Conservative
   disre-mixed                    = false
   dr-fc                          = 1000
   dr-tau                         = 0
   nstdisreout                    = 100
   orire-fc                       = 0
   orire-tau                      = 0
   nstorireout                    = 100
   free-energy                    = no
   cos-acceleration               = 0
   deform (3x3):
    | deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
    | deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
    | deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   simulated-tempering            = false
   E-x:
    | n = 0
   E-xt:
    | n = 0
   E-y:
    | n = 0
   E-yt:
    | n = 0
   E-z:
    | n = 0
   E-zt:
    | n = 0
   swapcoords                     = no
   userint1                       = 0
   userint2                       = 0
   userint3                       = 0
   userint4                       = 0
   userreal1                      = 0
   userreal2                      = 0
   userreal3                      = 0
   userreal4                      = 0
grpopts:
   nrdf:       65676
   ref-t:         298
   tau-t:         0.6
annealing:          No
annealing-npoints:           0
   acc:            0           0           0
   nfreeze:           N           N           N
   energygrp-flags[  0]: 0 0
   energygrp-flags[  1]: 0 0

Using 1 MPI process
Using 8 OpenMP threads

1 GPU user-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: 0

Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.28   Coulomb: 1.2   LJ: 1.2
System total charge: 0.000
Generated table with 1140 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1140 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1140 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176


Using GPU 8x8 non-bonded kernels


NOTE: With GPUs, reporting energy group contributions is not supported
NOTE: With GPUs, reporting energy group contributions is not supported

Removing pbc first time

Overriding thread affinity set outside gmx mdrun

Pinning threads with an auto-selected logical core stride of 1

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 3447

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------

Intra-simulation communication will occur every 10 steps.
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  System
There are: 32849 Atoms

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 1.74e-06
Initial temperature: 4.17475e-05 K

Started mdrun on rank 0 Thu Mar  1 16:05:31 2018
    |   |  Step           Time
    |   |   | 0        0.00000

   Energies (kJ/mol)
    |   |   U-B    Proper Dih.  Improper Dih.      CMAP Dih.          LJ-14
    8.35075e+03    8.52456e+03    4.70575e+02   -1.97674e+02    3.13716e+03
    |Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.
    3.11791e+04    3.80088e+04   -5.28805e+05    1.60428e+03    1.10424e-04
    | Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -4.37728e+05    1.29531e+03   -4.36432e+05    4.74422e+00   -7.64626e+02
   Constr. rmsd
	1.84421e-05