Log file opened on Tue Nov 3 15:45:02 2015 Host: op24th4 pid: 26295 rank ID: 0 number of ranks: 1 GROMACS: gmx mdrun, VERSION 5.0.1 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Peter Kasson 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 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) 2001-2014, 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 5.0.1 Executable: /fsnfs/users/persson/gmx/bin/gmx Library dir: /fsnfs/users/persson/gmx/share/gromacs/top Command line: mdrun -v -deffnm em -rdd 4 Gromacs version: VERSION 5.0.1 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) SIMD instructions: AVX_128_FMA FFT library: fftw-3.3.3-sse2 RDTSCP usage: enabled C++11 compilation: enabled TNG support: enabled Tracing support: disabled Built on: Wed Sep 10 09:15:58 CEST 2014 Built by: persson@op24th1 [CMAKE] Build OS/arch: Linux 3.4.63-2.44-desktop x86_64 Build CPU vendor: AuthenticAMD Build CPU brand: AMD Opteron(tm) Processor 6376 Build CPU family: 21 Model: 2 Stepping: 0 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c fma fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop C compiler: /usr/bin/cc GNU 4.7.1 C compiler flags: -mavx -mfma4 -mxop -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 4.7.1 C++ compiler flags: -mavx -mfma4 -mxop -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.49.0 (external) ++++ 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 --- -------- -------- Input Parameters: integrator = steep tinit = 0 dt = 0.001 nsteps = 5000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 3747088824 emtol = 100 emstep = 0.1 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 1 ns-type = Grid pbc = xyz periodic-molecules = FALSE verlet-buffer-tolerance = 0.005 rlist = 1 rlistlong = 1 nstcalclr = 1 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 208 fourier-ny = 52 fourier-nz = 28 pme-order = 4 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 = No nsttcouple = -1 nh-chain-length = 0 print-nose-hoover-chain-variables = FALSE pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 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 = no 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 adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 89001 ref-t: 0 tau-t: 0 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Initializing Domain Decomposition on 64 ranks Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Minimum cell size due to bonded interactions: 4.000 nm Guess for relative PME load: 0.20 Will use 48 particle-particle and 16 PME only ranks This is a guess, check the performance at the end of the log file Using 16 separate PME ranks, as guessed by mdrun Optimizing the DD grid for 48 cells with a minimum initial size of 4.000 nm The maximum allowed number of cells is: X 6 Y 1 Z 0 ------------------------------------------------------- Program mdrun, VERSION 5.0.1 Source code file: /fsnfs/users/persson/gromacs-5.0.1-newpol/src/gromacs/mdlib/domdec.c, line: 6881 Fatal error: There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 4 nm Change the number of ranks or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------