[gmx-users] my log file to the mdrun error message that on Tue 15, July...
Carsten Kutzner
ckutzne at gwdg.de
Wed Jul 16 10:32:02 CEST 2014
Hi,
it is not directly clear what problem you mean.
If you refer to the binary being compiled for SSE4.1 and the
hardware being capable of AVX instructions, then simply recompile
with -DGMX_CPU_ACCELERATION=AVX_256 added to your cmake line.
Carsten
On 16 Jul 2014, at 04:02, Andy Chao <achao at energiaq.com> wrote:
> Dear GROMACS Users:
>
> Here is my log file..
>
> Please let me know how to fix this problem.
>
> Thanks!
>
> Andy
>
> Log file opened on Tue Jul 15 21:01:52 2014
> Host: server-Virtual-Machine pid: 10019 nodeid: 0 nnodes: 1
> Gromacs version: VERSION 4.6.5
> Precision: single
> Memory model: 32 bit
> MPI library: thread_mpi
> OpenMP support: enabled
> GPU support: disabled
> invsqrt routine: gmx_software_invsqrt(x)
> CPU acceleration: SSE4.1
> FFT library: fftw-3.3.3-sse2-avx
> Large file support: enabled
> RDTSCP usage: enabled
> Built on: Sun Dec 15 03:59:22 UTC 2013
> Built by: buildd at roseapple [CMAKE]
> Build OS/arch: Linux 3.2.0-37-generic i686
> Build CPU vendor: GenuineIntel
> Build CPU brand: Intel(R) Xeon(R) CPU E5530 @ 2.40GHz
> Build CPU family: 6 Model: 26 Stepping: 5
> Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> nonstop_tsc pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
> C compiler: /usr/bin/i686-linux-gnu-gcc GNU gcc-4.8.real
> (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2
> C compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter
> -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
> -DNDEBUG
>
>
> :-) G R O M A C S (-:
>
> Gromacs Runs On Most of All Computer Systems
>
> :-) VERSION 4.6.5 (-:
>
> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
> Berk Hess, David van der Spoel, and Erik Lindahl.
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2012,2013, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> This program 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.
>
> :-) mdrun (-:
>
>
> ++++ 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 --- -------- --------
>
>
> Changing rlist from 1.05 to 1 for non-bonded 4x4 atom kernels
>
> Input Parameters:
> integrator = steep
> nsteps = 200
> init-step = 0
> cutoff-scheme = Verlet
> ns_type = Grid
> nstlist = 10
> ndelta = 2
> nstcomm = 100
> comm-mode = Linear
> nstlog = 1000
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstcalcenergy = 100
> nstenergy = 1000
> nstxtcout = 0
> init-t = 0
> delta-t = 0.001
> xtcprec = 1000
> fourierspacing = 0.12
> nkx = 48
> nky = 48
> nkz = 48
> pme-order = 4
> ewald-rtol = 1e-05
> ewald-geometry = 0
> epsilon-surface = 0
> optimize-fft = FALSE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = No
> bPrintNHChains = FALSE
> nsttcouple = -1
> epc = No
> epctype = Isotropic
> nstpcouple = -1
> tau-p = 1
> 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}
> compress (3x3):
> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 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
> verlet-buffer-drift = 0.005
> rlist = 1
> rlistlong = 1
> nstcalclr = 10
> rtpi = 0.05
> coulombtype = PME
> coulomb-modifier = Potential-shift
> rcoulomb-switch = 0
> rcoulomb = 1
> vdwtype = Cut-off
> vdw-modifier = Potential-shift
> rvdw-switch = 0
> rvdw = 1
> epsilon-r = 1
> epsilon-rf = inf
> tabext = 1
> implicit-solvent = No
> gb-algorithm = Still
> gb-epsilon-solvent = 80
> nstgbradii = 1
> rgbradii = 1
> 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
> DispCorr = No
> bSimTemp = FALSE
> free-energy = no
> nwall = 0
> wall-type = 9-3
> wall-atomtype[0] = -1
> wall-atomtype[1] = -1
> wall-density[0] = 0
> wall-density[1] = 0
> wall-ewald-zfac = 3
> pull = no
> rotation = FALSE
> disre = No
> disre-weighting = Conservative
> disre-mixed = FALSE
> dr-fc = 1000
> dr-tau = 0
> nstdisreout = 100
> orires-fc = 0
> orires-tau = 0
> nstorireout = 100
> dihre-fc = 0
> em-stepsize = 0.01
> em-tol = 10
> niter = 20
> fc-stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake-tol = 0.0001
> lincs-order = 4
> lincs-warnangle = 30
> lincs-iter = 1
> bd-fric = 0
> ld-seed = 1993
> cos-accel = 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}
> adress = FALSE
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 22677
> ref-t: 0
> tau-t: 0
> anneal: No
> ann-npoints: 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp-flags[ 0]: 0
> efield-x:
> n = 0
> efield-xt:
> n = 0
> efield-y:
> n = 0
> efield-yt:
> n = 0
> efield-z:
> n = 0
> efield-zt:
> n = 0
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm-opts:
> ngQM = 0
> Using 1 MPI thread
> Using 1 OpenMP thread
>
> Detecting CPU-specific acceleration.
> Present hardware specification:
> Vendor: GenuineIntel
> Brand: Intel(R) Xeon(R) CPU E5-1603 0 @ 2.80GHz
> Family: 6 Model: 45 Stepping: 7
> Features: aes apic avx clfsh cmov cx8 cx16 lahf_lm mmx msr pclmuldq popcnt
> pse sse2 sse3 sse4.1 sse4.2 ssse3
> Acceleration most likely to fit this hardware: AVX_256
> Acceleration selected at GROMACS compile time: SSE4.1
>
>
> Binary not matching hardware - you might be losing performance.
> Acceleration most likely to fit this hardware: AVX_256
> Acceleration selected at GROMACS compile time: SSE4.1
>
> Will do PME sum in reciprocal space.
>
> ++++ 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 0.320163 nm for Ewald
> Cut-off's: NS: 1 Coulomb: 1 LJ: 1
> System total charge: 0.000
> Generated table with 1000 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Using SSE4.1 4x4 non-bonded kernels
>
> Using geometric Lennard-Jones combination rule
>
> Potential shift: LJ r^-12: 1.000 r^-6 1.000, Ewald 1.000e-05
> Initialized non-bonded Ewald correction tables, spacing: 6.60e-04 size: 3033
>
> Removing pbc first time
> 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 --- -------- --------
> --
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa
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