I followed the below instructions to install Gromacs-5.1.4 after patching up with plumed. and then ran gromacs-plumed simulations end up with following errors. I didnt see any errors, while installation. I also ran on gpu and endup with same error.
Could you please instruct me that where i did wrong?.
Thanking you
note : attched md.log file
Error while running on HPC
[srp106@hpc1 TOPO]$ gmx_mpi mdrun -s topolA.tpr -nsteps 10000 -plumed plumed.dat
:-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
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 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) 2001-2015, 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 5.1.4
Executable: /home/srp106/software/gromacs-5.1.4/gmxbuild/bin/gmx_mpi
Data prefix: /home/srp106/software/gromacs-5.1.4/gmxbuild
Command line:
gmx_mpi mdrun -s topolA.tpr -nsteps 10000 -plumed plumed.dat
Back Off! I just backed up md.log to ./#md.log.2#
NOTE: Error occurred during GPU detection:
CUDA driver version is insufficient for CUDA runtime version
Can not use GPU acceleration, will fall back to CPU kernels.
Running on 1 node with total 12 cores, 12 logical cores, 2 compatible GPUs
Hardware detected on host hpc1 (the node of MPI rank 0):
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU X5660 @ 2.80GHz
SIMD instructions most likely to fit this hardware: SSE4.1
SIMD instructions selected at GROMACS compile time: SSE4.1
Reading file topolA.tpr, VERSION 4.6.7 (single precision)
Note: file tpx version 83, software tpx version 103
Overriding nsteps with value passed on the command line: 10000 steps, 20 ps
Using 1 MPI process
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.
Back Off! I just backed up traj_comp.xtc to ./#traj_comp.xtc.5#
Back Off! I just backed up ener.edr to ./#ener.edr.5#
starting mdrun 'alanine dipeptide in vacuum'
10000 steps, 20.0 ps.
[hpc1:27984] *** Process received signal ***
[hpc1:27984] Signal: Segmentation fault (11)
[hpc1:27984] Signal code: Address not mapped (1)
[hpc1:27984] Failing at address: (nil)
[hpc1:27984] [ 0] /lib64/libpthread.so.0[0x393a60f7e0]
[hpc1:27984] *** End of error message ***
Segmentation fault (core dumped)
md log out file while running on HPC
Log file opened on Thu Aug 3 16:13:51 2017
Host: hpc1 pid: 18034 rank ID: 0 number of ranks: 1
:-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
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 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) 2001-2015, 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 itA
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 5.1.4
Executable: /home/srp106/software/gromacs-5.1.4/gmxbuild/bin/gmx_mpi
Data prefix: /home/srp106/software/gromacs-5.1.4/gmxbuild
Command line:
gmx_mpi mdrun -s topolA.tpr -nsteps 10000 -plumed plumed.dat
GROMACS version: VERSION 5.1.4
Precision: single
Memory model: 64 bit
MPI library: MPI
OpenMP support: disabled
GPU support: enabled
OpenCL support: disabled
invsqrt routine: gmx_software_invsqrt(x)
SIMD instructions: SSE4.1
FFT library: fftw-3.3.6-pl2-fma-sse2-avx-avx2-avx2_128
RDTSCP usage: enabled
C++11 compilation: disabled
TNG support: enabled
Tracing support: disabled
Built on: Thu Jul 27 14:09:08 EDT 2017
Built by: srp106@hpc1 [CMAKE]
Build OS/arch: Linux 2.6.32-696.3.1.el6.x86_64 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU X5660 @ 2.80GHz
Build CPU family: 6 Model: 44 Stepping: 2
Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
C compiler: /usr/local/openmpi/1.8.8/bin/mpicc Intel 15.0.3.20150407
C compiler flags: -msse4.1 -std=gnu99 -w3 -wd177 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd3180 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
C++ compiler: /usr/local/openmpi/1.8.8/bin/mpic++ Intel 15.0.3.20150407
C++ compiler flags: -msse4.1 -w3 -wd177 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd1782 -wd2282 -wd3180 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
Boost version: 1.58.0 (external)
CUDA compiler: /usr/local/cuda-7.5/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;-gcc-version=450; ;-msse4.1;-w3;-wd177;-wd271;-wd304;-wd383;-wd424;-wd444;-wd522;-wd593;-wd869;-wd981;-wd1418;-wd1419;-wd1572;-wd1599;-wd2259;-wd2415;-wd2547;-wd2557;-wd3280;-wd3346;-wd11074;-wd11076;-wd1782;-wd2282;-wd3180;-O3;-DNDEBUG;-ip;-funroll-all-loops;-alias-const;-ansi-alias;
CUDA driver: 0.0
CUDA runtime: 0.0
NOTE: Error occurred during GPU detection:
CUDA driver version is insufficient for CUDA runtime version
Can not use GPU acceleration, will fall back to CPU kernels.
Running on 1 node with total 12 cores, 12 logical cores, 0 compatible GPUs
Hardware detected on host hpc1 (the node of MPI rank 0):
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU X5660 @ 2.80GHz
Family: 6 model: 44 stepping: 2
CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
SIMD instructions most likely to fit this hardware: SSE4.1
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 --- -------- --------
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 1000
init-step = 0
simulation-part = 1
comm-mode = Angular
nstcomm = 100
bd-fric = 0
ld-seed = 1993
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstcalcenergy = 100
nstenergy = 100
nstxout-compressed = 100
compressed-x-precision = 1000
cutoff-scheme = Group
nstlist = 10
ns-type = Grid
pbc = no
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 1.2
rlistlong = 1.2
nstcalclr = 0
coulombtype = Cut-off
coulomb-modifier = None
rcoulomb-switch = 0
rcoulomb = 1.2
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = None
rvdw-switch = 0
rvdw = 1.2
DispCorr = No
table-extension = 1
fourierspacing = 0.12
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 1e-05
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 = V-rescale
nsttcouple = 10
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 = 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
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 39
ref-t: 300
tau-t: 0.1
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Overriding nsteps with value passed on the command line: 10000 steps, 20 ps
Using 1 MPI process
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge: -0.000
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Coulomb -0e+00
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 21
Center of mass motion removal mode is Angular
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
Gromacs-plumed installation
[srp106@hpc1 TOPO]$
./configure --prefix=/home/srp106/ software/plumed2
make -j 16
make install
cd gromacs-5.1.4
plumed patch -p --runtime -e
module load base gcc libmatheval gsl xdrfile boost fftw/3.3.6-pl2 lapack/3.7.0
module load cuda/7.5
CXX=mpic++ CC=mpicc FC=mpifort LDFLAGS=-lmpi_cxx cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/srp106/software/gromacs-5.1.4/gmxbuild -DFFTWF_INCLUDE_DIR=/usr/local/fftw/3.3.6-pl2/include -DBoost_INCLUDE_DIR=/usr/local/boost/1_58_0/include -DBoost_DIR=/usr/local/boost/1_58_0 -DZLIB_INCLUDE_DIR=/usr/local/base/8.0/include -DZLIB_LIBRARY_RELEASE=/usr/local/base/8.0/lib/libz.so -DFFTWF_LIBRARY=/usr/local/fftw/3.3.6-pl2/lib/libfftw3f.so
make -j 16
make install
md log out file while running on GPU
Log file opened on Thu Aug 3 16:30:51 2017
Host: gpu013t pid: 29484 rank ID: 0 number of ranks: 1
:-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
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 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 a
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) 2001-2015, 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 5.1.4
Executable: /home/srp106/software/gromacs-5.1.4/gmxbuild/bin/gmx_mpi
Data prefix: /home/srp106/software/gromacs-5.1.4/gmxbuild
Command line:
gmx_mpi mdrun -s topolA.tpr -nsteps 10000 -plumed plumed.dat
GROMACS version: VERSION 5.1.4
Precision: single
Memory model: 64 bit
MPI library: MPI
OpenMP support: disabled
GPU support: enabled
OpenCL support: disabled
invsqrt routine: gmx_software_invsqrt(x)
SIMD instructions: SSE4.1
FFT library: fftw-3.3.6-pl2-fma-sse2-avx-avx2-avx2_128
RDTSCP usage: enabled
C++11 compilation: disabled
TNG support: enabled
Tracing support: disabled
Built on: Thu Jul 27 14:09:08 EDT 2017
Built by: srp106@hpc1 [CMAKE]
Build OS/arch: Linux 2.6.32-696.3.1.el6.x86_64 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU X5660 @ 2.80GHz
Build CPU family: 6 Model: 44 Stepping: 2
Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
C compiler: /usr/local/openmpi/1.8.8/bin/mpicc Intel 15.0.3.20150407
C compiler flags: -msse4.1 -std=gnu99 -w3 -wd177 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd3180 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
C++ compiler: /usr/local/openmpi/1.8.8/bin/mpic++ Intel 15.0.3.20150407
C++ compiler flags: -msse4.1 -w3 -wd177 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd1782 -wd2282 -wd3180 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
Boost version: 1.58.0 (external)
CUDA compiler: /usr/local/cuda-7.5/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;-gcc-version=450; ;-msse4.1;-w3;-wd177;-wd271;-wd304;-wd383;-wd424;-wd444;-wd522;-wd593;-wd869;-wd981;-wd1418;-wd1419;-wd1572;-wd1599;-wd2259;-wd2415;-wd2547;-wd2557;-wd3280;-wd3346;-wd11074;-wd11076;-wd1782;-wd2282;-wd3180;-O3;-DNDEBUG;-ip;-funroll-all-loops;-alias-const;-ansi-alias;
CUDA driver: 7.50
CUDA runtime: 7.50
Running on 1 node with total 12 cores, 12 logical cores, 2 compatible GPUs
Hardware detected on host gpu013t (the node of MPI rank 0):
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
Family: 6 model: 44 stepping: 2
CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
SIMD instructions most likely to fit this hardware: SSE4.1
SIMD instructions selected at GROMACS compile time: SSE4.1
GPU info:
Number of GPUs detected: 2
#0: NVIDIA Tesla M2090, compute cap.: 2.0, ECC: yes, stat: compatible
#1: NVIDIA Tesla M2090, compute cap.: 2.0, ECC: yes, stat: compatible
++++ 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 --- -------- --------
NOTE: GPU(s) found, but the current simulation can not use GPUs
To use a GPU, set the mdp option: cutoff-scheme = Verlet
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 1000
init-step = 0
simulation-part = 1
comm-mode = Angular
nstcomm = 100
bd-fric = 0
ld-seed = 1993
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstcalcenergy = 100
nstenergy = 100
nstxout-compressed = 100
compressed-x-precision = 1000
cutoff-scheme = Group
nstlist = 10
ns-type = Grid
pbc = no
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 1.2
rlistlong = 1.2
nstcalclr = 0
coulombtype = Cut-off
coulomb-modifier = None
rcoulomb-switch = 0
rcoulomb = 1.2
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = None
rvdw-switch = 0
rvdw = 1.2
DispCorr = No
table-extension = 1
fourierspacing = 0.12
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 1e-05
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 = V-rescale
nsttcouple = 10
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 = 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
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 39
ref-t: 300
tau-t: 0.1
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Overriding nsteps with value passed on the command line: 10000 steps, 20 ps
Using 1 MPI process
2 compatible GPUs detected in the system, but none will be used.
Consider trying GPU acceleration with the Verlet scheme!
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge: -0.000
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Coulomb -0e+00
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 21
Center of mass motion removal mode is Angular
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
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