Code: Select all
04:33:39:WU01:FS00:0xa7:*********************** Log Started 2020-03-30T04:33:38Z ***********************
04:33:39:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
04:33:39:WU01:FS00:0xa7: Type: 0xa7
04:33:39:WU01:FS00:0xa7: Core: Gromacs
04:33:39:WU01:FS00:0xa7: Args: -dir 01 -suffix 01 -version 705 -lifeline 33987 -checkpoint 15 -np
04:33:39:WU01:FS00:0xa7: 15
04:33:39:WU01:FS00:0xa7:************************************ CBang *************************************
04:33:39:WU01:FS00:0xa7: Date: Nov 5 2019
04:33:39:WU01:FS00:0xa7: Time: 06:06:57
04:33:39:WU01:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
04:33:39:WU01:FS00:0xa7: Branch: master
04:33:39:WU01:FS00:0xa7: Compiler: GNU 8.3.0
04:33:39:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
04:33:39:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
04:33:39:WU01:FS00:0xa7: Bits: 64
04:33:39:WU01:FS00:0xa7: Mode: Release
04:33:39:WU01:FS00:0xa7:************************************ System ************************************
04:33:39:WU01:FS00:0xa7: CPU: Intel(R) Xeon(R) E-2286M CPU @ 2.40GHz
04:33:39:WU01:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 158 Stepping 13
04:33:39:WU01:FS00:0xa7: CPUs: 16
04:33:39:WU01:FS00:0xa7: Memory: 15.48GiB
04:33:39:WU01:FS00:0xa7:Free Memory: 3.88GiB
04:33:39:WU01:FS00:0xa7: Threads: POSIX_THREADS
04:33:39:WU01:FS00:0xa7: OS Version: 5.5
04:33:39:WU01:FS00:0xa7:Has Battery: true
04:33:39:WU01:FS00:0xa7: On Battery: false
04:33:39:WU01:FS00:0xa7: UTC Offset: -5
04:33:39:WU01:FS00:0xa7: PID: 33991
04:33:39:WU01:FS00:0xa7: CWD: /var/lib/fahclient/work
04:33:39:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
04:33:39:WU01:FS00:0xa7: Version: 0.0.18
04:33:39:WU01:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
04:33:39:WU01:FS00:0xa7: Copyright: 2019 foldingathome.org
04:33:39:WU01:FS00:0xa7: Homepage: https://foldingathome.org/
04:33:39:WU01:FS00:0xa7: Date: Nov 5 2019
04:33:39:WU01:FS00:0xa7: Time: 06:13:26
04:33:39:WU01:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
04:33:39:WU01:FS00:0xa7: Branch: master
04:33:39:WU01:FS00:0xa7: Compiler: GNU 8.3.0
04:33:39:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
04:33:39:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
04:33:39:WU01:FS00:0xa7: Bits: 64
04:33:39:WU01:FS00:0xa7: Mode: Release
04:33:39:WU01:FS00:0xa7:************************************ Build *************************************
04:33:39:WU01:FS00:0xa7: SIMD: avx_256
04:33:39:WU01:FS00:0xa7:********************************************************************************
04:33:39:WU01:FS00:0xa7:Project: 16401 (Run 153, Clone 0, Gen 0)
04:33:39:WU01:FS00:0xa7:Unit: 0x0000000096880e6e5e814c9dec360f60
04:33:39:WU01:FS00:0xa7:Reading tar file core.xml
04:33:39:WU01:FS00:0xa7:Reading tar file frame0.tpr
04:33:39:WU01:FS00:0xa7:Digital signatures verified
04:33:39:WU01:FS00:0xa7:Calling: mdrun -s frame0.tpr -o frame0.trr -x frame0.xtc -cpt 15 -nt 15
04:33:39:WU01:FS00:0xa7:Steps: first=0 total=500000
04:33:39:WU01:FS00:0xa7:ERROR:
04:33:39:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
04:33:39:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
04:33:39:WU01:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/mdlib/domdec.c, line: 6902
04:33:39:WU01:FS00:0xa7:ERROR:
04:33:39:WU01:FS00:0xa7:ERROR:Fatal error:
04:33:39:WU01:FS00:0xa7:ERROR:There is no domain decomposition for 15 ranks that is compatible with the given box and a minimum cell size of 1.40508 nm
04:33:39:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
04:33:39:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
04:33:39:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
04:33:39:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
04:33:39:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
04:33:44:WU01:FS00:0xa7:WARNING:Unexpected exit() call
04:33:44:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
04:33:44:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
04:33:44:WU01:FS00:0xa7:Saving result file md.log
04:33:44:WU01:FS00:0xa7:Saving result file science.log
04:33:44:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)Code: Select all
Log file opened on Sun Mar 29 23:33:38 2020
Host: localhost pid: 33991 rank ID: 0 number of ranks: 1
GROMACS: GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
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: GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
Gromacs version: VERSION 5.0.4-20191026-456f0d636-unknown
GIT SHA1 hash: 456f0d636b694d70ef483843dbb1b1383643ee12
Branched from: unknown
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
SIMD instructions: AVX_256
FFT library: fftw-3.3.8-sse2-avx
RDTSCP usage: disabled
C++11 compilation: disabled
TNG support: enabled
Tracing support: disabled
Built on: Wed Mar 22 01:02:31 UTC 2017
Built by: root@69562b3fdcef [CMAKE]
Build OS/arch: Linux 4.9.0-1-amd64 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i7-3770S CPU @ 3.10GHz
Build CPU family: 6 Model: 58 Stepping: 9
Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 8.3.0
C compiler flags: -mavx -I/host/debian-stable-64bit-core-a7-avx-release/libfah/build/src -I/host/debian-stable-64bit-core-a7-avx-release/cbang/build/include -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wno-unknown-pragmas -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
C++ compiler: /usr/bin/c++ GNU 8.3.0
C++ compiler flags: -mavx -I/host/debian-stable-64bit-core-a7-avx-release/libfah/build/src -I/host/debian-stable-64bit-core-a7-avx-release/cbang/build/include -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -Wno-unknown-pragmas -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
Boost version: 1.55.0 (internal)
++++ 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 --- -------- --------
Can not increase nstlist because verlet-buffer-tolerance is not set or used
Input Parameters:
integrator = md
tinit = 0
dt = 0.004
nsteps = 500000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 5
bd-fric = 0
ld-seed = 1764347182
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 0
nstcalcenergy = 0
nstenergy = 0
nstxout-compressed = 5000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 10
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = -1
rlist = 1.1
rlistlong = 1.1
nstcalclr = 10
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 0.9
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 0.9
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.12
fourier-nx = 64
fourier-ny = 64
fourier-nz = 64
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 = V-rescale
nsttcouple = 10
nh-chain-length = 0
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 = All
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 = 6
lincs-iter = 2
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: 56191
ref-t: 300
tau-t: 0.1
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Initializing Domain Decomposition on 15 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.419 nm, LJ-14, atoms 849 858
multi-body bonded interactions: 0.419 nm, Proper Dih., atoms 849 858
Minimum cell size due to bonded interactions: 0.461 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.124 nm
Estimated maximum distance required for P-LINCS: 1.124 nm
This distance will limit the DD cell size, you can override this with -rcon
Using 0 separate PME ranks, as there are too few total
ranks for efficient splitting
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 15 cells with a minimum initial size of 1.405 nm
The maximum allowed number of cells is: X 4 Y 4 Z 3