LMDE3 setup
Code: Select all
*********************** Log Started 2020-03-04T23:33:27Z ***********************
23:33:27:************************* Folding@home Client *************************
23:33:27: Website: https://foldingathome.org/
23:33:27: Copyright: (c) 2009-2018 foldingathome.org
23:33:27: Author: Joseph Coffland <[email protected]>
23:33:27: Args: --child --lifeline 990 /etc/fahclient/config.xml --run-as
23:33:27: fahclient --pid-file=/var/run/fahclient.pid --daemon
23:33:27: Config: /etc/fahclient/config.xml
23:33:27:******************************** Build ********************************
23:33:27: Version: 7.5.1
23:33:27: Date: May 11 2018
23:33:27: Time: 19:59:04
23:33:27: Repository: Git
23:33:27: Revision: 4705bf53c635f88b8fe85af7675557e15d491ff0
23:33:27: Branch: master
23:33:27: Compiler: GNU 6.3.0 20170516
23:33:27: Options: -std=gnu++98 -O3 -funroll-loops
23:33:27: Platform: linux2 4.14.0-3-amd64
23:33:27: Bits: 64
23:33:27: Mode: Release
23:33:27:******************************* System ********************************
23:33:27: CPU: Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
23:33:27: CPU ID: GenuineIntel Family 6 Model 60 Stepping 3
23:33:27: CPUs: 8
23:33:27: Memory: 15.63GiB
23:33:27: Free Memory: 15.12GiB
23:33:27: Threads: POSIX_THREADS
23:33:27: OS Version: 4.9
23:33:27: Has Battery: false
23:33:27: On Battery: false
23:33:27: UTC Offset: -8
23:33:27: PID: 992
23:33:27: CWD: /var/lib/fahclient
23:33:27: OS: Linux 4.9.0-11-amd64 x86_64
23:33:27: OS Arch: AMD64
23:33:27: GPUs: 1
23:33:27: GPU 0: Bus:1 Slot:0 Func:0 NVIDIA:2 GF116 [GeForce GT 635]
23:33:27:CUDA Device 0: Platform:0 Device:0 Bus:1 Slot:0 Compute:3.5 Driver:9.1
23:33:27: OpenCL: Not detected: Failed to open dynamic library 'libOpenCL.so':
23:33:27: libOpenCL.so: cannot open shared object file: No such file or
23:33:27: directory
23:33:27:***********************************************************************
23:33:27:<config>
23:33:27: <!-- Client Control -->
23:33:27: <fold-anon v='true'/>
23:33:27:
23:33:27: <!-- Folding Slot Configuration -->
23:33:27: <gpu v='false'/>
23:33:27:
23:33:27: <!-- Network -->
23:33:27: <proxy v=':8080'/>
23:33:27:
23:33:27: <!-- User Information -->
23:33:27: <passkey v='********************************'/>
23:33:27: <team v='45104'/>
23:33:27: <user v='dooley'/>
23:33:27:
23:33:27: <!-- Folding Slots -->
23:33:27: <slot id='0' type='CPU'>
23:33:27: <cpus v='6'/>
23:33:27: <next-unit-percentage v='100'/>
23:33:27: </slot>
23:33:27: <slot id='1' type='GPU'>
23:33:27: <opencl-index v='0'/>
23:33:27: </slot>
23:33:27:</config>
Code: Select all
*********************** Log Started 2020-03-07T12:44:26Z ***********************
************************** Gromacs Folding@home Core ***************************
Type: 0xa7
Core: Gromacs
Args: -dir 00 -suffix 01 -version 705 -lifeline 807 -checkpoint 15 -np 6
************************************ CBang *************************************
Date: Nov 5 2019
Time: 06:06:57
Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
Branch: master
Compiler: GNU 8.3.0
Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
Platform: linux2 4.19.0-5-amd64
Bits: 64
Mode: Release
************************************ System ************************************
CPU: Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
CPU ID: GenuineIntel Family 6 Model 60 Stepping 3
CPUs: 8
Memory: 15.63GiB
Free Memory: 5.55GiB
Threads: POSIX_THREADS
OS Version: 4.9
Has Battery: false
On Battery: false
UTC Offset: -8
PID: 811
CWD: /var/lib/fahclient/work
******************************** Build - libFAH ********************************
Version: 0.0.18
Author: Joseph Coffland <[email protected]>
Copyright: 2019 foldingathome.org
Homepage: https://foldingathome.org/
Date: Nov 5 2019
Time: 06:13:26
Revision: 490c9aa2957b725af319379424d5c5cb36efb656
Branch: master
Compiler: GNU 8.3.0
Options: -std=c++11 -O3 -funroll-loops -fno-pie
Platform: linux2 4.19.0-5-amd64
Bits: 64
Mode: Release
************************************ Build *************************************
SIMD: avx_256
********************************************************************************
Project: 14314 (Run 0, Clone 132, Gen 2)
Unit: 0x000000030002894b5e62c389eb15dc0a
Reading tar file core.xml
Reading tar file frame2.tpr
Digital signatures verified
Calling: mdrun -s frame2.tpr -o frame2.trr -cpt 15 -nt 6
Steps: first=1000000 total=500000
ERROR:
ERROR:-------------------------------------------------------
ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/mdlib/domdec.c, line: 6902
ERROR:
ERROR:Fatal error:
ERROR:There is no domain decomposition for 6 ranks that is compatible with the given box and a minimum cell size of 2.42412 nm
ERROR:Change the number of ranks or mdrun option -rdd or -dds
ERROR:Look in the log file for details on the domain decomposition
ERROR:For more information and tips for troubleshooting, please check the GROMACS
ERROR:website at http://www.gromacs.org/Documentation/Errors
ERROR:-------------------------------------------------------
WARNING:Unexpected exit() call
WARNING:Unexpected exit from science code
Saving result file ../logfile_01.txt
Saving result file md.log
Saving result file science.log
Code: Select all
Log file opened on Sat Mar 7 04:51:26 2020
Host: sol2 pid: 1035 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 --- -------- --------
Changing nstlist from 10 to 20, rlist from 0.9 to 0.931
Input Parameters:
integrator = sd
tinit = 0
dt = 0.002
nsteps = 500000
init-step = 1000000
simulation-part = 1
comm-mode = Linear
nstcomm = 10
bd-fric = 0
ld-seed = 1090642883
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 500000
nstvout = 500000
nstfout = 0
nstlog = 50000
nstcalcenergy = 10
nstenergy = 50000
nstxout-compressed = 5000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 20
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 0.931
rlistlong = 0.931
nstcalclr = 10
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 0.9
epsilon-r = 1
epsilon-rf = 1
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 0.9
DispCorr = No
table-extension = 1
fourierspacing = 0.12
fourier-nx = 60
fourier-ny = 60
fourier-nz = 60
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 = TRUE
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 = yes
init-lambda = -1
init-lambda-state = 19
delta-lambda = 0
nstdhdl = 10
n-lambdas = 20
separate-dvdl:
fep-lambdas = TRUE
mass-lambdas = FALSE
coul-lambdas = FALSE
vdw-lambdas = FALSE
bonded-lambdas = FALSE
restraint-lambdas = FALSE
temperature-lambdas = FALSE
all-lambdas:
fep-lambdas = 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
mass-lambdas = 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
coul-lambdas = 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
vdw-lambdas = 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
bonded-lambdas = 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
restraint-lambdas = 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
temperature-lambdas = 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1
calc-lambda-neighbors = -1
dhdl-print-energy = no
sc-alpha = 0
sc-power = 0
sc-r-power = 6
sc-sigma = 0.3
sc-sigma-min = 0.3
sc-coul = FALSE
dh-hist-size = 0
dh-hist-spacing = 0.1
separate-dhdl-file = yes
dhdl-derivatives = yes
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: 3483.86 69916.1
ref-t: 300 300
tau-t: 1 1
annealing: No No
annealing-npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0 0 0
energygrp-flags[ 1]: 0 0 0
energygrp-flags[ 2]: 0 0 0
Code: Select all
-------------------------------------------------------
Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/mdlib/domdec.c, line: 6902
Fatal error:
There is no domain decomposition for 6 ranks that is compatible with the given box and a minimum cell size of 2.42412 nm
Change the number of ranks or mdrun option -rdd or -dds
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
-------------------------------------------------------
WARNING:Unexpected exit() call
WARNING:Unexpected exit from science code
Saving result file ../logfile_01.txt
Saving result file md.log
Saving result file science.log
Calling: mdrun -s frame2.tpr -o frame2.trr -cpt 15 -nt 6
Steps: first=1000000 total=500000
ERROR:
ERROR:-------------------------------------------------------
ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/mdlib/domdec.c, line: 6902
ERROR:
ERROR:Fatal error:
ERROR:There is no domain decomposition for 6 ranks that is compatible with the given box and a minimum cell size of 2.42412 nm
ERROR:Change the number of ranks or mdrun option -rdd or -dds
ERROR:Look in the log file for details on the domain decomposition
ERROR:For more information and tips for troubleshooting, please check the GROMACS
ERROR:website at http://www.gromacs.org/Documentation/Errors
ERROR:-------------------------------------------------------
Reading file frame2.tpr, VERSION 5.0.4 (single precision)
Changing nstlist from 10 to 20, rlist from 0.9 to 0.931