As far as I can see then I currently having WU (they refere to slots?)
WU01 is the cpu and withing /var/lib/fahclient/work/01 find a log file called logfile_01.txt:
Code: Select all
*------------------------------*
Folding@Home Gromacs GB Core
Version 2.27 (Dec. 15, 2010)
Preparing to commence simulation
- Ensuring status. Please wait.
- Looking at optimizations...
- Working with standard loops on this execution.
Examination of work files indicates 8 consecutive improper terminations of core.
- Expanded 825690 -> 1402156 (decompressed 169.8 percent)
Called DecompressByteArray: compressed_data_size=825690 data_size=1402156, decompressed_data_size=1402156 diff=0
- Digital signature verified
Project: 9035 (Run 154, Clone 0, Gen 1055)
Entering M.D.
However the others does (/var/lib/fahclient/work/00/01) and in here I found a log that looks like this
Code: Select all
Project: 11432 (Run 0, Clone 981, Gen 40)
Unit: 0x000000338ca304e85a5a6c4686da8781
CPU: 0x00000000000000000000000000000000
Machine: 1
Reading tar file core.xml
Reading tar file integrator.xml
Reading tar file state.xml
Reading tar file system.xml
Digital signatures verified
*************************** Core21 Folding@home Core ***************************
Type: 33
Core: Core21
Website: http://folding.stanford.edu/
Copyright: (c) 2009-2014 Stanford University
Author: Yutong Zhao <[email protected]>
Args: -dir 00 -suffix 01 -version 704 -lifeline 8816 -checkpoint 30
-gpu-vendor nvidia -opencl-platform 0 -opencl-device 0 -cuda-device
0 -gpu 0
Config: <none>
************************************ Build *************************************
Version: 0.0.18
Date: Jan 20 2017
Time: 03:42:31
Repository: Git
Revision: 2745fc8067662d2e7b9e455232edb5ebd8790640
Branch: HEAD
Compiler: GNU 4.4.7 20120313 (Red Hat 4.4.7-17)
Options: -std=gnu++98 -O3 -funroll-loops -mfpmath=sse -ffast-math
-fno-unsafe-math-optimizations -msse2
Platform: linux2 4.4.39-moby
Bits: 64
Mode: Release
************************************ System ************************************
CPU: Intel(R) Core(TM) i7-4770S CPU @ 3.10GHz
CPU ID: GenuineIntel Family 6 Model 60 Stepping 3
CPUs: 8
Memory: 7.73GiB
Free Memory: 4.68GiB
Threads: POSIX_THREADS
OS Version: 4.14
Has Battery: false
On Battery: false
UTC Offset: 1
PID: 8820
CWD: /var/lib/fahclient/work
OS: Linux 4.14.0-3-amd64 x86_64
OS Arch: AMD64
GPUs: 0
CUDA: Not detected
OpenCL: Not detected
********************************************************************************
Folding@home GPU Core21 Folding@home Core
Version 0.0.18
[1] compatible platform(s):
-- 0 --
PROFILE = FULL_PROFILE
VERSION = OpenCL 1.2 CUDA 9.0.282
NAME = NVIDIA CUDA
VENDOR = NVIDIA Corporation
(1) device(s) found on platform 0:
-- 0 --
DEVICE_NAME = GeForce GTX 1070
DEVICE_VENDOR = NVIDIA Corporation
DEVICE_VERSION = OpenCL 1.2 CUDA
[ Entering Init ]
Launch time: 2018-02-21T17:14:26Z
Arguments passed: -dir 00 -suffix 01 -version 704 -lifeline 8816 -checkpoint 30 -gpu-vendor nvidia -opencl-platform 0 -opencl-device 0 -cuda-device 0 -gpu 0
For testState comparison of CPU and GPU, will use:
forceTolerance: 5 kJ/mol/nm
energyTolerance: 10 kJ/mol
[ Leaving Init ]
[ Entering Main ]
Reading core settings...
Total number of steps: 5000000
XTC write frequency: 250000
Checkpoint write frequency: 250000 (5%)
Number of frames per WU: 20
[ Initializing Core Contexts ]
Using platform OpenCL
Looking for vendor: nvidia...found on platformId 0
Setting platform precision to mixed
Deserializing System...
Found MonteCarloBarostat @ 1.01325 (default) Bar, 300 Kelvin, 50 pressure change frequency.
Found: 58738 atoms, 9 forces.
Deserializing State... done.
Ewald error tolerance in force 6 is 0.0005
Ewald parameters: alpha 2.920289872087185 nx 75 ny 75 nz 75
Integrator Type: N6OpenMM18LangevinIntegratorE
Constraint Tolerance: 1e-05
Time Step in PS: 0.002
Temperature: 300
Friction Coeff: 5
Using CPU platform for reference calculations.
Checking core state against reference...
Checking checkpoint state against reference...
[ Initialized Core Contexts... ]
Using OpenCL on platformId 0 and gpu 0
v(^_^)v MD ready starting from step 0
Completed 0 out of 5000000 steps (0%)
Temperature control disabled. Requirements: single Nvidia GPU, tmax must be < 110 and twait >= 900
Completed 50000 out of 5000000 steps (1%)
Completed 100000 out of 5000000 steps (2%)
Completed 150000 out of 5000000 steps (3%)
Completed 200000 out of 5000000 steps (4%)
Code: Select all
Log file opened on Wed Feb 21 18:33:46 2018
Host: debian pid: 9564 rank ID: 0 number of ranks: 1
GROMACS: GROMACS, VERSION 5.0.4-20161122-4846b12-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 5.0.4-20161122-4846b12-unknown
Gromacs version: VERSION 5.0.4-20161122-4846b12-unknown
GIT SHA1 hash: 4846b12ba1ad097bbb8e24164b2e54ab4c5dc17b
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-3.3.4-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 4.9.2
C compiler flags: -mavx -I/host/debian-stable-64bit-core-a7-avx-release/libfah/build/src -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 4.9.2
C++ compiler flags: -mavx -I/host/debian-stable-64bit-core-a7-avx-release/libfah/build/src -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: 1.62.0 (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 = md
tinit = 0
dt = 0.002
nsteps = 2500000
init-step = 47500000
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 1959294850
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 = 100
nstenergy = 50000
nstxout-compressed = 50000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 10
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 0.903
rlistlong = 0.903
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 = 0.16
fourier-nx = 24
fourier-ny = 24
fourier-nz = 24
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 = Nose-Hoover
nsttcouple = 10
nh-chain-length = 1
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 = 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: 761.79 10122.2
ref-t: 360 360
tau-t: 1 1
annealing: No No
annealing-npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Initializing Domain Decomposition on 6 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: 0.404 nm, LJ-14, atoms 19 30
multi-body bonded interactions: 0.454 nm, CMAP Dih., atoms 175 184
Minimum cell size due to bonded interactions: 0.500 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm
Estimated maximum distance required for P-LINCS: 0.222 nm
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 6 cells with a minimum initial size of 0.625 nm
The maximum allowed number of cells is: X 5 Y 5 Z 5
Domain decomposition grid 3 x 2 x 1, separate PME ranks 0
PME domain decomposition: 3 x 2 x 1
Domain decomposition rank 0, coordinates 0 0 0
Using 6 MPI threads
Detecting CPU SIMD instructions.
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-4770S CPU @ 3.10GHz
Family: 6 Model: 60 Stepping: 3
Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX_256
Binary not matching hardware - you might be losing performance.
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX_256
The current CPU can measure timings more accurately than the code in
GROMACS was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding GROMACS with the GMX_USE_RDTSCP=OFF CMake option.
Will do PME sum in reciprocal space for electrostatic interactions.
++++ 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 0.288146 nm for Ewald
Cut-off's: NS: 0.903 Coulomb: 0.9 LJ: 0.9
Long Range LJ corr.: <C6> 3.0399e-04
System total charge: 0.000
Generated table with 951 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 951 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 951 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 951 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 951 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 951 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Using AVX_256 4x4 non-bonded kernels
Using Lorentz-Berthelot Lennard-Jones combination rule
Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 8.85e-04 size: 2151
NOTE: The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto: will not pin thread to cores.
This can lead to significant performance degradation.
Consider using -pin on (and -pinoffset in case you run multiple jobs).
Initializing Parallel LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------
The number of constraints is 150
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Setting the maximum number of constraint warnings to -1
maxwarn < 0, will not stop on constraint errors
Linking all bonded interactions to atoms
There are 6745 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 1.23 nm Y 1.85 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 0.903 nm
two-body bonded interactions (-rdd) 0.903 nm
multi-body bonded interactions (-rdd) 0.903 nm
atoms separated by up to 5 constraints (-rcon) 1.233 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1
The minimum size for domain decomposition cells is 0.903 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.73 Y 0.49
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 0.903 nm
two-body bonded interactions (-rdd) 0.903 nm
multi-body bonded interactions (-rdd) 0.903 nm
atoms separated by up to 5 constraints (-rcon) 0.903 nm
Making 2D domain decomposition grid 3 x 2 x 1, home cell index 0 0 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 5365 Atoms
Charge group distribution at step 47500000: 911 881 887 890 889 907
Initial temperature: 365.706 K
Started mdrun on rank 0 Wed Feb 21 18:33:47 2018
Step Time Lambda
47500000 95000.00000 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
2.81980e+02 8.53134e+02 4.00920e+02 5.02920e+01 -8.66576e+01
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
2.30543e+02 4.01757e+03 1.04793e+04 -9.91009e+02 -8.30525e+04
Coul. recip. Potential Kinetic En. Total Energy Conserved En.
8.03228e+02 -6.70131e+04 1.65673e+04 -5.04458e+04 -5.04458e+04
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
3.66149e+02 -3.25382e+02 2.53839e+03 3.14117e-06
DD step 47500009 load imb.: force 20.7%
At step 47500010 the performance loss due to force load imbalance is 3.9 %
NOTE: Turning on dynamic load balancing
DD step 47549999 vol min/aver 0.807 load imb.: force 1.7%
Step Time Lambda
47550000 95100.00000 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
3.09016e+02 8.04182e+02 3.14941e+02 5.97698e+01 -8.77557e+01
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
1.88819e+02 4.01889e+03 1.01774e+04 -9.91009e+02 -8.17578e+04
Coul. recip. Potential Kinetic En. Total Energy Conserved En.
7.75933e+02 -6.61877e+04 1.63524e+04 -4.98353e+04 -5.01356e+04
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
3.61398e+02 -3.25382e+02 2.19064e+03 3.08043e-06
Does any of those logs help?
