Page 2 of 3
Re: Issues, perhaps bad WU? - 16417
Posted: Thu Apr 09, 2020 12:24 pm
by MMaatttt
Will do.
Re: Issues, perhaps bad WU? - 16417
Posted: Thu Apr 09, 2020 7:27 pm
by Roadpower
I just woke up so posting this and will continue to wake up so I can digest this better.
The following is md.log
Code: Select all
Log file opened on Thu Apr 9 15:24:29 2020
Host: omitted pid: 6496 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 = 250000
init-step = 5500000
simulation-part = 1
comm-mode = Linear
nstcomm = 5
bd-fric = 0
ld-seed = 620990457
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 125000
nstvout = 125000
nstfout = 0
nstlog = 0
nstcalcenergy = 0
nstenergy = 2500
nstxout-compressed = 2500
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 = 80
fourier-ny = 80
fourier-nz = 80
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 = TRUE
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: 95890
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 166 174
multi-body bonded interactions: 0.419 nm, Proper Dih., atoms 166 174
Minimum cell size due to bonded interactions: 0.461 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.166 nm
Estimated maximum distance required for P-LINCS: 1.166 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 1.457 nm
The maximum allowed number of cells is: X 4 Y 4 Z 4
The CPU hang up appears to be project 13833. It cycles right at the top. Projected time of completion five days.
Code: Select all
20:16:30:WU01:FS00:0xa7:************************************ Build *************************************
20:16:30:WU01:FS00:0xa7: SIMD: avx_256
20:16:30:WU01:FS00:0xa7:********************************************************************************
20:16:30:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 1548, Gen 22)
20:16:30:WU01:FS00:0xa7:Unit: 0x0000001e80fccb095e6e5656a6e3070c
20:16:30:WU01:FS00:0xa7:Reading tar file core.xml
20:16:30:WU01:FS00:0xa7:Reading tar file frame22.tpr
20:16:30:WU01:FS00:0xa7:Digital signatures verified
20:16:30:WU01:FS00:0xa7:Calling: mdrun -s frame22.tpr -o frame22.trr -x frame22.xtc -cpt 15 -nt 15
20:16:30:WU01:FS00:0xa7:Steps: first=5500000 total=250000
20:16:30:WU01:FS00:0xa7:ERROR:
20:16:30:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
20:16:30:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
20:16:30: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
20:16:30:WU01:FS00:0xa7:ERROR:
20:16:30:WU01:FS00:0xa7:ERROR:Fatal error:
20:16:30: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 1.45733 nm
20:16:30:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
20:16:30:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
20:16:30:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
20:16:30:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
20:16:30:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
20:16:35:WU01:FS00:0xa7:WARNING:Unexpected exit() call
20:16:35:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
20:16:35:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
20:16:35:WU01:FS00:0xa7:Saving result file md.log
20:16:35:WU01:FS00:0xa7:Saving result file science.log
20:16:35:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
I'm thinking to remove CPU slot, wait a while and then add it back in to clear the stuck project.
Re: Issues, perhaps bad WU? - 16417
Posted: Thu Apr 09, 2020 7:38 pm
by HendricksSA
Project: 16417 (Run 1642, Clone 2, Gen 2) does not work at 48 threads. Lost nearly 4 days of folding to a Linux machine hung on this probably bad WU.
Code: Select all
*********************** Log Started 2020-03-25T22:55:43Z ***********************
22:55:43:************************* Folding@home Client *************************
22:55:43: Website: https://foldingathome.org/
22:55:43: Copyright: (c) 2009-2018 foldingathome.org
22:55:43: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
22:55:43: Args: --child --lifeline 1946 /etc/fahclient/config.xml --run-as
22:55:43: fahclient --pid-file=/var/run/fahclient.pid --daemon
22:55:43: Config: /etc/fahclient/config.xml
22:55:43:******************************** Build ********************************
22:55:43: Version: 7.5.1
22:55:43: Date: May 11 2018
22:55:43: Time: 19:59:04
22:55:43: Repository: Git
22:55:43: Revision: 4705bf53c635f88b8fe85af7675557e15d491ff0
22:55:43: Branch: master
22:55:43: Compiler: GNU 6.3.0 20170516
22:55:43: Options: -std=gnu++98 -O3 -funroll-loops
22:55:43: Platform: linux2 4.14.0-3-amd64
22:55:43: Bits: 64
22:55:43: Mode: Release
22:55:43:******************************* System ********************************
22:55:43: CPU: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
22:55:43: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
22:55:43: CPUs: 48
22:55:43: Memory: 62.80GiB
22:55:43:Free Memory: 61.70GiB
22:55:43: Threads: POSIX_THREADS
22:55:43: OS Version: 5.3
22:55:43:Has Battery: false
22:55:43: On Battery: false
22:55:43: UTC Offset: -5
22:55:43: PID: 1949
22:55:43: CWD: /var/lib/fahclient
22:55:43: OS: Linux 5.3.0-42-generic x86_64
22:55:43: OS Arch: AMD64
22:55:43: GPUs: 0
22:55:43: CUDA: Not detected: Failed to open dynamic library 'libcuda.so':
22:55:43: libcuda.so: cannot open shared object file: No such file or
22:55:43: directory
22:55:43: OpenCL: Not detected: Failed to open dynamic library 'libOpenCL.so':
22:55:43: libOpenCL.so: cannot open shared object file: No such file or
22:55:43: directory
22:55:43:***********************************************************************
22:55:43:<config>
22:55:43: <!-- Folding Slot Configuration -->
22:55:43: <client-type v='advanced'/>
22:55:43: <max-packet-size v='big'/>
22:55:43:
22:55:43: <!-- Slot Control -->
22:55:43: <pause-on-start v='true'/>
22:55:43: <power v='full'/>
22:55:43:
22:55:43: <!-- User Information -->
22:55:43: <passkey v='********************************'/>
22:55:43: <user v='HendricksSA'/>
22:55:43:
22:55:43: <!-- Work Unit Control -->
22:55:43: <next-unit-percentage v='100'/>
22:55:43:
22:55:43: <!-- Folding Slots -->
22:55:43: <slot id='0' type='CPU'/>
22:55:43:</config>
22:55:43:Switching to user fahclient
22:55:43:Trying to access database...
22:55:43:Successfully acquired database lock
22:55:43:Enabled folding slot 00: PAUSED cpu:48 (by user)
23:17:11:FS00:Unpaused
…
04:24:05:WU00:FS00:Starting
04:24:05:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 00 -suffix 01 -version 705 -lifeline 1949 -checkpoint 15 -np 48
04:24:05:WU00:FS00:Started FahCore on PID 1074
04:24:05:WU00:FS00:Core PID:1078
04:24:05:WU00:FS00:FahCore 0xa7 started
04:24:05:WU00:FS00:0xa7:*********************** Log Started 2020-04-06T04:24:05Z ***********************
04:24:05:WU00:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
04:24:05:WU00:FS00:0xa7: Type: 0xa7
04:24:05:WU00:FS00:0xa7: Core: Gromacs
04:24:05:WU00:FS00:0xa7: Args: -dir 00 -suffix 01 -version 705 -lifeline 1074 -checkpoint 15 -np
04:24:05:WU00:FS00:0xa7: 48
04:24:05:WU00:FS00:0xa7:************************************ CBang *************************************
04:24:05:WU00:FS00:0xa7: Date: Nov 5 2019
04:24:05:WU00:FS00:0xa7: Time: 06:06:57
04:24:05:WU00:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
04:24:05:WU00:FS00:0xa7: Branch: master
04:24:05:WU00:FS00:0xa7: Compiler: GNU 8.3.0
04:24:05:WU00:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
04:24:05:WU00:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
04:24:05:WU00:FS00:0xa7: Bits: 64
04:24:05:WU00:FS00:0xa7: Mode: Release
04:24:05:WU00:FS00:0xa7:************************************ System ************************************
04:24:05:WU00:FS00:0xa7: CPU: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
04:24:05:WU00:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
04:24:05:WU00:FS00:0xa7: CPUs: 48
04:24:05:WU00:FS00:0xa7: Memory: 62.80GiB
04:24:05:WU00:FS00:0xa7:Free Memory: 59.17GiB
04:24:05:WU00:FS00:0xa7: Threads: POSIX_THREADS
04:24:05:WU00:FS00:0xa7: OS Version: 5.3
04:24:05:WU00:FS00:0xa7:Has Battery: false
04:24:05:WU00:FS00:0xa7: On Battery: false
04:24:05:WU00:FS00:0xa7: UTC Offset: -5
04:24:05:WU00:FS00:0xa7: PID: 1078
04:24:05:WU00:FS00:0xa7: CWD: /var/lib/fahclient/work
04:24:05:WU00:FS00:0xa7:******************************** Build - libFAH ********************************
04:24:05:WU00:FS00:0xa7: Version: 0.0.18
04:24:05:WU00:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
04:24:05:WU00:FS00:0xa7: Copyright: 2019 foldingathome.org
04:24:05:WU00:FS00:0xa7: Homepage: https://foldingathome.org/
04:24:05:WU00:FS00:0xa7: Date: Nov 5 2019
04:24:05:WU00:FS00:0xa7: Time: 06:13:26
04:24:05:WU00:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
04:24:05:WU00:FS00:0xa7: Branch: master
04:24:05:WU00:FS00:0xa7: Compiler: GNU 8.3.0
04:24:05:WU00:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
04:24:05:WU00:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
04:24:05:WU00:FS00:0xa7: Bits: 64
04:24:05:WU00:FS00:0xa7: Mode: Release
04:24:05:WU00:FS00:0xa7:************************************ Build *************************************
04:24:05:WU00:FS00:0xa7: SIMD: avx_256
04:24:05:WU00:FS00:0xa7:********************************************************************************
04:24:05:WU00:FS00:0xa7:Project: 16417 (Run 1642, Clone 2, Gen 2)
04:24:05:WU00:FS00:0xa7:Unit: 0x0000000396880e6e5e8a60945e03cfee
04:24:05:WU00:FS00:0xa7:Reading tar file core.xml
04:24:05:WU00:FS00:0xa7:Reading tar file frame2.tpr
04:24:05:WU00:FS00:0xa7:Digital signatures verified
04:24:05:WU00:FS00:0xa7:Calling: mdrun -s frame2.tpr -o frame2.trr -x frame2.xtc -cpt 15 -nt 48
04:24:05:WU00:FS00:0xa7:Steps: first=500000 total=250000
04:24:05:WU00:FS00:0xa7:ERROR:
04:24:05:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
04:24:05:WU00:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
04:24:05:WU00: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
04:24:05:WU00:FS00:0xa7:ERROR:
04:24:05:WU00:FS00:0xa7:ERROR:Fatal error:
04:24:05:WU00:FS00:0xa7:ERROR:There is no domain decomposition for 40 ranks that is compatible with the given box and a minimum cell size of 1.4227 nm
04:24:05:WU00:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
04:24:05:WU00:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
04:24:05:WU00:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
04:24:05:WU00:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
04:24:05:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
04:24:10:WU00:FS00:0xa7:WARNING:Unexpected exit() call
04:24:10:WU00:FS00:0xa7:WARNING:Unexpected exit from science code
04:24:10:WU00:FS00:0xa7:Saving result file ../logfile_01.txt
04:24:10:WU00:FS00:0xa7:Saving result file md.log
04:24:10:WU00:FS00:0xa7:Saving result file science.log
04:24:11:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
04:24:11:WU01:FS00:Upload 91.17%
04:24:11:WU00:FS00:Starting
04:24:11:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 00 -suffix 01 -version 705 -lifeline 1949 -checkpoint 15 -np 48
04:24:11:WU00:FS00:Started FahCore on PID 1131
04:24:11:WU00:FS00:Core PID:1135
04:24:11:WU00:FS00:FahCore 0xa7 started
04:24:11:WU00:FS00:0xa7:*********************** Log Started 2020-04-06T04:24:11Z ***********************
04:24:11:WU00:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
04:24:11:WU00:FS00:0xa7: Type: 0xa7
04:24:11:WU00:FS00:0xa7: Core: Gromacs
04:24:11:WU00:FS00:0xa7: Args: -dir 00 -suffix 01 -version 705 -lifeline 1131 -checkpoint 15 -np
04:24:11:WU00:FS00:0xa7: 48
04:24:11:WU00:FS00:0xa7:************************************ CBang *************************************
04:24:11:WU00:FS00:0xa7: Date: Nov 5 2019
04:24:11:WU00:FS00:0xa7: Time: 06:06:57
04:24:11:WU00:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
04:24:11:WU00:FS00:0xa7: Branch: master
04:24:11:WU00:FS00:0xa7: Compiler: GNU 8.3.0
04:24:11:WU00:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
04:24:11:WU00:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
04:24:11:WU00:FS00:0xa7: Bits: 64
04:24:11:WU00:FS00:0xa7: Mode: Release
04:24:11:WU00:FS00:0xa7:************************************ System ************************************
04:24:11:WU00:FS00:0xa7: CPU: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
04:24:11:WU00:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
04:24:11:WU00:FS00:0xa7: CPUs: 48
04:24:11:WU00:FS00:0xa7: Memory: 62.80GiB
04:24:11:WU00:FS00:0xa7:Free Memory: 59.16GiB
04:24:11:WU00:FS00:0xa7: Threads: POSIX_THREADS
04:24:11:WU00:FS00:0xa7: OS Version: 5.3
04:24:11:WU00:FS00:0xa7:Has Battery: false
04:24:11:WU00:FS00:0xa7: On Battery: false
04:24:11:WU00:FS00:0xa7: UTC Offset: -5
04:24:11:WU00:FS00:0xa7: PID: 1135
04:24:11:WU00:FS00:0xa7: CWD: /var/lib/fahclient/work
04:24:11:WU00:FS00:0xa7:******************************** Build - libFAH ********************************
04:24:11:WU00:FS00:0xa7: Version: 0.0.18
04:24:11:WU00:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
04:24:11:WU00:FS00:0xa7: Copyright: 2019 foldingathome.org
04:24:11:WU00:FS00:0xa7: Homepage: https://foldingathome.org/
04:24:11:WU00:FS00:0xa7: Date: Nov 5 2019
04:24:11:WU00:FS00:0xa7: Time: 06:13:26
04:24:11:WU00:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
04:24:11:WU00:FS00:0xa7: Branch: master
04:24:11:WU00:FS00:0xa7: Compiler: GNU 8.3.0
04:24:11:WU00:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
04:24:11:WU00:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
04:24:11:WU00:FS00:0xa7: Bits: 64
04:24:11:WU00:FS00:0xa7: Mode: Release
04:24:11:WU00:FS00:0xa7:************************************ Build *************************************
04:24:11:WU00:FS00:0xa7: SIMD: avx_256
04:24:11:WU00:FS00:0xa7:********************************************************************************
04:24:11:WU00:FS00:0xa7:Project: 16417 (Run 1642, Clone 2, Gen 2)
04:24:11:WU00:FS00:0xa7:Unit: 0x0000000396880e6e5e8a60945e03cfee
04:24:11:WU00:FS00:0xa7:Reading tar file core.xml
04:24:11:WU00:FS00:0xa7:Reading tar file frame2.tpr
04:24:11:WU00:FS00:0xa7:Digital signatures verified
04:24:11:WU00:FS00:0xa7:Calling: mdrun -s frame2.tpr -o frame2.trr -x frame2.xtc -cpt 15 -nt 48
04:24:11:WU00:FS00:0xa7:Steps: first=500000 total=250000
04:24:11:WU00:FS00:0xa7:ERROR:
04:24:11:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
04:24:11:WU00:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
04:24:11:WU00: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
04:24:11:WU00:FS00:0xa7:ERROR:
04:24:11:WU00:FS00:0xa7:ERROR:Fatal error:
04:24:11:WU00:FS00:0xa7:ERROR:There is no domain decomposition for 40 ranks that is compatible with the given box and a minimum cell size of 1.4227 nm
04:24:11:WU00:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
04:24:11:WU00:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
04:24:11:WU00:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
04:24:11:WU00:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
04:24:11:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
04:24:12:WU01:FS00:Upload complete
04:24:12:WU01:FS00:Server responded WORK_ACK (400)
04:24:12:WU01:FS00:Final credit estimate, 16533.00 points
04:24:12:WU01:FS00:Cleaning up
04:24:16:WU00:FS00:0xa7:WARNING:Unexpected exit() call
04:24:16:WU00:FS00:0xa7:WARNING:Unexpected exit from science code
04:24:16:WU00:FS00:0xa7:Saving result file ../logfile_01.txt
04:24:16:WU00:FS00:0xa7:Saving result file md.log
04:24:16:WU00:FS00:0xa7:Saving result file science.log
04:24:17:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
04:25:11:WU00:FS00:Starting
04:25:11:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 00 -suffix 01 -version 705 -lifeline 1949 -checkpoint 15 -np 48
04:25:11:WU00:FS00:Started FahCore on PID 1194
04:25:11:WU00:FS00:Core PID:1198
04:25:11:WU00:FS00:FahCore 0xa7 started
04:25:11:WU00:FS00:0xa7:*********************** Log Started 2020-04-06T04:25:11Z ***********************
…
06:52:15:WU00:FS00:0xa7:*********************** Log Started 2020-04-06T06:52:15Z ***********************
06:52:15:WU00:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
06:52:15:WU00:FS00:0xa7: Type: 0xa7
06:52:15:WU00:FS00:0xa7: Core: Gromacs
06:52:15:WU00:FS00:0xa7: Args: -dir 00 -suffix 01 -version 705 -lifeline 10446 -checkpoint 15 -np
06:52:15:WU00:FS00:0xa7: 48
06:52:15:WU00:FS00:0xa7:************************************ CBang *************************************
06:52:15:WU00:FS00:0xa7: Date: Nov 5 2019
06:52:15:WU00:FS00:0xa7: Time: 06:06:57
06:52:15:WU00:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
06:52:15:WU00:FS00:0xa7: Branch: master
06:52:15:WU00:FS00:0xa7: Compiler: GNU 8.3.0
06:52:15:WU00:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
06:52:15:WU00:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
06:52:15:WU00:FS00:0xa7: Bits: 64
06:52:15:WU00:FS00:0xa7: Mode: Release
06:52:15:WU00:FS00:0xa7:************************************ System ************************************
06:52:15:WU00:FS00:0xa7: CPU: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
06:52:15:WU00:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
06:52:15:WU00:FS00:0xa7: CPUs: 48
06:52:15:WU00:FS00:0xa7: Memory: 62.80GiB
06:52:15:WU00:FS00:0xa7:Free Memory: 59.20GiB
06:52:15:WU00:FS00:0xa7: Threads: POSIX_THREADS
06:52:15:WU00:FS00:0xa7: OS Version: 5.3
06:52:15:WU00:FS00:0xa7:Has Battery: false
06:52:15:WU00:FS00:0xa7: On Battery: false
06:52:15:WU00:FS00:0xa7: UTC Offset: -5
06:52:15:WU00:FS00:0xa7: PID: 10450
06:52:15:WU00:FS00:0xa7: CWD: /var/lib/fahclient/work
06:52:15:WU00:FS00:0xa7:******************************** Build - libFAH ********************************
06:52:15:WU00:FS00:0xa7: Version: 0.0.18
06:52:15:WU00:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
06:52:15:WU00:FS00:0xa7: Copyright: 2019 foldingathome.org
06:52:15:WU00:FS00:0xa7: Homepage: https://foldingathome.org/
06:52:15:WU00:FS00:0xa7: Date: Nov 5 2019
06:52:15:WU00:FS00:0xa7: Time: 06:13:26
06:52:15:WU00:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
06:52:15:WU00:FS00:0xa7: Branch: master
06:52:15:WU00:FS00:0xa7: Compiler: GNU 8.3.0
06:52:15:WU00:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
06:52:15:WU00:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
06:52:15:WU00:FS00:0xa7: Bits: 64
06:52:15:WU00:FS00:0xa7: Mode: Release
06:52:15:WU00:FS00:0xa7:************************************ Build *************************************
06:52:15:WU00:FS00:0xa7: SIMD: avx_256
06:52:15:WU00:FS00:0xa7:********************************************************************************
06:52:15:WU00:FS00:0xa7:Project: 16417 (Run 1642, Clone 2, Gen 2)
06:52:15:WU00:FS00:0xa7:Unit: 0x0000000396880e6e5e8a60945e03cfee
06:52:15:WU00:FS00:0xa7:Reading tar file core.xml
06:52:15:WU00:FS00:0xa7:Reading tar file frame2.tpr
06:52:15:WU00:FS00:0xa7:Digital signatures verified
06:52:15:WU00:FS00:0xa7:Calling: mdrun -s frame2.tpr -o frame2.trr -x frame2.xtc -cpt 15 -nt 48
06:52:15:WU00:FS00:0xa7:Steps: first=500000 total=250000
06:52:15:WU00:FS00:0xa7:ERROR:
06:52:15:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
06:52:15:WU00:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
06:52:15:WU00: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
06:52:15:WU00:FS00:0xa7:ERROR:
06:52:15:WU00:FS00:0xa7:ERROR:Fatal error:
06:52:15:WU00:FS00:0xa7:ERROR:There is no domain decomposition for 40 ranks that is compatible with the given box and a minimum cell size of 1.4227 nm
06:52:15:WU00:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
06:52:15:WU00:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
06:52:15:WU00:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
06:52:15:WU00:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
06:52:15:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
06:52:20:WU00:FS00:0xa7:WARNING:Unexpected exit() call
06:52:20:WU00:FS00:0xa7:WARNING:Unexpected exit from science code
06:52:20:WU00:FS00:0xa7:Saving result file ../logfile_01.txt
06:52:20:WU00:FS00:0xa7:Saving result file md.log
06:52:20:WU00:FS00:0xa7:Saving result file science.log
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
06:52:20:WU00:FS00:0xa7:Caught signal SIGSEGV(11) on PID 10450
…
This repeats for 37 mb of log file consuming 4 days. Hope this helps.
Re: Issues, perhaps bad WU? - 16417
Posted: Thu Apr 09, 2020 8:59 pm
by Roadpower
Roadpower wrote:I just woke up so posting this and will continue to wake up so I can digest this better.
The following is md.log
Code: Select all
Log file opened on Thu Apr 9 15:24:29 2020
Host: omitted pid: 6496 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 = 250000
init-step = 5500000
simulation-part = 1
comm-mode = Linear
nstcomm = 5
bd-fric = 0
ld-seed = 620990457
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 125000
nstvout = 125000
nstfout = 0
nstlog = 0
nstcalcenergy = 0
nstenergy = 2500
nstxout-compressed = 2500
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 = 80
fourier-ny = 80
fourier-nz = 80
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 = TRUE
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: 95890
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 166 174
multi-body bonded interactions: 0.419 nm, Proper Dih., atoms 166 174
Minimum cell size due to bonded interactions: 0.461 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.166 nm
Estimated maximum distance required for P-LINCS: 1.166 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 1.457 nm
The maximum allowed number of cells is: X 4 Y 4 Z 4
The CPU hang up appears to be project 13833. It cycles right at the top. Projected time of completion five days.
Code: Select all
20:16:30:WU01:FS00:0xa7:************************************ Build *************************************
20:16:30:WU01:FS00:0xa7: SIMD: avx_256
20:16:30:WU01:FS00:0xa7:********************************************************************************
20:16:30:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 1548, Gen 22)
20:16:30:WU01:FS00:0xa7:Unit: 0x0000001e80fccb095e6e5656a6e3070c
20:16:30:WU01:FS00:0xa7:Reading tar file core.xml
20:16:30:WU01:FS00:0xa7:Reading tar file frame22.tpr
20:16:30:WU01:FS00:0xa7:Digital signatures verified
20:16:30:WU01:FS00:0xa7:Calling: mdrun -s frame22.tpr -o frame22.trr -x frame22.xtc -cpt 15 -nt 15
20:16:30:WU01:FS00:0xa7:Steps: first=5500000 total=250000
20:16:30:WU01:FS00:0xa7:ERROR:
20:16:30:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
20:16:30:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
20:16:30: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
20:16:30:WU01:FS00:0xa7:ERROR:
20:16:30:WU01:FS00:0xa7:ERROR:Fatal error:
20:16:30: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 1.45733 nm
20:16:30:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
20:16:30:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
20:16:30:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
20:16:30:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
20:16:30:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
20:16:35:WU01:FS00:0xa7:WARNING:Unexpected exit() call
20:16:35:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
20:16:35:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
20:16:35:WU01:FS00:0xa7:Saving result file md.log
20:16:35:WU01:FS00:0xa7:Saving result file science.log
20:16:35:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
I'm thinking to remove CPU slot, wait a while and then add it back in to clear the stuck project.
Okay I wasn't ready to read through and digest this thread but getting the gist of the issue I lowered my CPU thread count from -01 (FAHClient determined) down to 8 threads, and now the project is running. I'm not sure how many hours it was stuck on that as I was sleeping but I don't think it matters that much. I'm happy the CPU is back to work and that this wasn't a difficult issue to resolve.
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 10:02 am
by rogermateer
My FAH Client seems to be stuck trying to run PRCG 13833 (0,2146,7).
It repeatedly starts, makes a couple of % progress, and then stops (perhaps crashing).
I'm on a Linux i7-5820K hexacore with 12 threads.
According to /var/lib/fahclient/work/01/01/md.log, it seems to be using 10 threads:
Code: Select all
Initializing Domain Decomposition on 10 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: 0.423 nm, LJ-14, atoms 166 174
multi-body bonded interactions: 0.423 nm, Proper Dih., atoms 166 174
Minimum cell size due to bonded interactions: 0.465 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.166 nm
Estimated maximum distance required for P-LINCS: 1.166 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 10 cells with a minimum initial size of 1.457 nm
The maximum allowed number of cells is: X 4 Y 4 Z 4
I've kind of read through this posting, but i don't seem to have access to an
mdrun executable to change the thread count to 8 (which it seems would be more stable in my situation).
Is there a way to change the thread count from the FAHControl GUI?
Or where would i get the
mdrun executable?
I want to contribute, but it's frustrating when the system gets gummed up like this.
(This is the first time it's happened to me though.)
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 10:28 am
by PantherX
Welcome to the F@H Forum rogermateer,
You can easily change the CPU value from FAHControl. You need to go to Configure -> Slots -> CPU Slot -> Edit -> Change the value to 8 -> Click OK -> Click Save and that's it.
You may want to post the start of the log which has the system configuration so we can see if there's anything that can be optimized on your system.
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 11:15 am
by rogermateer
thanks, PantherX
i have set my cpu slot to use 8 threads, and it seems to be running better now.
here is a failed log file:
Code: Select all
*********************** Log Started 2020-04-11T11:06:33Z ***********************
************************** Gromacs Folding@home Core ***************************
Type: 0xa7
Core: Gromacs
Args: -dir 01 -suffix 01 -version 705 -lifeline 14140 -checkpoint 15 -np
11
************************************ 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) i7-5820K CPU @ 3.30GHz
CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
CPUs: 12
Memory: 15.56GiB
Free Memory: 4.96GiB
Threads: POSIX_THREADS
OS Version: 4.15
Has Battery: false
On Battery: false
UTC Offset: 2
PID: 14144
CWD: /var/lib/fahclient/work
******************************** Build - libFAH ********************************
Version: 0.0.18
Author: Joseph Coffland <joseph@cauldrondevelopment.com>
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: 13833 (Run 0, Clone 2146, Gen 7)
Unit: 0x0000000b80fccb095e6e562caf863c2a
Reading tar file core.xml
Reading tar file frame7.tpr
Digital signatures verified
Reducing thread count from 11 to 10 to avoid domain decomposition by a prime number > 3
Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 10
Steps: first=1750000 total=250000
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 10 ranks that is compatible with the given box and a minimum cell size of 1.45733 nm
ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
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
and here is the new log file so far (after the adjustment):
Code: Select all
*********************** Log Started 2020-04-11T11:07:33Z ***********************
************************** Gromacs Folding@home Core ***************************
Type: 0xa7
Core: Gromacs
Args: -dir 01 -suffix 01 -version 705 -lifeline 26749 -checkpoint 15 -np
8
************************************ 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) i7-5820K CPU @ 3.30GHz
CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
CPUs: 12
Memory: 15.56GiB
Free Memory: 4.95GiB
Threads: POSIX_THREADS
OS Version: 4.15
Has Battery: false
On Battery: false
UTC Offset: 2
PID: 26753
CWD: /var/lib/fahclient/work
******************************** Build - libFAH ********************************
Version: 0.0.18
Author: Joseph Coffland <joseph@cauldrondevelopment.com>
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: 13833 (Run 0, Clone 2146, Gen 7)
Unit: 0x0000000b80fccb095e6e562caf863c2a
Reading tar file core.xml
Reading tar file frame7.tpr
Digital signatures verified
Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 8
Steps: first=1750000 total=250000
Completed 1 out of 250000 steps (0%)
Completed 2500 out of 250000 steps (1%)
Completed 5000 out of 250000 steps (2%)
Completed 7500 out of 250000 steps (3%)
Completed 10000 out of 250000 steps (4%)
Completed 12500 out of 250000 steps (5%)
Completed 15000 out of 250000 steps (6%)
Completed 17500 out of 250000 steps (7%)
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 11:44 am
by PantherX
Sorry, I forgot to clarify, when I mentioned the start of the log, I meant the log file which is seen in FAHControl, not the md.log file. Here's what the starting of the log file would look like:
Code: Select all
*********************** Log Started 2020-04-11T03:29:02Z ***********************
03:29:02:************************* Folding@home Client *************************
03:29:02: Website: https://foldingathome.org/
03:29:02: Copyright: (c) 2009-2018 foldingathome.org
03:29:02: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
03:29:02: Args:
03:29:02: Config: C:\Users\PantherX-H\AppData\Roaming\FAHClient\config.xml
03:29:02:******************************** Build ********************************
03:29:02: Version: 7.5.1
03:29:02: Date: May 11 2018
03:29:02: Time: 13:06:32
03:29:02: Repository: Git
03:29:02: Revision: 4705bf53c635f88b8fe85af7675557e15d491ff0
03:29:02: Branch: master
03:29:02: Compiler: Visual C++ 2008
03:29:02: Options: /TP /nologo /EHa /wd4297 /wd4103 /Ox /MT
03:29:02: Platform: win32 10
03:29:02: Bits: 32
03:29:02: Mode: Release
03:29:02:******************************* System ********************************
03:29:02: CPU: Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
03:29:02: CPU ID: GenuineIntel Family 6 Model 94 Stepping 3
03:29:02: CPUs: 8
03:29:02: Memory: 31.94GiB
03:29:02: Free Memory: 27.89GiB
03:29:02: Threads: WINDOWS_THREADS
03:29:02: OS Version: 6.2
03:29:02: Has Battery: false
03:29:02: On Battery: false
03:29:02: UTC Offset: 12
03:29:02: PID: 1532
03:29:02: CWD: C:\Users\PantherX-H\AppData\Roaming\FAHClient
03:29:02: OS: Windows 10 Enterprise
03:29:02: OS Arch: AMD64
03:29:02: GPUs: 1
03:29:02: GPU 0: Bus:1 Slot:0 Func:0 NVIDIA:8 GP102 [GeForce GTX 1080 Ti] 11380
03:29:02: CUDA Device 0: Platform:0 Device:0 Bus:1 Slot:0 Compute:6.1 Driver:10.2
03:29:02:OpenCL Device 0: Platform:0 Device:0 Bus:1 Slot:0 Compute:1.2 Driver:442.19
03:29:02: Win32 Service: false
03:29:02:***********************************************************************
03:29:02:<config>
03:29:02: <!-- Network -->
03:29:02: <proxy v=':8080'/>
03:29:02:
03:29:02: <!-- Slot Control -->
03:29:02: <power v='full'/>
03:29:02:
03:29:02: <!-- User Information -->
03:29:02: <passkey v='********************************'/>
03:29:02: <team v='69411'/>
03:29:02: <user v='PantherX'/>
03:29:02:
03:29:02: <!-- Folding Slots -->
03:29:02: <slot id='1' type='GPU'>
03:29:02: <next-unit-percentage v='100'/>
03:29:02: <pause-on-start v='true'/>
03:29:02: </slot>
03:29:02:</config>
03:29:02:Trying to access database...
03:29:02:Successfully acquired database lock
03:29:02:Enabled folding slot 01: PAUSED gpu:0:GP102 [GeForce GTX 1080 Ti] 11380 (by user)
03:30:05:FS01:Unpaused
03:30:05:WU01:FS01:Starting
03:30:05:WU01:FS01:Running FahCore: "C:\Program Files (x86)\FAHClient/FAHCoreWrapper.exe" C:\Users\PantherX-H\AppData\Roaming\FAHClient\cores/cores.foldingathome.org/v7/win/64bit/Core_22.fah/FahCore_22.exe -dir 01 -suffix 01 -version 705 -lifeline 1532 -checkpoint 15 -gpu-vendor nvidia -opencl-platform 0 -opencl-device 0 -cuda-device 0 -gpu 0
03:30:05:WU01:FS01:Started FahCore on PID 8052
03:30:06:WU01:FS01:Core PID:1800
03:30:06:WU01:FS01:FahCore 0x22 started
03:30:06:WU01:FS01:0x22:*********************** Log Started 2020-04-11T03:30:06Z ***********************
03:30:06:WU01:FS01:0x22:*************************** Core22 Folding@home Core ***************************
03:30:06:WU01:FS01:0x22: Type: 0x22
03:30:06:WU01:FS01:0x22: Core: Core22
03:30:06:WU01:FS01:0x22: Website: https://foldingathome.org/
03:30:06:WU01:FS01:0x22: Copyright: (c) 2009-2018 foldingathome.org
03:30:06:WU01:FS01:0x22: Author: John Chodera <john.chodera@choderalab.org> and Rafal Wiewiora
03:30:06:WU01:FS01:0x22: <rafal.wiewiora@choderalab.org>
03:30:06:WU01:FS01:0x22: Args: -dir 01 -suffix 01 -version 705 -lifeline 8052 -checkpoint 15
03:30:06:WU01:FS01:0x22: -gpu-vendor nvidia -opencl-platform 0 -opencl-device 0 -cuda-device
03:30:06:WU01:FS01:0x22: 0 -gpu 0
03:30:06:WU01:FS01:0x22: Config: <none>
03:30:06:WU01:FS01:0x22:************************************ Build *************************************
03:30:06:WU01:FS01:0x22: Version: 0.0.2
03:30:06:WU01:FS01:0x22: Date: Dec 6 2019
03:30:06:WU01:FS01:0x22: Time: 21:30:31
03:30:06:WU01:FS01:0x22: Repository: Git
03:30:06:WU01:FS01:0x22: Revision: abeb39247cc72df5af0f63723edafadb23d5dfbe
03:30:06:WU01:FS01:0x22: Branch: HEAD
03:30:06:WU01:FS01:0x22: Compiler: Visual C++ 2008
03:30:06:WU01:FS01:0x22: Options: /TP /nologo /EHa /wd4297 /wd4103 /Ox /MT
03:30:06:WU01:FS01:0x22: Platform: win32 10
03:30:06:WU01:FS01:0x22: Bits: 64
03:30:06:WU01:FS01:0x22: Mode: Release
03:30:06:WU01:FS01:0x22:************************************ System ************************************
03:30:06:WU01:FS01:0x22: CPU: Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
03:30:06:WU01:FS01:0x22: CPU ID: GenuineIntel Family 6 Model 94 Stepping 3
03:30:06:WU01:FS01:0x22: CPUs: 8
03:30:06:WU01:FS01:0x22: Memory: 31.94GiB
03:30:06:WU01:FS01:0x22:Free Memory: 27.29GiB
03:30:06:WU01:FS01:0x22: Threads: WINDOWS_THREADS
03:30:06:WU01:FS01:0x22: OS Version: 6.2
03:30:06:WU01:FS01:0x22:Has Battery: false
03:30:06:WU01:FS01:0x22: On Battery: false
03:30:06:WU01:FS01:0x22: UTC Offset: 12
03:30:06:WU01:FS01:0x22: PID: 1800
03:30:06:WU01:FS01:0x22: CWD: C:\Users\PantherX-H\AppData\Roaming\FAHClient\work
03:30:06:WU01:FS01:0x22: OS: Windows 10 Pro
03:30:06:WU01:FS01:0x22: OS Arch: AMD64
03:30:06:WU01:FS01:0x22:********************************************************************************
03:30:06:WU01:FS01:0x22:Project: 11761 (Run 0, Clone 7538, Gen 10)
03:30:06:WU01:FS01:0x22:Unit: 0x0000001a80fccb0a5e7001958353bbf1
03:30:06:WU01:FS01:0x22:Digital signatures verified
03:30:06:WU01:FS01:0x22:Folding@home GPU Core22 Folding@home Core
03:30:06:WU01:FS01:0x22:Version 0.0.2
03:30:06:WU01:FS01:0x22: Found a checkpoint file
03:30:11:WU01:FS01:0x22:Completed 1050000 out of 2000000 steps (52%)
03:30:11:WU01:FS01:0x22:Temperature control disabled. Requirements: single Nvidia GPU, tmax must be < 110 and twait >= 900
03:30:36:WU01:FS01:0x22:Completed 1060000 out of 2000000 steps (53%)
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 12:12 pm
by rogermateer
I don't think it contains any information substantially different from the logs i have already shown you.
It doesn't look the same as what you've quoted above; maybe there's a difference between how Windows vs Linux clients log?
It also seems truncated (I have done ballpark 10 WUs). I also had to truncate it further (removing duplicate lines of the following form from the top to fit the 60000 character posting limit...)
Code: Select all
11:00:38:WU01:FS00:0xa7:Caught signal SIGSEGV(11) on PID 2566
But here is the log visible in my FAHControl:
Code: Select all
11:00:38:WU01:FS00:0xa7:Caught signal SIGSEGV(11) on PID 2566
...
<<<many identical lines cut>>>
...
11:00:38:WU01:FS00:0xa7:Caught signal SIGSEGV(11) on PID 2566
11:00:38:WU01:FS00:0xa7:Caught signal SIGSEGV(11) on PID 2566
11:00:38:WU01:FS00:0xa7:Caught signal SIGSEGV(11) on PID 2566
11:00:38:WU01:FS00:0xa7:Caught signal SIGSEGV(11) on PID 2566
11:00:38:WU01:FS00:0xa7:Caught signal SIGSEGV(11) on PID 2566
11:00:38:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
11:01:33:WU01:FS00:Starting
11:01:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:01:33:WU01:FS00:Removing old file './work/01/logfile_01-20200411-102932.txt'
11:01:33:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 705 -lifeline 1927 -checkpoint 15 -np 11
11:01:33:WU01:FS00:Started FahCore on PID 4924
11:01:33:WU01:FS00:Core PID:4931
11:01:33:WU01:FS00:FahCore 0xa7 started
11:01:33:WU01:FS00:0xa7:*********************** Log Started 2020-04-11T11:01:33Z ***********************
11:01:33:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
11:01:33:WU01:FS00:0xa7: Type: 0xa7
11:01:33:WU01:FS00:0xa7: Core: Gromacs
11:01:33:WU01:FS00:0xa7: Args: -dir 01 -suffix 01 -version 705 -lifeline 4924 -checkpoint 15 -np
11:01:33:WU01:FS00:0xa7: 11
11:01:33:WU01:FS00:0xa7:************************************ CBang *************************************
11:01:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:01:33:WU01:FS00:0xa7: Time: 06:06:57
11:01:33:WU01:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
11:01:33:WU01:FS00:0xa7: Branch: master
11:01:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:01:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
11:01:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:01:33:WU01:FS00:0xa7: Bits: 64
11:01:33:WU01:FS00:0xa7: Mode: Release
11:01:33:WU01:FS00:0xa7:************************************ System ************************************
11:01:33:WU01:FS00:0xa7: CPU: Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
11:01:33:WU01:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
11:01:33:WU01:FS00:0xa7: CPUs: 12
11:01:33:WU01:FS00:0xa7: Memory: 15.56GiB
11:01:33:WU01:FS00:0xa7:Free Memory: 5.00GiB
11:01:33:WU01:FS00:0xa7: Threads: POSIX_THREADS
11:01:33:WU01:FS00:0xa7: OS Version: 4.15
11:01:33:WU01:FS00:0xa7:Has Battery: false
11:01:33:WU01:FS00:0xa7: On Battery: false
11:01:33:WU01:FS00:0xa7: UTC Offset: 2
11:01:33:WU01:FS00:0xa7: PID: 4931
11:01:33:WU01:FS00:0xa7: CWD: /var/lib/fahclient/work
11:01:33:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
11:01:33:WU01:FS00:0xa7: Version: 0.0.18
11:01:33:WU01:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
11:01:33:WU01:FS00:0xa7: Copyright: 2019 foldingathome.org
11:01:33:WU01:FS00:0xa7: Homepage: https://foldingathome.org/
11:01:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:01:33:WU01:FS00:0xa7: Time: 06:13:26
11:01:33:WU01:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
11:01:33:WU01:FS00:0xa7: Branch: master
11:01:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:01:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
11:01:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:01:33:WU01:FS00:0xa7: Bits: 64
11:01:33:WU01:FS00:0xa7: Mode: Release
11:01:33:WU01:FS00:0xa7:************************************ Build *************************************
11:01:33:WU01:FS00:0xa7: SIMD: avx_256
11:01:33:WU01:FS00:0xa7:********************************************************************************
11:01:33:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 2146, Gen 7)
11:01:33:WU01:FS00:0xa7:Unit: 0x0000000b80fccb095e6e562caf863c2a
11:01:33:WU01:FS00:0xa7:Reading tar file core.xml
11:01:33:WU01:FS00:0xa7:Reading tar file frame7.tpr
11:01:33:WU01:FS00:0xa7:Digital signatures verified
11:01:33:WU01:FS00:0xa7:Reducing thread count from 11 to 10 to avoid domain decomposition by a prime number > 3
11:01:33:WU01:FS00:0xa7:Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 10
11:01:33:WU01:FS00:0xa7:Steps: first=1750000 total=250000
11:01:33:WU01:FS00:0xa7:ERROR:
11:01:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:01:33:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
11:01:33: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
11:01:33:WU01:FS00:0xa7:ERROR:
11:01:33:WU01:FS00:0xa7:ERROR:Fatal error:
11:01:33:WU01:FS00:0xa7:ERROR:There is no domain decomposition for 10 ranks that is compatible with the given box and a minimum cell size of 1.45733 nm
11:01:33:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
11:01:33:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
11:01:33:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
11:01:33:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
11:01:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:01:38:WU01:FS00:0xa7:WARNING:Unexpected exit() call
11:01:38:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
11:01:38:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
11:01:38:WU01:FS00:0xa7:Saving result file md.log
11:01:38:WU01:FS00:0xa7:Saving result file science.log
11:01:38:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
11:02:33:WU01:FS00:Starting
11:02:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:02:33:WU01:FS00:Removing old file './work/01/logfile_01-20200411-103032.txt'
11:02:33:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 705 -lifeline 1927 -checkpoint 15 -np 11
11:02:33:WU01:FS00:Started FahCore on PID 32177
11:02:33:WU01:FS00:Core PID:32184
11:02:33:WU01:FS00:FahCore 0xa7 started
11:02:33:WU01:FS00:0xa7:*********************** Log Started 2020-04-11T11:02:33Z ***********************
11:02:33:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
11:02:33:WU01:FS00:0xa7: Type: 0xa7
11:02:33:WU01:FS00:0xa7: Core: Gromacs
11:02:33:WU01:FS00:0xa7: Args: -dir 01 -suffix 01 -version 705 -lifeline 32177 -checkpoint 15 -np
11:02:33:WU01:FS00:0xa7: 11
11:02:33:WU01:FS00:0xa7:************************************ CBang *************************************
11:02:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:02:33:WU01:FS00:0xa7: Time: 06:06:57
11:02:33:WU01:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
11:02:33:WU01:FS00:0xa7: Branch: master
11:02:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:02:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
11:02:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:02:33:WU01:FS00:0xa7: Bits: 64
11:02:33:WU01:FS00:0xa7: Mode: Release
11:02:33:WU01:FS00:0xa7:************************************ System ************************************
11:02:33:WU01:FS00:0xa7: CPU: Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
11:02:33:WU01:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
11:02:33:WU01:FS00:0xa7: CPUs: 12
11:02:33:WU01:FS00:0xa7: Memory: 15.56GiB
11:02:33:WU01:FS00:0xa7:Free Memory: 5.00GiB
11:02:33:WU01:FS00:0xa7: Threads: POSIX_THREADS
11:02:33:WU01:FS00:0xa7: OS Version: 4.15
11:02:33:WU01:FS00:0xa7:Has Battery: false
11:02:33:WU01:FS00:0xa7: On Battery: false
11:02:33:WU01:FS00:0xa7: UTC Offset: 2
11:02:33:WU01:FS00:0xa7: PID: 32184
11:02:33:WU01:FS00:0xa7: CWD: /var/lib/fahclient/work
11:02:33:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
11:02:33:WU01:FS00:0xa7: Version: 0.0.18
11:02:33:WU01:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
11:02:33:WU01:FS00:0xa7: Copyright: 2019 foldingathome.org
11:02:33:WU01:FS00:0xa7: Homepage: https://foldingathome.org/
11:02:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:02:33:WU01:FS00:0xa7: Time: 06:13:26
11:02:33:WU01:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
11:02:33:WU01:FS00:0xa7: Branch: master
11:02:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:02:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
11:02:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:02:33:WU01:FS00:0xa7: Bits: 64
11:02:33:WU01:FS00:0xa7: Mode: Release
11:02:33:WU01:FS00:0xa7:************************************ Build *************************************
11:02:33:WU01:FS00:0xa7: SIMD: avx_256
11:02:33:WU01:FS00:0xa7:********************************************************************************
11:02:33:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 2146, Gen 7)
11:02:33:WU01:FS00:0xa7:Unit: 0x0000000b80fccb095e6e562caf863c2a
11:02:33:WU01:FS00:0xa7:Reading tar file core.xml
11:02:33:WU01:FS00:0xa7:Reading tar file frame7.tpr
11:02:33:WU01:FS00:0xa7:Digital signatures verified
11:02:33:WU01:FS00:0xa7:Reducing thread count from 11 to 10 to avoid domain decomposition by a prime number > 3
11:02:33:WU01:FS00:0xa7:Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 10
11:02:33:WU01:FS00:0xa7:Steps: first=1750000 total=250000
11:02:33:WU01:FS00:0xa7:ERROR:
11:02:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:02:33:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
11:02:33: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
11:02:33:WU01:FS00:0xa7:ERROR:
11:02:33:WU01:FS00:0xa7:ERROR:Fatal error:
11:02:33:WU01:FS00:0xa7:ERROR:There is no domain decomposition for 10 ranks that is compatible with the given box and a minimum cell size of 1.45733 nm
11:02:33:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
11:02:33:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
11:02:33:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
11:02:33:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
11:02:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:02:38:WU01:FS00:0xa7:WARNING:Unexpected exit() call
11:02:38:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
11:02:38:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
11:02:38:WU01:FS00:0xa7:Saving result file md.log
11:02:38:WU01:FS00:0xa7:Saving result file science.log
11:02:38:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
11:03:33:WU01:FS00:Starting
11:03:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:03:33:WU01:FS00:Removing old file './work/01/logfile_01-20200411-103132.txt'
11:03:33:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 705 -lifeline 1927 -checkpoint 15 -np 11
11:03:33:WU01:FS00:Started FahCore on PID 9366
11:03:33:WU01:FS00:Core PID:9370
11:03:33:WU01:FS00:FahCore 0xa7 started
11:03:33:WU01:FS00:0xa7:*********************** Log Started 2020-04-11T11:03:33Z ***********************
11:03:33:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
11:03:33:WU01:FS00:0xa7: Type: 0xa7
11:03:33:WU01:FS00:0xa7: Core: Gromacs
11:03:33:WU01:FS00:0xa7: Args: -dir 01 -suffix 01 -version 705 -lifeline 9366 -checkpoint 15 -np
11:03:33:WU01:FS00:0xa7: 11
11:03:33:WU01:FS00:0xa7:************************************ CBang *************************************
11:03:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:03:33:WU01:FS00:0xa7: Time: 06:06:57
11:03:33:WU01:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
11:03:33:WU01:FS00:0xa7: Branch: master
11:03:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:03:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
11:03:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:03:33:WU01:FS00:0xa7: Bits: 64
11:03:33:WU01:FS00:0xa7: Mode: Release
11:03:33:WU01:FS00:0xa7:************************************ System ************************************
11:03:33:WU01:FS00:0xa7: CPU: Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
11:03:33:WU01:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
11:03:33:WU01:FS00:0xa7: CPUs: 12
11:03:33:WU01:FS00:0xa7: Memory: 15.56GiB
11:03:33:WU01:FS00:0xa7:Free Memory: 5.00GiB
11:03:33:WU01:FS00:0xa7: Threads: POSIX_THREADS
11:03:33:WU01:FS00:0xa7: OS Version: 4.15
11:03:33:WU01:FS00:0xa7:Has Battery: false
11:03:33:WU01:FS00:0xa7: On Battery: false
11:03:33:WU01:FS00:0xa7: UTC Offset: 2
11:03:33:WU01:FS00:0xa7: PID: 9370
11:03:33:WU01:FS00:0xa7: CWD: /var/lib/fahclient/work
11:03:33:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
11:03:33:WU01:FS00:0xa7: Version: 0.0.18
11:03:33:WU01:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
11:03:33:WU01:FS00:0xa7: Copyright: 2019 foldingathome.org
11:03:33:WU01:FS00:0xa7: Homepage: https://foldingathome.org/
11:03:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:03:33:WU01:FS00:0xa7: Time: 06:13:26
11:03:33:WU01:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
11:03:33:WU01:FS00:0xa7: Branch: master
11:03:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:03:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
11:03:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:03:33:WU01:FS00:0xa7: Bits: 64
11:03:33:WU01:FS00:0xa7: Mode: Release
11:03:33:WU01:FS00:0xa7:************************************ Build *************************************
11:03:33:WU01:FS00:0xa7: SIMD: avx_256
11:03:33:WU01:FS00:0xa7:********************************************************************************
11:03:33:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 2146, Gen 7)
11:03:33:WU01:FS00:0xa7:Unit: 0x0000000b80fccb095e6e562caf863c2a
11:03:33:WU01:FS00:0xa7:Reading tar file core.xml
11:03:33:WU01:FS00:0xa7:Reading tar file frame7.tpr
11:03:33:WU01:FS00:0xa7:Digital signatures verified
11:03:33:WU01:FS00:0xa7:Reducing thread count from 11 to 10 to avoid domain decomposition by a prime number > 3
11:03:33:WU01:FS00:0xa7:Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 10
11:03:33:WU01:FS00:0xa7:Steps: first=1750000 total=250000
11:03:33:WU01:FS00:0xa7:ERROR:
11:03:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:03:33:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
11:03:33: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
11:03:33:WU01:FS00:0xa7:ERROR:
11:03:33:WU01:FS00:0xa7:ERROR:Fatal error:
11:03:33:WU01:FS00:0xa7:ERROR:There is no domain decomposition for 10 ranks that is compatible with the given box and a minimum cell size of 1.45733 nm
11:03:33:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
11:03:33:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
11:03:33:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
11:03:33:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
11:03:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:03:38:WU01:FS00:0xa7:WARNING:Unexpected exit() call
11:03:38:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
11:03:38:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
11:03:38:WU01:FS00:0xa7:Saving result file md.log
11:03:38:WU01:FS00:0xa7:Saving result file science.log
11:03:38:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
11:04:33:WU01:FS00:Starting
11:04:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:04:33:WU01:FS00:Removing old file './work/01/logfile_01-20200411-103232.txt'
11:04:33:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 705 -lifeline 1927 -checkpoint 15 -np 11
11:04:33:WU01:FS00:Started FahCore on PID 13777
11:04:33:WU01:FS00:Core PID:13781
11:04:33:WU01:FS00:FahCore 0xa7 started
11:04:33:WU01:FS00:0xa7:*********************** Log Started 2020-04-11T11:04:33Z ***********************
11:04:33:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
11:04:33:WU01:FS00:0xa7: Type: 0xa7
11:04:33:WU01:FS00:0xa7: Core: Gromacs
11:04:33:WU01:FS00:0xa7: Args: -dir 01 -suffix 01 -version 705 -lifeline 13777 -checkpoint 15 -np
11:04:33:WU01:FS00:0xa7: 11
11:04:33:WU01:FS00:0xa7:************************************ CBang *************************************
11:04:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:04:33:WU01:FS00:0xa7: Time: 06:06:57
11:04:33:WU01:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
11:04:33:WU01:FS00:0xa7: Branch: master
11:04:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:04:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
11:04:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:04:33:WU01:FS00:0xa7: Bits: 64
11:04:33:WU01:FS00:0xa7: Mode: Release
11:04:33:WU01:FS00:0xa7:************************************ System ************************************
11:04:33:WU01:FS00:0xa7: CPU: Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
11:04:33:WU01:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
11:04:33:WU01:FS00:0xa7: CPUs: 12
11:04:33:WU01:FS00:0xa7: Memory: 15.56GiB
11:04:33:WU01:FS00:0xa7:Free Memory: 5.00GiB
11:04:33:WU01:FS00:0xa7: Threads: POSIX_THREADS
11:04:33:WU01:FS00:0xa7: OS Version: 4.15
11:04:33:WU01:FS00:0xa7:Has Battery: false
11:04:33:WU01:FS00:0xa7: On Battery: false
11:04:33:WU01:FS00:0xa7: UTC Offset: 2
11:04:33:WU01:FS00:0xa7: PID: 13781
11:04:33:WU01:FS00:0xa7: CWD: /var/lib/fahclient/work
11:04:33:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
11:04:33:WU01:FS00:0xa7: Version: 0.0.18
11:04:33:WU01:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
11:04:33:WU01:FS00:0xa7: Copyright: 2019 foldingathome.org
11:04:33:WU01:FS00:0xa7: Homepage: https://foldingathome.org/
11:04:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:04:33:WU01:FS00:0xa7: Time: 06:13:26
11:04:33:WU01:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
11:04:33:WU01:FS00:0xa7: Branch: master
11:04:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:04:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
11:04:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:04:33:WU01:FS00:0xa7: Bits: 64
11:04:33:WU01:FS00:0xa7: Mode: Release
11:04:33:WU01:FS00:0xa7:************************************ Build *************************************
11:04:33:WU01:FS00:0xa7: SIMD: avx_256
11:04:33:WU01:FS00:0xa7:********************************************************************************
11:04:33:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 2146, Gen 7)
11:04:33:WU01:FS00:0xa7:Unit: 0x0000000b80fccb095e6e562caf863c2a
11:04:33:WU01:FS00:0xa7:Reading tar file core.xml
11:04:33:WU01:FS00:0xa7:Reading tar file frame7.tpr
11:04:33:WU01:FS00:0xa7:Digital signatures verified
11:04:33:WU01:FS00:0xa7:Reducing thread count from 11 to 10 to avoid domain decomposition by a prime number > 3
11:04:33:WU01:FS00:0xa7:Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 10
11:04:33:WU01:FS00:0xa7:Steps: first=1750000 total=250000
11:04:33:WU01:FS00:0xa7:ERROR:
11:04:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:04:33:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
11:04:33: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
11:04:33:WU01:FS00:0xa7:ERROR:
11:04:33:WU01:FS00:0xa7:ERROR:Fatal error:
11:04:33:WU01:FS00:0xa7:ERROR:There is no domain decomposition for 10 ranks that is compatible with the given box and a minimum cell size of 1.45733 nm
11:04:33:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
11:04:33:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
11:04:33:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
11:04:33:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
11:04:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:04:38:WU01:FS00:0xa7:WARNING:Unexpected exit() call
11:04:38:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
11:04:38:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
11:04:38:WU01:FS00:0xa7:Saving result file md.log
11:04:38:WU01:FS00:0xa7:Saving result file science.log
11:04:38:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
11:05:33:WU01:FS00:Starting
11:05:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:05:33:WU01:FS00:Removing old file './work/01/logfile_01-20200411-103332.txt'
11:05:33:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 705 -lifeline 1927 -checkpoint 15 -np 11
11:05:33:WU01:FS00:Started FahCore on PID 1063
11:05:33:WU01:FS00:Core PID:1067
11:05:33:WU01:FS00:FahCore 0xa7 started
11:05:33:WU01:FS00:0xa7:*********************** Log Started 2020-04-11T11:05:33Z ***********************
11:05:33:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
11:05:33:WU01:FS00:0xa7: Type: 0xa7
11:05:33:WU01:FS00:0xa7: Core: Gromacs
11:05:33:WU01:FS00:0xa7: Args: -dir 01 -suffix 01 -version 705 -lifeline 1063 -checkpoint 15 -np
11:05:33:WU01:FS00:0xa7: 11
11:05:33:WU01:FS00:0xa7:************************************ CBang *************************************
11:05:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:05:33:WU01:FS00:0xa7: Time: 06:06:57
11:05:33:WU01:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
11:05:33:WU01:FS00:0xa7: Branch: master
11:05:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:05:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
11:05:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:05:33:WU01:FS00:0xa7: Bits: 64
11:05:33:WU01:FS00:0xa7: Mode: Release
11:05:33:WU01:FS00:0xa7:************************************ System ************************************
11:05:33:WU01:FS00:0xa7: CPU: Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
11:05:33:WU01:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
11:05:33:WU01:FS00:0xa7: CPUs: 12
11:05:33:WU01:FS00:0xa7: Memory: 15.56GiB
11:05:33:WU01:FS00:0xa7:Free Memory: 5.03GiB
11:05:33:WU01:FS00:0xa7: Threads: POSIX_THREADS
11:05:33:WU01:FS00:0xa7: OS Version: 4.15
11:05:33:WU01:FS00:0xa7:Has Battery: false
11:05:33:WU01:FS00:0xa7: On Battery: false
11:05:33:WU01:FS00:0xa7: UTC Offset: 2
11:05:33:WU01:FS00:0xa7: PID: 1067
11:05:33:WU01:FS00:0xa7: CWD: /var/lib/fahclient/work
11:05:33:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
11:05:33:WU01:FS00:0xa7: Version: 0.0.18
11:05:33:WU01:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
11:05:33:WU01:FS00:0xa7: Copyright: 2019 foldingathome.org
11:05:33:WU01:FS00:0xa7: Homepage: https://foldingathome.org/
11:05:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:05:33:WU01:FS00:0xa7: Time: 06:13:26
11:05:33:WU01:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
11:05:33:WU01:FS00:0xa7: Branch: master
11:05:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:05:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
11:05:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:05:33:WU01:FS00:0xa7: Bits: 64
11:05:33:WU01:FS00:0xa7: Mode: Release
11:05:33:WU01:FS00:0xa7:************************************ Build *************************************
11:05:33:WU01:FS00:0xa7: SIMD: avx_256
11:05:33:WU01:FS00:0xa7:********************************************************************************
11:05:33:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 2146, Gen 7)
11:05:33:WU01:FS00:0xa7:Unit: 0x0000000b80fccb095e6e562caf863c2a
11:05:33:WU01:FS00:0xa7:Reading tar file core.xml
11:05:33:WU01:FS00:0xa7:Reading tar file frame7.tpr
11:05:33:WU01:FS00:0xa7:Digital signatures verified
11:05:33:WU01:FS00:0xa7:Reducing thread count from 11 to 10 to avoid domain decomposition by a prime number > 3
11:05:33:WU01:FS00:0xa7:Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 10
11:05:33:WU01:FS00:0xa7:Steps: first=1750000 total=250000
11:05:33:WU01:FS00:0xa7:ERROR:
11:05:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:05:33:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
11:05:33: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
11:05:33:WU01:FS00:0xa7:ERROR:
11:05:33:WU01:FS00:0xa7:ERROR:Fatal error:
11:05:33:WU01:FS00:0xa7:ERROR:There is no domain decomposition for 10 ranks that is compatible with the given box and a minimum cell size of 1.45733 nm
11:05:33:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
11:05:33:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
11:05:33:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
11:05:33:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
11:05:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:05:38:WU01:FS00:0xa7:WARNING:Unexpected exit() call
11:05:38:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
11:05:38:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
11:05:38:WU01:FS00:0xa7:Saving result file md.log
11:05:38:WU01:FS00:0xa7:Saving result file science.log
11:05:38:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
11:06:33:WU01:FS00:Starting
11:06:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:06:33:WU01:FS00:Removing old file './work/01/logfile_01-20200411-103432.txt'
11:06:33:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 705 -lifeline 1927 -checkpoint 15 -np 11
11:06:33:WU01:FS00:Started FahCore on PID 14140
11:06:33:WU01:FS00:Core PID:14144
11:06:33:WU01:FS00:FahCore 0xa7 started
11:06:33:WU01:FS00:0xa7:*********************** Log Started 2020-04-11T11:06:33Z ***********************
11:06:33:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
11:06:33:WU01:FS00:0xa7: Type: 0xa7
11:06:33:WU01:FS00:0xa7: Core: Gromacs
11:06:33:WU01:FS00:0xa7: Args: -dir 01 -suffix 01 -version 705 -lifeline 14140 -checkpoint 15 -np
11:06:33:WU01:FS00:0xa7: 11
11:06:33:WU01:FS00:0xa7:************************************ CBang *************************************
11:06:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:06:33:WU01:FS00:0xa7: Time: 06:06:57
11:06:33:WU01:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
11:06:33:WU01:FS00:0xa7: Branch: master
11:06:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:06:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
11:06:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:06:33:WU01:FS00:0xa7: Bits: 64
11:06:33:WU01:FS00:0xa7: Mode: Release
11:06:33:WU01:FS00:0xa7:************************************ System ************************************
11:06:33:WU01:FS00:0xa7: CPU: Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
11:06:33:WU01:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
11:06:33:WU01:FS00:0xa7: CPUs: 12
11:06:33:WU01:FS00:0xa7: Memory: 15.56GiB
11:06:33:WU01:FS00:0xa7:Free Memory: 4.96GiB
11:06:33:WU01:FS00:0xa7: Threads: POSIX_THREADS
11:06:33:WU01:FS00:0xa7: OS Version: 4.15
11:06:33:WU01:FS00:0xa7:Has Battery: false
11:06:33:WU01:FS00:0xa7: On Battery: false
11:06:33:WU01:FS00:0xa7: UTC Offset: 2
11:06:33:WU01:FS00:0xa7: PID: 14144
11:06:33:WU01:FS00:0xa7: CWD: /var/lib/fahclient/work
11:06:33:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
11:06:33:WU01:FS00:0xa7: Version: 0.0.18
11:06:33:WU01:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
11:06:33:WU01:FS00:0xa7: Copyright: 2019 foldingathome.org
11:06:33:WU01:FS00:0xa7: Homepage: https://foldingathome.org/
11:06:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:06:33:WU01:FS00:0xa7: Time: 06:13:26
11:06:33:WU01:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
11:06:33:WU01:FS00:0xa7: Branch: master
11:06:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:06:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
11:06:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:06:33:WU01:FS00:0xa7: Bits: 64
11:06:33:WU01:FS00:0xa7: Mode: Release
11:06:33:WU01:FS00:0xa7:************************************ Build *************************************
11:06:33:WU01:FS00:0xa7: SIMD: avx_256
11:06:33:WU01:FS00:0xa7:********************************************************************************
11:06:33:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 2146, Gen 7)
11:06:33:WU01:FS00:0xa7:Unit: 0x0000000b80fccb095e6e562caf863c2a
11:06:33:WU01:FS00:0xa7:Reading tar file core.xml
11:06:33:WU01:FS00:0xa7:Reading tar file frame7.tpr
11:06:33:WU01:FS00:0xa7:Digital signatures verified
11:06:33:WU01:FS00:0xa7:Reducing thread count from 11 to 10 to avoid domain decomposition by a prime number > 3
11:06:33:WU01:FS00:0xa7:Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 10
11:06:33:WU01:FS00:0xa7:Steps: first=1750000 total=250000
11:06:33:WU01:FS00:0xa7:ERROR:
11:06:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:06:33:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
11:06:33: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
11:06:33:WU01:FS00:0xa7:ERROR:
11:06:33:WU01:FS00:0xa7:ERROR:Fatal error:
11:06:33:WU01:FS00:0xa7:ERROR:There is no domain decomposition for 10 ranks that is compatible with the given box and a minimum cell size of 1.45733 nm
11:06:33:WU01:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
11:06:33:WU01:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
11:06:33:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
11:06:33:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
11:06:33:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
11:06:38:WU01:FS00:0xa7:WARNING:Unexpected exit() call
11:06:38:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
11:06:38:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
11:06:38:WU01:FS00:0xa7:Saving result file md.log
11:06:38:WU01:FS00:0xa7:Saving result file science.log
11:06:38:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
11:07:33:WU01:FS00:Starting
11:07:33:WARNING:WU01:FS00:Changed SMP threads from 12 to 8 this can cause some work units to fail
11:07:33:WU01:FS00:Removing old file './work/01/logfile_01-20200411-103532.txt'
11:07:33:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 705 -lifeline 1927 -checkpoint 15 -np 8
11:07:33:WU01:FS00:Started FahCore on PID 26749
11:07:33:WU01:FS00:Core PID:26753
11:07:33:WU01:FS00:FahCore 0xa7 started
11:07:33:WU01:FS00:0xa7:*********************** Log Started 2020-04-11T11:07:33Z ***********************
11:07:33:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
11:07:33:WU01:FS00:0xa7: Type: 0xa7
11:07:33:WU01:FS00:0xa7: Core: Gromacs
11:07:33:WU01:FS00:0xa7: Args: -dir 01 -suffix 01 -version 705 -lifeline 26749 -checkpoint 15 -np
11:07:33:WU01:FS00:0xa7: 8
11:07:33:WU01:FS00:0xa7:************************************ CBang *************************************
11:07:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:07:33:WU01:FS00:0xa7: Time: 06:06:57
11:07:33:WU01:FS00:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
11:07:33:WU01:FS00:0xa7: Branch: master
11:07:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:07:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
11:07:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:07:33:WU01:FS00:0xa7: Bits: 64
11:07:33:WU01:FS00:0xa7: Mode: Release
11:07:33:WU01:FS00:0xa7:************************************ System ************************************
11:07:33:WU01:FS00:0xa7: CPU: Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
11:07:33:WU01:FS00:0xa7: CPU ID: GenuineIntel Family 6 Model 63 Stepping 2
11:07:33:WU01:FS00:0xa7: CPUs: 12
11:07:33:WU01:FS00:0xa7: Memory: 15.56GiB
11:07:33:WU01:FS00:0xa7:Free Memory: 4.95GiB
11:07:33:WU01:FS00:0xa7: Threads: POSIX_THREADS
11:07:33:WU01:FS00:0xa7: OS Version: 4.15
11:07:33:WU01:FS00:0xa7:Has Battery: false
11:07:33:WU01:FS00:0xa7: On Battery: false
11:07:33:WU01:FS00:0xa7: UTC Offset: 2
11:07:33:WU01:FS00:0xa7: PID: 26753
11:07:33:WU01:FS00:0xa7: CWD: /var/lib/fahclient/work
11:07:33:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
11:07:33:WU01:FS00:0xa7: Version: 0.0.18
11:07:33:WU01:FS00:0xa7: Author: Joseph Coffland <joseph@cauldrondevelopment.com>
11:07:33:WU01:FS00:0xa7: Copyright: 2019 foldingathome.org
11:07:33:WU01:FS00:0xa7: Homepage: https://foldingathome.org/
11:07:33:WU01:FS00:0xa7: Date: Nov 5 2019
11:07:33:WU01:FS00:0xa7: Time: 06:13:26
11:07:33:WU01:FS00:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
11:07:33:WU01:FS00:0xa7: Branch: master
11:07:33:WU01:FS00:0xa7: Compiler: GNU 8.3.0
11:07:33:WU01:FS00:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
11:07:33:WU01:FS00:0xa7: Platform: linux2 4.19.0-5-amd64
11:07:33:WU01:FS00:0xa7: Bits: 64
11:07:33:WU01:FS00:0xa7: Mode: Release
11:07:33:WU01:FS00:0xa7:************************************ Build *************************************
11:07:33:WU01:FS00:0xa7: SIMD: avx_256
11:07:33:WU01:FS00:0xa7:********************************************************************************
11:07:33:WU01:FS00:0xa7:Project: 13833 (Run 0, Clone 2146, Gen 7)
11:07:33:WU01:FS00:0xa7:Unit: 0x0000000b80fccb095e6e562caf863c2a
11:07:33:WU01:FS00:0xa7:Reading tar file core.xml
11:07:33:WU01:FS00:0xa7:Reading tar file frame7.tpr
11:07:33:WU01:FS00:0xa7:Digital signatures verified
11:07:33:WU01:FS00:0xa7:Calling: mdrun -s frame7.tpr -o frame7.trr -x frame7.xtc -cpt 15 -nt 8
11:07:33:WU01:FS00:0xa7:Steps: first=1750000 total=250000
11:07:35:WU01:FS00:0xa7:Completed 1 out of 250000 steps (0%)
11:08:30:WU01:FS00:0xa7:Completed 2500 out of 250000 steps (1%)
11:09:23:WU01:FS00:0xa7:Completed 5000 out of 250000 steps (2%)
11:10:18:WU01:FS00:0xa7:Completed 7500 out of 250000 steps (3%)
11:11:12:WU01:FS00:0xa7:Completed 10000 out of 250000 steps (4%)
11:12:06:WU01:FS00:0xa7:Completed 12500 out of 250000 steps (5%)
11:13:00:WU01:FS00:0xa7:Completed 15000 out of 250000 steps (6%)
11:13:54:WU01:FS00:0xa7:Completed 17500 out of 250000 steps (7%)
11:14:48:WU01:FS00:0xa7:Completed 20000 out of 250000 steps (8%)
11:15:43:WU01:FS00:0xa7:Completed 22500 out of 250000 steps (9%)
11:16:37:WU01:FS00:0xa7:Completed 25000 out of 250000 steps (10%)
11:17:31:WU01:FS00:0xa7:Completed 27500 out of 250000 steps (11%)
11:18:25:WU01:FS00:0xa7:Completed 30000 out of 250000 steps (12%)
11:19:18:WU01:FS00:0xa7:Completed 32500 out of 250000 steps (13%)
11:20:12:WU01:FS00:0xa7:Completed 35000 out of 250000 steps (14%)
11:21:05:WU01:FS00:0xa7:Completed 37500 out of 250000 steps (15%)
11:21:59:WU01:FS00:0xa7:Completed 40000 out of 250000 steps (16%)
11:22:52:WU01:FS00:0xa7:Completed 42500 out of 250000 steps (17%)
11:23:46:WU01:FS00:0xa7:Completed 45000 out of 250000 steps (18%)
11:24:39:WU01:FS00:0xa7:Completed 47500 out of 250000 steps (19%)
11:25:32:WU01:FS00:0xa7:Completed 50000 out of 250000 steps (20%)
11:26:25:WU01:FS00:0xa7:Completed 52500 out of 250000 steps (21%)
11:27:18:WU01:FS00:0xa7:Completed 55000 out of 250000 steps (22%)
11:28:11:WU01:FS00:0xa7:Completed 57500 out of 250000 steps (23%)
11:29:04:WU01:FS00:0xa7:Completed 60000 out of 250000 steps (24%)
11:29:56:WU01:FS00:0xa7:Completed 62500 out of 250000 steps (25%)
11:30:49:WU01:FS00:0xa7:Completed 65000 out of 250000 steps (26%)
11:31:42:WU01:FS00:0xa7:Completed 67500 out of 250000 steps (27%)
11:32:35:WU01:FS00:0xa7:Completed 70000 out of 250000 steps (28%)
11:33:28:WU01:FS00:0xa7:Completed 72500 out of 250000 steps (29%)
11:34:22:WU01:FS00:0xa7:Completed 75000 out of 250000 steps (30%)
11:35:14:WU01:FS00:0xa7:Completed 77500 out of 250000 steps (31%)
11:36:07:WU01:FS00:0xa7:Completed 80000 out of 250000 steps (32%)
11:37:00:WU01:FS00:0xa7:Completed 82500 out of 250000 steps (33%)
11:37:53:WU01:FS00:0xa7:Completed 85000 out of 250000 steps (34%)
11:38:46:WU01:FS00:0xa7:Completed 87500 out of 250000 steps (35%)
11:39:40:WU01:FS00:0xa7:Completed 90000 out of 250000 steps (36%)
11:40:34:WU01:FS00:0xa7:Completed 92500 out of 250000 steps (37%)
11:41:28:WU01:FS00:0xa7:Completed 95000 out of 250000 steps (38%)
11:42:21:WU01:FS00:0xa7:Completed 97500 out of 250000 steps (39%)
11:43:14:WU01:FS00:0xa7:Completed 100000 out of 250000 steps (40%)
11:44:07:WU01:FS00:0xa7:Completed 102500 out of 250000 steps (41%)
11:45:00:WU01:FS00:0xa7:Completed 105000 out of 250000 steps (42%)
11:45:53:WU01:FS00:0xa7:Completed 107500 out of 250000 steps (43%)
11:46:46:WU01:FS00:0xa7:Completed 110000 out of 250000 steps (44%)
11:47:40:WU01:FS00:0xa7:Completed 112500 out of 250000 steps (45%)
11:48:33:WU01:FS00:0xa7:Completed 115000 out of 250000 steps (46%)
11:49:27:WU01:FS00:0xa7:Completed 117500 out of 250000 steps (47%)
11:50:20:WU01:FS00:0xa7:Completed 120000 out of 250000 steps (48%)
11:51:14:WU01:FS00:0xa7:Completed 122500 out of 250000 steps (49%)
11:52:07:WU01:FS00:0xa7:Completed 125000 out of 250000 steps (50%)
11:53:02:WU01:FS00:0xa7:Completed 127500 out of 250000 steps (51%)
11:53:55:WU01:FS00:0xa7:Completed 130000 out of 250000 steps (52%)
11:54:47:WU01:FS00:0xa7:Completed 132500 out of 250000 steps (53%)
11:55:40:WU01:FS00:0xa7:Completed 135000 out of 250000 steps (54%)
11:56:33:WU01:FS00:0xa7:Completed 137500 out of 250000 steps (55%)
11:57:28:WU01:FS00:0xa7:Completed 140000 out of 250000 steps (56%)
11:58:22:WU01:FS00:0xa7:Completed 142500 out of 250000 steps (57%)
11:59:16:WU01:FS00:0xa7:Completed 145000 out of 250000 steps (58%)
12:00:10:WU01:FS00:0xa7:Completed 147500 out of 250000 steps (59%)
12:01:08:WU01:FS00:0xa7:Completed 150000 out of 250000 steps (60%)
12:02:05:WU01:FS00:0xa7:Completed 152500 out of 250000 steps (61%)
12:03:02:WU01:FS00:0xa7:Completed 155000 out of 250000 steps (62%)
What information specifically are you after?
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 12:16 pm
by PantherX
The messages printed by the FAHClient at the start of the log are same across all the OS. What I am after is the FAHClient configuration that your system is using. You can post the config.xml file here as long as you remove your passkey from it. The reason the log from your FAHControl didn't match mine is because you need to click "Refresh" at the bottom right corner to reload the log from disk as opposed to what's in memory.
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 1:06 pm
by rogermateer
My /etc/fahclient/config.xml doesn't have a passkey - perhaps because i'm folding anonymously... (I don't want to play the points game
)
I've noticed now that the problematic WU has finished, I'm getting curious warnings and errors in the FAHControl log when it tries to get more work:
Code: Select all
*********************** Log Started 2020-04-11T08:31:23Z ***********************
09:02:30:WARNING:WU01:FS00:Changed SMP threads from 11 to 12 this can cause some work units to fail
09:02:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:03:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:04:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:05:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:06:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:07:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:08:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:09:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:10:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:11:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:12:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:13:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:14:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:15:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:16:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:17:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:18:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:19:30:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:20:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:21:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:22:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:23:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:24:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:25:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:26:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:27:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:28:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:29:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:30:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:31:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:32:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:33:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:34:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:35:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:36:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:37:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:38:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:39:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:40:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:41:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:42:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:43:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:44:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:45:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:46:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:47:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:48:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:49:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:50:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:51:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:52:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:53:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:54:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:55:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:56:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:57:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:58:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
09:59:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:00:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:01:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:02:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:03:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:04:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:05:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:06:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:07:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:08:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:09:31:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:10:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:11:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:12:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:13:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:14:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:15:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:16:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:17:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:18:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:19:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:20:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:21:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:22:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:23:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:24:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:25:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:26:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:27:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:28:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:29:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:30:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:31:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:32:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:33:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:34:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:35:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:36:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:37:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:38:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:39:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:40:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:41:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:42:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:43:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:44:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:45:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:46:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:47:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:48:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:49:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:50:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:51:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:52:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:53:32:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:54:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:55:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:56:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:57:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:58:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
10:59:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:00:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:01:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:02:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:03:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:04:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:05:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:06:33:WARNING:WU01:FS00:AS lowered CPUs from 12 to 11
11:07:33:WARNING:WU01:FS00:Changed SMP threads from 12 to 8 this can cause some work units to fail
12:36:41:WARNING:WU00:FS00:Failed to get assignment from '65.254.110.245:8080': No WUs available for this configuration
12:36:48:ERROR:WU00:FS00:Exception: Server did not assign work unit
12:36:54:WARNING:WU00:FS00:Failed to get assignment from '65.254.110.245:8080': No WUs available for this configuration
12:37:04:WARNING:WU00:FS00:Failed to get assignment from '18.218.241.186:80': No WUs available for this configuration
12:37:04:ERROR:WU00:FS00:Exception: Could not get an assignment
12:37:49:WARNING:WU00:FS00:Failed to get assignment from '65.254.110.245:8080': No WUs available for this configuration
12:41:36:ERROR:WU00:FS00:Exception: Transfer failed
12:41:39:WARNING:WU00:FS00:Failed to get assignment from '65.254.110.245:8080': No WUs available for this configuration
12:41:44:WARNING:WU00:FS00:Failed to get assignment from '18.218.241.186:80': No WUs available for this configuration
12:41:44:ERROR:WU00:FS00:Exception: Could not get an assignment
12:44:18:ERROR:WU00:FS00:Exception: Server did not assign work unit
12:48:29:WARNING:WU00:FS00:Failed to get assignment from '65.254.110.245:8080': No WUs available for this configuration
12:48:31:WARNING:WU00:FS00:Failed to get assignment from '18.218.241.186:80': No WUs available for this configuration
12:48:31:ERROR:WU00:FS00:Exception: Could not get an assignment
12:55:20:WARNING:WU00:FS00:Failed to get assignment from '65.254.110.245:8080': No WUs available for this configuration
12:55:22:WARNING:WU00:FS00:Failed to get assignment from '18.218.241.186:80': No WUs available for this configuration
12:55:22:ERROR:WU00:FS00:Exception: Could not get an assignment
So I'm fiddling around with the CPU slot threads setting (between 8 or 12 or -1) to try to persuade the server to give it some more compatible work.
When it is set to 8, my /etc/fahclient/config.xml looks like this:
Code: Select all
<config>
<!-- Client Control -->
<fold-anon v='true'/>
<!-- Folding Slot Configuration -->
<gpu v='false'/>
<!-- Network -->
<proxy v=':8080'/>
<!-- Slot Control -->
<power v='full'/>
<!-- Folding Slots -->
<slot id='0' type='CPU'>
<cpus v='8'/>
</slot>
</config>
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 1:31 pm
by rogermateer
It's now folding a cancer cause WU - 14307.
Hopefully some more covid-19 work will be available soon...
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 2:03 pm
by _r2w_ben
You could try 9 instead of 8 next time. I'm not sure which is more efficient to schedule: 8 threads on 6 cores + 2 HT or 9 threads on 6 cores + 3 HT.
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 2:19 pm
by PantherX
If you're not folding for points, everything looks fine. However, I didn't expect the AS to reduce your CPUs from 12 to 11 since 11 is not a good number at all for folding CPU WUs. Nonetheless, you have 8 and 12 and depending on the situation, can adjust so it will work out in the end
I haven't head anything about 9 CPUs since it is not a "typical" value. If you do get WUs that fold on 9, that's cool.
Re: Issues, perhaps bad WU? - 16417
Posted: Sat Apr 11, 2020 6:50 pm
by rogermateer
Thanks for all your attention.