GROMACS version:2021.6-plumed-2.7.5
GROMACS modification: Yes
I am running
mpirun -np 35 gmx_mpi mdrun -plumed plumed.dat -deffnm topolmd -multidir ./steprest/MD_[0123456] -replex 1000 -hrex -dlb no
however, the process broke down with segmentation fault below:
[localhost:2845343] *** Process received signal ***
[localhost:2845343] Signal: Segmentation fault (11)
[localhost:2845343] Signal code: Address not mapped (1)
[localhost:2845343] Failing at address: (nil)
[localhost:2845387] *** Process received signal ***
[localhost:2845387] Signal: Segmentation fault (11)
[localhost:2845387] Signal code: Address not mapped (1)
[localhost:2845387] Failing at address: (nil)
[localhost:2845351] *** Process received signal ***
[localhost:2845351] Signal: Segmentation fault (11)
[localhost:2845351] Signal code: Address not mapped (1)
[localhost:2845351] Failing at address: (nil)
[localhost:2845351] [localhost:2845370] *** Process received signal ***
[localhost:2845370] Signal: Segmentation fault (11)
[localhost:2845370] Signal code: Address not mapped (1)
[localhost:2845370] Failing at address: (nil)
[localhost:2845370] [ 0] [localhost:2845319] *** Process received signal ***
[localhost:2845319] Signal: Segmentation fault (11)
[localhost:2845319] Signal code: Address not mapped (1)
[localhost:2845319] Failing at address: (nil)
[localhost:2845305] *** Process received signal ***
[localhost:2845305] Signal: Segmentation fault (11)
[localhost:2845305] Signal code: Address not mapped (1)
[localhost:2845305] Failing at address: (nil)
[localhost:2845307] *** Process received signal ***
[localhost:2845307] Signal: Segmentation fault (11)
[localhost:2845307] Signal code: Address not mapped (1)
[localhost:2845307] Failing at address: (nil)
[localhost:2845303] *** Process received signal ***
[localhost:2845303] Signal: Segmentation fault (11)
[localhost:2845303] Signal code: Address not mapped (1)
[localhost:2845303] Failing at address: (nil)
[localhost:2845303] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7fca6074acf0]
[localhost:2845303] *** End of error message ***
[localhost:2845377] *** Process received signal ***
[localhost:2845377] Signal: Segmentation fault (11)
[localhost:2845377] Signal code: Address not mapped (1)
[localhost:2845377] Failing at address: (nil)
[localhost:2845383] *** Process received signal ***
[localhost:2845383] Signal: Segmentation fault (11)
[localhost:2845383] Signal code: Address not mapped (1)
[localhost:2845383] Failing at address: (nil)
[localhost:2845383] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f1ecb0a4cf0]
[localhost:2845383] *** End of error message ***
[localhost:2845310] *** Process received signal ***
[localhost:2845310] Signal: Segmentation fault (11)
[localhost:2845310] Signal code: Address not mapped (1)
[localhost:2845310] Failing at address: (nil)
[localhost:2845314] *** Process received signal ***
[localhost:2845314] Signal: Segmentation fault (11)
[localhost:2845314] Signal code: Address not mapped (1)
[localhost:2845314] Failing at address: (nil)
[localhost:2845314] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7fdbf309ccf0]
[localhost:2845314] *** End of error message ***
[localhost:2845353] *** Process received signal ***
[localhost:2845353] Signal: Segmentation fault (11)
[localhost:2845353] Signal code: Address not mapped (1)
[localhost:2845353] Failing at address: (nil)
[localhost:2845353] [ 0] [localhost:2845302] *** Process received signal ***
[localhost:2845302] Signal: Segmentation fault (11)
[localhost:2845302] Signal code: Address not mapped (1)
[localhost:2845302] Failing at address: (nil)
[localhost:2845302] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7fa82cd51cf0]
[localhost:2845302] *** End of error message ***
[localhost:2845300] *** Process received signal ***
[localhost:2845300] Signal: Segmentation fault (11)
[localhost:2845300] Signal code: Address not mapped (1)
[localhost:2845300] Failing at address: (nil)
[localhost:2845300] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f7151343cf0]
[localhost:2845300] *** End of error message ***
[localhost:2845312] *** Process received signal ***
[localhost:2845312] Signal: Segmentation fault (11)
[localhost:2845312] Signal code: Address not mapped (1)
[localhost:2845312] Failing at address: (nil)
[localhost:2845312] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7fdd0fedccf0]
[localhost:2845312] *** End of error message ***
[localhost:2845334] *** Process received signal ***
[localhost:2845334] Signal: Segmentation fault (11)
[localhost:2845334] Signal code: Address not mapped (1)
[localhost:2845334] Failing at address: (nil)
[localhost:2845334] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7fa99db15cf0]
[localhost:2845334] *** End of error message ***
[localhost:2845327] *** Process received signal ***
[localhost:2845327] Signal: Segmentation fault (11)
[localhost:2845327] Signal code: Address not mapped (1)
[localhost:2845327] Failing at address: (nil)
[localhost:2845327] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f62cc6cacf0]
[localhost:2845327] *** End of error message ***
[localhost:2845372] *** Process received signal ***
[localhost:2845372] Signal: Segmentation fault (11)
[localhost:2845372] Signal code: Address not mapped (1)
[localhost:2845372] Failing at address: (nil)
[localhost:2845372] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f564ff42cf0]
[localhost:2845372] *** End of error message ***
[localhost:2845308] *** Process received signal ***
[localhost:2845308] Signal: Segmentation fault (11)
[localhost:2845308] Signal code: Address not mapped (1)
[localhost:2845308] Failing at address: (nil)
[localhost:2845308] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7fb97726ccf0]
[localhost:2845308] *** End of error message ***
[localhost:2845360] *** Process received signal ***
[localhost:2845360] Signal: Segmentation fault (11)
[localhost:2845360] Signal code: Address not mapped (1)
[localhost:2845360] Failing at address: (nil)
[localhost:2845360] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f735694ccf0]
[localhost:2845360] *** End of error message ***
[localhost:2845343] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f84b5a04cf0]
[localhost:2845343] *** End of error message ***
[localhost:2845387] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7fb88eececf0]
[localhost:2845387] *** End of error message ***
[ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f6afd839cf0]
[localhost:2845351] *** End of error message ***
/lib64/libpthread.so.0(+0x12cf0)[0x7faffe9adcf0]
[localhost:2845370] *** End of error message ***
[localhost:2845319] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f173e6d2cf0]
[localhost:2845319] *** End of error message ***
[localhost:2845305] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f3d69c44cf0]
[localhost:2845305] *** End of error message ***
[localhost:2845307] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7fc8aa8b2cf0]
[localhost:2845307] *** End of error message ***
[localhost:2845377] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7ff254529cf0]
[localhost:2845377] *** End of error message ***
[localhost:2845310] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f414ee2dcf0]
[localhost:2845310] *** End of error message ***
/lib64/libpthread.so.0(+0x12cf0)[0x7f3e50ed6cf0]
[localhost:2845353] *** End of error message ***
mpirun noticed that process rank 5 with PID 0 on node localhost exited on signal 11 (Segmentation fault).
more, the files like .xtc, .edr were output without content.
one of the MD .log files:
:-) GROMACS - gmx mdrun, 2021.6-plumed-2.7.5 (-:
GROMACS is written by:
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and the project leaders:
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GROMACS: gmx mdrun, version 2021.6-plumed-2.7.5
Executable: /home/Liws2021/gmx202106_mpi_plumed/bin/gmx_mpi
Data prefix: /home/Liws2021/gmx202106_mpi_plumed
Working dir: /data/Liws2021/AT8/rest/steprest/MD_5
Process ID: 2848572
Command line:
gmx_mpi mdrun -plumed plumed.dat -deffnm topolmd -multidir ./steprest/MD_0 ./steprest/MD_1 ./steprest/MD_2 ./steprest/MD_3 ./steprest/MD_4 ./steprest/MD_5 ./steprest/MD_6 -replex 1000 -hrex -dlb no
GROMACS version: 2021.6-plumed-2.7.5
Precision: mixed
Memory model: 64 bit
MPI library: MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: AVX_512
FFT library: fftw-3.3.10-sse2-avx-avx2-avx2_128
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 8.5.0
C compiler flags: -mavx512f -mfma -pthread -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 8.5.0
C++ compiler flags: -mavx512f -mfma -pthread -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
Running on 1 node with total 40 cores, 80 logical cores
Hardware detected on host localhost.localdomain (the node of MPI rank 10):
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) Silver 4316 CPU @ 2.30GHz
Family: 6 Model: 106 Stepping: 6
Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
Number of AVX-512 FMA units: 2
Hardware topology: Basic
Sockets, cores, and logical processors:
Socket 0: [ 0 40] [ 1 41] [ 2 42] [ 3 43] [ 4 44] [ 5 45] [ 6 46] [ 7 47] [ 8 48] [ 9 49] [ 10 50] [ 11 51] [ 12 52] [ 13 53] [ 14 54] [ 15 55] [ 16 56] [ 17 57] [ 18 58] [ 19 59]
Socket 1: [ 20 60] [ 21 61] [ 22 62] [ 23 63] [ 24 64] [ 25 65] [ 26 66] [ 27 67] [ 28 68] [ 29 69] [ 30 70] [ 31 71] [ 32 72] [ 33 73] [ 34 74] [ 35 75] [ 36 76] [ 37 77] [ 38 78] [ 39 79]
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. P谩ll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- — Thank You — -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. P谩ll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- — Thank You — -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. P谩ll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- — Thank You — -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- — Thank You — -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- — Thank You — -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- — Thank You — -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- — Thank You — -------- --------
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 50000
init-step = 0
simulation-part = 1
mts = false
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = -2015371314
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 10
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 1
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.16
fourier-nx = 40
fourier-ny = 40
fourier-nz = 36
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
tcoupl = V-rescale
nsttcouple = 10
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = No
pcoupltype = Isotropic
nstpcouple = -1
tau-p = 1
compressibility (3x3):
compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p (3x3):
ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
QMMM = false
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = true
Shake-SOR = false
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = false
awh = false
rotation = false
interactiveMD = false
disre = No
disre-weighting = Conservative
disre-mixed = false
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = no
cos-acceleration = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
simulated-tempering = false
swapcoords = no
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
applied-forces:
electric-field:
x:
E0 = 0
omega = 0
t0 = 0
sigma = 0
y:
E0 = 0
omega = 0
t0 = 0
sigma = 0
z:
E0 = 0
omega = 0
t0 = 0
sigma = 0
density-guided-simulation:
active = false
group = protein
similarity-measure = inner-product
atom-spreading-weight = unity
force-constant = 1e+09
gaussian-transform-spreading-width = 0.2
gaussian-transform-spreading-range-in-multiples-of-width = 4
reference-density-filename = reference.mrc
nst = 1
normalize-densities = true
adaptive-force-scaling = false
adaptive-force-scaling-time-constant = 4
shift-vector =
transformation-matrix =
grpopts:
nrdf: 4920.62 34287.4
ref-t: 300 300
tau-t: 0.1 0.1
annealing: No No
annealing-npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Changing nstlist from 10 to 50, rlist from 1 to 1.102
Initializing Domain Decomposition on 2 ranks
Dynamic load balancing: off
Using update groups, nr 6720, average size 2.8 atoms, max. radius 0.104 nm
Minimum cell size due to atom displacement: 0.398 nm
Initial maximum distances in bonded interactions:
two-body bonded interactions: 0.443 nm, LJ-14, atoms 1156 1405
multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1156 1405
Minimum cell size due to bonded interactions: 0.487 nm
Using 0 separate PME ranks, as there are too few total
ranks for efficient splitting
Optimizing the DD grid for 2 cells with a minimum initial size of 0.487 nm
The maximum allowed number of cells is: X 11 Y 12 Z 11
Domain decomposition grid 1 x 2 x 1, separate PME ranks 0
PME domain decomposition: 1 x 2 x 1
Domain decomposition rank 0, coordinates 0 0 0
The initial number of communication pulses is: Y 1
The initial domain decomposition cell size is: Y 3.12 nm
The maximum allowed distance for atom groups involved in interactions is:
non-bonded interactions 1.310 nm
two-body bonded interactions (-rdd) 1.310 nm
multi-body bonded interactions (-rdd) 1.310 nm
This is simulation 5 out of 7 running as a composite GROMACS
multi-simulation job. Setup for this simulation:
Using 2 MPI processes
Non-default thread affinity set, disabling internal thread affinity
Using 5 OpenMP threads per MPI process
System total charge: 0.000
Will do PME sum in reciprocal space for electrostatic interactions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- — Thank You — -------- --------
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Coulomb Ewald tables, spacing: 9.33e-04 size: 1073
Generated table with 1051 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1051 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1051 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Long Range LJ corr.: 3.2623e-04
Using SIMD 4x8 nonbonded short-range kernels
Using a dual 4x8 pair-list setup updated with dynamic pruning:
outer list: updated every 50 steps, buffer 0.102 nm, rlist 1.102 nm
inner list: updated every 13 steps, buffer 0.003 nm, rlist 1.003 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
outer list: updated every 50 steps, buffer 0.229 nm, rlist 1.229 nm
inner list: updated every 13 steps, buffer 0.051 nm, rlist 1.051 nm
Using Lorentz-Berthelot Lennard-Jones combination rule
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- — Thank You — -------- --------
The number of constraints is 959
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- — Thank You — -------- --------
Linking all bonded interactions to atoms
Intra-simulation communication will occur every 10 steps.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- — Thank You — -------- --------
There are: 19101 Atoms
Atom distribution over 2 domains: av 9550 stddev 98 min 9549 max 9552
Initializing Replica Exchange
Repl There are 7 replicas:
Multi-checking the number of atoms … OK
Multi-checking the integrator … OK
Multi-checking init_step+nsteps … OK
Multi-checking first exchange step: init_step/-replex … OK
Multi-checking the temperature coupling … OK
Multi-checking the number of temperature coupling groups … OK
Multi-checking the pressure coupling … OK
Multi-checking free energy … OK
Multi-checking number of lambda states … OK
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
Y. Sugita, Y. Okamoto
Replica-exchange molecular dynamics method for protein folding
Chem. Phys. Lett. 314 (1999) pp. 141-151
-------- -------- — Thank You — -------- --------
Though I know the fault is probably related to plumed or openmpi, how can I deal with it.