What is causing this error?
C:\Users\Sadat Abdullah\LAMMPS 64-bit 29Aug2024-MSMPI\bin> mpiexec -np 8 lmp -in in.relax
LAMMPS (29 Aug 2024 - Update 1)
job aborted:
[ranks] message
[0-2] terminated
[3] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 1, comm rank 3
[4] terminated
[5] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 1, comm rank 5
[6] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 1, comm rank 6
[7] terminated
---- error analysis -----
[3,5-6] on LAPTOP-S968HDJK
lmp aborted the job. abort code 1
---- error analysis -----
This is the input script:
# This is the control script for LAMMPS
echo both
#-------------------------------------------------------------------------------
# Stage 2.1: Initialize LAMMPS run
#-------------------------------------------------------------------------------
units metal
atom_style charge
boundary p p p
processors * * * grid numa
read_data Bi2Te3.data
replicate 8 8 4
# group watom type 1
# group seatom type 2
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
pair_style hybrid/overlay morse 30.0 coul/long 11.0
pair_coeff * * coul/long
pair_coeff 1 2 morse 0.975 1.285 3.089
pair_coeff 1 3 morse 0.582 1.257 3.251
pair_coeff 2 2 morse 0.076 1.675 3.642
pair_coeff 1 1 morse 0.085 2.212 4.203
pair_coeff 2 3 morse 0.807 0.731 4.497
pair_coeff 3 3 morse 0.066 2.876 4.312
kspace_style pppm 1.0e-5
thermo_style custom step temp pe ke etotal press vol
thermo 50
dump 1 all atom 100 dump.min
min_style cg
minimize 1.0e-8 1.0e-8 5000 10000
undump 1
velocity all create 10.00 156467 mom yes rot yes dist gaussian
fix 1 all npt temp 10.00 10.00 100 iso 0.0 0.0 1000
dump 2 all atom 50000 dumpheat.npt
timestep 0.001
run 100000
unfix 1
# heat from 10 to 100K
velocity all create 100.00 156467 mom yes rot yes dist gaussian
fix 2a all nve
run 20000
velocity all create 100.00 156467 mom yes rot yes dist gaussian
run 20000
velocity all create 100.00 156467 mom yes rot yes dist gaussian
run 20000
velocity all create 100.00 156467 mom yes rot yes dist gaussian
run 20000
velocity all create 100.00 156467 mom yes rot yes dist gaussian
run 20000
unfix 2a
fix 2b all npt temp 100.00 100.00 100 iso 0.0 0.0 1000
run 200000
unfix 2b
undump 2
# final relaxation run
fix 5 all nve
dump 4 all atom 50000 dump300.nve
run 300000
unfix 5
write_restart Bi2Te3.restart
Impossible to say from this information. Please try running without ‘mpiexec -np 8’ and report back what output you get.
If that is successful, then try to add the flags -echo screen -nb and report back what the output is.
Without the data file to try reproduce what you see on a different platform, there is not much to do.
C:\Users\Sadat Abdullah\LAMMPS 64-bit 29Aug2024-MSMPI\bin>lmp -in in.relax
LAMMPS (29 Aug 2024 - Update 1)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Loaded 0 plugins from D:\LAMMPS 64-bit 29Aug2024-MSMPI\plugins
#-------------------------------------------------------------------------------
# Stage 2.1: Initialize LAMMPS run
#-------------------------------------------------------------------------------
units metal
atom_style charge
boundary p p p
processors * * * grid numa
read_data Bi2Te3.data
Reading data file ...
triclinic box = (0 0 0) to (4.4181304 3.8262132 32.257299) with tilt (-2.2090652 0 0)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
1 by 1 by 1 MPI processor grid
1 by 1 by 1 core grid within node
reading atoms ...
15 atoms
read_data CPU = 0.002 seconds
replicate 8 8 4
Replication is creating a 8x8x4 = 256 times larger system...
triclinic box = (0 0 0) to (35.345044 30.609706 129.0292) with tilt (-17.672522 0 0)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
1 by 1 by 1 MPI processor grid
1 by 1 by 1 core grid within node
3840 atoms
replicate CPU = 0.001 seconds
# group watom type 1
# group seatom type 2
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
pair_style hybrid/overlay morse 30.0 coul/long 11.0
pair_coeff * * coul/long
pair_coeff 1 2 morse 0.975 1.285 3.089
pair_coeff 1 3 morse 0.582 1.257 3.251
pair_coeff 2 2 morse 0.076 1.675 3.642
pair_coeff 1 1 morse 0.085 2.212 4.203
pair_coeff 2 3 morse 0.807 0.731 4.497
pair_coeff 3 3 morse 0.066 2.876 4.312
kspace_style pppm 1.0e-5
thermo_style custom step temp pe ke etotal press vol
thermo 50
dump 1 all atom 100 dump.min
min_style cg
minimize 1.0e-8 1.0e-8 5000 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.24879243
grid = 20 27 54
stencil order = 5
estimated absolute RMS force accuracy = 0.00010939985
estimated relative force accuracy = 7.5973993e-06
using double precision FFTW3
3d grid and FFT values/proc = 54162 29160
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 32
ghost atom cutoff = 32
binsize = 16, bins = 4 2 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair morse, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton/tri
stencil: half/bin/3d/tri
bin: standard
(2) pair coul/long, perpetual, trim from (1)
attributes: half, newton on, cut 13
pair build: trim
stencil: none
bin: none
Setting up cg style minimization ...
Unit style : metal
Current step : 0
ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_bin.cpp:248)
Last command: minimize 1.0e-8 1.0e-8 5000 10000
job aborted:
[ranks] message
[0] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 1, comm rank 0
This is the data file
# LAMMPS data file written by OVITO Basic 3.10.6
15 atoms
3 atom types
0.0 4.41813045 xlo xhi
0.0 3.8262132069 ylo yhi
0.0 32.25729904 zlo zhi
-2.209065225 0.0 0.0 xy xz yz
Masses
1 208.98038 # Bi3+
2 127.6 # Te2-
3 127.6
Atoms # charge
1 1 +0.38 0.0 0.0 12.8006565589
2 1 +0.38 0.0 0.0 19.4566424811
3 1 +0.38 2.209065225 1.2754044023 23.5530895722
4 1 +0.38 2.209065225 1.2754044023 30.2090754945
5 1 +0.38 4.4408920985e-16 2.5508088046 2.0482235455
6 1 +0.38 4.4408920985e-16 2.5508088046 8.7042094678
7 2 -0.26 0.0 0.0 6.9936321034
8 3 -0.24 0.0 0.0 25.2636669366
9 2 -0.26 2.209065225 1.2754044023 17.7460651167
10 2 -0.26 2.209065225 1.2754044023 3.75880091
11 3 -0.24 4.4408920985e-16 2.5508088046 28.49849813
12 2 -0.26 4.4408920985e-16 2.5508088046 14.5112339233
13 2 -0.26 0.0 0.0 0.0
14 3 -0.24 2.209065225 1.2754044023 10.7524330133
15 2 -0.26 4.4408920985e-16 2.5508088046 21.5048660267
C:\Users\Sadat Abdullah\LAMMPS 64-bit 29Aug2024-MSMPI\bin>lmp -in in.relax -echo screen -nb
LAMMPS (29 Aug 2024 - Update 1)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Loaded 0 plugins from D:\LAMMPS 64-bit 29Aug2024-MSMPI\plugins
# This is the control script for LAMMPS
echo both
#-------------------------------------------------------------------------------
# Stage 2.1: Initialize LAMMPS run
#-------------------------------------------------------------------------------
units metal
atom_style charge
boundary p p p
processors * * * grid numa
read_data Bi2Te3.data
Reading data file ...
triclinic box = (0 0 0) to (4.4181304 3.8262132 32.257299) with tilt (-2.2090652 0 0)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
1 by 1 by 1 MPI processor grid
1 by 1 by 1 core grid within node
reading atoms ...
15 atoms
read_data CPU = 0.001 seconds
replicate 8 8 4
Replication is creating a 8x8x4 = 256 times larger system...
triclinic box = (0 0 0) to (35.345044 30.609706 129.0292) with tilt (-17.672522 0 0)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
1 by 1 by 1 MPI processor grid
1 by 1 by 1 core grid within node
3840 atoms
replicate CPU = 0.001 seconds
# group watom type 1
# group seatom type 2
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
pair_style hybrid/overlay morse 30.0 coul/long 11.0
pair_coeff * * coul/long
pair_coeff 1 2 morse 0.975 1.285 3.089
pair_coeff 1 3 morse 0.582 1.257 3.251
pair_coeff 2 2 morse 0.076 1.675 3.642
pair_coeff 1 1 morse 0.085 2.212 4.203
pair_coeff 2 3 morse 0.807 0.731 4.497
pair_coeff 3 3 morse 0.066 2.876 4.312
kspace_style pppm 1.0e-5
thermo_style custom step temp pe ke etotal press vol
thermo 50
dump 1 all atom 100 dump.min
min_style cg
minimize 1.0e-8 1.0e-8 5000 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.24879243
grid = 20 27 54
stencil order = 5
estimated absolute RMS force accuracy = 0.00010939985
estimated relative force accuracy = 7.5973993e-06
using double precision FFTW3
3d grid and FFT values/proc = 54162 29160
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 32
ghost atom cutoff = 32
binsize = 16, bins = 4 2 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair morse, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton/tri
stencil: half/bin/3d/tri
bin: standard
(2) pair coul/long, perpetual, trim from (1)
attributes: half, newton on, cut 13
pair build: trim
stencil: none
bin: none
Setting up cg style minimization ...
Unit style : metal
Current step : 0
ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_bin.cpp:248)
Last command: minimize 1.0e-8 1.0e-8 5000 10000
job aborted:
[ranks] message
[0] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 1, comm rank 0
Here is the error that is terminating your run. The default neighbor list settings in LAMMPS are sufficient for the simulation of typical molecular systems are normal densities and with a typical interaction cutoff of 10-15 Angstrom. You are, however, using a cutoff of 30 Angstrom for the Morse potential and thus the number of neighbors is much larger (remember that the number of neighbors grows O(N^3) with the cutoff). So you either need to reduce the cutoff or increase the size of the neighbor list storage using neigh_modify.
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