Dear LAMMPS community,
I am having difficulty running a simulation using the 30 Aug 2013 distribution. My simulation size is fairly large, 305793 atoms. The input data consists of the final positions of a previous dump file (a heated and cooled block of Cu). I am encountering a neighbor list overflow error at the beginning of the run with the script below. When I increase the page size in nigh_modify to a very large number (maybe 5000000000), I get a ‘segmentation fault error, address not mapped’ error from the OS (see below). It’s not clear to me why I am seeing the list overflow error, especially since I am running the same configuration with the same .eam potential that was used previously. I am relatively new to LAMMPS, so any insight/education/advice would be greatly appreciated.
#---------Initialize Sim---------------
clear
units metal
dimension 3
boundary p p p
atom_style atomic
#---------Create Atoms -----------------
read_data start.data.txt
--------Define Interatomic Potential —
pair_style eam/alloy
pair_coeff * * Cu_mishin1.eam.alloy Cu
neighbor 2.0 bin
neigh_modify delay 10 every 2 check yes page 500000 one 50000
#---------Run-----------------------------
reset_timestep 0
timestep 0.001
fix 1 all nvt temp 700 700 0.1
Set thermo output
thermo 1000
thermo_style custom step lx ly lz press pe ke etotal vol temp
dump 1 all atom 40000 dump_up.atom
Run for 3 nanosectons (1 fs timestep)
run 3000000
unfix 1
OS ERROR
LAMMPS (30 Aug 2013)
Reading data file …
orthogonal box = (0 0 0) to (100 100 100)
2 by 4 by 4 MPI processor grid
305793 atoms
Setting up run …
[n072:30924] *** Process received signal ***
[n072:30924] Signal: Segmentation fault (11)
[n072:30924] Signal code: Address not mapped (1)
[n072:30924] Failing at address: (nil)
[n072:30924] [ 0] /lib64/libpthread.so.0 [0x36c2a0eb10]
[n072:30924] [ 1] lmp_openmpi(_ZN9LAMMPS_NS8Neighbor15half_bin_newtonEPNS_9NeighListE+0x35c) [0x72fbfc]
[n072:30924] [ 2] lmp_openmpi(_ZN9LAMMPS_NS8Neighbor5buildEi+0x483) [0x722753]
[n072:30924] [ 3] lmp_openmpi(_ZN9LAMMPS_NS6Verlet5setupEv+0x156) [0x986346]
[n072:30924] [ 4] lmp_openmpi(_ZN9LAMMPS_NS3Run7commandEiPPc+0xd1e) [0x94f2ae]
[n072:30924] [ 5] lmp_openmpi(_ZN9LAMMPS_NS5Input15command_creatorINS_3RunEEEvPNS_6LAMMPSEiPPc+0x29) [0x6b27b9]
[n072:30924] [ 6] lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0x2225) [0x6b7f65]
[n072:30924] [ 7] lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x1cb) [0x6b42cb]
[n072:30924] [ 8] lmp_openmpi(main+0x94) [0x6cccc4]
[n072:30924] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x36c1e1d994]
[n072:30924] [10] lmp_openmpi(_ZNSt8ios_base4InitD1Ev+0x41) [0x490929]
[n072:30924] *** End of error message ***