Error debugging

LAMMPS LAMMPS Beginners
1

Hi, all,

Does anybody solve this problem?

The following is the error message:

PPPM initialization …
[virtualO:11497] *** Process received signal ***
[virtualO:11497] Signal: Segmentation fault: 11 (11)
[virtualO:11497] Signal code: Invalid permissions (2)
[virtualO:11497] Failing at address: 0x10
[virtualO:11497] [ 0] 0 libsystem_platform.dylib 0x00000001828b7584 _sigtramp + 56
[virtualO:11497] [ 1] 0 libfftw3.3.dylib 0x00000001036b6c60 fftw_plan_awake + 32
[virtualO:11497] [ 2] 0 liblammps_mpi.0.dylib 0x000000010490cc60 _ZN9LAMMPS_NS5FFT3dD0Ev + 36
[virtualO:11497] [ 3] 0 liblammps_mpi.0.dylib 0x000000010493e354 _ZN9LAMMPS_NS4PPPM10deallocateEv + 796
… … … (very long)

prterun noticed that process rank 2 with PID 11499 on node virtualO exited on
signal 11 (Segmentation fault: 11).

The code is as follows:

units real
atom_style full
atom_modify map array

newton off
processors * * 1
region box block -100 100 -100 100 -100 100
create_box 6 box

mass 1 15.9994 # O(water)
mass 2 1.008 # H(water)
mass 3 1.0e-3 # TIP5P M-site
mass 4 14.0067 # N(N2)
mass 5 15.9994 # O(TiO2)
mass 6 47.867 # Ti(TiO2)

special_bonds lj/coul 0.0 0.0 0.0

molecule water tip5p.mol
molecule n2 n2.mol toff 3

create_atoms 0 random 21600 34564 box mol water 25678 overlap 2.0
create_atoms 0 random 2160 13456 box mol n2 12536 overlap 3.0

region nanoparticle_void sphere 0 0 0 15
delete_atoms region nanoparticle_void mol yes

read_data tio2_neutral.data add append offset 4 0 0 0 0

group water_group type 1 2 3
group n2_group type 4
group tio2_group type 5 6
group rigid_group union water_group n2_group

neighbor 3.0 bin
neigh_modify delay 0 every 1 check yes
comm_modify vel yes

thermo_style custom step temp pe ke etotal press density
thermo 2000

pair_style hybrid/overlay lj/cut/coul/cut 12.0 buck 12.0
kspace_style none

pair_coeff * * lj/cut/coul/cut 0.0 1.0
pair_coeff 1 1 lj/cut/coul/cut 0.1780 3.0970
pair_coeff 2 2 lj/cut/coul/cut 0.0 1.0
pair_coeff 3 3 lj/cut/coul/cut 0.0 1.0
pair_coeff 4 4 lj/cut/coul/cut 0.0720 3.3000
pair_coeff 5 5 lj/cut/coul/cut 0.00261 3.1180
pair_coeff 6 6 lj/cut/coul/cut 0.00405 2.7660
pair_coeff 1 2 lj/cut/coul/cut 0.0 1.0
pair_coeff 1 3 lj/cut/coul/cut 0.0 1.0
pair_coeff 1 4 lj/cut/coul/cut 0.1130 3.1985
pair_coeff 1 5 lj/cut/coul/cut 0.0215 3.1075
pair_coeff 1 6 lj/cut/coul/cut 0.0269 2.9315
pair_coeff 2 3 lj/cut/coul/cut 0.0 1.0
pair_coeff 2 4 lj/cut/coul/cut 0.0 1.0
pair_coeff 2 5 lj/cut/coul/cut 0.0 1.0
pair_coeff 2 6 lj/cut/coul/cut 0.0 1.0
pair_coeff 3 4 lj/cut/coul/cut 0.0 1.0
pair_coeff 3 5 lj/cut/coul/cut 0.0 1.0
pair_coeff 3 6 lj/cut/coul/cut 0.0 1.0
pair_coeff 4 5 lj/cut/coul/cut 0.0137 3.2090
pair_coeff 4 6 lj/cut/coul/cut 0.0171 3.0330
pair_coeff 5 6 lj/cut/coul/cut 0.00326 2.9420

pair_coeff 5 5 buck 9547.9 0.2192 32.0
pair_coeff 6 6 buck 0.0 1.0 0.0
pair_coeff 5 6 buck 1638.2 0.3170 0.0

reset_timestep 0
timestep 0.2
fix rig_pre rigid_group rigid/nvt/small molecule temp 50.0 200.0 100.0
fix int_pre tio2_group nve/limit 0.02
fix lan_pre tio2_group langevin 50.0 200.0 100.0 12345 zero yes
run 10000
unfix rig_pre
unfix int_pre
unfix lan_pre

pair_style hybrid/overlay lj/cut/coul/long 12.0 buck 12.0
kspace_style pppm 1.0e-4
kspace_modify order 5 fftbench no mesh 48 48 48 gewald 0.16093

pair_coeff * * lj/cut/coul/long 0.0 1.0
pair_coeff 1 1 lj/cut/coul/long 0.1780 3.0970
pair_coeff 2 2 lj/cut/coul/long 0.0 1.0
pair_coeff 3 3 lj/cut/coul/long 0.0 1.0
pair_coeff 4 4 lj/cut/coul/long 0.0720 3.3000
pair_coeff 5 5 lj/cut/coul/long 0.00261 3.1180
pair_coeff 6 6 lj/cut/coul/long 0.00405 2.7660
pair_coeff 1 2 lj/cut/coul/long 0.0 1.0
pair_coeff 1 3 lj/cut/coul/long 0.0 1.0
pair_coeff 1 4 lj/cut/coul/long 0.1130 3.1985
pair_coeff 1 5 lj/cut/coul/long 0.0215 3.1075
pair_coeff 1 6 lj/cut/coul/long 0.0269 2.9315
pair_coeff 2 3 lj/cut/coul/long 0.0 1.0
pair_coeff 2 4 lj/cut/coul/long 0.0 1.0
pair_coeff 2 5 lj/cut/coul/long 0.0 1.0
pair_coeff 2 6 lj/cut/coul/long 0.0 1.0
pair_coeff 3 4 lj/cut/coul/long 0.0 1.0
pair_coeff 3 5 lj/cut/coul/long 0.0 1.0
pair_coeff 3 6 lj/cut/coul/long 0.0 1.0
pair_coeff 4 5 lj/cut/coul/long 0.0137 3.2090
pair_coeff 4 6 lj/cut/coul/long 0.0171 3.0330
pair_coeff 5 6 lj/cut/coul/long 0.00326 2.9420
pair_coeff 5 5 buck 9547.9 0.2192 32.0
pair_coeff 6 6 buck 0.0 1.0 0.0
pair_coeff 5 6 buck 1638.2 0.3170 0.0

reset_timestep 0
timestep 0.25
fix rig_eq rigid_group rigid/nvt/small molecule temp 233.0 233.0 100.0
fix tio2_eq tio2_group nvt temp 233.0 233.0 100.0

variable s equal step
run 50070000 every 1 &
“if ‘$s == 20000’ then ‘timestep 0.5’” &
“if ‘$s == 70000’ then ‘timestep 1.0’”

2

Hi @testpilot,

please try to follow the forum guidelines and format your post accordingly.

You’re more likely to get relevant advice if you present the lammps version your using, how it was compiled, where the error appears and if it still does with some minimal example (i.e. not your production run script).

As this appears to be an error related to the call of fft library, check for the installation and compilation of the LAMMPS executable you’re using with the people in charge if necessary.

3

@testpilot
Yup. Looks like a defective FFTW installation. Try compiling LAMMPS using the internal KISS FFT library. The speed difference between the two on any reasonable input that you can run on a local machine is negligible. Since you seem to be on macOS, I would suggest you also experiment with a pre-compiled macOS package from here: Releases · lammps/lammps · GitHub

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