I Installed lammps by pre-compiled RPM packages , but I get "mpirun noticed ..... exited on signal 11 (Segmentation fault)."

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1

Hi everyone
I installed lammps by pre-compiled RPM packages (Non-MPI LAMMPS executable compiled multi-threading support via OpenMP. The name of the executable is: lmp_g++
). Then I installed openmpi myself. I can successfully run ReaxFF simulations (RDX) in examples with 4 core.However, when I run my own input I got this error:

mpirun noticed that process rank 0 with PID 14438 on node localhost.localdomain exited on signal 11 (Segmentation fault).

Here is my input and data.file

input:
units real
boundary p p p
atom_style full
read_data coro.data

pair_style reax/c NULL
pair_coeff * * ffield.reax C H

compute reax all pair reax/c

variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]

neighbor 2.0 bin
neigh_modify every 10 delay 0 check no

fix 1 all nvt temp 0 2000 100
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 3 all reax/c/bonds 200 bonds.coro
fix 4 all reax/c/species 10 10 100 corospecies.out

thermo 100
thermo_style custom step temp epair etotal &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq

timestep 1.0

dump 1 all atom 100 dump.reaxc.rdx

#dump 2 all image 25 image.*.jpg type type &

axes yes 0.8 0.02 view 60 -30

#dump_modify 2 pad 3

#dump 3 all movie 25 movie.mpg type type &

axes yes 0.8 0.02 view 60 -30

#dump_modify 3 pad 3

run 100000

coro.data

Pair Coeffs

2

There is too little information to tell. What version of LAMMPS are you using? It seems you have pre-defined bonds. Can you run without bonds?

Ray

3

Hi everyone
I installed lammps by pre-compiled RPM packages (Non-MPI LAMMPS executable
compiled multi-threading support via OpenMP. The name of the executable is:
lmp_g++
). Then I installed openmpi myself. I can successfully run ReaxFF
simulations (RDX) in examples with 4 core.However, when I run my own input
I got this error:

​please note that OpenMPI != OpenMP. thus ​there is no point in installing
an openmpi, when you are using the non-mpi rpm.
please also note that for the user-reaxc package, there is no OpenMP
support. ​

mpirun noticed that process rank 0 with PID 14438 on node

localhost.localdomain exited on signal 11 (Segmentation fault).

the examples provided examples with LAMMPS work, but your own input gives
an error, it is most likely, that there is an error in your input.
inputs for reax can be tricky and yours look needlessly complicated. try
starting by building an input for a simple system from scratch and thus
verify that your understanding of how to set up such a calculation is
correct. if you cannot get this simple input going, post the complete input
deck with a detailed description here and see if people here can help you.

axel.​

4

Also try with a smaller timestep first (e.g. 0.1 fs), and if that does not work, try without the reax/c/bonds and reax/c/species fixes. If that does not work still, post a complete input deck.

Ray

5

Hi everyone
I solve my problem. This error is due to that I set the start temperature as 0.
Change this line of input " 1 all nvt temp 0 2000 100" to " 1 all nvt temp 10 (any value is ok except 0) 2000 100 "

Thanks
everyone

6

It is true that an absolute zero is a bad temperature in MD, but are you sure you changed nothing else? I am just wondering.

Thanks,
Ray