Error Lammps: MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.

LAMMPS LAMMPS General Discussion
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1

I’m encountering an error in my LAMMPS/Mace NEB calculation for oxygen vacancy diffusion. The log.err file shows “ERROR: Incorrect atom format in NEB file (src/REPLICA/neb.cpp:502)”, but the log.out file does not. I’ve checked my input file multiple times and don’t believe there’s a syntax error.

srun: Job step aborted: Waiting up to 32 seconds for job step to finish.

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with error code 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

srun lmp -partition 4x1 -in in.mace(this is the command I am using for parallelisation)

input file : neb 0.0 0e-3 2000 6000 4 final poscar_b_neb.data

write_dump all custom 100 neb.lammpstrj id type x y z,

2

Clearly, LAMMPS thinks differently and you cannot argue with software. Thus you have to change your NEB file so that LAMMPS will accept it.

3

Hi Axel,

Thanks for your reply. If possible, can you please see my initial and final file, and provide me with feedback on what the error is by my part, which is triggering this error and below is my input file:

units metal
atom_style atomic
atom_modify map yes
newton on
boundary p p p

#log lscf_mace_restart.log # write thermo info to this file

read_data initial.data

pair_style mace no_domain_decomposition
pair_coeff * * /home/parul.goel/mace/mace_matpes.model-lammps.pt La Sr Ni Fe O

mass 1 138.90547 # La
mass 2 87.62 # Sr
mass 3 58.6934 #Ni
mass 4 55.845 # Fe
mass 5 15.999 # O

neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes

#thermo 100

timestep 0.001 # ps (in units metal)

neb 0.0 1.0e-4 4000 8000 4 final final.data

write_dump all custom 100 neb.lammpstrj id type x y z

initial.data (40.7 KB)

final.data (21.4 KB) i just renamed the file as initial and final for easier understanding

4

You are feeding the “neb” command a data file in the format suitable for “read_data”, but the format for that file is very different. Please read the documentation more carefully and follow what it says.

5

Thanks Alex,

For your piece of advice, I identified my mistake and converted my final file into the correct format as per neb documentation. Now its runnig successfully !