2.3.1. Running LAMMPS and Python in serial

To run a LAMMPS in serial, type these lines into Python interactively from the bench directory:

from lammps import lammps
lmp = lammps()

Or put the same lines in the file test.py and run it as

python3 test.py

Either way, you should see the results of running the in.lj benchmark on a single processor appear on the screen, the same as if you had typed something like:

lmp_serial -in in.lj

2.3.2. Running LAMMPS and Python in parallel with MPI

To run LAMMPS in parallel, assuming you have installed the mpi4py package as discussed Extending Python to run in parallel, create a test.py file containing these lines:

from mpi4py import MPI
from lammps import lammps
lmp = lammps()
me = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
print("Proc %d out of %d procs has" % (me,nprocs),lmp)

You can run the script in parallel as:

mpirun -np 4 python3 test.py

and you should see the same output as if you had typed

mpirun -np 4 lmp_mpi -in in.lj

Note that without the mpi4py specific lines from test.py

from lammps import lammps
lmp = lammps()

running the script with mpirun on \(P\) processors would lead to \(P\) independent simulations to run parallel, each with a single processor. Therefore, if you use the mpi4py lines and you see multiple LAMMPS single processor outputs, mpi4py is not working correctly.

Also note that once you import the mpi4py module, mpi4py initializes MPI for you, and you can use MPI calls directly in your Python script, as described in the mpi4py documentation. The last line of your Python script should be MPI.finalize(), to ensure MPI is shut down correctly.

2.3.3. Running Python scripts

Note that any Python script (not just for LAMMPS) can be invoked in one of several ways:

python script.py
python -i script.py

The last command requires that the first line of the script be something like this:



#!/usr/bin/env python

where the path in the first case needs to point to where you have Python installed (the second option is workaround for when this may change), and that you have made the script file executable:

chmod +x script.py

Without the -i flag, Python will exit when the script finishes. With the -i flag, you will be left in the Python interpreter when the script finishes, so you can type subsequent commands. As mentioned above, you can only run Python interactively when running Python on a single processor, not in parallel.