12.5. Extending Python to run in parallel

If you wish to run LAMMPS in parallel from Python, you need to extend your Python with an interface to MPI. This also allows you to make MPI calls directly from Python in your script, if you desire.

We have tested this with mpi4py and pypar:

• MPI for Python

• pypar

We recommend the use of mpi4py as it is the more complete MPI interface, and as of version 2.0.0 mpi4py allows passing a custom MPI communicator to the LAMMPS constructor, which means one can easily run one or more LAMMPS instances on subsets of the total MPI ranks.

To install mpi4py (version mpi4py-3.0.3 as of Nov 2019), unpack it and from its main directory, type

python setup.py build
sudo python setup.py install

Again, the “sudo” is only needed if required to copy mpi4py files into your Python distribution’s site-packages directory. To install with user privilege into the user local directory type

python setup.py install --user

If you have successfully installed mpi4py, you should be able to run Python and type

from mpi4py import MPI

without error. You should also be able to run python in parallel on a simple test script

% mpirun -np 4 python test.py

where test.py contains the lines

from mpi4py import MPI
comm = MPI.COMM_WORLD
print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size())

and see one line of output for each processor you run on.

Note

To use mpi4py and LAMMPS in parallel from Python, you must insure both are using the same version of MPI. If you only have one MPI installed on your system, this is not an issue, but it can be if you have multiple MPIs. Your LAMMPS build is explicit about which MPI it is using, since you specify the details in your low-level src/MAKE/Makefile.foo file. Mpi4py uses the “mpicc” command to find information about the MPI it uses to build against. And it tries to load “libmpi.so” from the LD_LIBRARY_PATH. This may or may not find the MPI library that LAMMPS is using. If you have problems running both mpi4py and LAMMPS together, this is an issue you may need to address, e.g. by moving other MPI installations so that mpi4py finds the right one.