LAMMPS and MLIP on Mac

Install OpenMPI

First, install OpenMPI following directions here

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cd openmpi*
./configure
make all install

OpenMPI creates the following files on /usr/local/bin . Check it is in your PATH

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❯ ll mpi*
Permissions Size User     Date Modified Date Created Date Accessed Name
lrwxr-xr-x    12 chinchay  9 Apr 23:15   9 Apr 23:15  9 Apr 23:15  mpic++ -> opal_wrapper
lrwxr-xr-x    12 chinchay  9 Apr 23:15   9 Apr 23:15  9 Apr 23:15  mpicc -> opal_wrapper
lrwxr-xr-x    12 chinchay  9 Apr 23:15   9 Apr 23:15  9 Apr 23:15  mpicxx -> opal_wrapper
lrwxr-xr-x     7 chinchay  9 Apr 23:14   9 Apr 23:14  9 Apr 23:14  mpiexec -> orterun
lrwxr-xr-x    12 chinchay  9 Apr 23:15   9 Apr 23:15  9 Apr 23:15  mpif77 -> opal_wrapper
lrwxr-xr-x    12 chinchay  9 Apr 23:15   9 Apr 23:15  9 Apr 23:15  mpif90 -> opal_wrapper
lrwxr-xr-x    12 chinchay  9 Apr 23:15   9 Apr 23:15  9 Apr 23:15  mpifort -> opal_wrapper
lrwxr-xr-x     7 chinchay  9 Apr 23:14   9 Apr 23:14  9 Apr 23:14  mpirun -> orterun
❯ pwd
/usr/local/bin

LAMMPS as shared library

First, use virtualenv (in Graham) or pyenv (in my local machine) to define the python version:

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pyenv local <myenv>

Download LAMMSP:

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git clone https://github.com/lammps/lammps.git
cd lammps/src/MAKE/OPTIONS

I tried with other options (Makefile.mpi, Makefile.serial, Makefile.mac) but they didn’t work, MacOS Big Sur complains about not finding compatibility with c++11. Makefile.g++_openmpi worked and it already contains the flag mpicxx -std=c++11.

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cd ../../ # return to lammps/src
make yes-molecule
make g++_openmpi mode=shlib

At this point, *.so libraries have been created in lammps/src.

MLIP

Download MLIP and cd into the directory

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export mylammps="<path/to/LAMMPS>"
./configure --lammps=$mylammps

For Big Sur, I needed to modify configuration files:

• MLIP will be unable to find the gfortran library (errors with -lgfortran). Tell it manually where to search for the library through the flag -L (while -l is used to make reference to the library itself). I ended up installing gfortran by downloading it, instead of using it using brew, so in my case, I need to check for the following lines in make/config.mk:

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LDFLAGS += $(LIB_DIR)/lib_mlip_cblas.a -L/usr/local/gfortran/lib -lgfortran
...
LAMMPS_SYSLIB =  $(abspath $(LIB_DIR)/lib_mlip_cblas.a) -L/usr/local/gfortran/lib -lgfortran

If using gfortran from brew, check libgfortran.a is in /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 (or modifiy it according to your gcc version), and add it. Example: -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10

• In a later step installation, LAMMPS will complain again about compatibiligy issues with c++11, so add this flag in make/config.mk:

  1	CXX_EXE = mpicxx -std=c++11

• Also, modify the make/config.mk to the type of machine you chose in LAMMPS installation:

  1	LAMMPS_TARGET_MPI = g++_openmpi

• The default value of LAMMPS_TARGET_SERIAL = serial in make/config.mk will look for Makefile.serial in <path/to/LAMMPS>/src/MAKE and errors about std=c++11 will be found if not adding the following to the Makefile:

  1	CC = g++ -std=c++11

Now you are ready to install MLIP, and use it through LAMMPS:

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make clean
make mlp
make lammps-shlib

Finally, save the paths into .bash_profile or .zshrc:

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export mylammps="<path/to/LAMMPS>"
export mymlip="<path/to/MLIP>" # not the bin/ directory, but the parent one, needed to find lib/
export PYTHONPATH=$mylammps/python:$PYTHONPATH
export LD_LIBRARY_PATH=$mylammps/src:/mymlip/lib:$LD_LIBRARY_PATH ## will search for $mylammps/src/liblammps_intel_cpu_intelmpi.so and /mlip/lib/liblammps_mpi.so

In python:

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from lammps import lammps
lmp = lammps()

Change the extension of liblammps.so to liblammps.dylib if python can’t find the library. <path/to/LAMMPS>/python/lammps/core.py will look for the extension *.dylib for Darwin (Mac) instead of *.so for Linux.