$\renewcommand{\AA}{\text{Å}}$

3.3. Link LAMMPS as a library to another code

LAMMPS is designed as a library of C++ objects that can be integrated into other applications, including Python scripts. The files src/library.cpp and src/library.h define a C-style API for using LAMMPS as a library. See the Library interface to LAMMPS page for a description of the interface and how to use it for your needs.

The Basic build options page explains how to build LAMMPS as either a shared or static library. This results in a file in the compilation folder called liblammps.a or liblammps_<name>.a in case of building a static library. In case of a shared library, the name is the same only that the suffix is going to be either .so or .dylib or .dll instead of .a depending on the OS. In some cases, the .so file may be a symbolic link to a file with the suffix .so.0 (or some other number).

Note

Care should be taken to use the same MPI library for the calling code and the LAMMPS library, unless LAMMPS is to be compiled without (real) MPI support using the included STUBS MPI library.

3.3.1. Link with LAMMPS as a static library

The calling application can link to LAMMPS as a static library with compilation and link commands, as in the examples shown below. These are examples for a code written in C in the file caller.c. The benefit of linking to a static library is, that the resulting executable is independent of that library since all required executable code from the library is copied into the calling executable.

This assumes that LAMMPS has been configured without setting a LAMMPS_MACHINE name, installed with “make install”, and the PKG_CONFIG_PATH environment variable has been updated to include the liblammps.pc file installed into the configured destination folder. The commands to compile and link a coupled executable are then:

mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)

This assumes that LAMMPS has been compiled in the folder ${HOME}/lammps/src with “make mpi”. The commands to compile and link a coupled executable are then:

mpicc -c -O -I${HOME}/lammps/src caller.c
mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi

The -I argument is the path to the location of the library.h header file containing the interface to the LAMMPS C-style library interface. The -L argument is the path to where the liblammps_mpi.a file is located. The -llammps_mpi argument is shorthand for telling the compiler to link the file liblammps_mpi.a. If LAMMPS has been built as a shared library, then the linker will use liblammps_mpi.so instead. If both files are available, the linker will usually prefer the shared library. In case of a shared library, you may need to update the LD_LIBRARY_PATH environment variable or running the caller executable will fail since it cannot find the shared library at runtime.

However, it is only as simple as shown above for the case of a plain LAMMPS library without any optional packages that depend on libraries (bundled or external) or when using a shared library. Otherwise, you need to include all flags, libraries, and paths for the coupled executable, that are also required to link the LAMMPS executable.

When using CMake, additional libraries with sources in the lib folder are built, but not included in liblammps.a and (currently) not installed with make install and not included in the pkgconfig configuration file. They can be found in the top level build folder, but you have to determine the necessary link flags manually. It is therefore recommended to either use the traditional make procedure to build and link with a static library or build and link with a shared library instead.

After you have compiled a static LAMMPS library using the conventional build system for example with “make mode=static serial”. And you also have installed the POEMS package after building its bundled library in lib/poems. Then the commands to build and link the coupled executable change to:

gcc -c -O -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
             -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src \
             -llammps_serial -lpoems -lmpi_stubs

Note, that you need to link with g++ instead of gcc even if you have written your code in C, since LAMMPS itself is C++ code. You can display the currently applied settings for building LAMMPS for the “serial” machine target by using the command:

make mode=print serial

Which should output something like:

# Compiler:
CXX=g++
# Linker:
LD=g++
# Compilation:
CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
# Linking:
LDFLAGS=-g -O
# Libraries:
LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs

From this you can gather the necessary paths and flags. With makefiles for other machine configurations you need to do the equivalent and replace “serial” with the corresponding “machine” name of the makefile.

3.3.2. Link with LAMMPS as a shared library

When linking to LAMMPS built as a shared library, the situation becomes much simpler, as all dependent libraries and objects are either included in the shared library or registered as a dependent library in the shared library file. Thus, those libraries need not be specified when linking the calling executable. Only the -I flags are needed. So the example case from above of the serial version static LAMMPS library with the POEMS package installed becomes:

The commands with a shared LAMMPS library compiled with the CMake build process are the same as for the static library.

mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf --libs)

The commands with a shared LAMMPS library compiled with the traditional make build using make mode=shared serial becomes:

gcc -c -O -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial

Locating liblammps.so at runtime

Unlike with a static link, now the liblammps.so file is required at runtime and needs to be in a folder, where the shared linker program of the operating system can find it. This would be either a folder like /usr/local/lib64 or ${HOME}/.local/lib64 or a folder pointed to by the LD_LIBRARY_PATH environment variable. You can type

printenv LD_LIBRARY_PATH

to see what directories are in that list.

Or you can add the LAMMPS src directory or the directory you performed a CMake style build in to your LD_LIBRARY_PATH environment variable, so that the current version of the shared library is always available to programs that use it.

For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you would add something like this to your ${HOME}/.profile file:

LD_LIBRARY_PATH ${LD_LIBRARY_PATH-/usr/lib64}:${HOME}/lammps/src
export LD_LIBRARY_PATH

For the csh or tcsh shells, you would equivalently add something like this to your ${HOME}/.cshrc file:

setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src

You can verify whether all required shared libraries are found with the ldd tool. Example:

LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
     linux-vdso.so.1 (0x00007ffe729e0000)
     liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
     libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
     libm.so.6 => /lib64/libm.so.6 (0x00007fc91b83e000)
     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fc91b824000)
     libc.so.6 => /lib64/libc.so.6 (0x00007fc91b65b000)
     /lib64/ld-linux-x86-64.so.2 (0x00007fc91c094000)

If a required library is missing, you would get a ‘not found’ entry:

ldd caller
     linux-vdso.so.1 (0x00007ffd672fe000)
     liblammps.so => not found
     libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)
     libm.so.6 => /usr/lib64/libm.so.6 (0x00007fb7c7d40000)
     libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007fb7c7d26000)
     libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
     /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)