3.4. Basic build options¶

The following topics are covered on this page, for building with both CMake and make:

Serial vs parallel build
Choice of compiler and compile/link options
Build the LAMMPS executable and library
Including and removing debug support
Install LAMMPS after a build

3.4.1. Serial vs parallel build¶

LAMMPS is written to use the ubiquitous MPI (Message Passing Interface) library API for distributed memory parallel computation. You need to have such a library installed for building and running LAMMPS in parallel using a domain decomposition parallelization. It is compatible with the MPI standard version 2.x and later. LAMMPS can also be built into a “serial” executable for use with a single processor using the bundled MPI STUBS library.

Independent of the distributed memory MPI parallelization, parts of LAMMPS are also written with support for shared memory parallelization using the OpenMP threading standard. A more detailed discussion of that is below.

-D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
-D BUILD_OMP=value        # yes or no, default is yes if a compatible compiler is detected
-D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
                          # no default value

The executable created by CMake (after running make) is named lmp unless the LAMMPS_MACHINE option is set. When setting LAMMPS_MACHINE=name the executable will be called lmp_name. Using BUILD_MPI=no will enforce building a serial executable using the MPI STUBS library.

The build with traditional makefiles has to be done inside the source folder src.

make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
make serial             # serial build, produces lmp_serial using Makefile/serial
make mybox              # uses Makefile.mybox to produce lmp_mybox

Any make machine command will look up the make settings from a file Makefile.machine in the folder src/MAKE or one of its sub-directories MINE, MACHINES, or OPTIONS, create a folder Obj_machine with all objects and generated files and an executable called lmp_machine. The standard parallel build with make mpi assumes a standard MPI installation with MPI compiler wrappers where all necessary compiler and linker flags to get access and link with the suitable MPI headers and libraries are set by the wrapper programs. For other cases or the serial build, you have to adjust the make file variables MPI_INC, MPI_PATH, MPI_LIB as well as CC and LINK. To enable OpenMP threading usually a compiler specific flag needs to be added to the compile and link commands. For the GNU compilers, this is -fopenmp, which can be added to the CC and LINK makefile variables.

For the serial build the following make variables are set (see src/MAKE/Makefile.serial):

CC =            g++
LINK =          g++
MPI_INC =       -I../STUBS
MPI_PATH =      -L../STUBS
MPI_LIB =       -lmpi_stubs

You also need to build the STUBS library for your platform before making LAMMPS itself. A make serial build does this for you automatically, otherwise, type make mpi-stubs from the src directory, or make from the src/STUBS dir. If the build fails, you may need to edit the STUBS/Makefile for your platform. The stubs library does not provide MPI/IO functions required by some LAMMPS packages, e.g. MPIIO or LATBOLTZ, and thus is not compatible with those packages.

Note

The file src/STUBS/mpi.cpp provides a CPU timer function called MPI_Wtime() that calls gettimeofday(). If your operating system does not support gettimeofday(), you will need to insert code to call another timer. Note that the ANSI-standard function clock() rolls over after an hour or so, and is therefore insufficient for timing long LAMMPS simulations.

MPI and OpenMP support in LAMMPS¶

If you are installing MPI yourself to build a parallel LAMMPS executable, we recommend either MPICH or OpenMPI which are regularly used and tested with LAMMPS by the LAMMPS developers. MPICH can be downloaded from the MPICH home page and OpenMPI can be downloaded correspondingly from the OpenMPI home page. Other MPI packages should also work. No specific vendor provided and standard compliant MPI library is currently known to be incompatible with LAMMPS. If you are running on a large parallel machine, your system admins or the vendor should have already installed a version of MPI, which is likely to be faster than a self-installed MPICH or OpenMPI, so you should study the provided documentation to find out how to build and link with it.

The majority of OpenMP (threading) support in LAMMPS is provided by the OPENMP package; see the OPENMP package page for details. The INTEL package also includes OpenMP threading (it is compatible with OPENMP and will usually fall back on styles from that package, if a INTEL does not exist) and adds vectorization support when compiled with compatible compilers, in particular the Intel compilers on top of OpenMP. Also, the KOKKOS package can be compiled to include OpenMP threading.

In addition, there are a few commands in LAMMPS that have native OpenMP support included as well. These are commands in the MPIIO, ML-SNAP, DIFFRACTION, and DPD-REACT packages. In addition some packages support OpenMP threading indirectly through the libraries they interface to: e.g. LATTE, KSPACE, and COLVARS. See the Packages details page for more info on these packages and the pages for their respective commands for OpenMP threading info.

For CMake, if you use BUILD_OMP=yes, you can use these packages and turn on their native OpenMP support and turn on their native OpenMP support at run time, by setting the OMP_NUM_THREADS environment variable before you launch LAMMPS.

For building via conventional make, the CCFLAGS and LINKFLAGS variables in Makefile.machine need to include the compiler flag that enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel compilers it is -qopenmp. If you are using a different compiler, please refer to its documentation.

OpenMP Compiler compatibility¶

Some compilers do not fully support the default(none) directive and others (e.g. GCC version 9 and beyond, Clang version 10 and later) may implement strict OpenMP 4.0 and later semantics, which are incompatible with the OpenMP 3.1 semantics used in LAMMPS for maximal compatibility with compiler versions in use. If compilation with OpenMP enabled fails because of your compiler requiring strict OpenMP 4.0 semantics, you can change the behavior by adding -D LAMMPS_OMP_COMPAT=4 to the LMP_INC variable in your makefile, or add it to the command line while configuring with CMake. LAMMPS will auto-detect a suitable setting for most GNU, Clang, and Intel compilers.

3.4.2. Choice of compiler and compile/link options¶

The choice of compiler and compiler flags can be important for maximum performance. Vendor provided compilers for a specific hardware can produce faster code than open-source compilers like the GNU compilers. On the most common x86 hardware most popular C++ compilers are quite similar in performance of C/C++ code at high optimization levels. When using the INTEL package, there is a distinct advantage in using the Intel C++ compiler due to much improved vectorization through SSE and AVX instructions on compatible hardware as the source code includes changes and Intel compiler specific directives to enable high degrees of vectorization. This may change over time as equivalent vectorization directives are included into OpenMP standard revisions and other compilers adopt them.

On parallel clusters or supercomputers which use “environment modules” for their compile/link environments, you can often access different compilers by simply loading the appropriate module before building LAMMPS.

By default CMake will use the compiler it finds according to internal preferences and it will add optimization flags appropriate to that compiler and any accelerator packages you have included in the build. CMake will check if the detected or selected compiler is compatible with the C++ support requirements of LAMMPS and stop with an error, if this is not the case.

You can tell CMake to look for a specific compiler with setting CMake variables (listed below) during configuration. For a few common choices, there are also presets in the cmake/presets folder. For convenience, there is a CMAKE_TUNE_FLAGS variable that can be set to apply global compiler options (applied to compilation only), to be used for adding compiler or host specific optimization flags in addition to the “flags” variables listed below. You may also specify the corresponding CMAKE_*_FLAGS variables individually, if you want to experiment with alternate optimization flags. You should specify all 3 compilers, so that the (few) LAMMPS source files written in C or Fortran are built with a compiler consistent with the one used for the C++ files:

-D CMAKE_CXX_COMPILER=name            # name of C++ compiler
-D CMAKE_C_COMPILER=name              # name of C compiler
-D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler

-D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
-D CMAKE_C_FLAGS=string               # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler

A few example command lines are:

# Building with GNU Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
# Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
# Building with Intel oneAPI Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
# Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
# Building with PGI/Nvidia Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran

For compiling with the Clang/LLVM compilers a CMake preset is provided that can be loaded with -C ../cmake/presets/clang.cmake. Similarly, -C ../cmake/presets/intel.cmake should switch the compiler toolchain to the legacy Intel compilers, -C ../cmake/presets/oneapi.cmake will switch to the LLVM based oneAPI Intel compilers, and -C ../cmake/presets/pgi.cmake will switch the compiler to the PGI compilers.

In addition you can set CMAKE_TUNE_FLAGS to specifically add compiler flags to tune for optimal performance on given hosts. By default this variable is empty.

Note

When the cmake command completes, it prints a summary to the screen which compilers it is using and what flags and settings will be used for the compilation. Note that if the top-level compiler is mpicxx, it is simply a wrapper on a real compiler. The underlying compiler info is what CMake will try to determine and report. You should check to confirm you are using the compiler and optimization flags you want.

The “compiler/linker settings” section of a Makefile.machine lists compiler and linker settings for your C++ compiler, including optimization flags. For a parallel build it is recommended to use mpicxx or mpiCC, since these compiler wrappers will include a variety of settings appropriate for your MPI installation and thus avoiding the guesswork of finding the right flags.

Parallel build (see src/MAKE/Makefile.mpi):

CC =            mpicxx
CCFLAGS =       -g -O3
LINK =          mpicxx
LINKFLAGS =     -g -O

Serial build with GNU gcc (see src/MAKE/Makefile.serial):

CC =            g++
CCFLAGS =       -g -O3
LINK =          g++
LINKFLAGS =     -g -O

Note

If compilation stops with a message like the following:

g++ -g -O3  -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64    -I../STUBS     -c ../main.cpp
In file included from ../pointers.h:24:0,
           from ../input.h:17,
           from ../main.cpp:16:
../lmptype.h:34:2: error: #error LAMMPS requires a C++11 (or later) compliant compiler. Enable C++11 compatibility or upgrade the compiler.

then you have either an unsupported (old) compiler or you have to turn on C++11 mode. The latter applies to GCC 4.8.x shipped with RHEL 7.x and CentOS 7.x or GCC 5.4.x shipped with Ubuntu16.04. For those compilers, you need to add the -std=c++11 flag. If there is no compiler that supports this flag (or equivalent), you would have to install a newer compiler that supports C++11; either as a binary package or through compiling from source.

If you build LAMMPS with any Accelerator packages included, there may be specific compiler or linker flags that are either required or recommended to enable required features and to achieve optimal performance. You need to include these in the CCFLAGS and LINKFLAGS settings above. For details, see the documentation for the individual packages listed on the Accelerator packages page. Or examine these files in the src/MAKE/OPTIONS directory. They correspond to each of the 5 accelerator packages and their hardware variants:

Makefile.opt                   # OPT package
Makefile.omp                   # OPENMP package
Makefile.intel_cpu             # INTEL package for CPUs
Makefile.intel_coprocessor     # INTEL package for KNLs
Makefile.gpu                   # GPU package
Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP)

3.4.3. Build the LAMMPS executable and library¶

LAMMPS is always built as a library of C++ classes plus an executable. The executable is a simple main() function that sets up MPI and then creates a LAMMPS class instance from the LAMMPS library, which will then process commands provided via a file or from the console input. The LAMMPS library can also be called from another application or a scripting language. See the Howto couple doc page for more info on coupling LAMMPS to other codes. See the Python page for more info on wrapping and running LAMMPS from Python via its library interface.

For CMake builds, you can select through setting CMake variables between building a shared or a static LAMMPS library and what kind of suffix is added to them (in case you want to concurrently install multiple variants of binaries with different settings). If none are set, defaults are applied.

-D BUILD_SHARED_LIBS=value   # yes or no (default)
-D LAMMPS_MACHINE=name       # name = mpi, serial, mybox, titan, laptop, etc
                             # no default value

The compilation will always produce a LAMMPS library and an executable linked to it. By default this will be a static library named liblammps.a and an executable named lmp Setting BUILD_SHARED_LIBS=yes will instead produce a shared library called liblammps.so (or liblammps.dylib or liblammps.dll depending on the platform) If LAMMPS_MACHINE=name is set in addition, the name of the generated libraries will be changed to either liblammps_name.a or liblammps_name.so, respectively and the executable will be called lmp_name.

With the traditional makefile based build process, the choice of the generated executable or library depends on the “mode” setting. Several options are available and mode=static is the default.

make machine               # build LAMMPS executable lmp_machine
make mode=static machine   # same as "make machine"
make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so instead

The “static” build will generate a static library called liblammps_machine.a and an executable named lmp_machine, while the “shared” build will generate a shared library liblammps_machine.so instead and lmp_machine will be linked to it. The build step will also create generic soft links, named liblammps.a and liblammps.so, which point to the specific liblammps_machine.a/so files.

Additional information¶

Note that for creating a shared library, all the libraries it depends on must be compiled to be compatible with shared libraries. This should be the case for libraries included with LAMMPS, such as the dummy MPI library in src/STUBS or any package libraries in the lib directory, since they are always built in a shared library compatible way using the -fPIC compiler switch. However, if an auxiliary library (like MPI or FFTW) does not exist as a compatible format, the shared library linking step may generate an error. This means you will need to install a compatible version of the auxiliary library. The build instructions for that library should tell you how to do this.

As an example, here is how to build and install the MPICH library, a popular open-source version of MPI, as a shared library in the default /usr/local/lib location:

./configure --enable-shared
make
make install

You may need to use sudo make install in place of the last line if you do not have write privileges for /usr/local/lib or use the --prefix configuration option to select an installation folder, where you do have write access. The end result should be the file /usr/local/lib/libmpich.so. On many Linux installations the folder ${HOME}/.local is an alternative to using /usr/local and does not require superuser or sudo access. In that case the configuration step becomes:

./configure --enable-shared --prefix=${HOME}/.local

Avoiding to use “sudo” for custom software installation (i.e. from source and not through a package manager tool provided by the OS) is generally recommended to ensure the integrity of the system software installation.

3.4.4. Including or removing debug support¶

By default the compilation settings will include the -g flag which instructs the compiler to include debug information (e.g. which line of source code a particular instruction correspond to). This can be extremely useful in case LAMMPS crashes and can help to provide crucial information in tracking down the origin of a crash and help the LAMMPS developers fix bugs in the source code. However, this increases the storage requirements for object files, libraries, and the executable 3-5 fold.

If this is a concern, you can change the compilation settings or remove the debug information from the LAMMPS executable:

Traditional make: edit your Makefile.<machine> to remove the -g flag from the CCFLAGS and LINKFLAGS definitions
CMake: use -D CMAKE_BUILD_TYPE=Release or explicitly reset the applicable compiler flags (best done using the text mode or graphical user interface).
Remove debug info: If you are only concerned about the executable being too large, you can use the strip tool (e.g. strip lmp_serial) to remove the debug information from the executable file. Do not strip libraries or object files, as that will render them unusable.

3.4.5. Build LAMMPS tools¶

Some tools described in Auxiliary tools can be built directly using CMake or Make.

-D BUILD_TOOLS=value         # yes or no (default)
-D BUILD_LAMMPS_SHELL=value  # yes or no (default)

The generated binaries will also become part of the LAMMPS installation (see below).

cd lammps/tools
make all              # build all binaries of tools
make binary2txt       # build only binary2txt tool
make chain            # build only chain tool
make micelle2d        # build only micelle2d tool
make thermo_extract   # build only thermo_extract tool

cd lammps/tools/lammps-shell
make                  # build LAMMPS shell

3.4.6. Install LAMMPS after a build¶

After building LAMMPS, you may wish to copy the LAMMPS executable of library, along with other LAMMPS files (library header, doc files) to a globally visible place on your system, for others to access. Note that you may need super-user privileges (e.g. sudo) if the directory you want to copy files to is protected.

cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
make                        # perform make after CMake command
make install                # perform the installation into prefix

During the installation process CMake will by default remove any runtime path settings for loading shared libraries. Because of this you may have to set or modify the LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH) environment variable, if you are installing LAMMPS into a non-system location and/or are linking to libraries in a non-system location that depend on such runtime path settings. As an alternative you may set the CMake variable LAMMPS_INSTALL_RPATH to on and then the runtime paths for any linked shared libraries and the library installation folder for the LAMMPS library will be embedded and thus the requirement to set environment variables is avoided. The off setting is usually preferred for packaged binaries or when setting up environment modules, the on setting is more convenient for installing software into a non-system or personal folder.

There is no “install” option in the src/Makefile for LAMMPS. If you wish to do this you will need to first build LAMMPS, then manually copy the desired LAMMPS files to the appropriate system directories.