3.4. Basic build options
The following topics are covered on this page, for building both with CMake and make:
3.4.1. Serial vs parallel build
LAMMPS can be built to run in parallel using the ubiquitous MPI (message-passing interface) library. Or it can built to run on a single processor (serial) without MPI. It can also be built with support for OpenMP threading (see more discussion below).
CMake variables:
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no
-D BUILD_OMP=value # yes or no (default)
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
The executable created by CMake (after running make) is lmp_name. If the LAMMPS_MACHINE variable is not specified, the executable is just lmp. Using BUILD_MPI=no will produce a serial executable.
Traditional make:
cd lammps/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
Serial build (see src/MAKE/Makefile.serial):
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs
For a parallel build, if MPI is installed on your system in the usual place (e.g. under /usr/local), you do not need to specify the 3 variables MPI_INC, MPI_PATH, MPI_LIB. The MPI wrapper on the compiler (e.g. mpicxx, mpiCC) knows where to find the needed include and library files. Failing this, these 3 variables can be used to specify where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH) are found, and the name of the library files (MPI_LIB).
For a serial build, you need to specify the 3 variables, as shown above.
For a serial LAMMPS build, use the dummy MPI library provided in src/STUBS. You also need to build the STUBS library for your platform before making LAMMPS itself. A “make serial” build does this for. Otherwise, type “make mpi-stubs” from the src directory, or “make” from the src/STUBS dir. If the build fails, you will need to edit the STUBS/Makefile for your platform.
The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime() that calls gettimeofday() . If your system doesn’t support gettimeofday() , you’ll 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.
CMake and make info:
If you are installing MPI yourself, we recommend MPICH2 from Argonne National Laboratory or OpenMPI. MPICH can be downloaded from the Argonne MPI site. OpenMPI can be downloaded from the OpenMPI site. Other MPI packages should also work. 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 find out how to build and link with it.
The majority of OpenMP (threading) support in LAMMPS is provided by the USER-OMP package; see the Speed omp doc page for details. The USER-INTEL package also provides OpenMP support (it is compatible with USER-OMP) and adds vectorization support when compiled with the Intel compilers on top of that. Also, the KOKKOS package can be compiled for using OpenMP threading.
However, there are a few commands in LAMMPS that have native OpenMP support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and USER-DPD packages. In addition some packages support OpenMP threading indirectly through the libraries they interface to: e.g. LATTE and USER-COLVARS. See the Packages details doc page for more info on these packages and the doc 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 info:
Some compilers do not fully support the ‘default(none)’ directive and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0 semantics, which are incompatible with the OpenMP 3.1 directives used in LAMMPS (for maximal compatibility with compiler versions in use). In those case, all ‘default(none)’ directives (which aid in detecting incorrect and unwanted sharing) can be replaced with ‘default(shared)’ while dropping all ‘shared()’ directives. The script ‘src/USER-OMP/hack_openmp_for_pgi_gcc9.sh’ can be used to automate this conversion.
3.4.2. Choice of compiler and compile/link options
The choice of compiler and compiler flags can be important for performance. Vendor compilers can produce faster code than open-source compilers like GNU. On boxes with Intel CPUs, we suggest trying the Intel C++ compiler.
On parallel clusters or supercomputers which use “modules” for their compile/link environments, you can often access different compilers by simply loading the appropriate module before building LAMMPS.
CMake variables:
-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
By default CMake will use a compiler it finds and it will add optimization flags appropriate to that compiler and any accelerator packages you have included in the build.
You can tell CMake to look for a specific compiler with these variable settings. Likewise you can specify the FLAGS variables if you want to experiment with alternate optimization flags. You should specify all 3 compilers, so that the small number of LAMMPS source files written in C or Fortran are built with a compiler consistent with the one used for all the C++ files:
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 LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
Note
When the cmake command completes, it prints info to the screen as to which compilers it is using, and what flags will be used in 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 will be listed in the CMake output. You should check to insure you are using the compiler and optimization flags are the ones you want.
Makefile.machine settings:
Parallel build (see src/MAKE/Makefile.mpi):
CC = mpicxx
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O
Serial build (see src/MAKE/Makefile.serial):
CC = g++
CCFLAGS = -g -O3
LINK = g++
LINKFLAGS = -g -O
The “compiler/linker settings” section of a Makefile.machine lists compiler and linker settings for your C++ compiler, including optimization flags. You should always use mpicxx or mpiCC for a parallel build, since these compiler wrappers will include a variety of settings appropriate for your MPI installation.
Note
If you build LAMMPS with any accelerator packages included, they have specific optimization flags that are either required or recommended for optimal performance. You need to include these in the CCFLAGS and LINKFLAGS settings above. For details, see the individual package doc pages listed on the Speed packages doc 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 # USER-OMP package
Makefile.intel_cpu # USER-INTEL package for CPUs
Makefile.intel_coprocessor # USER-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 LAMMPS as an executable or a library
LAMMPS can be built as either an executable or as a static or shared library. The LAMMPS library can 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 doc page for more info on wrapping and running LAMMPS from Python via its library interface.
CMake variables:
-D BUILD_EXE=value # yes (default) or no
-D BUILD_LIB=value # yes or no (default)
-D BUILD_SHARED_LIBS=value # yes or no (default)
Setting BUILD_EXE=no will not produce an executable. Setting BUILD_LIB=yes will produce a static library named liblammps.a. Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a shared library named liblammps.so.
Traditional make:
cd lammps/src
make machine # build LAMMPS executable lmp_machine
make mode=lib machine # build LAMMPS static lib liblammps_machine.a
make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so
The two library builds also create generic soft links, named liblammps.a and liblammps.so, which point to the liblammps_machine files.
CMake and make info:
Note that for a shared library to be usable by a calling program, all the auxiliary libraries it depends on must also exist as shared libraries. This will be the case for libraries included with LAMMPS, such as the dummy MPI library in src/STUBS or any package libraries in the lib/packages directory, since they are always built as shared libraries using the -fPIC switch. However, if a library like MPI or FFTW does not exist as a shared library, the shared library build will generate an error. This means you will need to install a shared library version of the auxiliary library. The build instructions for the 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, distributed by Argonne National Lab, 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. The end result should be the file /usr/local/lib/libmpich.so.
3.4.4. Build the LAMMPS documentation
CMake variable:
-D BUILD_DOC=value # yes or no (default)
This will create the HTML doc pages within the CMake build directory. The reason to do this is if you want to “install” LAMMPS on a system after the CMake build via “make install”, and include the doc pages in the install.
Traditional make:
cd lammps/doc
make html # html doc pages
make pdf # single Manual.pdf file
This will create a lammps/doc/html dir with the HTML doc pages so that you can browse them locally on your system. Type “make” from the lammps/doc dir to see other options.
Note
You can also download a tarball of the documentation for the current LAMMPS version (HTML and PDF files), from the website download page.
3.4.5. 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 variable:
cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
make # perform make after CMake command
make install # perform the installation into prefix
Traditional make:
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.