3.5. Optional build settings

LAMMPS can be built with several optional settings. Each sub-section explain how to do this for building both with CMake and make.

3.5.1. C++11 standard compliance

The LAMMPS developers plan to transition to make the C++11 standard the minimum requirement for compiling LAMMPS. Currently this only applies to some packages like KOKKOS while the rest aims to be compatible with the C++98 standard. Most currently used compilers are compatible with C++11; some need to set extra flags to enable C++11 compliance. Example for GNU c++:

CCFLAGS = -g -O3 -std=c++11

3.5.2. FFT library

When the KSPACE package is included in a LAMMPS build, the kspace_style pppm command performs 3d FFTs which require use of an FFT library to compute 1d FFTs. The KISS FFT library is included with LAMMPS but other libraries can be faster. LAMMPS can use them if they are available on your system.

CMake variables:

-D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_SINGLE=value       # yes or no (default), no = double precision
-D FFT_PACK=value         # array (default) or pointer or memcpy

Note

The values for the FFT variable must be in upper-case. This is an exception to the rule that all CMake variables can be specified with lower-case values.

Usually these settings are all that is needed. If FFTW3 is selected, then CMake will try to detect, if threaded FFTW libraries are available and enable them by default. This setting is independent of whether OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is used. If CMake cannot detect the FFT library, you can set these variables to assist:

-D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
-D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
-D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
-D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
-D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARIES=path

Makefile.machine settings:

FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
                              # default is KISS if not specified
FFT_INC = -DFFT_SINGLE        # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY

# default is FFT_PACK_ARRAY if not specified

FFT_INC =       -I/usr/local/include
FFT_PATH =      -L/usr/local/lib
FFT_LIB =       -lfftw3             # FFTW3 double precision
FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compier, serial interface
FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs

As with CMake, you do not need to set paths in FFT_INC or FFT_PATH, if the compiler can find the FFT header and library files in its default search path. You must specify FFT_LIB with the appropriate FFT libraries to include in the link.

CMake and make info:

The KISS FFT library is included in the LAMMPS distribution. It is portable across all platforms. Depending on the size of the FFTs and the number of processors used, the other libraries listed here can be faster.

However, note that long-range Coulombics are only a portion of the per-timestep CPU cost, FFTs are only a portion of long-range Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel communication can be costly). A breakdown of these timings is printed to the screen at the end of a run when using the kspace_style pppm command. The Run output doc page gives more details. A more detailed (and time consuming) report of the FFT performance is generated with the kspace_modify fftbench yes command.

FFTW is a fast, portable FFT library that should also work on any platform and can be faster than the KISS FFT library. You can download it from www.fftw.org. LAMMPS requires version 3.X; the legacy version 2.1.X is no longer supported.

Building FFTW for your box should be as simple as ./configure; make; make install. The install command typically requires root privileges (e.g. invoke it via sudo), unless you specify a local directory with the “–prefix” option of configure. Type “./configure –help” to see various options.

The Intel MKL math library is part of the Intel compiler suite. It can be used with the Intel or GNU compiler (see FFT_LIB setting above).

Performing 3d FFTs in parallel can be time consuming due to data access and required communication. This cost can be reduced by performing single-precision FFTs instead of double precision. Single precision means the real and imaginary parts of a complex datum are 4-byte floats. Double precision means they are 8-byte doubles. Note that Fourier transform and related PPPM operations are somewhat less sensitive to floating point truncation errors and thus the resulting error is less than the difference in precision. Using the -DFFT_SINGLE setting trades off a little accuracy for reduced memory use and parallel communication costs for transposing 3d FFT data.

When using -DFFT_SINGLE with FFTW3 you may need to build the FFTW library a second time with support for single-precision.

For FFTW3, do the following, which should produce the additional library libfftw3f.a or libfftw3f.so.

make clean
./configure --enable-single; make; make install

Performing 3d FFTs requires communication to transpose the 3d FFT grid. The data packing/unpacking for this can be done in one of 3 modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above. Depending on the machine, the size of the FFT grid, the number of processors used, one option may be slightly faster. The default is ARRAY mode.

3.5.3. Size of LAMMPS data types

LAMMPS has a few integer data types which can be defined as 4-byte or 8-byte integers. The default setting of “smallbig” is almost always adequate.

CMake variable:

-D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall

Makefile.machine setting:

LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL

# default is LAMMPS_SMALLBIG if not specified CMake and make info:

The default “smallbig” setting allows for simulations with:

  • total atom count = 2^63 atoms (about 9e18)

  • total timesteps = 2^63 (about 9e18)

  • atom IDs = 2^31 (about 2 billion)

  • image flags = roll over at 512

The “bigbig” setting increases the latter two limits. It allows for:

  • total atom count = 2^63 atoms (about 9e18)

  • total timesteps = 2^63 (about 9e18)

  • atom IDs = 2^63 (about 9e18)

  • image flags = roll over at about 1 million (2^20)

The “smallsmall” setting is only needed if your machine does not support 8-byte integers. It allows for:

  • total atom count = 2^31 atoms (about 2 billion)

  • total timesteps = 2^31 (about 2 billion)

  • atom IDs = 2^31 (about 2 billion)

  • image flags = roll over at 512 (2^9)

Atom IDs are not required for atomic systems which do not store bond topology information, though IDs are enabled by default. The atom_modify id no command will turn them off. Atom IDs are required for molecular systems with bond topology (bonds, angles, dihedrals, etc). Thus if you model a molecular system with more than 2 billion atoms, you need the “bigbig” setting.

Image flags store 3 values per atom which count the number of times an atom has moved through the periodic box in each dimension. See the dump doc page for a discussion. If an atom moves through the periodic box more than this limit, the value will “roll over”, e.g. from 511 to -512, which can cause diagnostics like the mean-squared displacement, as calculated by the compute msd command, to be faulty.

Note that the USER-ATC package and the USER-INTEL package are currently not compatible with the “bigbig” setting. Also, there are limitations when using the library interface. Some functions with known issues have been replaced by dummy calls printing a corresponding error rather than crashing randomly or corrupting data.

Also note that the GPU package requires its lib/gpu library to be compiled with the same size setting, or the link will fail. A CMake build does this automatically. When building with make, the setting in whichever lib/gpu/Makefile is used must be the same as above.

3.5.4. Output of JPG, PNG, and movie files

The dump image command has options to output JPEG or PNG image files. Likewise the dump movie command outputs movie files in MPEG format. Using these options requires the following settings:

CMake variables:

-D WITH_JPEG=value      # yes or no
                        # default = yes if CMake finds JPEG files, else no
-D WITH_PNG=value       # yes or no
                        # default = yes if CMake finds PNG and ZLIB files, else no
-D WITH_FFMPEG=value    # yes or no
                        # default = yes if CMake can find ffmpeg, else no

Usually these settings are all that is needed. If CMake cannot find the graphics header, library, executable files, you can set these variables:

-D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
-D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file
-D PNG_INCLUDE_DIR=path     # path to png.h header file
-D PNG_LIBRARIES=path       # path to libpng.a (.so) file
-D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
-D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable

Makefile.machine settings:

LMP_INC = -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_PNG
LMP_INC = -DLAMMPS_FFMPEG

JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz       # library names

As with CMake, you do not need to set JPG_INC or JPG_PATH, if make can find the graphics header and library files. You must specify JPG_LIB with a list of graphics libraries to include in the link. You must insure ffmpeg is in a directory where LAMMPS can find it at runtime, that is a directory in your PATH environment variable.

CMake and make info:

Using ffmpeg to output movie files requires that your machine supports the “popen” function in the standard runtime library.

Note

On some clusters with high-speed networks, using the fork() library call (required by popen()) can interfere with the fast communication library and lead to simulations using ffmpeg to hang or crash.

3.5.5. Read or write compressed files

If this option is enabled, large files can be read or written with gzip compression by several LAMMPS commands, including read_data, rerun, and dump.

CMake variables:

-D WITH_GZIP=value       # yes or no
                         # default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it

Makefile.machine setting:

LMP_INC = -DLAMMPS_GZIP

CMake and make info:

This option requires that your machine supports the “popen()” function in the standard runtime library and that a gzip executable can be found by LAMMPS during a run.

Note

On some clusters with high-speed networks, using the fork() library call (required by popen()) can interfere with the fast communication library and lead to simulations using compressed output or input to hang or crash. For selected operations, compressed file I/O is also available using a compression library instead, which is what the COMPRESS package enables.

3.5.6. Memory allocation alignment

This setting enables the use of the posix_memalign() call instead of malloc() when LAMMPS allocates large chunks or memory. This can make vector instructions on CPUs more efficient, if dynamically allocated memory is aligned on larger-than-default byte boundaries. On most current systems, the malloc() implementation returns pointers that are aligned to 16-byte boundaries. Using SSE vector instructions efficiently, however, requires memory blocks being aligned on 64-byte boundaries.

CMake variable:

-D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)

Use a LAMMPS_MEMALIGN value of 0 to disable using posix_memalign() and revert to using the malloc() C-library function instead. When compiling LAMMPS for Windows systems, malloc() will always be used and this setting ignored.

Makefile.machine setting:

LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64

Do not set -DLAMMPS_MEMALIGN, if you want to have memory allocated with the malloc() function call instead. -DLAMMPS_MEMALIGN cannot be used on Windows, as it does use different function calls for allocating aligned memory, that are not compatible with how LAMMPS manages its dynamical memory.

3.5.7. Workaround for long long integers

If your system or MPI version does not recognize “long long” data types, the following setting will be needed. It converts “long long” to a “long” data type, which should be the desired 8-byte integer on those systems:

CMake variable:

-D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)

Makefile.machine setting:

LMP_INC = -DLAMMPS_LONGLONG_TO_LONG

3.5.8. Exception handling when using LAMMPS as a library

This setting is useful when external codes drive LAMMPS as a library. With this option enabled, LAMMPS errors do not kill the calling code. Instead, the call stack is unwound and control returns to the caller, e.g. to Python. Of course the calling code has to be set up to catch exceptions from within LAMMPS.

CMake variable:

-D LAMMPS_EXCEPTIONS=value        # yes or no (default)

Makefile.machine setting:

LMP_INC = -DLAMMPS_EXCEPTIONS