This section gives an overview of the optional packages that extend SPARTA functionality with instructions on how to build SPARTA with each of them. Packages are groups of files that enable a specific set of features. For example, the KOKKOS package provides styles that can run on different hardware such as GPUs. You can see the list of all packages and "make" commands to manage them by typing "make package" from within the src directory of the SPARTA distribution. Section 2.3 gives general info on how to install and un-install packages as part of the SPARTA build process.
Packages may require some additional code compiled located in the lib folder, or may require an external library to be downloaded, compiled, installed, and SPARTA configured to know about its location and additional compiler flags.
Following the next two tables is a sub-section for each package. It lists authors (if applicable) and summarizes the package contents. It has specific instructions on how to install the package, including (if necessary) downloading or building any extra library it requires. It also gives links to documentation, example scripts, and pictures/movies (if available) that illustrate use of the package.
NOTE: To see the complete list of commands a package adds to SPARTA, just look at the files in its src directory, e.g. "ls src/KOKKOS". Files with names that start with fix, compute, etc correspond to commands with the same style names.
In these two tables, the "Example" column is a sub-directory in the examples directory of the distribution which has an input script that uses the package. E.g. "fft" refers to the examples/fft directory; The "Library" column indicates whether an extra library is needed to build and use the package:
|FFT||fast Fourier transforms||compute_style compute/fft/grid||fft||int or ext|
|KOKKOS||Kokkos-enabled styles||Section 5.3.3||Benchmarks||-|
Apply Fast Fourier Transforms (FFTs) to simulation data. The FFT library is specified in the Makefile.machine using the FFT_INC, FFT_PATH, and FFT_LIB variables. Supported external FFT libraries that can be specified include FFTW2, FFTW3, and MKL.If no FFT library is specified in the Makefile, SPARTA will use the internal KISS FFT library that is included with SPARTA. See the see discussion in doc/Section_start.html#2_2 (step 6).
Install or un-install:
make yes-fft make machine
make no-fft make machine
Styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their style name. Section 5.3.3 gives details of what hardware and software is required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf kk" or "-suffix kk" command-line switches.
You must have a C++11 compatible compiler to use this package.
Authors: The KOKKOS package was created primarily by Stan Moore (Sandia), with contributions from other folks as well. It uses the open-source Kokkos library which was developed by Carter Edwards, Christian Trott, and others at Sandia, and which is included in the SPARTA distribution in lib/kokkos.
Install or un-install:
For the KOKKOS package, you have 3 choices when building. You can build with either CPU or KNL or GPU support. Each choice requires additional settings in your Makefile.machine for the KOKKOS_DEVICES and KOKKOS_ARCH settings. See the src/MAKE/OPTIONS/Makefile.kokkos* files for examples.
For multicore CPUs using OpenMP:
KOKKOS_DEVICES = OpenMP KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc
For Intel KNLs using OpenMP:
KOKKOS_DEVICES = OpenMP KOKKOS_ARCH = KNL
For NVIDIA GPUs using CUDA:
KOKKOS_DEVICES = Cuda KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc
For GPUs, you also need these 2 lines in your Makefile.machine before the CC line is defined, in this case for use with OpenMPI mpicxx. The 2 lines define a nvcc wrapper compiler, which will use nvcc for compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA files.
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper CC = mpicxx
Once you have an appropriate Makefile.machine, you can install/un-install the package and build SPARTA in the usual manner. Note that you cannot build one executable to run on multiple hardware targets (CPU or KNL or GPU). You need to build SPARTA once for each hardware target, to produce a separate executable.
make yes-kokkos make machine
make no-kokkos make machine