Updating Kokkos lib
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15556 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
stamoor
127
lib/kokkos/doc/Doxyfile
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lib/kokkos/doc/Doxyfile
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#
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# Include the global look and feel options
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#
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@INCLUDE = ../../common/Doxyfile
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#
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# Package options
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#
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PROJECT_NAME = "Kokkos Core Kernels Package"
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PROJECT_NUMBER = "Version of the Day"
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OUTPUT_DIRECTORY = .
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OUTPUT_LANGUAGE = English
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EXTRACT_ALL = NO
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EXTRACT_PRIVATE = NO
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EXTRACT_STATIC = YES
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HIDE_UNDOC_MEMBERS = YES
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HIDE_UNDOC_CLASSES = YES
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BRIEF_MEMBER_DESC = YES
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REPEAT_BRIEF = YES
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ALWAYS_DETAILED_SEC = YES
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FULL_PATH_NAMES = NO
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STRIP_FROM_PATH =
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INTERNAL_DOCS = NO
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CLASS_DIAGRAMS = YES
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SOURCE_BROWSER = YES
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INLINE_SOURCES = NO
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STRIP_CODE_COMMENTS = YES
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REFERENCED_BY_RELATION = NO
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REFERENCES_RELATION = NO
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CASE_SENSE_NAMES = YES
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HIDE_SCOPE_NAMES = NO
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VERBATIM_HEADERS = YES
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SHOW_INCLUDE_FILES = YES
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#JAVADOC_AUTOBRIEF = YES
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INHERIT_DOCS = YES
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INLINE_INHERITED_MEMB = YES
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INLINE_INFO = YES
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SORT_MEMBER_DOCS = NO
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TAB_SIZE = 2
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ENABLED_SECTIONS =
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SORT_BRIEF_DOCS = NO
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GENERATE_TODOLIST = YES
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GENERATE_TESTLIST = YES
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QUIET = NO
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WARNINGS = YES
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WARN_IF_UNDOCUMENTED = YES
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WARN_FORMAT = "$file:$line: $text"
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#
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# INPUT: Where to find files that Doxygen should process. ../classic
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# has a doc/ subdirectory with its own Doxyfile that points to its own
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# files. The other Kokkos subpackages don't currently have their own
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# Doxyfile files, so we have to do it manually here.
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#
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# mfh 26 Sep 2013: I've only added those directories in the Core
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# subpackage that constitute the "public interface" of that
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# subpackage. Please feel free to include additional subdirectories
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# of ../core if you want to generate their documentation as well.
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#
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# mfh 26 Sep 2013: I've only added the Kokkos subpackages here that I
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# think are ready for Doxygen documentation generation. Please feel
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# free to amend this list as you see fit.
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#
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INPUT = index.doc ../classic ../core/src ../containers/src ../linalg/src
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FILE_PATTERNS = *.hpp *.cpp *.cuh *.cu
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RECURSIVE = NO
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EXCLUDE_PATTERNS = *.x *.o *.out
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EXAMPLE_PATH =
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EXAMPLE_RECURSIVE = YES
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EXAMPLE_PATTERNS = *.cpp *.hpp
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IMAGE_PATH =
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INPUT_FILTER =
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ALPHABETICAL_INDEX = YES
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COLS_IN_ALPHA_INDEX = 4
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IGNORE_PREFIX =
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#
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# What diagrams are created
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#
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CLASS_GRAPH = YES
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COLLABORATION_GRAPH = NO
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INCLUDE_GRAPH = NO
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INCLUDED_BY_GRAPH = NO
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GRAPHICAL_HIERARCHY = YES
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#
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# Preprocessing
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#
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ENABLE_PREPROCESSING = YES
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MACRO_EXPANSION = YES
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EXPAND_ONLY_PREDEF = YES
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SEARCH_INCLUDES = YES
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INCLUDE_FILE_PATTERNS =
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PREDEFINED = DOXYGEN_SHOULD_SKIP_THIS DOXYGEN_USE_ONLY
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INCLUDE_PATH = ../src
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EXPAND_AS_DEFINED =
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#
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# Links to other packages
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#
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TAGFILES = ../../common/tag_files/teuchos.tag=../../../teuchos/doc/html ../../common/tag_files/epetra.tag=../../../epetra/doc/html \
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../../common/tag_files/belos.tag=../../../belos/doc/html ../../common/tag_files/anasazi.tag=../../../anasazi/doc/html \
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../../common/tag_files/kokkos.tag=../../../kokkos/doc/html
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GENERATE_TAGFILE = ../../common/tag_files/tpetra.tag
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ALLEXTERNALS = NO
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EXTERNAL_GROUPS = NO
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#
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# Environment
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#
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PERL_PATH = /usr/bin/perl
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HAVE_DOT = YES
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DOT_PATH =
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MAX_DOT_GRAPH_WIDTH = 1024
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MAX_DOT_GRAPH_HEIGHT = 1024
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#
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# What kind of documentation is generated
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#
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#GENERATE_HTML = YES
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#HTML_OUTPUT = html
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#HTML_HEADER = includes/header.html
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#HTML_FOOTER = includes/footer.html
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#HTML_STYLESHEET = includes/stylesheet.css
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#HTML_ALIGN_MEMBERS = YES
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GENERATE_HTMLHELP = NO
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DISABLE_INDEX = NO
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GENERATE_LATEX = NO
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GENERATE_RTF = NO
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GENERATE_MAN = NO
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GENERATE_XML = NO
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BIN
lib/kokkos/doc/Kokkos_PG.pdf
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BIN
lib/kokkos/doc/Kokkos_PG.pdf
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Binary file not shown.
32
lib/kokkos/doc/README
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lib/kokkos/doc/README
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Kokkos uses the Doxygen tool for providing three documentation
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sources:
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- man pages
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- Latex User Guide
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- HTML Online User Guide.
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Man Pages
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Man pages are available for all files and functions in the directory
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TRILINOS_HOME/doc/kokkos/man, where TRILINOS_HOME is the location of your
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copy of Trilinos. To use these pages with the Unix man utility, add
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the directory to your man path as follows:
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setenv MANPATH `echo $MANPATH`:TRILINOS_HOME/doc/kokkos/man
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LaTeX User Guide
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A postscript version of this guide is in
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TRILINOS_HOME/doc/kokkos/latex/user_guide.ps. The LaTeX source is in the
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directory TRILINOS_HOME/doc/kokkos/latex.
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HTML Online User Guide
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The online guide is initiated by pointing your browser to
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TRILINOS_HOME/doc/kokkos/html/index.html
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Any question, comments or suggestions are welcome. Please send to
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Mike Heroux at
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320-845-7695
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maherou@sandia.gov
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15
lib/kokkos/doc/build_docs
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lib/kokkos/doc/build_docs
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#!/bin/sh
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if [ $TRILINOS_HOME ]; then
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echo "TRILINOS_HOME has already been set!"
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else
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echo "TRILINOS_HOME has not been set. Setting it!"
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export TRILINOS_HOME=`pwd`/../../..
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fi
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echo
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echo "Generating main Kokkos doxygen documentation ..."
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echo
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doxygen Doxyfile
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72
lib/kokkos/doc/index.doc
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lib/kokkos/doc/index.doc
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/*!
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\mainpage Trilinos/Kokkos: Shared-memory programming interface and computational kernels
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\section Kokkos_Intro Introduction
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The %Kokkos package has two main components. The first, sometimes
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called "%Kokkos Array" or just "%Kokkos," implements a
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performance-portable shared-memory parallel programming model and data
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containers. The second, called "%Kokkos Classic," consists of
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computational kernels that support the %Tpetra package.
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\section Kokkos_Kokkos The %Kokkos programming model
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%Kokkos implements a performance-portable shared-memory parallel
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programming model and data containers. It lets you write an algorithm
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once, and just change a template parameter to get the optimal data
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layout for your hardware. %Kokkos has back-ends for the following
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parallel programming models:
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- Kokkos::Threads: POSIX Threads (Pthreads)
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- Kokkos::OpenMP: OpenMP
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- Kokkos::Cuda: NVIDIA's CUDA programming model for graphics
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processing units (GPUs)
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- Kokkos::Serial: No thread parallelism
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%Kokkos also has optimizations for shared-memory parallel systems with
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nonuniform memory access (NUMA). Its containers can hold data of any
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primitive ("plain old") data type (and some aggregate types). %Kokkos
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Array may be used as a stand-alone programming model.
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%Kokkos' parallel operations include the following:
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- parallel_for: a thread-parallel "for loop"
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- parallel_reduce: a thread-parallel reduction
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- parallel_scan: a thread-parallel prefix scan operation
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as well as expert-level platform-independent interfaces to thread
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"teams," per-team "shared memory," synchronization, and atomic update
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operations.
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%Kokkos' data containers include the following:
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- Kokkos::View: A multidimensional array suitable for thread-parallel
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operations. Its layout (e.g., row-major or column-major) is
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optimized by default for the particular thread-parallel device.
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- Kokkos::Vector: A drop-in replacement for std::vector that eases
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porting from standard sequential C++ data structures to %Kokkos'
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parallel data structures.
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- Kokkos::UnorderedMap: A parallel lookup table comparable in
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functionality to std::unordered_map.
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%Kokkos also uses the above basic containers to implement higher-level
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data structures, like sparse graphs and matrices.
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A good place to start learning about %Kokkos would be <a href="http://trilinos.sandia.gov/events/trilinos_user_group_2013/presentations/2013-11-TUG-Kokkos-Tutorial.pdf">these tutorial slides</a> from the 2013 Trilinos Users' Group meeting.
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\section Kokkos_Classic %Kokkos Classic
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"%Kokkos Classic" consists of computational kernels that support the
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%Tpetra package. These kernels include sparse matrix-vector multiply,
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sparse triangular solve, Gauss-Seidel, and dense vector operations.
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They are templated on the type of objects (\c Scalar) on which they
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operate. This component was not meant to be visible to users; it is
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an implementation detail of the %Tpetra distributed linear algebra
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package.
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%Kokkos Classic also implements a shared-memory parallel programming
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model. This inspired and preceded the %Kokkos programming model
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described in the previous section. Users should consider the %Kokkos
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Classic programming model deprecated, and prefer the new %Kokkos
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programming model.
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*/
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