Add core source files

.gitignore

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+# editors temporary files
+*~
+.*.swp
+\#*\#
+TAGS
+cscope.*
+
+# files generated by compiler/linker
+.libs
+*.o
+*.lo
+*.la
+*.diff
+*.orig
+*.rej
+*.gcda
+*.gcno
+
+# files generated by configure
+.deps/
+/autom4te.cache/
+/config.h
+/config.log
+/config.status
+/libtool
+/stamp-h1
+Makefile
+.dirstamp
+Makefile.in

ChangeLog

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+NEWS

Makefile.am

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+SUBDIRS = src
+dist_doc_DATA = README.md
+

NEWS

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+* Changes in hp2p-3.1 - 01/04/2016
+=====================
+
+   -- introduces SHIFT algorithm for choosing pairs
+   -- reporting results in standard output
+
+* Changes in hp2p-2.0 - 2012
+=====================
+
+   -- add python gui for visualization
+
+* Initial release hp2p-1.0 - 2010
+=====================
+

README

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+README.md

autogen.sh

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+#!/bin/env bash
+
+autoreconf --install

clean.sh

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+#!/bin/env bash
+
+rm -rf *~ */*~ \
+   aclocal.m4 \
+   autom4te.cache \
+   depcomp \
+   install-sh \
+   missing \
+   configure \
+   config.h.in \
+   Makefile.in \
+   */Makefile.in
+
+

configure.ac

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+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ([2.63])
+AC_INIT([HP2P], [3.1], [laurent.nguyen@cea.fr])
+AM_INIT_AUTOMAKE([-Wall])
+AC_CONFIG_SRCDIR([src/hp2p.cpp])
+AC_CONFIG_HEADERS([config.h])
+
+# use the C++ compiler for the following checks
+AC_LANG([C++])
+
+# use Python
+AM_PATH_PYTHON([2.6])
+
+# Checks for programs.
+AC_PROG_CXX([mpic++ mpicxx])
+AC_LANG_PUSH(C++)
+AC_LANG_POP(C++)
+AC_PROG_RANLIB
+
+# Checks for libraries.
+
+# Checks for header files.
+AC_HEADER_STDC
+AC_CHECK_HEADERS([cstdlib cstring])
+AC_CHECK_HEADERS([string])
+AC_CHECK_HEADERS([vector algorithm list])
+AC_CHECK_HEADERS([iostream fstream sstream])
+AC_CHECK_HEADERS([sys/time.h unistd.h])
+AC_CHECK_HEADERS([mpi.h])
+
+# distribute additional compiler and linker flags among Makefiles
+# --> set and change these variables instead of CXXFLAGS or LDFLAGS (for user only)
+AC_SUBST([AM_CXXFLAGS])
+AC_SUBST([AM_LDFLAGS])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_TYPE_SIZE_T
+
+# Checks for library functions.
+AC_CHECK_FUNCS([gettimeofday])
+AC_CHECK_FUNCS([getopt])
+
+# Checks for MPI library functions.
+AC_CHECK_FUNCS([MPI_Init MPI_Finalize])
+AC_CHECK_FUNCS([MPI_File_open MPI_File_close])
+
+
+AC_CONFIG_FILES([Makefile
+	src/Makefile])
+AC_OUTPUT

src/.clang-format

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+---
+Language:        Cpp
+BasedOnStyle:  LLVM
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: false
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: false
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Allman
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeCategories: 
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '$'
+IndentCaseLabels: false
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Right
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Always
+...
+

src/Makefile.am

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+bin_PROGRAMS = hp2p.exe
+hp2p_exe_SOURCES = hp2p.cpp
+bin_SCRIPTS = vizhp2p
+