move tools. change some chain_complex internals..

Author: rhl-

.gitignore

@@ -1,30 +1,38 @@
+**/test_multi
+deps
+distributed/distributed_persistence
+ctl/chain_complex/tm
+ctl/cube/test_cube
+ctl/distributed/distributed_persistence_serial
+tools/vr
+tools/ngraph
 ctl/vr/incremental_test
 ctl/vr/test
 tools/convert_asc_format
 tools/ctl2phat
 doc/doxygen/*
-ctl/tools/convert_asc_format
-ctl/tools/ctl2phat
+tools/convert_asc_format
+tools/ctl2phat
 doc/doxygen/*
 ctl/distributed/distributed_persistence
 Doxyfile
-ctl/tools/distributed_persistence
+tools/distributed_persistence
 examples/
-ctl/tools/cover_homology
-ctl/tools/concurrent_homology
-ctl/tools/write_filtration
+tools/cover_homology
+tools/concurrent_homology
+tools/write_filtration
 cover_test
 bin/
 include/
 install_manifest.txt
-ctl/tools/gpcover
+tools/gpcover
 ctl/parallel/build_blowup_complex/blowup_test
 ctl/product_cell/test_product_cell
-ctl/tools/metowgh
-ctl/tools/oneskeleton
-ctl/tools/wghtomet
-ctl/tools/complex_size
-ctl/tools/persistence
+tools/metowgh
+tools/oneskeleton
+tools/wghtomet
+tools/complex_size
+tools/persistence
 build_clique
 duplicate
 euler

CMakeLists.txt

@@ -9,54 +9,65 @@ if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" VERSION_GREATER 2.6)
   endif()
 endif()
 
-set(CMAKE_BUILD_TYPE RELWITHDEBINFO)
+set(CMAKE_BUILD_TYPE Release)
+add_definitions(" -fno-omit-frame-pointer -Wall -ansi -std=c++11")
 
 set(CTL_INCLUDE_INSTALL_DIR ${CMAKE_SOURCE_DIR}/include)
 set(CTL_DOC_INSTALL_DIR ${CMAKE_SOURCE_DIR}/doc)
 set(CTL_BIN_INSTALL_DIR ${CMAKE_SOURCE_DIR}/bin)
 set(CTL_EXAMPLES_INSTALL_DIR ${CMAKE_SOURCE_DIR}/examples)
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/CMakeModules")
+set(CMAKE_PREFIX_PATH /usr/lib64/openmpi)
+
 if (NOT APPLE)
 	set(DSO_FIXES rt)
 endif (NOT APPLE)
 
-find_package( ANN REQUIRED)
-find_package(Boost COMPONENTS program_options serialization MPI REQUIRED)
-message( "Boost_LIBRARIES = " ${Boost_LIBRARIES}) 
-include_directories(/usr/local/inlcude ${ANN_INCLUDE_DIRS})
-link_directories(/usr/local/lib ${ANN_LIBRARY_DIR} ${Boost_LIBRARY_DIR})
-
-set(Boost_USE_MULTITHREADED ON)
-add_definitions(" -fno-omit-frame-pointer -Wall -ansi -std=c++11")
-
+find_package(Boost COMPONENTS program_options serialization mpi REQUIRED)
+find_package(MPI REQUIRED)
+find_package(ANN REQUIRED)
 find_package(TBB REQUIRED) 
 find_package(METIS REQUIRED) 
 find_package(Doxygen)
+
+set(GTEST_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/deps/gtest/include)
+message( ${GTEST_INCLUDE_DIR})
+set(GTEST_LIBRARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/deps/gtest)
+set(GTEST_LIBRARIES gtest gtest_main)
+
 if(DOXYGEN_FOUND)
-configure_file(${CMAKE_SOURCE_DIR}/doc/Doxyfile.in ${CMAKE_BINARY_DIR}/Doxyfile @ONLY)
-add_custom_target(doc
-${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile
+configure_file(${CMAKE_SOURCE_DIR}/doc/Doxyfile.in 
+	       ${CMAKE_BINARY_DIR}/Doxyfile @ONLY)
+add_custom_target(doc ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile
 WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
 COMMENT "Generating API documentation with Doxygen" VERBATIM
 )
 endif(DOXYGEN_FOUND)
 
+add_custom_target(deps COMMAND cmake . COMMAND make 
+		  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/deps)
 
 include_directories(${CMAKE_SOURCE_DIR} ${Boost_INCLUDE_DIR})
+include_directories(/usr/local/include ${MPI_INCLUDE_DIR})
+include_directories(${ANN_INCLUDE_DIRS} ${GTEST_INCLUDE_DIR})
 include_directories(${METIS_INCLUDE_DIR} ${TBB_INCLUDE_DIR})
 
+link_directories(/usr/local/lib ${ANN_LIBRARY_DIR} ${Boost_LIBRARY_DIR})
+link_directories( ${MPI_LIBRARY_DIR} ${GTEST_LIBRARY_DIR})
 link_directories(/usr/local/lib ${Boost_LIBRARY_DIR})
 link_directories(${METIS_LIBRARY_DIR} ${TBB_LIBRARY_DIR})
 
 add_subdirectory( ctl)
+add_subdirectory( tools)
+#add_subdirectory( distributed)
 
 install( DIRECTORY ${CMAKE_SOURCE_DIR}/ctl 
 	 DESTINATION include 
 	 FILES_MATCHING PATTERN "*.h"
 	 PATTERN "CMakeFiles" EXCLUDE)
 
-install( DIRECTORY ${CMAKE_SOURCE_DIR}/ctl
-	 DESTINATION share/ctl/examples
+install( DIRECTORY ${CMAKE_SOURCE_DIR}/tools
+	 DESTINATION share/ctl/tools
 	 FILES_MATCHING PATTERN "*.cpp"
 	 PATTERN "CMakeLists.txt"
 	 PATTERN "CMakeFiles" EXCLUDE)

README

@@ -13,10 +13,12 @@ CTL is BSD See LICENSE for more info.
 
 === DEPENDENCIES ==
 C++11 compiler (clang or gcc)
-Boost
+Boost with MPI
 Intel's TBB
 METIS (graph partitioning)
-ANN (soon)
+ANN 
+MPI
+Doxygen (Optional)
 
 === BUILDING ====
 To build the library type:

ctl/CMakeLists.txt

@@ -5,7 +5,6 @@ add_subdirectory( chain)
 add_subdirectory( chain_complex)
 add_subdirectory( finite_field)
 add_subdirectory( filtration)
-add_subdirectory( tools)
 add_subdirectory( product_cell)
 add_subdirectory( parallel)
 add_subdirectory( vr)

ctl/chain_complex/CMakeLists.txt

@@ -1,3 +1 @@
-#include_directories(${CMAKE_SOURCE_DIR})
-add_executable(tc test_chain_complex.cpp)
-add_executable(tm test_multi_array.cpp)
+add_subdirectory( tests)

ctl/chain_complex/chain_complex.h

@@ -56,8 +56,8 @@
 #include <ctl/hash/hash.h>
 #include <ctl/chain_complex/detail/data_wrapper.h>
 #include <ctl/chain_complex/detail/default_complex_storage.h>
-#include <ctl/chain_complex/detail/cubical_complex.h>
-#include <ctl/chain_complex/detail/generic_complex.h>
+#include <ctl/chain_complex/cubical_complex.h>
+#include <ctl/chain_complex/simplicial_chain_complex.h>
 
 namespace ctl {
 
@@ -135,18 +135,17 @@ typename std::conditional<
 std::is_same< typename detail::recombine< Cell, detail::Dummy>::type, 
 	      ctl::Cube< detail::Dummy> >::value, 
 //then we create a Cubical_complex which optimizes storage.
- ctl::detail::Cubical_complex< Cell, 
-			       Boundary, 
-			       detail::Data_wrapper< Data>, 
-			       Hash, 
-			       Storage
-		              >,
+ ctl::Cubical_complex< Cell, 
+		       Boundary, 
+		       Data, 
+		       Hash, 
+		       Storage>,
 //Otherwise all other cell types are stored generically
- ctl::detail::Generic_complex< Cell, 
-			       Boundary, 
-			       detail::Data_wrapper< Data>, 
-			       Hash, 
-			       Storage> 
+ ctl::Simplicial_chain_complex< Cell, 
+			        Boundary, 
+			        detail::Data_wrapper< Data>, 
+			        Hash, 
+			        Storage> 
 	    >::type;
 
 //! Utility to read a complex and any associated data