Merge pull request #146 from yanurag994/master

Merging Distributed Helix Algorithm into Master Branch

.github/workflows/ccpp.yml

@@ -63,7 +63,7 @@ jobs:
       run:  vcpkg update && vcpkg install cgal eigen3 msmpi
 
     # Checkout v2 : https://github.com/actions/checkout
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     # Check CMake Version 
     - name: Check CMake (${{ matrix.mpi }})

Complex/CMakeLists.txt

@@ -6,27 +6,27 @@ cmake_minimum_required(VERSION 3.10)
 
 find_package(OpenMP REQUIRED)
 
-add_library(simplexBase STATIC simplexBase.cpp simplexBase.hpp)
+add_library(simplexBase STATIC simplexBase.cpp)
 target_link_libraries(simplexBase PUBLIC utils pipePacket simplexTree simplexArrayList alphaComplex witnessComplex betaComplex)
 target_include_directories(simplexBase PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${PROJECT_SOURCE_DIR}/Utils)
 
-add_library(simplexArrayList STATIC simplexArrayList.cpp simplexArrayList.hpp)
+add_library(simplexArrayList STATIC simplexArrayList.cpp)
 target_link_libraries(simplexArrayList PUBLIC simplexBase)
 target_include_directories(simplexArrayList PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(alphaComplex STATIC alphaComplex.cpp alphaComplex.hpp)
+add_library(alphaComplex STATIC alphaComplex.cpp)
 target_link_libraries(alphaComplex PUBLIC utils kdTree simplexArrayList OpenMP::OpenMP_CXX)
 target_include_directories(alphaComplex PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(witnessComplex STATIC witnessComplex.cpp witnessComplex.hpp)
+add_library(witnessComplex STATIC witnessComplex.cpp)
 target_link_libraries(witnessComplex PUBLIC simplexArrayList)
 target_include_directories(witnessComplex PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(simplexTree STATIC simplexTree.cpp simplexTree.hpp)
+add_library(simplexTree STATIC simplexTree.cpp)
 target_link_libraries(simplexTree PUBLIC utils kdTree simplexBase)
 target_include_directories(simplexTree PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(betaComplex STATIC betaComplex.cpp betaComplex.hpp)
+add_library(betaComplex STATIC betaComplex.cpp)
 target_link_libraries(betaComplex PUBLIC alphaComplex)
 target_include_directories(betaComplex PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 

LHFmain/CMakeLists.txt

@@ -15,7 +15,7 @@ include_directories(SYSTEM ${MPI_INCLUDE_PATH})
 find_package(OpenMP REQUIRED)
 
 #Add Source to this project's executable
-add_library(LHFlib SHARED "LHF.cpp" "LHF.hpp")
+add_library(LHFlib SHARED LHF.cpp)
 set_target_properties(LHFlib PROPERTIES VERSION ${PROJECT_VERSION})
 set_target_properties(LHFlib PROPERTIES SOVERSION 1)
 set_target_properties(LHFlib PROPERTIES POSITION_INDEPENDENT_CODE ON)

Pipes/CMakeLists.txt

@@ -49,77 +49,83 @@ endif()
 find_package(OpenMP REQUIRED)
 find_package(Eigen3 REQUIRED)
 find_package(TBB)
+find_package(MPI REQUIRED)
 
-add_library(pipePacket STATIC "pipePacket.cpp" "pipePacket.hpp")
+add_library(pipePacket STATIC pipePacket.cpp)
 target_link_libraries(pipePacket PUBLIC simplexBase)
 target_include_directories(pipePacket PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${PROJECT_SOURCE_DIR}/Complex)
 
-add_library(basePipe STATIC "basePipe.cpp" "basePipe.hpp")
+add_library(basePipe STATIC basePipe.cpp)
 target_link_libraries(basePipe PUBLIC
  distMatrixPipe neighGraphPipe 
  ripsPipe betaSkeletonBasedComplex betaSubSkeletonComplex
  upscalePipe slidingWindow fastPersistence 
- incrementalPersistence naiveWindow qhullPipe delaunayPipe incrementalPipe)
+ incrementalPersistence naiveWindow qhullPipe delaunayPipe helixPipe helixDistPipe)
 target_include_directories(basePipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(distMatrixPipe STATIC "distMatrixPipe.cpp" "distMatrixPipe.hpp")
+add_library(distMatrixPipe STATIC distMatrixPipe.cpp)
 target_link_libraries(distMatrixPipe PUBLIC utils basePipe)
 target_include_directories(distMatrixPipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(neighGraphPipe STATIC "neighGraphPipe.cpp" "neighGraphPipe.hpp")
+add_library(neighGraphPipe STATIC neighGraphPipe.cpp)
 target_link_libraries(neighGraphPipe PUBLIC basePipe)
 target_include_directories(neighGraphPipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(ripsPipe STATIC "ripsPipe.cpp" "ripsPipe.hpp")
+add_library(ripsPipe STATIC ripsPipe.cpp)
 target_link_libraries(ripsPipe PUBLIC utils basePipe)
 target_include_directories(ripsPipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(betaSkeletonBasedComplex STATIC "betaSkeletonBasedComplex.cpp" "betaSkeletonBasedComplex.hpp")
+add_library(betaSkeletonBasedComplex STATIC betaSkeletonBasedComplex.cpp)
 target_link_libraries(betaSkeletonBasedComplex PUBLIC basePipe alphaComplex qhullPipe readInput utils kdTree qhullcpp qhull_r)
 target_include_directories(betaSkeletonBasedComplex PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${qhullext_SOURCE_DIR}/src)
 
-add_library(betaSubSkeletonComplex STATIC "betaSubSkeletonComplex.cpp" "betaSubSkeletonComplex.hpp")
+add_library(betaSubSkeletonComplex STATIC betaSubSkeletonComplex.cpp)
 target_link_libraries(betaSubSkeletonComplex PUBLIC basePipe alphaComplex readInput utils kdTree)
 target_include_directories(betaSubSkeletonComplex PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(upscalePipe STATIC "upscalePipe.cpp" "upscalePipe.hpp")
+add_library(upscalePipe STATIC upscalePipe.cpp)
 target_link_libraries(upscalePipe PUBLIC basePipe utils)
 target_include_directories(upscalePipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(slidingWindow STATIC "slidingWindow.cpp" "slidingWindow.hpp")
+add_library(slidingWindow STATIC slidingWindow.cpp)
 target_link_libraries(slidingWindow PUBLIC basePipe readInput utils)
 target_include_directories(slidingWindow PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(fastPersistence STATIC "fastPersistence.cpp" "fastPersistence.hpp")
+add_library(fastPersistence STATIC fastPersistence.cpp)
 target_link_libraries(fastPersistence PUBLIC basePipe utils unionFind)
 target_include_directories(fastPersistence PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(incrementalPersistence STATIC "incrementalPersistence.cpp" "incrementalPersistence.hpp")
+add_library(incrementalPersistence STATIC incrementalPersistence.cpp)
 target_link_libraries(incrementalPersistence PUBLIC basePipe simplexBase simplexArrayList utils unionFind)
 target_include_directories(incrementalPersistence PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(naiveWindow STATIC "naiveWindow.cpp" "naiveWindow.hpp")
+add_library(naiveWindow STATIC naiveWindow.cpp)
 target_link_libraries(naiveWindow PUBLIC basePipe readInput utils)
 target_include_directories(naiveWindow PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
-add_library(qhullPipe STATIC "qhullPipe.cpp" "qhullPipe.hpp")
+add_library(qhullPipe STATIC qhullPipe.cpp)
 target_link_libraries(qhullPipe PUBLIC basePipe utils alphaComplex qhullcpp qhull_r)
 target_include_directories(qhullPipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${qhullext_SOURCE_DIR}/src)
 
-add_library(delaunayPipe STATIC "delaunayPipe.cpp" "delaunayPipe.hpp")
+add_library(delaunayPipe STATIC delaunayPipe.cpp)
 target_link_libraries(delaunayPipe PUBLIC basePipe alphaComplex utils CGAL::CGAL OpenMP::OpenMP_CXX)
 target_include_directories(delaunayPipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
 if(APPLE)
     add_compile_definitions(NO_PARALLEL_ALGORITHMS=1)
 endif()
 
-add_library(incrementalPipe STATIC "incrementalPipe.cpp" "incrementalPipe.hpp")
-target_link_libraries(incrementalPipe PUBLIC basePipe utils OpenMP::OpenMP_CXX)
-target_include_directories(incrementalPipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${EIGEN3_INCLUDE_DIR})
+add_library(helixPipe STATIC helixPipe.cpp)
+target_link_libraries(helixPipe PUBLIC basePipe utils OpenMP::OpenMP_CXX)
+target_include_directories(helixPipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${EIGEN3_INCLUDE_DIR})
+
+add_library(helixDistPipe STATIC helixDistPipe.cpp)
+target_link_libraries(helixDistPipe PUBLIC basePipe readInput writeOutput multifileops utils OpenMP::OpenMP_CXX MPI::MPI_CXX)
+target_include_directories(helixDistPipe PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${EIGEN3_INCLUDE_DIR} ${MPI_INCLUDE_PATH})
 
 if(TBB_FOUND)
-target_link_libraries(incrementalPipe PUBLIC TBB::tbb)
+target_link_libraries(helixPipe PUBLIC TBB::tbb)
+target_link_libraries(helixDistPipe PUBLIC TBB::tbb)
 endif()
 
 

Pipes/basePipe.cpp

@@ -16,13 +16,14 @@
 #include "fastPersistence.hpp"
 #include "ripsPipe.hpp"
 #include "naiveWindow.hpp"
-// #include "betaSkeletonBasedComplex.hpp"
-// #include "betaSubSkeletonComplex.hpp"
+#include "betaSkeletonBasedComplex.hpp"
+#include "betaSubSkeletonComplex.hpp"
 #include "upscalePipe.hpp"
 #include "qhullPipe.hpp"
 #include "slidingWindow.hpp"
 #include "delaunayPipe.hpp"
-#include "incrementalPipe.hpp"
+#include "helixPipe.hpp"
+#include "helixDistPipe.hpp"
 
 template <typename nodeType>
 basePipe<nodeType> *basePipe<nodeType>::newPipe(const std::string &pipeType, const std::string &complexType)
@@ -65,12 +66,15 @@ basePipe<nodeType> *basePipe<nodeType>::newPipe(const std::string &pipeType, con
 	}
 	else if (pipeType == "upscale")
 	{
-		std::cout << "Building upscale" << std::endl;
 		return new upscalePipe<nodeType>();
-		//} else if (pipeType == "betaSkeletonBasedComplex"){
-		//	return new betaSkeletonBasedComplex<nodeType>();
-		//} else if (pipeType == "betaSubSkeletonComplex"){
-		//	return new betaSubSkeletonComplex<nodeType>();
+	}
+	else if (pipeType == "betaSkeletonBasedComplex")
+	{
+		return new betaSkeletonBasedComplex<nodeType>();
+	}
+	else if (pipeType == "betaSubSkeletonComplex")
+	{
+		return new betaSubSkeletonComplex<nodeType>();
 	}
 	else if (pipeType == "qhullPipe" || pipeType == "qhull" || pipeType == "alpha")
 	{
@@ -84,9 +88,13 @@ basePipe<nodeType> *basePipe<nodeType>::newPipe(const std::string &pipeType, con
 	{
 		return new delaunayPipe<nodeType>();
 	}
-	else if (pipeType == "incrementalPipe")
+	else if (pipeType == "helixPipe")
+	{
+		return new helixPipe<nodeType>();
+	}
+	else if (pipeType == "helixDistPipe")
 	{
-		return new incrementalPipe<nodeType>();
+		return new helixDistPipe<nodeType>();
 	}
 
 	return 0;