the decaps version

CMakeLists.txt

@@ -1,6 +1,8 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.9)
 project(bayestar)
 
+set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS TRUE)
+
 #
 # Use pkg-config to find some libraries
 #
@@ -26,74 +28,96 @@ IF(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git)
 	ELSE(GIT_FOUND)
 		SET(GIT_BUILD_VERSION 0)
 	ENDIF(GIT_FOUND)
+ELSE(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git)
+	SET(GIT_BUILD_VERSION "$ENV{BAYESTARCOMMIT}")
 ENDIF(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git)
 
 #
 # Configure a header file to pass some of the CMake
 # settings to the source code
 #
-#set(DATADIR "${CMAKE_INSTALL_PREFIX}/data/")
 set(DATADIR "${CMAKE_SOURCE_DIR}/data/")
 configure_file(
 	"${PROJECT_SOURCE_DIR}/src/bayestar_config.h.in"
-	"${PROJECT_BINARY_DIR}/src/bayestar_config.h"  
+	"${PROJECT_BINARY_DIR}/src/bayestar_config.h"
 	ESCAPE_QUOTES
 )
 include_directories("${PROJECT_BINARY_DIR}/src")
 
-#
-# Optimizations
-#
-IF(NOT CMAKE_COMPILER_IS_GNUCXX)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -ipo -axHOST -no-prec-div ")
-ELSE(NOT CMAKE_COMPILER_IS_GNUCXX)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 ") #-march=native
-ENDIF(NOT CMAKE_COMPILER_IS_GNUCXX)
-
 #
 # Profiling
 #
 IF(CMAKE_COMPILER_IS_GNUCXX)
 	IF(PROFILING_GEN)
-		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-generate -pg ")
-		#set(CMAKE_LD_FLAGS "${CMAKE_LD_FLAGS} -fprofile-generate=profiling/ -pg ")
+		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-generate=prof -lgcov ")
 		MESSAGE( STATUS "Setting flags to generate profiling information." )
 	ENDIF(PROFILING_GEN)
 	IF(PROFILING_USE)
-		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-use ")
-		#set(CMAKE_LD_FLAGS "${CMAKE_LD_FLAGS} -fprofile-use=profiling/ ")
+		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-use=prof ")
 		MESSAGE( STATUS "Setting flags to use profiling information." )
 	ENDIF(PROFILING_USE)
 ENDIF(CMAKE_COMPILER_IS_GNUCXX)
 
-### OpenCV
-pkg_check_modules(OPENCV opencv)
-include_directories(${OPENCV_INCLUDE_DIRS})
-link_directories(${OPENCV_LIBRARY_DIRS})
-MESSAGE( STATUS "OPENCV_LIBRARY_DIRS: ${OPENCV_LIBRARY_DIRS}" )
-MESSAGE( STATUS "OPENCV_INCLUDE_DIRS: ${OPENCV_INCLUDE_DIRS}" )
-MESSAGE( STATUS "OPENCV_LIBRARIES: ${OPENCV_LIBRARIES}" )
+#
+# Optimizations
+#
+IF(NOT CMAKE_COMPILER_IS_GNUCXX)
+	set(CMAKE_CXX_COMPILER icx)
+	# set(CMAKE_CXX_COMPILER icc)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -ipo -xHOST -fp-model precise ")
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14 ")
+ELSE(NOT CMAKE_COMPILER_IS_GNUCXX)
+	set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -O3 -march=native ")
+	set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -O1 -g ")
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --std=c++14 ")
+ENDIF(NOT CMAKE_COMPILER_IS_GNUCXX)
 
-### GSL
-find_package(GSL REQUIRED)
-include_directories(${GSL_INCLUDE_DIR})
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_INLINE=1 -DGSL_RANGE_CHECK=0")
+MESSAGE( STATUS "CMAKE_COMPILER_IS_GNUCXX: ${CMAKE_COMPILER_IS_GNUCXX}" )
+MESSAGE( STATUS "CMAKE_CXX_FLAGS_RELEASE: ${CMAKE_CXX_FLAGS_RELEASE}" )
+
+### HDF5
+find_package(HDF5 COMPONENTS C CXX HL REQUIRED)
+include_directories(${HDF5_INCLUDE_DIRS})
+MESSAGE( STATUS "HDF5_INCLUDE_DIRS: ${HDF5_INCLUDE_DIRS}" )
+MESSAGE( STATUS "HDF5_LIBRARY_DIRS: ${HDF5_LIBRARY_DIRS}" )
+MESSAGE( STATUS "HDF5_LIBRARIES: ${HDF5_LIBRARIES}" )
+MESSAGE( STATUS "HDF5_CXX_LIBRARIES: ${HDF5_CXX_LIBRARIES}" )
+
+### OpenCV
+find_package(OpenCV 4 REQUIRED)
+include_directories(${OpenCV_INCLUDE_DIRS})
+link_directories(${OpenCV_LIBRARY_DIRS})
+MESSAGE( STATUS "OPENCV_LIBRARY_DIRS: ${OpenCV_LIBRARY_DIRS}" )
+MESSAGE( STATUS "OPENCV_INCLUDE_DIRS: ${OpenCV_INCLUDE_DIRS}" )
+MESSAGE( STATUS "OPENCV_LIBRARIES: ${OpenCV_LIBRARIES}" )
 
 ### Boost
 find_package(Boost REQUIRED COMPONENTS program_options)
 include_directories(${Boost_INCLUDE_DIRS})
 MESSAGE( STATUS "Boost_INCLUDE_DIRS: ${Boost_INCLUDE_DIRS}" )
 MESSAGE( STATUS "Boost_LIBRARIES: ${Boost_LIBRARIES}" )
 
-
 ### OpenMP support
-#find_package(OpenMP REQUIRED)
 IF(NOT CMAKE_COMPILER_IS_GNUCXX)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -openmp")
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -qopenmp")
 ELSE(NOT CMAKE_COMPILER_IS_GNUCXX)
 	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
 ENDIF(NOT CMAKE_COMPILER_IS_GNUCXX)
-#set(CMAKE_C_FLAGS ${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS})
+
+### EIGEN3
+pkg_check_modules(EIGEN3 eigen3)
+#find_package(Eigen3 REQUIRED NO_MODULES)
+include_directories(${EIGEN3_INCLUDE_DIRS})
+MESSAGE( STATUS "EIGEN3_INCLUDE_DIRS: ${EIGEN3_INCLUDE_DIRS}" )
+MESSAGE( STATUS "EIGEN3_LIBRARIES: ${EIGEN3_LIBRARIES}" )
+
+### GSL
+pkg_check_modules(GSL gsl)
+#find_package(GSL REQUIRED)
+MESSAGE( STATUS "GSL_INCLUDE_DIRS: ${GSL_INCLUDE_DIR}" )
+MESSAGE( STATUS "GSL_LIBRARY_DIRS: ${GSL_LIBRARY_DIRS}" )
+include_directories(${GSL_INCLUDE_DIR})
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_INLINE=1 -DGSL_RANGE_CHECK=0")
 
 ### Fixed-size types
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__STDC_LIMIT_MACROS")
@@ -103,15 +127,23 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__STDC_LIMIT_MACROS")
 #
 add_executable(bayestar src/main.cpp src/model.cpp src/sampler.cpp
                         src/interpolation.cpp src/stats.cpp src/chain.cpp
-                        src/data.cpp src/binner.cpp src/los_sampler.cpp src/h5utils.cpp)
+                        src/data.cpp src/binner.cpp src/los_sampler.cpp
+                        src/h5utils.cpp src/star_exact.cpp
+                        src/program_opts.cpp src/gaussian_process.cpp
+                        src/healpix_tree.cpp src/neighbor_pixels.cpp
+			src/bridging_sampler.cpp)
 
 #
 # Link libraries
 #
 target_link_libraries(bayestar rt)
-target_link_libraries(bayestar hdf5 hdf5_cpp)
+target_link_libraries(bayestar ${HDF5_LIBRARIES} stdc++)
 target_link_libraries(bayestar ${GSL_LIBRARIES})
 target_link_libraries(bayestar ${Boost_LIBRARIES})
-target_link_libraries(bayestar opencv_core opencv_imgproc)
-#target_link_libraries(bayestar ${OPENCV_LIBRARIES})
+target_link_libraries(bayestar ${OpenCV_LIBRARIES})
 #target_link_libraries(bayestar ${OpenMP_LIBRARIES})
+target_link_libraries(bayestar ${EIGEN3_LIBRARIES})
+IF(ADDITIONAL_LINK_DIRS)
+	target_link_libraries(bayestar -L${ADDITIONAL_LINK_DIRS})
+    MESSAGE( STATUS "Additional link directories: ${ADDITIONAL_LINK_DIRS}" )
+ENDIF(ADDITIONAL_LINK_DIRS)

README.txt

@@ -0,0 +1 @@
+Andrew Saydjari updated this (forked) version of Bayestar for the DECaPS dust map run from Greg M. Green's original repo. The main changes were just to make it compile with modern compilers. The src/, cmake/, and data/ directories were updated accordingly. No guarantees are made about the scripts/ and input/ directories. A more recent config-example.txt file is also included. Any questions can be directed to andrew-saydjari or gregreen.