patched cmake from issue_136_paired_reads branch

sortmerna · Sep 4, 2019 · 7e31c75 · 7e31c75
1 parent 17ee60b
commit 7e31c75
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Showing 4 changed files with 148 additions and 52 deletions.
diff --git a/3rdparty/alp/CMakeLists.txt b/3rdparty/alp/CMakeLists.txt
@@ -8,6 +8,8 @@
 cmake_minimum_required(VERSION 3.13)
 project(alp CXX)
 
+set(CMAKE_CXX_STANDARD 11)
+
 set(ALP_HDRS
 	njn_approx.hpp
 	njn_doubletype.hpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -67,6 +67,12 @@ set(DIRENTWIN_URL https://github.com/tronkko/dirent CACHE STRING "Dirent-Windows
 set(DIRENTWIN_HOME ${EXTERNAL_DEPS}/dirent CACHE PATH "Dirent-Windows interface installation directory")
 set(CONCURRENTQUEUE_URL https://github.com/cameron314/concurrentqueue CACHE STRING "Concurrent queue library GitHub URL")
 set(CONCURRENTQUEUE_HOME ${EXTERNAL_DEPS}/concurrentqueue CACHE PATH "Concurrent queue library installation directory")
+#set(gflags_DIR  ${EXTERNAL_DEPS}/gflags/dist/lib/cmake/gflags CACHE PATH "GFlags library configuration")
+
+option(ROCKSDB_STATIC "Use static RocksDB library" ON)
+option(ZLIB_STATIC "Use static ZLib library" ON)
+
+option(PORTABLE "Build portable/statically linked executable" ON)
 
 option(WITH_MD_LIBRARY "build with MD" ON)
 if(WIN32 AND MSVC)
@@ -84,11 +90,29 @@ if(WIN32 AND MSVC)
 		CMAKE_C_FLAGS_RELWITHDEBINFO)
 	   if(${flag_var} MATCHES "/MD")
 		  string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
-	   endif(${flag_var} MATCHES "/MD")
+	   endif()
+	endforeach(flag_var)
+  endif()
+endif()
+
+option(WITH_RUNTIME_DEBUG "Build with MDd/MTd on Windows. Ignored on non-Windows" OFF)
+if(WIN32 AND MSVC)
+  if(NOT WITH_RUNTIME_DEBUG)
+	foreach(flag_var
+		CMAKE_CXX_FLAGS_DEBUG 
+		CMAKE_C_FLAGS_DEBUG
+		)
+	   if(${flag_var} MATCHES "/MDd")
+		  string(REGEX REPLACE "/MDd" "/MD" ${flag_var} "${${flag_var}}")
+		elseif(${flag_var} MATCHES "/MTd")
+		  string(REGEX REPLACE "/MTd" "/MT" ${flag_var} "${${flag_var}}")
+	   endif()
 	endforeach(flag_var)
   endif()
 endif()
 
+message("CMAKE_CXX_FLAGS_DEBUG: ${CMAKE_CXX_FLAGS_DEBUG}")
+message("CMAKE_C_FLAGS_DEBUG: ${CMAKE_C_FLAGS_DEBUG}")
 
 option(WITH_TESTS "Select whether to build tests" OFF)
 

diff --git a/src/sortmerna/CMakeLists.txt b/src/sortmerna/CMakeLists.txt
@@ -12,21 +12,61 @@ set(CMAKE_CXX_STANDARD 14)
 
 find_package(Threads REQUIRED)
 
-find_package(RocksDB 
-	REQUIRED
+find_package(RocksDB CONFIG REQUIRED
   PATHS ${ROCKSDB_HOME}
   NO_DEFAULT_PATH
 )
 
-# fix for RocksDBTargets.cmake, which makes both static and shared libraries always dependent on libz.so
+if(RocksDB_FOUND)
+	message("RocksDB package OK")
+else()
+	message("RocksDB package NOK")
+endif()
+
+# 
+get_target_property(lib RocksDB::rocksdb-shared LOCATION)
+message("RocksDB::rocksdb-shared LOCATION: ${lib}")
+get_target_property(lib RocksDB::rocksdb-shared LOCATION_DEBUG)
+message("RocksDB::rocksdb-shared LOCATION_DEBUG: ${lib}")
+get_target_property(lib RocksDB::rocksdb-shared IMPORTED_LOCATION_DEBUG)
+message("RocksDB::rocksdb-shared LOCATION_DEBUG: ${lib}")
+get_target_property(cfg RocksDB::rocksdb-shared IMPORTED_CONFIGURATIONS)
+message("RocksDB::rocksdb-shared IMPORTED_CONFIGURATIONS: ${cfg}")
+get_target_property(lib RocksDB::rocksdb-shared IMPORTED_IMPLIB)
+message("RocksDB::rocksdb-shared IMPORTED_IMPLIB: ${lib}")
+
+get_target_property(lib RocksDB::rocksdb LIBRARY_OUTPUT_NAME)
+message("RocksDB::rocksdb LIBRARY_OUTPUT_NAME: ${lib}")
+
+ if(ROCKSDB_STATIC)
+	message("Using Static RocksDB lib")
+    set(ROCKSDB_LIB RocksDB::rocksdb)
+ else()
+	message("Using Shared RocksDB lib")
+    set(ROCKSDB_LIB RocksDB::rocksdb-shared)
+	#if(WIN32 AND MSVC)
+	#	set_target_properties(RocksDB::rocksdb-shared PROPERTIES
+	#		IMPORTED_IMPLIB "${ROCKSDB_HOME}/lib/rocksdb-shared.lib"
+	#	)
+	#endif()
+endif()
+
+get_property(trans_deps TARGET ${ROCKSDB_LIB} PROPERTY INTERFACE_LINK_LIBRARIES)
+message("${ROCKSDB_LIB} transitive link dependencies: ${trans_deps}")
+
+# fix RocksDBTargets.cmake, which makes both static and shared libraries always dependent on libz.so
 if(NOT WIN32)
 	if(ZLIB_LIBRARY_RELEASE)
+		# modify the dependent libraries of the RocksDB::rocksdb target
 		set_target_properties(RocksDB::rocksdb PROPERTIES
-			INTERFACE_LINK_LIBRARIES "${ZLIB_LIBRARY_RELEASE};-lpthread"
+			INTERFACE_LINK_LIBRARIES "${ZLIB_LIBRARY_RELEASE};Threads::Threads"
 		)
 	endif()
 endif()
 
+get_property(trans_deps TARGET RocksDB::rocksdb PROPERTY INTERFACE_LINK_LIBRARIES)
+message("rocksdb transitive link dependencies AFTER modification: ${trans_deps}")
+
 include(FindZLIB)
 # prevent CONFIG search mode
 find_package(ZLIB MODULE REQUIRED)
@@ -35,6 +75,26 @@ include(FindRapidJson)
  # prevent CONFIG search mode
 find_package(RapidJson MODULE REQUIRED)
 
+# set additional compile flags
+if(MSVC)
+#  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Zi /nologo /EHsc /GS /Gd /GR /GF /fp:precise /Zc:wchar_t /Zc:forScope /errorReport:queue")
+#  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /FC /d2Zi+ /W4 /wd4127 /wd4800 /wd4996 /wd4351 /wd4100 /wd4204 /wd4324")
+else()
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -W -Wextra -Wall -Xlinker -v") # -Xlinker -v / --verbose (linked libraries info)   '-Wl,-Map,mapfile.txt'  '-Wl,-v'
+  #set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -v -da -Q") # for segfault
+  #                                                    |  |   |_show which function is causing the crash.
+  #                                                    |  |_dumps the RTL to a file after each stage
+  #                                                    |_show how the program was invoked
+  #set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -v -da -Q -O0") # for segfault
+#  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wsign-compare -Wshadow -Wno-unused-parameter -Wno-unused-variable -Woverloaded-virtual -Wnon-virtual-dtor -Wno-missing-field-initializers -Wno-strict-aliasing")
+endif()
+
+#set(MY_OPTS -g -Wall) # using quotes "-g -Wall" throws error
+#target_compile_options(smr_objs PUBLIC ${MY_OPTS})
+#target_compile_options(smr_objs PUBLIC "$<$<CONFIG:DEBUG>:${MY_OPTS}>")
+#target_compile_options(smr_objs PUBLIC "$<$<CONFIG:RELEASE>:${MY_OPTS}>")
+#set_target_properties(smr_objs PROPERTIES COMPILE_OPTIONS ${MY_OPTS})
+
 set(SMR_SRCS
 	alignment.cpp
 	bitvector.cpp
@@ -63,26 +123,36 @@ set(SMR_SRCS
 add_library(smr_objs OBJECT ${SMR_SRCS})
 target_link_libraries(smr_objs
 	PUBLIC
-		ZLIB::ZLIB
-		RocksDB::rocksdb
-		RapidJSON::RapidJSON
 		alp
+		${ROCKSDB_LIB}
+		RapidJSON::RapidJSON
+		ZLIB::ZLIB
 )
 if(WIN32)
 	target_include_directories(smr_objs 
-		PRIVATE
+		PUBLIC
 			${CMAKE_SOURCE_DIR}/include
 			$<TARGET_PROPERTY:winapi,INCLUDE_DIRECTORIES>
+			$<TARGET_PROPERTY:cmph,INCLUDE_DIRECTORIES>
 			${DIRENTWIN_HOME}/include
 			${EXTERNAL_DEPS}/concurrentqueue
 	)
 else()
-	target_include_directories(smr_objs PRIVATE
-		${CMAKE_SOURCE_DIR}/include
-		${EXTERNAL_DEPS}/concurrentqueue
+	target_include_directories(smr_objs 
+		PUBLIC
+			${CMAKE_SOURCE_DIR}/include
+			$<TARGET_PROPERTY:cmph,INCLUDE_DIRECTORIES>
+			${EXTERNAL_DEPS}/concurrentqueue
 	)
 endif()
 
+get_property(trans_deps TARGET smr_objs PROPERTY INTERFACE_LINK_LIBRARIES)
+message("SMR Objects transitive link dependencies: ${trans_deps}")
+
+get_target_property(COMPILE_OPT smr_objs COMPILE_OPTIONS)
+get_target_property(COMPILE_FLG smr_objs COMPILE_FLAGS)
+message("SMR Objects COMPILE_OPT: ${COMPILE_OPT}  COMPILE_FLG: ${COMPILE_FLG}")
+
 # SMR
 add_executable(sortmerna main.cpp)
 if(WIN32)
@@ -97,36 +167,33 @@ if(WIN32)
 		smr_objs
 		winapi
 		alp
+		$<TARGET_OBJECTS:cmph>
 		ZLIB::ZLIB
-		RocksDB::rocksdb
+		${ROCKSDB_LIB}
 		RapidJSON::RapidJSON
 		Rpcrt4.lib
 		Cabinet.lib # rocksdb:XPRESS::CreateCompressor,Compress,CloseCompressor,CreateDecompressor,Decompress,CloseDecompressor
 	)
-	add_dependencies(sortmerna 
-		winapi
-		alp
-		build_version
-		smr_objs
-	)
 else()
 	target_include_directories(sortmerna 
 		PRIVATE
 			${EXTERNAL_DEPS}/concurrentqueue
 			${CMAKE_SOURCE_DIR}/include
 	)
+	#get_property(rocksdb_trans_deps TARGET RocksDB::rocksdb PROPERTY INTERFACE_LINK_LIBRARIES)
+	#message("rocksdb_trans_deps: ${rocksdb_trans_deps}")
 	target_link_libraries(sortmerna
 		build_version
 		smr_objs
-		alp
-		ZLIB::ZLIB
-		RocksDB::rocksdb
-		RapidJSON::RapidJSON
-		${CMAKE_THREAD_LIBS_INIT}
-	)
-	add_dependencies(sortmerna 
-		alp 
-		smr_objs 
-		build_version
+		alp # this is a transitive dependency of smr_objs but the linking fails without it. Why?
+		$<TARGET_OBJECTS:cmph>
+		${ROCKSDB_LIB}
+		${CMAKE_DL_LIBS}
+		# the following are all transitive dependencies of smr_objs i.e. no need to link: 
+		# RapidJSON::RapidJSON ZLIB::ZLIB Threads::Threads (rockdb deps)
 	)
+
+	if(PORTABLE)
+		target_link_options(sortmerna PRIVATE -static)
+	endif(PORTABLE)
 endif()
diff --git a/tests/sortmerna/CMakeLists.txt b/tests/sortmerna/CMakeLists.txt
@@ -13,29 +13,32 @@ message("tests PROJECT_BINARY_DIR = ${PROJECT_BINARY_DIR}")
 message("tests CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
 message("tests CMAKE_CFG_INTDIR = ${CMAKE_CFG_INTDIR}")
 
-set(tests
-	kvdb
+set(TEST_SRCS
+	kvdb.cpp
+	#main.cpp
 )
 
-include_directories("${CMAKE_SOURCE_DIR}/include" ${CMAKE_SOURCE_DIR}/src/winapi/include)
+add_executable(tests ${TEST_SRCS})
+#target_include_directories(tests
+#PRIVATE
+#		${CMAKE_SOURCE_DIR}/include
+#		#${CMAKE_SOURCE_DIR}/src/winapi/include
+#)
+if(WIN32)
+	target_link_libraries(tests
+		build_version
+		alp
+		smr_objs
+		winapi
+		$<TARGET_OBJECTS:cmph>
+	)
+else()
+	target_link_libraries(tests
+		build_version
+		alp
+		smr_objs
+		$<TARGET_OBJECTS:cmph>
+	)
+endif()
 
-foreach(test ${tests})
-	add_executable("test_${test}" ${test}.cpp $<TARGET_OBJECTS:smr_objs>)
-	if(WIN32)
-		target_link_libraries( "test_${test}"
-			alp
-			z
-			rocksdb
-			Rpcrt4.lib
-			Cabinet.lib
-		)
-	else()
-		target_link_libraries( "test_${test}"
-			alp
-			z
-			rocksdb
-		)
-	endif()
-endforeach()
-
-add_dependencies(test_kvdb sortmerna)
+#add_executable("test_${test}" ${test}.cpp $<TARGET_OBJECTS:smr_objs>)