Merge pull request #3 from patflick/desa-new

Merging DESA code into master.

.travis.yml

@@ -78,6 +78,7 @@ script:
     - ./bin/test-ansv
     - ./bin/test-suffixtree
     - ./bin/test-gsa
+    - ./bin/test-desa
     - mpiexec -np 4 ./bin/test-psac
     - mpiexec -np 13 ./bin/test-psac
     - mpiexec -np 4 ./bin/test-ansv
@@ -86,6 +87,8 @@ script:
     - mpiexec -np 13 ./bin/test-gsa
     - mpiexec -np 4 ./bin/test-gsa
     - mpiexec -np 4 ./bin/test-ss
+    - mpiexec -np 4 ./bin/test-desa
+
 
 after_success:
   # only collect coverage if compiled with gcc

.ycm_extra_conf.py

@@ -86,6 +86,10 @@
 '-I',
 './ext',
 '-I',
+'./ext/mxx',
+'-I',
+'../ext/mxx',
+'-I',
 './ext/mxx/include',
 '-I',
 '../ext/mxx/include',

CMakeLists.txt

@@ -3,134 +3,64 @@ cmake_minimum_required(VERSION 2.6)
 # project settings
 project(psac)
 
+#### Options
+OPTION(PSAC_BUILD_EXES "Build all psac executables (command line tools & benchmark scripts)" ON)
+OPTION(PSAC_BUILD_TESTS "Build unit tests" ON)
+OPTION(PSAC_ENABLE_COVERAGE "Enable code coverage reporting" OFF)
+
 ##### General Compilation Settings
 
 # Initialize CXXFLAGS.
-#set(CMAKE_CXX_FLAGS                "-Wall -O0 -g --std=c++11 -D_GLIBCXX_DEBUG")
-#set(CMAKE_CXX_FLAGS                "-Wall -Wuninitialized -O0 -g --std=c++11")
-#set(CMAKE_CXX_FLAGS                "-Wall -O3 -funroll-loops -msse3 --std=c++11 -g -march=native")
-#set(CMAKE_CXX_FLAGS                "-Wall -O3 -funroll-loops -msse3 -DNDEBUG --std=c++11 -march=native")
-#set(CMAKE_CXX_FLAGS                "-Wall -O3 -DNDEBUG --std=c++11 -Wuninitialized -g")
-
-
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wuninitialized --std=c++11")
-set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0")
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG -march=native")
-set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELEASE} -g")
-
-# Add these standard paths to the search paths for FIND_LIBRARY
-# to find libraries from these locations first
-if(UNIX)
-    set(CMAKE_LIBRARY_PATH "${CMAKE_LIBRARY_PATH} /lib /usr/lib")
-endif()
-
-# --------------------------------------------------------------
-# Indicate CMake 2.7 and above that we don't want to mix relative
-#  and absolute paths in linker lib lists.
-# Run "cmake --help-policy CMP0003" for more information.
-# --------------------------------------------------------------
-if(COMMAND cmake_policy)
-    cmake_policy(SET CMP0003 NEW)
-endif()
-
-
-#### MPI
-find_package(MPI REQUIRED)
-if (MPI_FOUND)
-    #set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MPI_COMPILE_FLAGS}")
-    #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_COMPILE_FLAGS}")
-    #set(CMAKE_LINK_FLAGS "${CMAKE_LINK_FLAGS} ${MPI_LINK_FLAGS}")
-    set(EXTRA_LIBS ${EXTRA_LIBS} ${MPI_LIBRARIES})
-    include_directories(SYSTEM ${MPI_INCLUDE_PATH})
-else (MPI_FOUND)
-    message(SEND_ERROR "This application cannot compile without MPI")
-endif (MPI_FOUND)
-
-
-
-
-## add ScoreP support
-
-
-option(ENABLE_PROFILING_SCOREP "Enable ScoreP profiling support." OFF)
-
-#if(ENABLE_PROFILING_SCOREP)
-#    message(STATUS "Profiling with ScoreP enabled.")
-#
-#    execute_process(COMMAND scorep-config --cxxflags --nocompiler
-#                    OUTPUT_VARIABLE SCOREP_CXX_FLAGS)
-#                ##RESULT_VARIABLE SCOREP_CONFIG_RETURN)
-#                #if(NOT SCOREP_CONFIG_RETURN EQUAL 0)
-#                #    message(FATAL_ERROR "Can NOT execute 'scorep-config' at $ENV{SCOREP_ROOT}/bin/scorep-config - check file permissions")
-#                #endif()
-#    execute_process(COMMAND scorep-config --mpp=mpi --ldflags
-#                    OUTPUT_VARIABLE SCOREP_LD_FLAGS)
-#    execute_process(COMMAND scorep-config --mpp=mpi --libs
-#                    OUTPUT_VARIABLE SCOREP_LIBS)
-#                string(STRIP "${SCOREP_LIBS}" SCOREP_LIBS)
-#
-#                #execute_process(COMMAND scorep-config --mpp=mpi --libs
-#                #                OUTPUT_VARIABLE SCOREP_LIBFLAGS)
-#                #string(STRIP "${SCOREP_LIBFLAGS}" SCOREP_LIBFLAGS)
-#
-#    # subsystem iniialization file
-#    execute_process(COMMAND scorep-config --mpp=mpi --nocuda --noopencl --adapter-init
-#                    OUTPUT_VARIABLE SCOREP_INIT_FILE)
-#    file(WRITE ${CMAKE_BINARY_DIR}/scorep_init.c "${SCOREP_INIT_FILE}")
-#
-#    #if(SCOREP_ENABLE)
-#        set(SCOREP_SRCFILES "${CMAKE_BINARY_DIR}/scorep_init.c")
-#        #endif(SCOREP_ENABLE)
-#
-#
-#    # TODO: possibly put the LIBS to target_link_libraries
-#    set(CMAKE_CXX_LINK_FLAGS "${CMAKE_CXX_LINK_FLAGS} ${SCOREP_LD_FLAGS} ${SCOREP_LIBS}")
-#    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SCOREP_CXX_FLAGS}")
-#    #set(EXTRA_LIBS ${EXTRA_LIBS} ${SCOREP_LIBS})
-#endif(ENABLE_PROFILING_SCOREP)
-
-
-if(ENABLE_PROFILING_SCOREP)
-    message(STATUS "Profiling with ScoreP enabled.")
-    set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "scorep")
-    set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK "scorep")
-endif(ENABLE_PROFILING_SCOREP)
 
 ### Test Coverage
-OPTION(ENABLE_COVERAGE "Enable code coverage reporting" OFF)
-if(ENABLE_COVERAGE)
+if(PSAC_ENABLE_COVERAGE)
   # turn off stack protection for gcov coverage, because the stack protector shows
   # up as a never taken branch, and thus turns any last statement in a function
   # with a stack procetor into a partially covered statement.
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage -fno-stack-protector")
-endif(ENABLE_COVERAGE)
+endif(PSAC_ENABLE_COVERAGE)
 
 ###### Executable and Libraries
 # Save libs and executables in the same place
-set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib CACHE PATH "Output directory for libraries" )
-set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH "Output directory for applications" )
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
-include_directories("${PROJECT_SOURCE_DIR}/include")
-include_directories("${PROJECT_SOURCE_DIR}/ext/mxx")
-include_directories("${PROJECT_SOURCE_DIR}/ext/mxx/include")
-include_directories("${PROJECT_SOURCE_DIR}/ext")
-include_directories("${PROJECT_SOURCE_DIR}/ext/cxx-prettyprint")
+## psac header library
+add_library(psaclib INTERFACE)
+target_include_directories(psaclib INTERFACE include)
+
+## psac dependencies
 
 # load mxx and its gtest wrapper
-add_subdirectory("${PROJECT_SOURCE_DIR}/ext/mxx")
+set(MXX_BUILD_TESTS OFF CACHE BOOL "disable building mxx tests" FORCE)
+add_subdirectory(ext/mxx)
+target_link_libraries(psaclib INTERFACE mxx)
 
 # include libdivsufsort (with 64bit support but without examples)
 set(BUILD_DIVSUFSORT64 ON CACHE BOOL "enables divsufsort 64bit functions" FORCE)
-set(BUILD_EXAMPLES OFF CACHE BOOL "enables divsufsort 64bit functions" FORCE)
-add_subdirectory("${PROJECT_SOURCE_DIR}/ext/libdivsufsort")
-include_directories(${libdivsufsort_BINARY_DIR}/include)
-include_directories(${libdivsufsort_SOURCE_DIR}/include)
+set(BUILD_EXAMPLES OFF CACHE BOOL "enables divsufsort examples" FORCE)
+add_subdirectory(ext/libdivsufsort)
+
+# prettyprint
+target_include_directories(psaclib INTERFACE ext/cxx-prettyprint)
 
+# divsufsort (integrate into psac as `psac-dss-lib`)
+add_library(psac-dss-lib INTERFACE)
+target_link_libraries(psac-dss-lib INTERFACE psaclib)
+target_include_directories(psac-dss-lib INTERFACE ${libdivsufsort_BINARY_DIR}/include)
+target_link_libraries(psac-dss-lib INTERFACE divsufsort divsufsort64)
 
-# add own subdirectories
-add_subdirectory(src)
-add_subdirectory(src/tests)
+
+## build executables
+if(PSAC_BUILD_EXES)
+  add_subdirectory(src)
+endif()
 
 # build tests
-add_subdirectory(test)
+if (PSAC_BUILD_TESTS)
+  add_subdirectory(test)
+endif()