Fixing cmake files for Linux build and module.

femto-dev · Sep 30, 2014 · 8dd9996 · 8dd9996
1 parent 4c26934
commit 8dd9996
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Showing 8 changed files with 65 additions and 31 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.8)
-project(FEMTO)
+project(FEMTO C CXX)
 
 set(FEMTO_VERSION "femto 1.2.9.2 from http://github.com/femto-dev/femto")
 
@@ -24,6 +24,7 @@ else(NO_FLEX_BISON)
   find_package(BISON)
 endif(NO_FLEX_BISON)
 
+find_package(Threads REQUIRED)
 find_package(MPI)
 
 #if(NOT ${BISON_VERSION} EQUAL:
@@ -70,6 +71,12 @@ enable_testing()
 
 set(CMAKE_CXX_FLAGS "-g -Wall")
 
+# Add libaries used everywhere
+set(DEFAULT_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+if( DEFINED HAVE_CLOCK_GETTIME_RT OR DEFINED HAS_POSIX_AIO_RT)
+  set(DEFAULT_LIBRARIES "${DEFAULT_LIBRARIES} -lrt")
+endif()
+
 # Emulate make check
 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND})
 

diff --git a/cmake/FindAPXS.cmake b/cmake/FindAPXS.cmake
@@ -1,13 +1,23 @@
+FIND_PROGRAM(APXS_BIN NAMES apxs apxs2
+             PATH_SUFFIXES httpd apache apache2)
+
+if(APXS_BIN)
+  EXECUTE_PROCESS(COMMAND ${APXS_BIN} -q INCLUDEDIR OUTPUT_VARIABLE APXS_INCLUDE_DIR)
+  EXECUTE_PROCESS(COMMAND ${APXS_BIN} -q LIBEXECDIR OUTPUT_VARIABLE APXS_MODULE_DIR )
+  #message(WARNING "APXS was found ${AXPS_INCLUDE_DIR}")
+else(APXS_BIN)
+  # message(WARNING "APXS not found")
+
+endif(APXS_BIN)
+
+
+set(APACHE_INCLUDE_DIRS ${APXS_INCLUDE_DIR})
+set(APACHE_MODULE_DIRS ${APXS_MODULE_DIR})
+
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(APXS DEFAULT_MSG APXS_BIN APXS_INCLUDE_DIR APXS_MODULE_DIR)
+mark_as_advanced(APXS_BIN APXS_INCLUDE_DIR APXS_MODULE_DIR)
+
 
-if(NOT DEFINED APACHE_MODULE_DIR)
-   find_program(APXS_BIN NAMES apxs apxs2
-             PATH_SUFFIXES httpd apache apache2
-   )
-
-   if(APXS_BIN)
-      EXEC_PROGRAM(${APXS_BIN}
-         ARGS -q LIBEXECDIR
-         OUTPUT_VARIABLE APACHE_MODULE_DIR )
-   endif(APXS_BIN)
-endif(NOT DEFINED APACHE_MODULE_DIR)
 
diff --git a/src/dcx_cc/CMakeLists.txt b/src/dcx_cc/CMakeLists.txt
@@ -17,7 +17,12 @@ set(FEMTO_DCX_CC_SRCS
 
 add_library(femto_dcx_cc STATIC ${FEMTO_DCX_CC_SRCS})
 
-set(DCX_LIBS femto_dcx_cc femto_seq femto femto_bwt femto_mpi_cc femto_util_cc femto_util ssl crypto)
+set(DCX_LIBS femto_dcx_cc femto_seq femto femto_bwt femto_mpi_cc femto_util_cc femto_util ssl crypto ${DEFAULT_LIBRARIES})
+
+if(HAS_LINUX_LIBAIO)
+  set(DCX_LIBS "${DCX_LIBS} -laio")
+endif()
+
 
 set(DCX_TESTS dcover_test suffix_sort_test)
 

diff --git a/src/main/CMakeLists.txt b/src/main/CMakeLists.txt
@@ -89,15 +89,15 @@ add_library(femto_bwt STATIC ${FEMTO_BWT_SRCS})
 add_library(femto_seq STATIC ${FEMTO_SEQ_SRCS})
 
 add_executable(femto_multiquery query_tool.c)
-target_link_libraries(femto_multiquery femto femto_bwt femto_util)
+target_link_libraries(femto_multiquery femto femto_bwt femto_util ${DEFAULT_LIBRARIES})
 add_executable(femto_flatten flatten_tool.c)
-target_link_libraries(femto_flatten femto femto_bwt femto_util)
+target_link_libraries(femto_flatten femto femto_bwt femto_util ${DEFAULT_LIBRARIES})
 add_executable(femto_handle_request handle_request.c)
-target_link_libraries(femto_handle_request femto femto_bwt femto_util)
+target_link_libraries(femto_handle_request femto femto_bwt femto_util ${DEFAULT_LIBRARIES})
 add_executable(femto_info info_tool.c)
-target_link_libraries(femto_info femto femto_bwt femto_util)
+target_link_libraries(femto_info femto femto_bwt femto_util ${DEFAULT_LIBRARIES})
 add_executable(femto_common common_tool.c)
-target_link_libraries(femto_common femto femto_bwt femto_util)
+target_link_libraries(femto_common femto femto_bwt femto_util ${DEFAULT_LIBRARIES})
 install(TARGETS femto_flatten femto_handle_request femto_info femto_common
         ${INSTALL_TARGETS_DEFAULT_ARGS})
 
@@ -112,7 +112,7 @@ set(FEMTO_TESTS
 foreach(test ${FEMTO_TESTS})
   add_executable(${test} EXCLUDE_FROM_ALL ${test}.c)
   add_test(${test} ${test})
-  target_link_libraries(${test} femto femto_bwt femto_util)
+  target_link_libraries(${test} femto femto_bwt femto_util ${DEFAULT_LIBRARIES})
   add_dependencies(check ${test})
 endforeach(test)
 
@@ -124,7 +124,7 @@ set(BWT_TESTS
 foreach(test ${BWT_TESTS})
   add_executable(${test} EXCLUDE_FROM_ALL ${test}.c bwt_creator.h bwt_creator.c bwt_qsufsort.c)
   add_test(${test} ${test})
-  target_link_libraries(${test} femto femto_bwt femto_util)
+  target_link_libraries(${test} femto femto_bwt femto_util ${DEFAULT_LIBRARIES})
   add_dependencies(check ${test})
 endforeach(test)
 

diff --git a/src/main_cc/CMakeLists.txt b/src/main_cc/CMakeLists.txt
@@ -9,7 +9,7 @@ include_directories(${CMAKE_SOURCE_DIR}/src/re2/re2)
 add_executable(femto_search search_tool.cc)
 #link_directories(${RE2_LIB_DIR})
 #target_link_libraries(femto_search re2 femto_seq femto femto_util)
-target_link_libraries(femto_search ${RE2_LIB} femto_seq femto femto_util)
+target_link_libraries(femto_search ${RE2_LIB} femto_seq femto femto_util ${DEFAULT_LIBRARIES})
 add_dependencies(femto_search make_re2)
 
 install(TARGETS femto_search

diff --git a/src/mod_femto/CMakeLists.txt b/src/mod_femto/CMakeLists.txt
@@ -1,3 +1,13 @@
+# include ../util
+include_directories(${CMAKE_SOURCE_DIR}/src/utils)
+# include ../util_cc
+#include_directories(${CMAKE_SOURCE_DIR}/src/utils_cc)
+# include ../main
+include_directories(${CMAKE_SOURCE_DIR}/src/main)
+# include ../mpi
+#include_directories(${CMAKE_SOURCE_DIR}/src/mpi)
+# include ../re2
+#include_directories(${CMAKE_SOURCE_DIR}/src/re2/re2/)
 
 find_package(APR)
 find_package(APXS)
@@ -16,18 +26,18 @@ if(APR_FOUND)
     #apxs-install:
     #	${APXS} -i -a -n femto libmod_femto.la
     #
-    execute_process(COMMAND ${APXS} -q INCLUDEDIR OUTPUT_VARIABLE APXS_INCLUDE)
-    include_directories(${APXS_INCLUDE})
+    #    execute_process(COMMAND ${APXS} -q INCLUDEDIR OUTPUT_VARIABLE APXS_INCLUDE)
+    #include_directories(${APXS_INCLUDE})
 
+    add_library(libmod_femto mod_femto.c)
     target_link_libraries(libmod_femto ${APR_LIBRARY} ${APU_LIBRARY})
-    include_directories(${APR_INCLUDE_DIR} ${APU_INCLUDE_DIR})
+    include_directories(${APXS_INCLUDE_DIR} ${APR_INCLUDE_DIR} ${APU_INCLUDE_DIR})
     if(DEFINED APR_CPPFLAGS)
       add_definitions("${APR_CPPFLAGS}")
     endif(DEFINED APR_CPPFLAGS)
 
     add_definitions(-D_LARGEFILE64_SOURCE -D_GNU_SOURCE)
     #building just a library. 
-    add_library(libmod_femto mod_femto.c)
     target_link_libraries(libmod_femto libfemto libfemto_util -module)
   endif(APXS_FOUND)
 endif(APR_FOUND)

diff --git a/src/mpi/CMakeLists.txt b/src/mpi/CMakeLists.txt
@@ -13,7 +13,7 @@ set(MPI_CC_TESTS mpi_utils_test)
 foreach(test ${MPI_CC_TESTS})
   add_executable(${test} EXCLUDE_FROM_ALL ${test}.cc)
   add_test(${test} ${test})
-  target_link_libraries(${test} femto_mpi_cc femto_util_cc femto_util)
+  target_link_libraries(${test} femto_mpi_cc femto_util_cc femto_util ${DEFAULT_LIBRARIES})
   add_dependencies(check ${test})
 endforeach(test)
 
@@ -25,7 +25,7 @@ install(TARGETS femto_hello_mpi ${INSTALL_TARGETS_DEFAULT_ARGS})
 
 add_executable(femto_mpi_cp mpi_cp.cc)
 
-target_link_libraries(femto_mpi_cp femto_mpi_cc femto_util_cc femto_util)
+target_link_libraries(femto_mpi_cp femto_mpi_cc femto_util_cc femto_util ${DEFAULT_LIBRARIES})
 
 install(TARGETS femto_mpi_cp ${INSTALL_TARGETS_DEFAULT_ARGS})
 

diff --git a/src/utils_cc/CMakeLists.txt b/src/utils_cc/CMakeLists.txt
@@ -39,14 +39,16 @@ set(FEMTO_UTIL_CC_SRCS
     io_pipe.hh
     io_pipe.cc)
 
-  #if( DEFINED ${HAS_POSIX_AIO_RT} OR DEFINED ${HAS_POSIX_AIO_C})
+# Add libaries used everywhere
+set(LOCAL_DEFAULT_LIBRARIES "${DEFAULT_LIBRARIES}")
+
 if( DEFINED HAS_POSIX_AIO_RT OR DEFINED HAS_POSIX_AIO_C)
-  #if(${HAS_POSIX_AIO_RT} or ${HAS_POSIX_AIO_C})
   set(FEMTO_UTIL_CC_SRCS ${FEMTO_UTIL_CC_SRCS} aio_pipe.hh aio_pipe.cc)
 endif()
 
 if(HAS_LINUX_LIBAIO)
   set(FEMTO_UTIL_CC_SRCS ${FEMTO_UTIL_CC_SRCS} kaio_pipe.hh kaio_pipe.cc)
+  set(LOCAL_DEFAULT_LIBRARIES "${LOCAL_DEFAULT_LIBRARIES} -laio")
 endif()
 
 # include ../util
@@ -68,14 +70,14 @@ set(UTIL_CC_TESTS
 foreach(test ${UTIL_CC_TESTS})
   add_executable(${test} EXCLUDE_FROM_ALL ${test}.cc example_record.hh)
   add_test(${test} ${test})
-  target_link_libraries(${test} femto_util_cc femto_util)
+  target_link_libraries(${test} femto_util_cc femto_util ${LOCAL_DEFAULT_LIBRARIES})
   add_dependencies(check ${test})
 endforeach(test)
 
 
 add_executable(femto_sort_tests sort_tests.hh sort_tests.cc)
 
-target_link_libraries(femto_sort_tests femto_util_cc femto_util)
+target_link_libraries(femto_sort_tests femto_util_cc femto_util ${LOCAL_DEFAULT_LIBRARIES})
 
 install(TARGETS femto_sort_tests ${INSTALL_TARGETS_DEFAULT_ARGS})