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  1.   f28
  2.   apbs-cmake.patch
Blob Blame History Raw 
--- CMakeLists.txt_orig	2018-05-20 13:00:17.451341064 -0400
+++ CMakeLists.txt	2018-05-20 13:00:47.917440250 -0400
@@ -1,4 +1,5 @@
 cmake_minimum_required (VERSION 2.8.7)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 ################################################################################
 # TODO:  Add licensing and authorship information
@@ -63,10 +64,10 @@
 set(TOOLS_PATH ${APBS_BUILD}/tools)
 set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs)
 
-set(LIBRARY_INSTALL_PATH lib)
-set(HEADER_INSTALL_PATH include/apbs)
+set(LIBRARY_INSTALL_PATH ${LIB_INSTALL_DIR})
+set(HEADER_INSTALL_PATH ${INCLUDE_INSTALL_DIR}/apbs)
 set(EXECUTABLE_INSTALL_PATH bin)
-set(SHARE_INSTALL_PATH share/apbs)
+set(SHARE_INSTALL_PATH ${SHARE_INSTALL_PREFIX}/apbs)
 
 set(APBS_LIBS)
 set(APBS_LIB_DIRS)
@@ -78,7 +79,7 @@
   DOC "The path to the external git submodules"
   )
 
-set(SYS_LIBPATHS /usr/lib64)
+#set(SYS_LIBPATHS /usr/lib64)
 #list(APPEND SYS_LIBPATHS /usr/lib64)
 
 ################################################################################
@@ -105,9 +106,9 @@
 
 message(STATUS "Setting lookup paths for headers and libraries")
 
-set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
-list(APPEND CMAKE_INCLUDE_PATH /usr/include)
-list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
+#set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
+#list(APPEND CMAKE_INCLUDE_PATH /usr/include)
+#list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
 
 
 
@@ -259,11 +260,11 @@
 
 if(NOT ENABLE_FETK)
   # We'll use autotools to build MALOC if FETK is enabled.
-  set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc)
-  add_subdirectory(${MALOC_ROOT})
-  include_directories(${MALOC_ROOT}/src/base ${MALOC_ROOT}/src/vsys
-    ${MALOC_ROOT}/src/vsh ${MALOC_ROOT}/src/psh)
-  list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
+  #set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc)
+  # add_subdirectory(${MALOC_ROOT})
+  #include_directories(${MALOC_ROOT}/src/base ${MALOC_ROOT}/src/vsys
+  #  ${MALOC_ROOT}/src/vsh ${MALOC_ROOT}/src/psh)
+  #list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
   list(APPEND APBS_LIBS maloc)
 endif()
 
@@ -736,12 +737,12 @@
 # Set up additional directories to install                                     #
 ################################################################################
 
-install(
-    DIRECTORY ${APBS_ROOT}/doc
-    DESTINATION ${SHARE_INSTALL_PATH}
-    PATTERN "programmer" EXCLUDE
-    PATTERN "CMakeLists.txt" EXCLUDE
-)
+#install(
+#    DIRECTORY ${APBS_ROOT}/doc
+#    DESTINATION ${SHARE_INSTALL_PATH}
+#    PATTERN "programmer" EXCLUDE
+#    PATTERN "CMakeLists.txt" EXCLUDE
+#)
 
 if(BUILD_DOC)
     install(
@@ -753,24 +754,24 @@
     )
 endif()
 
-install(
-    DIRECTORY ${APBS_ROOT}/examples
-    DESTINATION ${SHARE_INSTALL_PATH}
-)
-
-install(
-    DIRECTORY ${APBS_ROOT}/tests
-    DESTINATION ${SHARE_INSTALL_PATH}
-    FILES_MATCHING
-        PATTERN "*.py"
-        PATTERN "README"
-)
-
-install(
-    DIRECTORY ${APBS_ROOT}/tools
-    DESTINATION ${SHARE_INSTALL_PATH}
-    PATTERN "CMakeLists.txt" EXCLUDE
-)
+#install(
+#    DIRECTORY ${APBS_ROOT}/examples
+#    DESTINATION ${SHARE_INSTALL_PATH}
+#)
+
+#install(
+#    DIRECTORY ${APBS_ROOT}/tests
+#    DESTINATION ${SHARE_INSTALL_PATH}
+#    FILES_MATCHING
+#        PATTERN "*.py"
+#        PATTERN "README"
+#)
+
+#install(
+#    DIRECTORY ${APBS_ROOT}/tools
+#    DESTINATION ${SHARE_INSTALL_PATH}
+#    PATTERN "CMakeLists.txt" EXCLUDE
+#)
 
 if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}")
     install(
--- src/CMakeLists.txt_orig	2018-05-20 13:00:20.518351049 -0400
+++ src/CMakeLists.txt	2018-05-20 13:00:47.917440250 -0400
@@ -32,11 +32,11 @@
     message(STATUS "With external header files ${EXTERNAL_HEADERS}")
     message(STATUS "With internal header files ${INTERNAL_HEADERS}")
     message(STATUS "With library dependencies ${LIBRARY_DEPENDENCIES}")
-    add_library(${LIBRARY_NAME} ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS})
-    target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES})
+    add_library(${LIBRARY_NAME} OBJECT ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS})
+    # target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES})
     #add_dependencies(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES})
     INSTALL(FILES ${EXTERNAL_HEADERS} DESTINATION ${HEADER_INSTALL_PATH}/${LIBRARY})
-    INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH})
+    # INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH})
     list(APPEND APBS_INTERNAL_LIBS ${LIBRARY_NAME})
     set(APBS_INTERNAL_LIBS ${APBS_INTERNAL_LIBS} PARENT_SCOPE)
     message(STATUS "Added ${LIBRARY_NAME}")
@@ -47,6 +47,11 @@
 add_subdirectory(generic)
 add_subdirectory(pmgc)
 add_subdirectory(mg)
+add_library(apbs SHARED $<TARGET_OBJECTS:apbs_generic> $<TARGET_OBJECTS:apbs_pmgc> $<TARGET_OBJECTS:apbs_mg>)
+# set a SOVERSION to keep packager happy
+SET_TARGET_PROPERTIES(apbs PROPERTIES SOVERSION "1")
+target_link_libraries(apbs ${LIBRARY_DEPENDENCIES})
+INSTALL(TARGETS apbs LIBRARY DESTINATION ${LIBRARY_INSTALL_PATH})
 
 if(ENABLE_FETK)
    add_subdirectory(fem)
@@ -57,7 +62,7 @@
 
 message(STATUS ${EXTERNAL_HEADERS})
 
-add_executable(apbs main.c apbs.h routines.c routines.h)
+add_executable(apbs-bin main.c apbs.h routines.c routines.h)
 message(***************************)
 message(STATUS " ")
 message(STATUS "APBS Libraries: ${APBS_LIBS}")
@@ -66,7 +71,8 @@
 message(***************************)
 
 #add_dependencies(apbs ${BEM_LIB})
-target_link_libraries(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${APBS_LIBS})
+target_link_libraries(apbs-bin ${APBS_LIBS} apbs)
+SET_TARGET_PROPERTIES(apbs-bin PROPERTIES OUTPUT_NAME apbs)
 #add_dependencies(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${APBS_LIBS})
 
 configure_file(
@@ -81,6 +87,6 @@
 endif()
 
 INSTALL(FILES apbs.h routines.h DESTINATION ${HEADER_INSTALL_PATH})
-INSTALL(TARGETS apbs DESTINATION ${EXECUTABLE_INSTALL_PATH})
+INSTALL(TARGETS apbs-bin DESTINATION ${EXECUTABLE_INSTALL_PATH})
 
 message(STATUS ${CMAKE_C_FLAGS})
--- tools/manip/CMakeLists.txt_orig	2018-05-20 13:00:31.831387880 -0400
+++ tools/manip/CMakeLists.txt	2018-05-20 13:07:07.742714938 -0400
@@ -1,9 +1,10 @@
 message(STATUS "Building manip")
 
 set(LIBS "")
-list(APPEND LIBS "apbs_generic")
-list(APPEND LIBS "apbs_mg")
-list(APPEND LIBS "apbs_pmgc")
+#list(APPEND LIBS "apbs_generic")
+#list(APPEND LIBS "apbs_mg")
+#list(APPEND LIBS "apbs_pmgc")
+list(APPEND LIBS "apbs")
 if(FETK_ENABLED)
     list(APPEND LIBS "apbs_fem")
 endif(FETK_ENABLED)
@@ -11,7 +12,9 @@
 message(STATUS "libraries: ${LIBS}")
 
 add_executable(coulomb coulomb.c)
-target_link_libraries(coulomb ${LIBS})
+target_link_libraries(coulomb ${LIBS} ${APBS_LIBS})
 
 add_executable(born born.c)
-target_link_libraries(born ${LIBS})
+target_link_libraries(born ${LIBS} ${APBS_LIBS})
+
+INSTALL(TARGETS coulomb born DESTINATION ${EXECUTABLE_INSTALL_PATH})
--- tools/mesh/CMakeLists.txt_orig	2018-05-20 13:00:26.966372042 -0400
+++ tools/mesh/CMakeLists.txt	2018-05-20 13:00:47.917440250 -0400
@@ -1,9 +1,10 @@
 message(STATUS "Building mesh")
 
 set(LIBS "")
-list(APPEND LIBS "apbs_generic")
-list(APPEND LIBS "apbs_mg")
-list(APPEND LIBS "apbs_pmgc")
+#list(APPEND LIBS "apbs_generic")
+#list(APPEND LIBS "apbs_mg")
+#list(APPEND LIBS "apbs_pmgc")
+list(APPEND LIBS "apbs")
 if(FETK_ENABLED)
     list(APPEND LIBS "apbs_fem")
 endif(FETK_ENABLED)
@@ -11,46 +12,48 @@
 message(STATUS "libraries: ${LIBS}")
 
 add_executable(mgmesh mgmesh.c)
-target_link_libraries(mgmesh ${LIBS})
+target_link_libraries(mgmesh ${LIBS} ${APBS_LIBS})
 
 add_executable(smooth smooth.c)
-target_link_libraries(smooth ${LIBS})
+target_link_libraries(smooth ${LIBS} ${APBS_LIBS})
 
 add_executable(dxmath dxmath.c)
-target_link_libraries(dxmath ${LIBS})
+target_link_libraries(dxmath ${LIBS} ${APBS_LIBS})
 
 add_executable(mergedx mergedx.c)
-target_link_libraries(mergedx ${LIBS})
+target_link_libraries(mergedx ${LIBS} ${APBS_LIBS})
 
 add_executable(mergedx2 mergedx2.c)
-target_link_libraries(mergedx2 ${LIBS})
+target_link_libraries(mergedx2 ${LIBS} ${APBS_LIBS})
 
 add_executable(value value.c)
-target_link_libraries(value ${LIBS})
+target_link_libraries(value ${LIBS} ${APBS_LIBS})
 
 add_executable(multivalue multivalue.c)
-target_link_libraries(multivalue ${LIBS})
+target_link_libraries(multivalue ${LIBS} ${APBS_LIBS})
 
 add_executable(benchmark benchmark.c)
-target_link_libraries(benchmark ${LIBS})
+target_link_libraries(benchmark ${LIBS} ${APBS_LIBS})
 
 add_executable(similarity similarity.c)
-target_link_libraries(similarity ${LIBS})
+target_link_libraries(similarity ${LIBS} ${APBS_LIBS})
 
 add_executable(analysis analysis.c)
-target_link_libraries(analysis ${LIBS})
+target_link_libraries(analysis ${LIBS} ${APBS_LIBS})
 
 add_executable(dx2mol dx2mol.c)
-target_link_libraries(dx2mol ${LIBS})
+target_link_libraries(dx2mol ${LIBS} ${APBS_LIBS})
 
 add_executable(dx2uhbd dx2uhbd.c)
-target_link_libraries(dx2uhbd ${LIBS})
+target_link_libraries(dx2uhbd ${LIBS} ${APBS_LIBS})
 
 add_executable(del2dx del2dx.c)
-target_link_libraries(del2dx ${LIBS})
+target_link_libraries(del2dx ${LIBS} ${APBS_LIBS})
 
 add_executable(tensor2dx tensor2dx.c)
-target_link_libraries(tensor2dx ${LIBS})
+target_link_libraries(tensor2dx ${LIBS} ${APBS_LIBS})
 
 add_executable(uhbd_asc2bin uhbd_asc2bin.c)
-target_link_libraries(uhbd_asc2bin ${LIBS})
+target_link_libraries(uhbd_asc2bin ${LIBS} ${APBS_LIBS})
+
+INSTALL(TARGETS mgmesh smooth dxmath mergedx mergedx2 value multivalue benchmark similarity analysis dx2mol dx2uhbd del2dx tensor2dx uhbd_asc2bin DESTINATION ${EXECUTABLE_INSTALL_PATH})
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