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apbs/apbs-cmake.patch
sagitter fa84d5a43e Release 3.0.0
2020-05-31 14:34:05 +02:00

272 lines
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--- a/apbs/CMakeLists.txt_orig 2018-05-20 13:00:17.451341064 -0400
+++ b/apbs/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400
@@ -1,4 +1,5 @@
cmake_minimum_required (VERSION 3.12)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
################################################################################
# TODO: Add licensing and authorship information
@@ -70,10 +71,10 @@
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 ${SHARE_INSTALL_PREFIX}/apbs)
set(APBS_LIBS)
set(APBS_LIB_DIRS)
@@ -85,7 +86,7 @@
PATHS "${APBS_ROOT}"
DOC "The path to the external git submodules")
-set(SYS_LIBPATHS /usr/lib64)
+#set(SYS_LIBPATHS /usr/lib64)
#list(APPEND SYS_LIBPATHS /usr/lib64)
@@ -139,11 +140,6 @@
################################################################################
message(STATUS "Setting lookup paths for headers and libraries")
-set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
-list(APPEND CMAKE_INCLUDE_PATH /usr/include)
-list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
-
-
################################################################################
# Enable ansi pedantic compiling #
################################################################################
@@ -307,12 +303,12 @@
################################################################################
if(NOT ENABLE_FETK)
# We'll use autotools to build MALOC if FETK is enabled.
- add_subdirectory(${EXTERNALS_PATH}/fetk/maloc)
- include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base
- ${EXTERNALS_PATH}/fetk/maloc/src/vsys
- ${EXTERNALS_PATH}/fetk/maloc/src/vsh
- ${EXTERNALS_PATH}/fetk/maloc/src/psh)
- list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
+ #add_subdirectory(${EXTERNALS_PATH}/fetk/maloc)
+ #include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base
+ # ${EXTERNALS_PATH}/fetk/maloc/src/vsys
+ # ${EXTERNALS_PATH}/fetk/maloc/src/vsh
+ # ${EXTERNALS_PATH}/fetk/maloc/src/psh)
+ #list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
list(APPEND APBS_LIBS maloc)
endif()
@@ -778,10 +774,10 @@
################################################################################
# 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(DIRECTORY ${APBS_BUILD}/doc/programmer
@@ -791,27 +787,11 @@
PATTERN "mainpage.h" EXCLUDE)
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")
-
-if(BUILD_TOOLS)
- install(DIRECTORY ${APBS_ROOT}/tools
- DESTINATION ${SHARE_INSTALL_PATH}
- USE_SOURCE_PERMISSIONS
- PATTERN "CMakeLists.txt"
- PATTERN "matlab" EXCLUDE)
-
- if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}")
- install(DIRECTORY ${APBS_BUILD}/tools/bin
+if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}")
+ install(
+ DIRECTORY ${APBS_BUILD}/tools/bin
DESTINATION ${SHARE_INSTALL_PATH}/tools
USE_SOURCE_PERMISSIONS)
- endif()
endif()
################################################################################
--- a/apbs/src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400
+++ b/apbs/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}")
@@ -45,6 +45,11 @@
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)
@@ -56,7 +61,7 @@
message(STATUS "External Headers: ${EXTERNAL_HEADERS}")
#add_executable(apbs main.c routines.c)
-add_executable(apbs main.c apbs.h routines.c routines.h)
+add_executable(apbs-bin main.c apbs.h routines.c routines.h)
message(STATUS " ")
message(STATUS "APBS Libraries: ${APBS_LIBS}")
message(STATUS "Internal Libraries: ${APBS_INTERNAL_LIBS}")
@@ -64,7 +69,8 @@
#add_dependencies(apbs ${BEM_LIB})
#target_include_directories(apbs PRIVATE apbs.h routines.h)
-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(
@@ -79,6 +85,6 @@
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})
--- a/apbs/tools/manip/CMakeLists.txt_orig 2018-05-20 13:00:31.831387880 -0400
+++ b/apbs/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})
--- a/apbs/tools/mesh/CMakeLists.txt_orig 2018-05-20 13:00:26.966372042 -0400
+++ b/apbs/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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