Attempt to fix linkage errors

CMakeLists.txt

@@ -42,6 +42,17 @@ ENDIF(BUILD_PYTHON)
 
 MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module")
 
+find_library(ZLIB_LIBRARY z)
+find_library(DL_LIBRARY dl)
+find_library(RT_LIBRARY rt)
+if (RT_LIBRARY)
+  SET(RT_DEP rt)
+  message(STATUS "RT found, linking against it")
+else()
+  SET(RT_DEP)
+endif()
+find_library(MATH_LIBRARY m)
+
 include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
 
 IF(YORICK_SUPPORT)
@@ -55,9 +66,6 @@ IF(YORICK_SUPPORT)
 ENDIF(YORICK_SUPPORT)
 
 find_program(CYTHON NAMES cython3 cython)
-find_library(ZLIB_LIBRARY z)
-find_library(DL_LIBRARY dl)
-find_library(MATH_LIBRARY m)
 
 set(NETCDF_FIND_REQUIRED ${YORICK_SUPPORT})
 set(GSL_FIND_REQUIRED TRUE)

external/external_build.cmake

@@ -105,7 +105,7 @@ if (INTERNAL_HDF5)
   SET(ENV{HDF5_ROOT} ${HDF5_BIN_DIR})
   SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
   SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib")
-  SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl")
+  SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl ${RT_LIBRARY}")
   set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5.a)
   set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl.a)
   set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
@@ -175,26 +175,28 @@ if (INTERNAL_NETCDF)
   string(REPLACE ";" "|" CMAKE_PREFIX_PATH_ALT_SEP "${CMAKE_PREFIX_PATH}")
   ExternalProject_Add(netcdf
     DEPENDS ${hdf5_built}
+    URL_HASH MD5=f48ee01534365006934f0c63d4055ea0
     PREFIX ${BUILD_PREFIX}/netcdf-prefix
     DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
     URL ${NETCDF_URL}
-  LIST_SEPARATOR |
-	CMAKE_ARGS
+    LIST_SEPARATOR |
+    CMAKE_ARGS
 		-DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH_ALT_SEP}
 		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
 		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                -DNC_EXTRA_DEPS=${RT_DEP}
 		-DBUILD_SHARED_LIBS=OFF
 		-DBUILD_TESTING=OFF
 		-DCMAKE_BUILD_TYPE=Release
 		-DENABLE_NETCDF4=ON
                 -DENABLE_BYTERANGE=FALSE
-    -DCMAKE_POSITION_INDEPENDENT_CODE=ON
-    -DENABLE_DAP=OFF
+		-DCMAKE_POSITION_INDEPENDENT_CODE=ON
+		-DENABLE_DAP=OFF
 		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
                 -DHDF5_C_LIBRARY=${HDF5_C_STATIC_LIBRARY}
                 -DHDF5_HL_LIBRARY=${HDF5_HL_STATIC_LIBRARY}
                 -DHDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIRS}
-    -DCMAKE_INSTALL_LIBDIR=lib
+		-DCMAKE_INSTALL_LIBDIR=lib
   )
   
   SET(NETCDFCXX_SOURCE_DIR ${BUILD_PREFIX}/netcdf-c++-prefix/src/netcdf-c++)