Fix compilation process. Fix compile error on new compiler

external/external_build.cmake

@@ -6,7 +6,8 @@ SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download
 SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE URL "URL to download Eigen from")
 SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
 SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.gz" CACHE STRING "URL to download HDF5 from")
-SET(NETCDF_URL "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz" CACHE STRING "URL to download NetCDF from")
+SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.4.1.1.tar.gz" CACHE STRING "URL to download NetCDF from")
+SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.0.tar.gz" CACHE STRING "URL to download NetCDF-C++ from")
 SET(BOOST_URL "http://sourceforge.net/projects/boost/files/boost/1.61.0/boost_1_61_0.tar.gz/download" CACHE STRING "URL to download Boost from")
 SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ")
 mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL)
@@ -77,13 +78,14 @@ if (INTERNAL_HDF5)
   ExternalProject_Add(hdf5
     PREFIX ${BUILD_PREFIX}/hdf5-prefix
     URL ${HDF5_URL}
-    CONFIGURE_COMMAND ${HDF5_SOURCE_DIR}/configure
-           --disable-shared --enable-cxx --with-pic
-	   --prefix=${HDF5_BIN_DIR} --libdir=${HDF5_BIN_DIR}/lib 
-	   CPPFLAGS=${CONFIGURE_CPP_FLAGS} CC=${CMAKE_C_COMPILER} 
-	   CXX=${CMAKE_CXX_COMPILER}
-    BUILD_IN_SOURCE 1
-    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+    CMAKE_ARGS
+       -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
+       -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+       -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+       -DHDF5_BUILD_CPP_LIB=ON
+       -DHDF5_BUILD_TOOLS=ON
+       -DHDF5_BUILD_HL_LIB=ON
+       -DBUILD_SHARED_LIBS=OFF
   )
   SET(cosmotool_DEPS ${cosmotool_DEPS} hdf5)
   SET(hdf5_built hdf5)
@@ -142,7 +144,7 @@ endforeach(include_dir)
 if (INTERNAL_NETCDF)
   SET(NETCDF_SOURCE_DIR ${BUILD_PREFIX}/netcdf-prefix/src/netcdf)
   SET(NETCDF_BIN_DIR ${EXT_INSTALL})
-#  SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${NETCDF_BIN_DIR}/include")
+  SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${NETCDF_BIN_DIR}/include")
   SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${NETCDF_BIN_DIR}/lib")
   SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LIBS=${CONFIGURE_LIBS} LDFLAGS=${CONFIGURE_LDFLAGS})
   SET(NETCDF_CONFIG_COMMAND ${NETCDF_SOURCE_DIR}/configure
@@ -155,15 +157,36 @@ if (INTERNAL_NETCDF)
     DEPENDS ${hdf5_built}
     PREFIX ${BUILD_PREFIX}/netcdf-prefix
     URL ${NETCDF_URL}
-    CONFIGURE_COMMAND  ${NETCDF_CONFIG_COMMAND}
-    BUILD_IN_SOURCE 1
-    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+	CMAKE_ARGS
+		-DCMAKE_PREFIX_PATH=${EXT_INSTALL}
+		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+		-DBUILD_SHARED_LIBS=OFF
+		-DBUILD_TESTING=OFF
+		-DCMAKE_BUILD_TYPE=Release
+		-DENABLE_NETCDF4=ON
+                -DENABLE_DAP=OFF
+		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
+  )
+  
+  SET(NETCDFCXX_SOURCE_DIR ${BUILD_PREFIX}/netcdf-c++-prefix/src/netcdf-c++)
+  ExternalProject_Add(netcdf-c++
+    DEPENDS ${hdf5_built} netcdf
+    PREFIX ${BUILD_PREFIX}/netcdf-c++-prefix
+    URL ${NETCDFCXX_URL}
+	CMAKE_ARGS
+		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+		-DBUILD_SHARED_LIBS=OFF
+		-DBUILD_TESTING=OFF
+		-DCMAKE_BUILD_TYPE=Release
+		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
   )
 #  SET(CONFIGURE_CPP_LDFLAGS "${CONFIGURE_LDFLAGS}")
 #  SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_CPP_LDFLAGS})
-  SET(cosmotool_DEPS ${cosmotool_DEPS} netcdf)
+  SET(cosmotool_DEPS ${cosmotool_DEPS} netcdf netcdf-c++)
   SET(NETCDF_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf.a CACHE STRING "NetCDF lib" FORCE)
-  SET(NETCDFCPP_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf_c++4.a CACHE STRING "NetCDF-C++ lib" FORCE)
+  SET(NETCDFCPP_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf-cxx4.a CACHE STRING "NetCDF-C++ lib" FORCE)
   SET(NETCDF_INCLUDE_PATH ${NETCDF_BIN_DIR}/include CACHE STRING "NetCDF include" FORCE)
   SET(NETCDFCPP_INCLUDE_PATH ${NETCDF_INCLUDE_PATH} CACHE STRING "NetCDF C++ include path" FORCE)
 

sample/simple3DFilter.cpp

@@ -62,7 +62,7 @@ void computeInterpolatedField(MyTree *tree1, double boxsize, int Nres, double cx
               {
                 double px = (rx)*boxsize/Nres-cx;
                 
-                MyTree::coords c = { px, py, pz };
+                MyTree::coords c = { float(px), float(py), float(pz) };
 
                 double r2 = c[0]*c[0]+c[1]*c[1]+c[2]*c[2];
                 if (r2 > rLimit2)
@@ -179,7 +179,7 @@ int main(int argc, char **argv)
               {
                 double px = (rx)*boxsize/Nres-cx;
                 
-                MyTree::coords c = { px, py, pz };
+                MyTree::coords c = { float(px), float(py), float(pz) };
 
                 double r2 = c[0]*c[0]+c[1]*c[1]+c[2]*c[2];
                 if (r2 > rLimit2)

sample/testSmooth.cpp

@@ -75,7 +75,7 @@ int main()
       cout << "iy=" << iy << endl;
       for (uint32_t ix = 0; ix < NX; ix++)
         {
-           MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX };
+           MyTree::coords c = { 1.0f*ix/NX, 1.0f*iy/NX };
            smooth.fetchNeighbours(c);
            smooth.addGridSite(c);
         }
@@ -92,7 +92,7 @@ int main()
       cout << "iy=" << iy << endl;
       for (uint32_t ix = 0; ix < NX; ix++)
         {
-           MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX };
+           MyTree::coords c = { 1.0f*ix/NX, 1.0f*iy/NX };
            smooth.fetchNeighbours(c, &state);
            out.put(smooth.computeSmoothedValue(c, unit_fun, &state));
 

src/CMakeLists.txt

@@ -1,5 +1,5 @@
 
-SET(CosmoTool_SRCS
+	SET(CosmoTool_SRCS
 		fortran.cpp
 		interpolate.cpp
 		load_data.cpp
@@ -9,9 +9,9 @@ SET(CosmoTool_SRCS
 		growthFactor.cpp
 		cosmopower.cpp
 	  cic.cpp
-)
+	)
 
-IF (Boost_FOUND)
+	IF (Boost_FOUND)
 	  include_directories(${Boost_INCLUDE_DIRS})
   SET(CosmoTool_SRCS
     ${CosmoTool_SRCS}
@@ -78,7 +78,7 @@ endif(YORICK_SUPPORT)
 
 if (HDF5_FOUND)
   set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${ZLIB})
-  include_directories(${HDF5_INCLUDE_DIRS})
+  include_directories(${HDF5_INCLUDE_DIR})
   message(STATUS "CosmoTool_LIBS: ${CosmoTool_LIBS}")
 endif (HDF5_FOUND)