merge the linking of netcdf and hdf5 libraries

Author: meihuisu

configure.ac

@@ -301,18 +301,37 @@ AC_ARG_WITH([proj-lib-path],
   [PROJ_LIB="-lproj -lpthread"])
 
 # Get optional netCDF library and include locations
+##if test "x$enable_netcdf" = xyes; then
+##   AC_ARG_WITH([netcdf-include-path],
+##   [AS_HELP_STRING([--with-netcdf-include-path],
+##   [location of the netCDF headers])],
+##   [NETCDF_INCL="-I$withval"],
+##   [NETCDF_INCL=""])
+##   AC_ARG_WITH([netcdf-lib-path],
+##   [AS_HELP_STRING([--with-netcdf-lib-path], [location of the netCDF libraries])],
+##   [NETCDF_LIB="-L$withval -lnetcdf  -lhdf5 -lm -lz -ldl -lxml2"],
+##   [NETCDF_LIB=" -lnetcdf -lhdf5 -lm -lz -ldl -lxml2"])
+##fi XX
+#
 if test "x$enable_netcdf" = xyes; then
-   AC_ARG_WITH([netcdf-include-path],
-   [AS_HELP_STRING([--with-netcdf-include-path],
-   [location of the netCDF headers])],
-   [NETCDF_INCL="-I$withval"],
-   [NETCDF_INCL=""])
-   AC_ARG_WITH([netcdf-lib-path],
-   [AS_HELP_STRING([--with-netcdf-lib-path], [location of the netCDF libraries])],
-   [NETCDF_LIB="-L$withval -lnetcdf -lm -ldl -lxml2 -lcurl"],
-   [NETCDF_LIB="-lnetcdf -lm -ldl -lxml2 -lcurl"])
+  AC_ARG_WITH([netcdf-include-path],
+    [AS_HELP_STRING([--with-netcdf-include-path],[location of NetCDF headers])],
+    [NETCDF_INCL="-I$withval"],
+    [NETCDF_INCL=""])
+
+  AC_ARG_WITH([netcdf-lib-path],
+    [AS_HELP_STRING([--with-netcdf-lib-path],[location of NetCDF libraries])],
+    [NETCDF_LIB="-L$withval -lnetcdf"],
+    [NETCDF_LIB="-lnetcdf"])
+
+  # Optional: HDF5 support if NetCDF-4 is enabled
+  AC_ARG_WITH([netcdf-extra-libs],
+    [AS_HELP_STRING([--netcdf-extra-libs],[location of NetCDF extra libraries, ie hdf5])],
+    [NETCDF_EXTRALIBS="-L$withval -lhdf5 -lhdf5_hl -lz -ldl -lm -lxml2"],
+    [NETCDF_EXTRALIBS=""])
 fi
 
+
 # Get optional HDF5 library and include locations
 if test "x$enable_hdf5" = xyes; then
    AC_ARG_WITH([hdf5-include-path],
@@ -961,20 +980,19 @@ AC_CHECK_LIB(proj, proj_create_crs_to_crs, [AC_CHECK_HEADER([proj.h], [], [AC_MS
 #  ], [AC_INCLUDES_DEFAULT])],[AC_MSG_ERROR(["Curl library not found; use --with-curl-lib-path"])], [???? -lssl -lcrypto])
 
 
-# Check optional NetCDF library
+## Check optional NetCDF library
 if test "x$enable_netcdf" = xyes; then
    echo "Checking for NetCDF library"
    CFLAGS="$NETCDF_INCL $CHECK_CFLAGS"
-   LDFLAGS="$CHECK_LDFLAGS $NETCDF_LIB"
+   LDFLAGS="$CHECK_LDFLAGS $NETCDF_LIB $NETCDF_EXTRALIBS"
    AC_CHECK_LIB(netcdf, nc_create,
 	[AM_CONDITIONAL(UCVM_HAVE_NETCDF, true)], 
 	[AC_MSG_ERROR([NetCDF library not found; use --with-netcdf-include-path"])],
-	[-lm -ldl -lxml2 -lcurl])
+	[])
    AC_CHECK_HEADER(netcdf.h,
 	[],
 	[AC_MSG_ERROR([NetCDF header not found; use --with-netcdf-lib-path"])],
 	[AC_INCLUDES_DEFAULT])
-
 else
 	AM_CONDITIONAL(UCVM_HAVE_NETCDF, false)
 fi
@@ -1001,7 +1019,7 @@ fi
 #
 
 CFLAGS="$CHECK_CFLAGS $ETREE_INCL $CURL_INCL $OPENSSL_INCL $PROJ_INCL $FFTW_INCL $NETCDF_INCL $HDF5_INCL"
-LDFLAGS="$CHECK_LDFLAGS $ETREE_LIB $CURL_LIB $OPENSSL_LIB $PROJ_LIB $FFTW_LIB $NETCDF_LIB $HDF5_LIB"
+LDFLAGS="$CHECK_LDFLAGS $ETREE_LIB $CURL_LIB $OPENSSL_LIB $PROJ_LIB $FFTW_LIB $NETCDF_LIB $NETCDF_EXTRALIBS $HDF5_LIB"
 LDFLAGS="$LDFLAGS -lm"
 
 # Check optional USGS CenCalVM installation

setup/note

@@ -12,6 +12,6 @@ GENERAL:
 
    Preprocess: Action dependency (example: bring in external code)
 
-NOTE:
-   SFCVM
+   
 
+NOTE:

setup/setup.list

@@ -436,10 +436,10 @@
 			"Path": "netcdf",
                         "Lib": "netcdf-c-4.9.2",
 			"URL": "https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz",
-			"Required": "no",
+			"Required": "yes",
+                        "Libraries": ["hdf5"],
 			"Prerequisites": "Dynamic",
-                        "oConfigureFlags": "--disable-byterange",
-                        "ConfigureFlags": "--disable-byterange --disable-hdf5",
+                        "ConfigureFlags": "--enable-shared --disable-static --enable-netcdf4 --disable-dap --disable-byterange --disable-doxygen CPPFLAGS='-I${UCVM_INSTALL_PATH}/lib/hdf5/include' LDFLAGS='-L${UCVM_INSTALL_PATH}/lib/hdf5/lib -Wl,-rpath,${UCVM_INSTALL_PATH}/lib/hdf5/lib' PKG_CONFIG_PATH='${UCVM_INSTALL_PATH}/lib/hdf5/lib/pkgconfig:${PKG_CONFIG_PATH}'",
                         "oUCVMConfigureFlags": "--enable-netcdf --with-netcdf-include-path=${UCVM_INSTALL_PATH}/lib/netcdf/include --with-netcdf-lib-path=${UCVM_INSTALL_PATH}/lib/netcdf/lib",
                         "UCVMConfigureFlags": "--with-netcdf-include-path=${UCVM_INSTALL_PATH}/lib/netcdf/include --with-netcdf-lib-path=${UCVM_INSTALL_PATH}/lib/netcdf/lib",
                         "md5sum": "f48ee01534365006934f0c63d4055ea0",

src/ucvm2mesh/mesh2hdf5.c

@@ -1,6 +1,7 @@
 /**
    mesh2hdf5.c
 
+     to mimick geomodelgrids' hdf5 file
 **/
 
 #include <stdio.h>

ucvm_setup.py

@@ -280,14 +280,18 @@ def installConfigMakeInstall(tarname, ucvmpath, type, config_data):
 
     createInstallTargetPath( ucvmpath + "/" + pathname + "/" + config_data["Path"])
 
+## mainly to pass environment variable available in setup.list environment
+## to the configure environment
     if "ConfigureEnv" in config_data.keys(): 
         needs_env = config_data["ConfigureEnv"]
     else:
         needs_env = [] 
 
     if "ConfigureFlags" in config_data and config_data["ConfigureFlags"] != "" :
-        configure_array += config_data["ConfigureFlags"].split(" ")
+        tmp = config_data["ConfigureFlags"].split(" ")
+        configure_array +=shlex.split(config_data["ConfigureFlags"])
     elif "Libraries" in config_data:
+## this is to work with our embedded libraries being installed in UCVM_INSTALL_PATH
         needs_array = config_data["Libraries"]
         if "euclid3" in needs_array:
           configure_array.append("--with-etree-lib-path=" + ucvmpath + "/lib/euclid3/lib")
@@ -296,8 +300,11 @@ def installConfigMakeInstall(tarname, ucvmpath, type, config_data):
           configure_array.append("--with-proj-lib-path=" + ucvmpath + "/lib/proj/lib")
           configure_array.append("--with-proj-include-path=" + ucvmpath + "/lib/proj/include")
         if "netcdf" in needs_array:
-          configure_array.append("LDFLAGS=-L" + ucvmpath + "/lib/netcdf/lib")
-          configure_array.append("CPPFLAGS=-I" + ucvmpath + "/lib/netcdf/include")
+          configure_array.append("LDFLAGS=-L" + ucvmpath + "/lib/netcdf/lib -L" + ucvmpath + "/lib/hdf5/lib")
+          configure_array.append("CPPFLAGS=-I" + ucvmpath + "/lib/netcdf/include -I" + ucvmpath + "/lib/hdf5/include")
+        if "hdf5" in needs_array:
+          configure_array.append("LDFLAGS=-L" + ucvmpath + "/lib/hdf5/lib")
+          configure_array.append("CPPFLAGS=-I" + ucvmpath + "/lib/hdf5/include")
 
 ## special case ??
     if config_data["Path"] == "cencal":
@@ -1030,11 +1037,11 @@ def _addPROJ_LIB_python() :
 if use_iobuf == True:
     ucvm_conf_command.append("--enable-iobuf")
 
-#if "NetCDF" in librariesToInstall:
-#    ucvm_conf_command.append("--enable-netcdf")
-#    ucvm_conf_command.append("--with-netcdf-include-path=" + ucvmpath + "/lib/netcdf/include")
-#    ucvm_conf_command.append("--with-netcdf-lib-path=" + ucvmpath + "/lib/netcdf/lib")
-#    ucvm_conf_command.append("LDFLAGS=-L" + ucvmpath + "/lib/hdf5/lib")
+if "NetCDF" in librariesToInstall:
+    ucvm_conf_command.append("--enable-netcdf")
+    ucvm_conf_command.append("--with-netcdf-include-path=" + ucvmpath + "/lib/netcdf/include")
+    ucvm_conf_command.append("--with-netcdf-lib-path=" + ucvmpath + "/lib/netcdf/lib")
+    ucvm_conf_command.append("--with-netcdf-extra-libs=" + ucvmpath + "/lib/hdf5/lib")
 
 #ucvm_conf_command.append("UCVM_INSTALL_PATH=" + ucvmpath)