Fix LDFLAGS definition and usage

`ld` flags are currently specified incorrectly. For example:
1. `-lnetcdf` is not required since it is a dependency of the netCDF
Fortran library - only `-lnetcdff` is needed.
2. `ld` flags are being split across two variables: `LDFLAGS` and `LD`
when there should only be one (`LD` typically refers to the path  to the
`ld` executable). Having the flags split across two variables allows for
the flags to be passed to the compiler in an inconsistent way.
See #198 for more details.

This change removes the `LD` variable and any hard-coded linker flags or
include flags in the Makefile or build script. Linker flags and include
flags are replaced with a query to `pkg-config` so that the build system
is insulated from changes to library versions and dependencies.

Fixes #198

src/offline/Makefile

@@ -147,26 +147,23 @@ PROG_MPI = cable-mpi
 # from the compiled object files
 OBJS := ${LSRC:.F90=.o}
 
-#compiler switches and flags
-CINC = -I$(NCMOD)
-
 #suffixes we use
 .SUFFIXES:
 .SUFFIXES: .F90 .o
 #default rules for these suffixes
 .F90.o:
-	$(FC) $(CFLAGS) $(CINC) -c $<
+	$(FC) $(CFLAGS) -c $<
 
 SUPPRESS_FLAGS := -warn nostderrors -diag-disable 10145
 
 # the first target is the default target
 .PHONY: serial
 serial: cable_driver.F90 $(OBJS)
-	$(FC) $(SUPPRESS_FLAGS) $(CFLAGS) $(LDFLAGS) $(LD) -o $(PROG_SERIAL) $^ $(CINC)
+	$(FC) $(SUPPRESS_FLAGS) $(CFLAGS) -o $(PROG_SERIAL) $^ $(LDFLAGS)
 
 .PHONY: mpi
 mpi: cable_mpidrv.F90 cable_mpicommon.o cable_mpimaster.o cable_mpiworker.o pop_mpi.o $(OBJS)
-	$(FC) $(SUPPRESS_FLAGS) $(CFLAGS) $(LDFLAGS) -o $(PROG_MPI) $^ $(CINC) $(LD)
+	$(FC) $(SUPPRESS_FLAGS) $(CFLAGS) -o $(PROG_MPI) $^ $(LDFLAGS)
 
 cable_mpicommon.o: cable_mpicommon.F90 $(OBJS)
 pop_mpi.o: pop_mpi.F90 cable_mpicommon.o $(OBJS)

src/offline/build3.sh

@@ -15,29 +15,37 @@ host_gadi()
    module purge
    module add intel-compiler/2019.5.281
    module add netcdf/4.6.3
+   # This is required so that the netcdf-fortran library is discoverable by
+   # pkg-config:
+   prepend_path PKG_CONFIG_PATH "${NETCDF_BASE}/lib/Intel/pkgconfig"
 
-   export NCDIR=$NETCDF_ROOT'/lib/Intel'
-   export NCMOD=$NETCDF_ROOT'/include/Intel'
-   export CFLAGS='-O2 -fp-model precise '
-   export LDFLAGS='-L'$NCDIR
-   export LD='-lnetcdf -lnetcdff'
+   if ! pkg-config --exists netcdf-fortran; then
+       echo -e "\nUnable to find netcdf-fortran via pkg-config. Exiting...\n"
+       exit 1
+   fi
 
    if [[ $1 = 'mpi' ]]; then
       module add intel-mpi/2019.5.281
       export FC='mpif90'
    else
       export FC='ifort'
    fi
+
+   CFLAGS="-O2 -fp-model precise"
 
    if [[ $1 = 'MGK' ]]; then
-      export CFLAGS='-O2'
-      #export NCMOD=$NETCDF_ROOT'/include'
+      CFLAGS='-O2'
    fi
 
    if [[ $1 = 'debug' ]]; then
-      export CFLAGS='-O0 -traceback -g -fp-model precise -ftz -fpe0'
-      #export CFLAGS='-O0 -traceback -g -fp-model precise -ftz -fpe0 -check all,noarg_temp_created'
+      CFLAGS='-O0 -traceback -g -fp-model precise -ftz -fpe0'
+      #CFLAGS='-O0 -traceback -g -fp-model precise -ftz -fpe0 -check all,noarg_temp_created'
    fi
+
+   CFLAGS+=" $(pkg-config --cflags netcdf-fortran)"
+   export CFLAGS
+   LDFLAGS=$(pkg-config --libs netcdf-fortran)
+   export LDFLAGS
 
    if [[ $1 = 'mpi' ]]; then
     build_build mpi
@@ -144,9 +152,6 @@ build_status()
       echo  ''
       echo 'Oooops. Something went wrong'
       echo  ''
-      echo 'Other than compiler messages, known build issues:'
-      echo 'Some systems require additional library. '
-      echo 'e.g. Edit Makefile; add -lnetcdff to LD = ...'
    fi
    exit
 }