Fix LDFLAGS definition and usage (#199)

`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 correct
flags are used. Using `pkg-config` also insulates the build system from
changes to library versions and dependencies.

~~This PR should ideally be done after #197 is merged so that we can
verify compiled object files have not been altered as a result of this
change.~~

Compiled object files are identical between this branch and the main
branch. However, the executables differ between the two branches due to
changes in the compiler arguments at the linking step.

Regression tests using
[benchcab](https://github.com/CABLE-LSM/benchcab)* (bitwise comparison
of model output via nccmp) show that model output is bitwise identical
between the current branch and the main branch for serial and MPI model
runs.

*executables were built manually for the spatial case (see this related
issue: CABLE-LSM/benchcab#244).

Fixes #198

<!-- readthedocs-preview cable start -->
----
📚 Documentation preview 📚:
https://cable--199.org.readthedocs.build/en/199/

<!-- readthedocs-preview cable end -->

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
 }