Manage Environments - simplify Make

.github/workflows/buildTest.yml

@@ -44,11 +44,13 @@ jobs:
           cd ../..
       - name: run resample example
         run: |
-          . arch/arch-GCC_LINUX_APT.env
-          . arch/arch-GCC_LINUX_APT.path
           export XIOS_BINDIR=$PWD/XIOS/bin
           export XIOS_INCDIR=$PWD/XIOS/inc
           export XIOS_LIBDIR=$PWD/XIOS/lib
+          export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/netcdf/mpi/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
+          export LDFLAGS="-L$XIOS_LIBDIR -lxios $(pkg-config --libs netcdf) $(pkg-config --libs netcdf-fortran) -lstdc++"
+          export FCFLAGS="-g -I$XIOS_INCDIR $(pkg-config --cflags-only-I netcdf) $(pkg-config --cflags-only-I netcdf-fortran)"
+          export FC=mpif90
 
           export MVER=${{ matrix.version }}
           export MPI_FLAVOUR='openmpi'

archerEnv

@@ -8,9 +8,6 @@ module load cray-netcdf-hdf5parallel
 module load cray-python
 module load netcdf4
 
-export NETCDF_LIBDIR=-L$NETCDF_DIR/lib
-export NETCDF_INCDIR=-I$NETCDF_DIR/include/
-
 # set XIOS build to XIOS3 marqh build, if not already set
 : ${XIOS_DIR=/work/n02/n02/marqh/metofficegit/tcd-XIOS3-extras}
 
@@ -19,6 +16,13 @@ export XIOS_INCDIR=$XIOS_DIR/inc
 export XIOS_LIBDIR=$XIOS_DIR/lib
 export XIOS_BINDIR=$XIOS_DIR/bin
 
+# ensure netcdf is on the LD path & flags
+export LD_LIBRARY_PATH=$NETCDF_LIBDIR:$LD_LIBRARY_PATH
+export LDFLAGS="-L$XIOS_LIBDIR -lxios -L$NETCDF_DIR/lib -lnetcdf -lnetcdff -lstdc++"
+
+export FCFLAGS="-g -I$XIOS_INCDIR -I$$NETCDF_DIR/include"
+export FC=mpif90
+
 # set env variable for run switching (mpiexec / srun) and iodef patching (transport)
 export PLATFORM=Archer2
 

azspiceEnv

@@ -0,0 +1,20 @@
+# this environment management script needs to be sourced in order to provide
+# equivalent functionality on the MO AZ Spice linux desktop to the Github CI environment.
+# `. azspiceEnv`
+
+# load Azure Spice Spack xios module
+module load xios
+
+# provide specific sub_paths for the demonstration build
+export XIOS_INCDIR=$XIOS_ROOT/include
+export XIOS_LIBDIR=$XIOS_ROOT/lib
+export XIOS_BINDIR=$XIOS_ROOT/bin
+
+# ensure netcdf is on the LD path & flags
+export LD_LIBRARY_PATH=${NETCDFF_ROOT}/lib:$LD_LIBRARY_PATH
+export LDFLAGS="-L$XIOS_LIBDIR -lxios $(pkg-config --libs netcdf) $(pkg-config --libs netcdf-fortran) -lstdc++"
+
+export FCFLAGS="-g -I$XIOS_INCDIR $(pkg-config --cflags-only-I netcdf) $(pkg-config --cflags-only-I netcdf-fortran)"
+export FC=mpif90
+
+export MVER=XIOS/trunk@2252

desktopEnv

@@ -10,17 +10,18 @@ module use /data/users/lfric/software/modulefiles.rhel7
 
 module load environment/lfric/gcc
 
-# provide explit path set to the arch script for netCDF linking
-export NETCDF_LIB_DIRS=$NETCDF_4_8_1_ROOT/lib:$NETCDF_4_8_1_ROOT/lib64
-export NETCDF_INC_DIRS=$NETCDF_4_8_1_ROOT/include
-
-. arch/arch-GCC_LINUX_APT.path
-
 # provide explicit paths to all XIOS components
 export XIOS_INCDIR=$XIOS_R2252_2_ROOT/include
 export XIOS_LIBDIR=$XIOS_R2252_2_ROOT/lib
 export XIOS_BINDIR=$XIOS_R2252_2_ROOT/bin
 
+# ensure netcdf is on the LD path & flags
+export LD_LIBRARY_PATH=$NETCDF_4_8_1_ROOT/lib:$NETCDF_4_8_1_ROOT/lib64:$LD_LIBRARY_PATH
+export LDFLAGS="-L$XIOS_LIBDIR -lxios -L$NETCDF_4_8_1_ROOT/lib -lnetcdf -L$NETCDF_4_8_1_ROOT/lib64 -lnetcdff -lstdc++"
+
+export FCFLAGS="-g -I$XIOS_INCDIR -I$NETCDF_4_8_1_ROOT/include"
+export FC=mpif90
+
 # use an extend LFRic Python environment
 # that includes netCDF4-python built w.r.t. the LFRIC
 # netCDF

jasminEnv

@@ -5,8 +5,8 @@
 module load jaspy/3.11 # need at least version 3.11 for parallel netcdf support
 
 # provide explit path set to the arch script for netCDF linking
-export NETCDF_LIBDIR=-L$(nc-config --libdir)
-export NETCDF_INCDIR=-I$(nc-config --includedir)
+export NETCDF_LIBDIR=$(nc-config --libdir)
+export NETCDF_INCDIR=$(nc-config --includedir)
 
 # set XIOS build to XIOS2 trunk revision 2628, if not already set
 : ${XIOS_DIR=/home/users/jcole/software/xios_trunk_r2628}
@@ -16,6 +16,13 @@ export XIOS_INCDIR=$XIOS_DIR/inc
 export XIOS_LIBDIR=$XIOS_DIR/lib
 export XIOS_BINDIR=$XIOS_DIR/bin
 
+# ensure netcdf is on the LD path & flags
+export LD_LIBRARY_PATH=$NETCDF_LIBDIR:$LD_LIBRARY_PATH
+export LDFLAGS="-L$XIOS_LIBDIR -lxios -L$NETCDF_LIBDIR -lnetcdf -lnetcdff -lstdc++"
+
+export FCFLAGS="-g -I$XIOS_INCDIR -I$NETCDF_INCDIR"
+export FC=mpif90
+
 # set env variable for run switching (mpiexec / srun) and iodef patching (transport)
 export PLATFORM=Jasmin
 #

xios_examples/Makefile

@@ -7,36 +7,12 @@
 #
 # Environment Variables expected by this MakeFile:
 #
-# NETCDF_LIBDIR: the directories for the netCDF lib files
-#                encoded as a -L string, e.g.
-#                "-L/dir1 -L/dir2"
-# NETCDF_INCDIR: the directories for the netCDF include files
-#                encoded as a -I string, e.g.
-#                "-I/dir3 -I/dir4"
-#     (note, this is for consistency with the XIOS build process
-#      required for the CI build machine.
-#      this is not required for other directories)
-#
-# XIOS_INCDIR: The directory for XIOS include files
-# XIOS_LIBDIR: The directory for XIOS lib files
+# FC: mpif90
+# FCFLAGS: -g & include files for netcdf & xios
+# LD_FLAGS: for xios, netcdf, netcdff, stfc++
+# LD_LIBRARY_PATH: for netCDF & XIOS libs
 # XIOS_BINDIR: The directory for XIOS binary files
 
-FCFLAGS = -g
-
-FC = mpif90       # compiler driver for MPI programs
-
-# compiler flag, includes
-FCFLAGS += -I$(XIOS_INCDIR) $(NETCDF_INCDIR)
-
-# loader flags
-LDFLAGS = \
-	-L$(XIOS_LIBDIR) \
-	$(NETCDF_LIBDIR) \
-	-lxios \
-	-lnetcdf \
-	-lnetcdff \
-	-lstdc++ 
-
 .PHONY: all, clean, run
 
 all: resample

xios_examples/context_test/Makefile

@@ -7,36 +7,12 @@
 #
 # Environment Variables expected by this MakeFile:
 #
-# NETCDF_LIBDIR: the directories for the netCDF lib files
-#                 encoded as a -L string, e.g.
-#                 "-L/dir1 -L/dir2"
-# NETCDF_INCDIR: the directories for the netCDF include files
-#                 encoded as a -I string, e.g.
-#                 "-I/dir3 -I/dir4"
-#     (note, this is for consistency with the XIOS build process
-#      required for the CI build machine.
-#      this is not required for other directories)
-#
-# XIOS_INCDIR: The directory for XIOS include files
-# XIOS_LIBDIR: The directory for XIOS lib files
+# FC: mpif90
+# FCFLAGS: -g & include files for netcdf & xios
+# LD_FLAGS: for xios, netcdf, netcdff, stfc++
+# LD_LIBRARY_PATH: for netCDF & XIOS libs
 # XIOS_BINDIR: The directory for XIOS binary files
 
-FCFLAGS = -g
-
-FC = mpif90 # compiler driver for MPI programs
-
-# compiler flag, includes
-FCFLAGS += -I$(XIOS_INCDIR) $(NETCDF_INCDIR)
-
-# loader flags
-LDFLAGS = \
-        -L$(XIOS_LIBDIR) \
-        $(NETCDF_LIBDIR) \
-        -lxios \
-        -lnetcdf \
-        -lnetcdff \
-        -lstdc++
-
 .PHONY: all, clean, run
 
 OBJ = custom_type_mod.o context_def_mod.o

xios_examples/packing_scale_offset/Makefile

@@ -7,36 +7,12 @@
 #
 # Environment Variables expected by this MakeFile:
 #
-# NETCDF_LIBDIR: the directories for the netCDF lib files
-#                encoded as a -L string, e.g.
-#                "-L/dir1 -L/dir2"
-# NETCDF_INCDIR: the directories for the netCDF include files
-#                encoded as a -I string, e.g.
-#                "-I/dir3 -I/dir4"
-#     (note, this is for consistency with the XIOS build process
-#      required for the CI build machine.
-#      this is not required for other directories)
-#
-# XIOS_INCDIR: The directory for XIOS include files
-# XIOS_LIBDIR: The directory for XIOS lib files
+# FC: mpif90
+# FCFLAGS: -g & include files for netcdf & xios
+# LD_FLAGS: for xios, netcdf, netcdff, stfc++
+# LD_LIBRARY_PATH: for netCDF & XIOS libs
 # XIOS_BINDIR: The directory for XIOS binary files
 
-FCFLAGS = -g
-
-FC = mpif90       # compiler driver for MPI programs
-
-# compiler flag, includes
-FCFLAGS += -I$(XIOS_INCDIR) $(NETCDF_INCDIR)
-
-# loader flags
-LDFLAGS = \
-	-L$(XIOS_LIBDIR) \
-	$(NETCDF_LIBDIR) \
-	-lxios \
-	-lnetcdf \
-	-lnetcdff \
-	-lstdc++ 
-
 .PHONY: all, clean, run
 
 all: pack

xios_examples/split_file_test/Makefile

@@ -7,35 +7,12 @@
 #
 # Environment Variables expected by this MakeFile:
 #
-# NETCDF_LIBDIR: the directories for the netCDF lib files
-#                encoded as a -L string, e.g.
-#                "-L/dir1 -L/dir2"
-# NETCDF_INCDIR: the directories for the netCDF include files
-#                encoded as a -I string, e.g.
-#                "-I/dir3 -I/dir4"
-#     (note, this is for consistency with the XIOS build process
-#      required for the CI build machine.
-#      this is not required for other directories)
-#
-# XIOS_INCDIR: The directory for XIOS include files
-# XIOS_LIBDIR: The directory for XIOS lib files
+# FC: mpif90
+# FCFLAGS: -g & include files for netcdf & xios
+# LD_FLAGS: for xios, netcdf, netcdff, stfc++
+# LD_LIBRARY_PATH: for netCDF & XIOS libs
 # XIOS_BINDIR: The directory for XIOS binary files
 
-FCFLAGS = -g
-
-FC = mpif90       # compiler driver for MPI programs
-
-# compiler flag, includes
-FCFLAGS += -I$(XIOS_INCDIR) $(NETCDF_INCDIR)
-
-# loader flags
-LDFLAGS = \
-	-L$(XIOS_LIBDIR) \
-	$(NETCDF_LIBDIR) \
-	-lxios \
-	-lnetcdf \
-	-lnetcdff \
-	-lstdc++ 
 
 .PHONY: all, clean, run
 
@@ -55,4 +32,4 @@ run:
 
 # cleanup
 clean:
-	rm -f *.exe *.o *.mod *.MOD *.out *.err *.nc
+	rm -f *.exe *.o *.mod *.MOD *.out *.err *.nc

xios_examples/write_domain_parallel/Makefile

@@ -7,36 +7,12 @@
 #
 # Environment Variables expected by this MakeFile:
 #
-# NETCDF_LIBDIR: the directories for the netCDF lib files
-#                 encoded as a -L string, e.g.
-#                 "-L/dir1 -L/dir2"
-# NETCDF_INCDIR: the directories for the netCDF include files
-#                 encoded as a -I string, e.g.
-#                 "-I/dir3 -I/dir4"
-#     (note, this is for consistency with the XIOS build process
-#      required for the CI build machine.
-#      this is not required for other directories)
-#
-# XIOS_INCDIR: The directory for XIOS include files
-# XIOS_LIBDIR: The directory for XIOS lib files
+# FC: mpif90
+# FCFLAGS: -g & include files for netcdf & xios
+# LD_FLAGS: for xios, netcdf, netcdff, stfc++
+# LD_LIBRARY_PATH: for netCDF & XIOS libs
 # XIOS_BINDIR: The directory for XIOS binary files
 
-FCFLAGS = -g
-
-FC = mpif90       # compiler driver for MPI programs
-
-# compiler flag, includes
-FCFLAGS += -I$(XIOS_INCDIR) $(NETCDF_INCDIR)
-
-# loader flags
-LDFLAGS = \
-	-L$(XIOS_LIBDIR) \
-	$(NETCDF_LIBDIR) \
-	-lxios \
-	-lnetcdf \
-	-lnetcdff \
-	-lstdc++ 
-
 all: write_parallel
 
 # fortran compilation