Merge pull request #199 from geco-bern/patch-interface

Patch for system specific compilation flags

cleanup

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+## a.out.dSYM may get created on OS X.
+rm -rf src/Makevars a.out.dSYM

configure

@@ -0,0 +1,29 @@
+#!/bin/sh
+
+# System dependent config script to deal with
+# CLANG / LLVM issues through custom compiler flags
+
+# taken from Writing R Extensions, 1.2. Configure and cleanup
+: ${R_HOME=`R RHOME`}
+if test -z "${R_HOME}"; then
+echo "could not determine R_HOME"
+exit 1
+fi
+
+# determine the Fortran 9x compiler
+FC="`"${R_HOME}/bin/R" CMD config FC`"
+
+# grab system specific flags already set
+SFLAGS="`"${R_HOME}/bin/R" CMD config FCFLAGS`"
+
+# Use --version output to determine the compiler
+# A different compiler will either accept --version and print something
+# else or fail due to "unknown argument". In both cases the branch will
+# 
+# use this routine to create the header / start of the Makevars file
+if "$FC" --version 2>/dev/null | grep -q 'flang'; then
+echo "PKG_FCFLAGS =  $SFLAGS -fc-prototypes-external" > src/Makevars
+fi
+
+# Complete the Makevars file with known system agnostic settings
+cat src/Makevars.in >> src/Makevars

src/Makevars → src/Makevars.in

@@ -6,9 +6,6 @@ C_OBJS = wrappersc.o
 # Fortran objects: refer to file names <name.o>, order reflects dependency structure
 FT_OBJS = params_core.mod.o sofunutils.mod.o grid_siterun.mod.o params_siml_pmodel.mod.o params_siml_biomee.mod.o forcing_siterun_pmodel.mod.o forcing_siterun_biomee.mod.o params_soil_biomee.mod.o interface_biosphere_pmodel.mod.o interface_biosphere_biomee.mod.o tile_pmodel.mod.o plant_pmodel.mod.o soiltemp_sitch.mod.o waterbal_splash.mod.o vegdynamics_pmodel.mod.o gpp_pmodel.mod.o gpp_biomee.mod.o photosynth_pmodel.mod.o biosphere_pmodel.mod.o biosphere_biomee.mod.o vegetation_biomee.mod.o soil_biomee.mod.o sofun_r.o  
 
-# Flags for the Fortran compiler, suggested by Prof. Ligges
-# PKG_FFLAGS = -fc-prototypes-external -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c
-
 all: $(SHLIB) clean
 
 $(SHLIB): $(FT_OBJS) $(C_OBJS)

src/Makevars.win

@@ -0,0 +1,68 @@
+# PKG_FFLAGS = -ffree-line-length-0 -fbacktrace -ffpe-trap=invalid,zero,overflow -O1 -Wall -Wextra -pedantic -fbacktrace -fPIC -fmax-errors=1 -ggdb -fcheck=all
+
+# C objects
+C_OBJS = wrappersc.o
+
+# Fortran objects: refer to file names <name.o>, order reflects dependency structure
+FT_OBJS = params_core.mod.o sofunutils.mod.o grid_siterun.mod.o params_siml_pmodel.mod.o params_siml_biomee.mod.o forcing_siterun_pmodel.mod.o forcing_siterun_biomee.mod.o params_soil_biomee.mod.o interface_biosphere_pmodel.mod.o interface_biosphere_biomee.mod.o tile_pmodel.mod.o plant_pmodel.mod.o soiltemp_sitch.mod.o waterbal_splash.mod.o vegdynamics_pmodel.mod.o gpp_pmodel.mod.o gpp_biomee.mod.o photosynth_pmodel.mod.o biosphere_pmodel.mod.o biosphere_biomee.mod.o vegetation_biomee.mod.o soil_biomee.mod.o sofun_r.o  
+
+all: $(SHLIB) clean
+
+$(SHLIB): $(FT_OBJS) $(C_OBJS)
+
+# Dependency of objects (?)
+# <name.o>: <modulename.o>
+sofun_r.o: interface_biosphere_pmodel.mod.o interface_biosphere_biomee.mod.o params_core.mod.o params_core.mod.o params_soil_biomee.mod.o params_siml_pmodel.mod.o params_siml_biomee.mod.o
+interface_biosphere_pmodel.mod.o: forcing_siterun_pmodel.mod.o params_siml_pmodel.mod.o params_core.mod.o
+interface_biosphere_biomee.mod.o: forcing_siterun_biomee.mod.o params_soil_biomee.mod.o params_siml_biomee.mod.o params_core.mod.o
+forcing_siterun_pmodel.mod.o: params_core.mod.o params_siml_pmodel.mod.o grid_siterun.mod.o sofunutils.mod.o
+forcing_siterun_biomee.mod.o: params_core.mod.o params_siml_biomee.mod.o grid_siterun.mod.o
+params_soil_biomee.mod.o: params_core.mod.o
+tile_pmodel.mod.o: params_core.mod.o interface_biosphere_pmodel.mod.o
+waterbal_splash.mod.o: params_core.mod.o tile_pmodel.mod.o plant_pmodel.mod.o sofunutils.mod.o
+gpp_pmodel.mod.o: params_core.mod.o sofunutils.mod.o plant_pmodel.mod.o tile_pmodel.mod.o interface_biosphere_pmodel.mod.o photosynth_pmodel.mod.o
+gpp_biomee.mod.o: datatypes.mod.o soil_biomee.mod.o forcing_siterun_biomee.mod.o photosynth_pmodel.mod.o params_core.mod.o sofunutils.mod.o
+photosynth_pmodel.mod.o: params_core.mod.o sofunutils.mod.o
+soiltemp_sitch.mod.o: params_core.mod.o sofunutils.mod.o tile_pmodel.mod.o interface_biosphere_pmodel.mod.o
+plant_pmodel.mod.o: params_core.mod.o sofunutils.mod.o interface_biosphere_pmodel.mod.o
+vegdynamics_pmodel.mod.o: params_core.mod.o tile_pmodel.mod.o plant_pmodel.mod.o gpp_pmodel.mod.o waterbal_splash.mod.o
+biosphere_pmodel.mod.o: params_core.mod.o classdefs.mod.o sofunutils.mod.o plant_pmodel.mod.o waterbal_splash.mod.o gpp_pmodel.mod.o vegdynamics_pmodel.mod.o tile_pmodel.mod.o interface_biosphere_pmodel.mod.o soiltemp_sitch.mod.o vegdynamics_pmodel.mod.o
+biosphere_biomee.mod.o: params_core.mod.o interface_biosphere_biomee.mod.o datatypes.mod.o soil_biomee.mod.o vegetation_biomee.mod.o
+soil_biomee.mod.o: datatypes.mod.o
+vegetation_biomee.mod.o: datatypes.mod.o soil_biomee.mod.o gpp_biomee.mod.o
+datatypes.mod.o: interface_biosphere_biomee.mod.o params_core.mod.o classdefs.mod.o
+sofunutils.mod.o: params_core.mod.o
+
+# Source (object) of Fortran modules
+# <modulename.mod>: <filename.o>
+sofun_r_mod.mod: sofun_r.o
+md_params_core.mod: params_core.mod.o
+md_params_siml_pmodel.mod: params_siml_pmodel.mod.o
+md_params_siml_biomee.mod: params_siml_biomee.mod.o
+md_forcing_pmodel.mod: forcing_siterun_pmodel.mod.o
+md_forcing_biomee.mod: forcing_siterun_biomee.mod.o
+md_params_soil_biomee.mod: params_soil_biomee.mod.o
+md_interface_pmodel.mod: interface_biosphere_pmodel.mod.o
+md_interface_biomee.mod: interface_biosphere_biomee.mod.o
+md_grid.mod: grid_siterun.mod.o
+md_biosphere_pmodel.mod: biosphere_pmodel.mod.o
+md_biosphere_biomee.mod: biosphere_biomee.mod.o
+md_classdefs.mod: classdefs.mod.o
+md_plant_pmodel.mod: plant_pmodel.mod.o
+md_waterbal.mod: waterbal_splash.mod.o
+md_sofunutils.mod: sofunutils.mod.o
+md_tile_pmodel.mod: tile_pmodel.mod.o
+md_gpp_pmodel.mod: gpp_pmodel.mod.o
+md_gpp_biomee.mod: gpp_biomee.mod.o
+md_photosynth.mod: photosynth_pmodel.mod.o
+md_soiltemp.mod: soiltemp_sitch.mod.o
+md_vegdynamics_pmodel.mod: vegdynamics_pmodel.mod.o
+datatypes.mod: datatypes.o
+md_soil_biomee.mod: soil_biomee.o
+md_vegetation_biomee.mod: vegetation_biomee.o
+
+# Dependency of the C wrapper
+wrappersc.o: sofun_r_mod.mod
+
+clean:
+	@rm -rf *.mod *.o