diff --git a/.gitignore b/.gitignore
index ef0cab950..8e156c547 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,4 @@
 *.o
-*.f
-*.f90
-*.F90
 *.mod
 *~
 Makefile.comm
@@ -23,3 +20,4 @@ README.md
 *pytest_cache*
 *.log
 compile_options.sh
+.DS_Store
diff --git a/trunk/NDHMS/CPL/CLM_cpl/Makefile b/trunk/NDHMS/CPL/CLM_cpl/Makefile
index 6eee09754..241bbee14 100644
--- a/trunk/NDHMS/CPL/CLM_cpl/Makefile
+++ b/trunk/NDHMS/CPL/CLM_cpl/Makefile
@@ -18,9 +18,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) -I ../../mod $(CLM_MOD) $(*).f
-	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -I$(NETCDFINC) -o $(@) $(F90FLAGS) $(MODFLAG) -I ../../mod $(CLM_MOD) $(*).F
 	@echo ""
 	ar -r ../../lib/libHYDRO.a $(@)
 
@@ -29,5 +27,5 @@ all:	$(OBJS)
 #
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f
+	rm -f *.o *.mod *.stb *~ 
 	cd ../..; make -f Makefile.comm clean
diff --git a/trunk/NDHMS/CPL/LIS_cpl/Makefile b/trunk/NDHMS/CPL/LIS_cpl/Makefile
index c38f6c637..e048032c9 100644
--- a/trunk/NDHMS/CPL/LIS_cpl/Makefile
+++ b/trunk/NDHMS/CPL/LIS_cpl/Makefile
@@ -18,9 +18,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) -I../../mod $(LIS_MOD) -I$(MOD_ESMF) $(*).f
-	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -I$(NETCDFINC) -o $(@) $(F90FLAGS) $(MODFLAG) -I../../mod $(LIS_MOD) -I$(MOD_ESMF) $(*).F
 	@echo ""
 	ar -r ../../lib/libHYDRO.a $(@)
 
@@ -29,4 +27,4 @@ all:	$(OBJS)
 #
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f
+	rm -f *.o *.mod *.stb *~ 
diff --git a/trunk/NDHMS/CPL/NoahMP_cpl/Makefile b/trunk/NDHMS/CPL/NoahMP_cpl/Makefile
index 8286d53d8..f70d27e29 100644
--- a/trunk/NDHMS/CPL/NoahMP_cpl/Makefile
+++ b/trunk/NDHMS/CPL/NoahMP_cpl/Makefile
@@ -16,10 +16,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-#	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I$(NETCDFINC) $(*).f
-	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I$(NETCDFINC) $(*).F
 	@echo ""
 	ar -r ../../lib/libHYDRO.a $(@)
 	cp *.mod ../../mod
@@ -33,4 +30,4 @@ hrldas_drv_HYDRO.o: module_hrldas_HYDRO.o ../../Data_Rec/module_namelist.o ../..
 
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f Noah_hrldas_beta
+	rm -f *.o *.mod *.stb *~ Noah_hrldas_beta
diff --git a/trunk/NDHMS/CPL/Noah_cpl/Makefile b/trunk/NDHMS/CPL/Noah_cpl/Makefile
index a8e04f3b3..655405022 100644
--- a/trunk/NDHMS/CPL/Noah_cpl/Makefile
+++ b/trunk/NDHMS/CPL/Noah_cpl/Makefile
@@ -16,10 +16,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-#	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) -I$(NETCDF_INC) $(*).f
-	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -o $(@) $(F90FLAGS) $(MODFLAG) -I$(NETCDF_INC) $(*).F
 	@echo ""
 	ar -r ../../lib/libHYDRO.a $(@)
 
@@ -32,4 +29,4 @@ hrldas_drv_HYDRO.o: module_hrldas_HYDRO.o ../../Data_Rec/module_namelist.o ../..
 
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f Noah_hrldas_beta
+	rm -f *.o *.mod *.stb *~ Noah_hrldas_beta
diff --git a/trunk/NDHMS/CPL/WRF_cpl/Makefile b/trunk/NDHMS/CPL/WRF_cpl/Makefile
index a37fbe0d7..fa196ae9d 100644
--- a/trunk/NDHMS/CPL/WRF_cpl/Makefile
+++ b/trunk/NDHMS/CPL/WRF_cpl/Makefile
@@ -17,9 +17,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) -I$(WRF_ROOT)/frame -I$(WRF_ROOT)/main -I$(WRF_ROOT)/external/esmf_time_f90 $(*).f
-	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -I$(NETCDFINC) -o $(@) $(F90FLAGS) $(MODFLAG) -I$(WRF_ROOT)/frame -I$(WRF_ROOT)/main -I$(WRF_ROOT)/external/esmf_time_f90 $(*).F
 	@echo ""
 	ar -r ../../lib/libHYDRO.a $(@)
 
@@ -31,4 +29,4 @@ module_wrf_HYDRO.o: ../../Data_Rec/module_RT_data.o ../../Data_Rec/module_nameli
 wrf_drv_HYDRO.o: module_wrf_HYDRO.o
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f
+	rm -f *.o *.mod *.stb *~
diff --git a/trunk/NDHMS/Data_Rec/Makefile b/trunk/NDHMS/Data_Rec/Makefile
index 49ac4e92e..2de17518d 100644
--- a/trunk/NDHMS/Data_Rec/Makefile
+++ b/trunk/NDHMS/Data_Rec/Makefile
@@ -14,9 +14,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I../mod $(*).f
-	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -I$(NETCDFINC) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I../mod $(*).F
 	@echo ""
 	ar -r ../lib/libHYDRO.a $(@)
 	cp *.mod ../mod
@@ -25,4 +23,4 @@ all:	$(OBJS)
 #
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f
+	rm -f *.o *.mod *.stb *~
diff --git a/trunk/NDHMS/Debug_Utilities/Makefile b/trunk/NDHMS/Debug_Utilities/Makefile
index 05a95c9b8..bbba71179 100644
--- a/trunk/NDHMS/Debug_Utilities/Makefile
+++ b/trunk/NDHMS/Debug_Utilities/Makefile
@@ -12,9 +12,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I../mod $(*).f
-	#$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -I$(NETCDFINC) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I../mod $(*).F
 	@echo ""
 	ar -r ../lib/libHYDRO.a $(@)
 	cp *.mod ../mod
@@ -23,4 +21,4 @@ all:	$(OBJS)
 #
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f
+	rm -f *.o *.mod *.stb *~
diff --git a/trunk/NDHMS/HYDRO_drv/Makefile b/trunk/NDHMS/HYDRO_drv/Makefile
index 0b92dda74..0bb462e09 100644
--- a/trunk/NDHMS/HYDRO_drv/Makefile
+++ b/trunk/NDHMS/HYDRO_drv/Makefile
@@ -11,10 +11,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-#	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) -I../mod $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I$(NETCDFINC) -I../mod $(*).f
-#	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I$(NETCDFINC) -I../mod $(*).F
 	@echo ""
 	ar -r ../lib/libHYDRO.a $(@)
 	cp *.mod ../mod
@@ -26,4 +23,4 @@ module_HYDRO_drv.o: ../Data_Rec/module_namelist.o ../Data_Rec/module_RT_data.o .
         ../Routing/module_GW_baseflow.o ../Routing/module_HYDRO_utils.o ../Routing/module_HYDRO_io.o ../Routing/module_RT.o
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f
+	rm -f *.o *.mod *.stb *~
diff --git a/trunk/NDHMS/Land_models/Noah/GRAPHICS/HORIZ/Makefile b/trunk/NDHMS/Land_models/Noah/GRAPHICS/HORIZ/Makefile
index 1e12d3fc5..6ec183f73 100644
--- a/trunk/NDHMS/Land_models/Noah/GRAPHICS/HORIZ/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/GRAPHICS/HORIZ/Makefile
@@ -34,10 +34,7 @@ all:	$(CMD)
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(*).F > $(*).f
-	$(F90) -c -I$(NETCDF)/include $(FFLAGS) $(MODDIR) $(*).f 
-	$(RM) $(*).f
+	$(F90) $(CPPINVOKE) $(CPPFLAGS) -c -I$(NETCDF)/include $(FFLAGS) $(MODDIR) $(*).F
 
 $(CMD):	$(OBJS)
 	$(F90) -o $(@) -I$(NETCDF)/include $(FFLAGS) $(OBJS) \
diff --git a/trunk/NDHMS/Land_models/Noah/GRAPHICS/TIME_SERIES/Makefile b/trunk/NDHMS/Land_models/Noah/GRAPHICS/TIME_SERIES/Makefile
index d8bbb6148..0bf9a76d4 100644
--- a/trunk/NDHMS/Land_models/Noah/GRAPHICS/TIME_SERIES/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/GRAPHICS/TIME_SERIES/Makefile
@@ -32,10 +32,7 @@ all:	$(CMD)
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(*).F > $(*).f
-	$(F90) -c -I$(NETCDF)/include $(FFLAGS) $(MODDIR) $(*).f 
-	$(RM) $(*).f
+	$(F90) $(CPPINVOKE) $(CPPFLAGS) -c -I$(NETCDF)/include $(FFLAGS) $(MODDIR) $(*).F
 
 $(CMD):	$(OBJS)
 	$(F90) -o $(@) -I$(NETCDF)/include $(FFLAGS) $(OBJS) \
diff --git a/trunk/NDHMS/Land_models/Noah/HRLDAS_COLLECT_DATA/Makefile b/trunk/NDHMS/Land_models/Noah/HRLDAS_COLLECT_DATA/Makefile
index 622e8b130..1d6547138 100644
--- a/trunk/NDHMS/Land_models/Noah/HRLDAS_COLLECT_DATA/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/HRLDAS_COLLECT_DATA/Makefile
@@ -20,10 +20,7 @@ lib/libsmda.a:
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(*).F > $(*).f
-	$(COMPILERF90) $(FREESOURCE) $(F90FLAGS) -c $(NETCDFMOD) -I./lib $(MODFLAG)./lib $(*).f 
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(FREESOURCE) $(F90FLAGS) -c $(NETCDFMOD) -I./lib $(MODFLAG)./lib $(*).F
 
 $(CMD):	lib/libsmda.a $(OBJS)
 	(cd lib; make)
diff --git a/trunk/NDHMS/Land_models/Noah/HRLDAS_COLLECT_DATA/lib/Makefile b/trunk/NDHMS/Land_models/Noah/HRLDAS_COLLECT_DATA/lib/Makefile
index 7eb47aa7d..9f6100cbd 100644
--- a/trunk/NDHMS/Land_models/Noah/HRLDAS_COLLECT_DATA/lib/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/HRLDAS_COLLECT_DATA/lib/Makefile
@@ -50,10 +50,7 @@ decode_jpeg2000.o:	decode_jpeg2000.c
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(GRIBCODE_OPT) $(BZIP_CPP) $(*).F > $(*).f
-	$(COMPILERF90) -c $(FREESOURCE) $(F90FLAGS) $(NETCDFMOD) $(*).f
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(GRIBCODE_OPT) $(BZIP_CPP) -c $(FREESOURCE) $(F90FLAGS) $(NETCDFMOD) $(*).F
 
 .c.o:
 	$(CC) -c $(BZIP_CPP) $(<)
diff --git a/trunk/NDHMS/Land_models/Noah/IO_code/Makefile b/trunk/NDHMS/Land_models/Noah/IO_code/Makefile
index a33d23449..75c81b46d 100644
--- a/trunk/NDHMS/Land_models/Noah/IO_code/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/IO_code/Makefile
@@ -15,27 +15,18 @@ all:	$(OBJS)
 
 Noah_hrldas_driver.o: Noah_hrldas_driver.F
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(MODFLAG). \
-	$(MODFLAG)../Noah $(MODFLAG)../Utility_routines $(NETCDFMOD) $(*).f
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(MODFLAG). \
+	$(MODFLAG)../Noah $(MODFLAG)../Utility_routines -I../../../MPP $(NETCDFMOD) $(*).F
 	@echo ""
 
 module_hrldas_netcdf_io.o: module_hrldas_netcdf_io.F
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(NETCDFMOD) $(CPPHRLDAS) $(*).F > $(*).f
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(MODFLAG)../Utility_routines $(NETCDFMOD)  $(*).f
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS)  -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(MODFLAG)../Utility_routines $(NETCDFMOD)  $(*).F
 	@echo ""
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(*).f
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(*).F
 	@echo ""
 
 
diff --git a/trunk/NDHMS/Land_models/Noah/Noah/Makefile b/trunk/NDHMS/Land_models/Noah/Noah/Makefile
index c1161082e..1881cc273 100644
--- a/trunk/NDHMS/Land_models/Noah/Noah/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/Noah/Makefile
@@ -15,10 +15,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f
-	$(COMPILERF90) -o $(@) -c $(MODFLAG). $(MODFLAG)../Utility_routines $(F90FLAGS) $(FREESOURCE) $(*).f
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(MODFLAG). $(MODFLAG)../Utility_routines $(F90FLAGS) $(FREESOURCE) $(*).F
 	@echo ""
 
 #
diff --git a/trunk/NDHMS/Land_models/Noah/Utility_programs/Makefile b/trunk/NDHMS/Land_models/Noah/Utility_programs/Makefile
index b7a260903..95a02fd30 100644
--- a/trunk/NDHMS/Land_models/Noah/Utility_programs/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/Utility_programs/Makefile
@@ -20,27 +20,18 @@ all: $(CMD)
 #
 module_date_utilities.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) ../Utility_routines/$(*).F > $(*).f
-	$(COMPILERF90) $(FREESOURCE) $(F90FLAGS) -c $(*).f 
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(FREESOURCE) $(F90FLAGS) -c ../Utility_routines/$(*).F
 
 #
 # Compile the arguments_module from the HRLDAS_COLLECT_DATA/lib directory
 #
 arguments_module.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) ../HRLDAS_COLLECT_DATA/lib/$(*).F > $(*).f
-	$(COMPILERF90) $(FREESOURCE) $(F90FLAGS) -c $(*).f 
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(FREESOURCE) $(F90FLAGS) -c ../HRLDAS_COLLECT_DATA/lib/$(*).F
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(*).F > $(*).f
-	$(COMPILERF90) $(FREESOURCE) $(F90FLAGS) -c $(NETCDFMOD) $(MODFLAG). $(*).f 
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(FREESOURCE) $(F90FLAGS) -c $(NETCDFMOD) $(MODFLAG). $(*).F
 
 
 hrldas_extract_point: hrldas_extract_point.o
diff --git a/trunk/NDHMS/Land_models/Noah/Utility_programs/gcip_sw_to_grib/Makefile b/trunk/NDHMS/Land_models/Noah/Utility_programs/gcip_sw_to_grib/Makefile
index ae8dba1bc..a94511513 100644
--- a/trunk/NDHMS/Land_models/Noah/Utility_programs/gcip_sw_to_grib/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/Utility_programs/gcip_sw_to_grib/Makefile
@@ -37,10 +37,7 @@ module_date_utilities.o:	../../Utility_routines/module_date_utilities.F
 	$(COMPILERF90) -c $(F90FLAGS) $(FREESOURCE) $(<)
 
 .F.o:
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(*).F > $(*).f
-	$(COMPILERF90) $(FREESOURCE) $(F90FLAGS) -c $(*).f 
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(FREESOURCE) $(F90FLAGS) -c $(*).F 
 
 
 neat:
diff --git a/trunk/NDHMS/Land_models/Noah/Utility_routines/Makefile b/trunk/NDHMS/Land_models/Noah/Utility_routines/Makefile
index b58244e51..64255c539 100644
--- a/trunk/NDHMS/Land_models/Noah/Utility_routines/Makefile
+++ b/trunk/NDHMS/Land_models/Noah/Utility_routines/Makefile
@@ -19,10 +19,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(*).f
-	$(RM) $(*).f
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS)  -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(*).F
 	@echo ""
 
 #
diff --git a/trunk/NDHMS/Land_models/NoahMP/HRLDAS_forcing/Makefile b/trunk/NDHMS/Land_models/NoahMP/HRLDAS_forcing/Makefile
index e1da7a2c3..ed619ffff 100644
--- a/trunk/NDHMS/Land_models/NoahMP/HRLDAS_forcing/Makefile
+++ b/trunk/NDHMS/Land_models/NoahMP/HRLDAS_forcing/Makefile
@@ -20,9 +20,7 @@ lib/libsmda.a:
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f90
-	$(CPP) $(CPPFLAGS) $(CPP_NETCDF4_COMPRESS) $(*).F > $(*).f90
-	$(COMPILERF90) $(FREESOURCE) $(F90FLAGS) $(LDFLAGS) -c $(NETCDFMOD) -I./lib -I./lib $(*).f90
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPP_NETCDF4_COMPRESS) $(FREESOURCE) $(F90FLAGS) $(LDFLAGS) -c $(NETCDFMOD) -I./lib -I./lib $(*).F
 
 $(CMD):	lib/libsmda.a $(OBJS)
 	(cd lib; make)
@@ -30,7 +28,7 @@ $(CMD):	lib/libsmda.a $(OBJS)
 		-L./lib -lsmda $(NETCDFLIB) $(BZIP2_LIB) $(LIBJASPER)
 
 clean:
-	$(RM) *.o *~ *.exe *.mod *.f90
+	$(RM) *.o *~ *.exe *.mod
 	(cd lib; make clean)
 #
 
diff --git a/trunk/NDHMS/Land_models/NoahMP/HRLDAS_forcing/lib/Makefile b/trunk/NDHMS/Land_models/NoahMP/HRLDAS_forcing/lib/Makefile
index b2f383d89..d0d5f1191 100644
--- a/trunk/NDHMS/Land_models/NoahMP/HRLDAS_forcing/lib/Makefile
+++ b/trunk/NDHMS/Land_models/NoahMP/HRLDAS_forcing/lib/Makefile
@@ -49,15 +49,13 @@ decode_jpeg2000.o:	decode_jpeg2000.c
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f90
-	$(CPP) $(CPPFLAGS) $(GRIBCODE_OPT) $(BZIP_CPP) $(*).F > $(*).f90
-	$(COMPILERF90) -c $(FREESOURCE) $(F90FLAGS) $(LDFLAGS) $(NETCDFMOD) $(*).f90
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(GRIBCODE_OPT) $(BZIP_CPP) -c $(FREESOURCE) $(F90FLAGS) $(LDFLAGS) $(NETCDFMOD) $(*).F
 
 .c.o:
 	$(CC) -c $(BZIP_CPP) $(<)
 
 clean:
-	$(RM) $(OBJS) $(CMD) *.mod *.f90 *~
+	$(RM) $(OBJS) $(CMD) *.mod *~
 #
 module_grib2.o:	module_grib2.F module_grib2_tables.o module_grib1.o module_mapinfo.o kwm_date_utilities.o module_grib_common.o
 module_grib1.o: module_grib1.F module_mapinfo.o kwm_date_utilities.o module_grib_common.o
diff --git a/trunk/NDHMS/Land_models/NoahMP/IO_code/Makefile b/trunk/NDHMS/Land_models/NoahMP/IO_code/Makefile
index f2aeb836d..009f1effc 100644
--- a/trunk/NDHMS/Land_models/NoahMP/IO_code/Makefile
+++ b/trunk/NDHMS/Land_models/NoahMP/IO_code/Makefile
@@ -19,34 +19,26 @@ NoahMP : $(OBJS_NoahMP) $(OBJS)
 
 module_NoahMP_hrldas_driver.o: module_NoahMP_hrldas_driver.F ../../../HYDRO_drv/module_HYDRO_drv.o  ../../../Data_Rec/module_namelist.o ../../../Data_Rec/module_RT_data.o ../../../CPL/NoahMP_cpl/module_hrldas_HYDRO.o
 	@echo ""
-	$(RM) $(*).f90
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f90
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(MODFLAG) -I. \
-	-I../phys -I../Utility_routines -I../../../mod $(NETCDFMOD) $(*).f90
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(MODFLAG) -I. \
+	-I../phys -I../Utility_routines -I../../../mod $(NETCDFMOD) $(*).F
 	@echo ""
 
 main_hrldas_driver.o: main_hrldas_driver.F
 	@echo ""
-	$(RM) $(*).f90
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f90
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) -I ../MPP -I. \
-	-I../phys -I../Utility_routines -I../../../mod -I../../../MPP $(NETCDFMOD) $(MODFLAG) $(*).f90
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) -I ../MPP -I. \
+	-I../phys -I../Utility_routines -I../../../mod -I../../../MPP $(NETCDFMOD) $(*).F
 #	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) -I ../MPP -I. \
 #	-I../phys -I../Utility_routines $(NETCDFMOD) $(*).f90
 	@echo ""
 
 module_hrldas_netcdf_io.o: module_hrldas_netcdf_io.F
 	@echo ""
-	$(RM) $(*).f90
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(NETCDFMOD) $(*).F > $(*).f90
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) -I ../MPP -I../Utility_routines $(NETCDFMOD) $(MODFLAG) $(*).f90
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(FREESOURCE) -I ../MPP -I../Utility_routines $(MODFLAG) $(NETCDFMOD) $(*).F
 	@echo ""
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f90
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f90
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(*).f90
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(*).F
 	@echo ""
 
 #
@@ -60,4 +52,4 @@ $(OBJS_NoahMP):	module_hrldas_netcdf_io.o
 
 # This command cleans up object files, etc.
 clean:
-	$(RM) *.o *.mod *.stb *~ *.f90
+	$(RM) *.o *.mod *.stb *~
diff --git a/trunk/NDHMS/Land_models/NoahMP/Utility_routines/Makefile b/trunk/NDHMS/Land_models/NoahMP/Utility_routines/Makefile
index 561efa1b6..d1fb97232 100644
--- a/trunk/NDHMS/Land_models/NoahMP/Utility_routines/Makefile
+++ b/trunk/NDHMS/Land_models/NoahMP/Utility_routines/Makefile
@@ -18,9 +18,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f90
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f90
-	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) $(*).f90
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) $(*).F
 	@echo ""
 
 #
@@ -32,5 +30,5 @@ all:	$(OBJS)
 #
 
 clean:
-	$(RM) *.o *.mod *.stb *~ *.f90
+	$(RM) *.o *.mod *.stb *~
 
diff --git a/trunk/NDHMS/Land_models/NoahMP/phys/Makefile b/trunk/NDHMS/Land_models/NoahMP/phys/Makefile
index 5437fa1c3..3cdaf1097 100644
--- a/trunk/NDHMS/Land_models/NoahMP/phys/Makefile
+++ b/trunk/NDHMS/Land_models/NoahMP/phys/Makefile
@@ -17,9 +17,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(RM) $(*).f90
-	$(CPP) $(CPPFLAGS) $(CPPHRLDAS) $(*).F > $(*).f90
-	$(COMPILERF90) -o $(@) -c -I../Utility_routines $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) $(*).f90
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c -I../Utility_routines $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) $(*).F
 	@echo ""
 
 #
@@ -33,5 +31,5 @@ module_sf_noahmp_groundwater.o: module_sf_noahmplsm.o
 #
 
 clean:
-	$(RM) *.o *.mod *.stb *~ *.f90
+	$(RM) *.o *.mod *.stb *~
 
diff --git a/trunk/NDHMS/MPP/Makefile b/trunk/NDHMS/MPP/Makefile
index 06333f586..0db500b02 100644
--- a/trunk/NDHMS/MPP/Makefile
+++ b/trunk/NDHMS/MPP/Makefile
@@ -16,9 +16,8 @@ mpp_land.o: mpp_land.F
 
 CPL_WRF.o: CPL_WRF.F
 	@echo ""
-	$(RMD) $(*).o $(*).mod $(*).stb *~ *.f
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) $(*).f
+	$(RMD) $(*).o $(*).mod $(*).stb *~
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -I$(NETCDFINC) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) $(*).F
         
 	$(COMPILER90) $(F90FLAGS) $(LDFLAGS) -c $(*).F
 	ar -r ../lib/libHYDRO.a $(@)
diff --git a/trunk/NDHMS/Routing/Makefile b/trunk/NDHMS/Routing/Makefile
index bfe77e2f5..6d933c58c 100644
--- a/trunk/NDHMS/Routing/Makefile
+++ b/trunk/NDHMS/Routing/Makefile
@@ -34,10 +34,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo "Routing Makefile:"
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-#	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I$(NETCDFINC) $(*).f
-#	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I$(NETCDFINC) $(*).F
 	@echo ""
 	ar -r ../lib/libHYDRO.a $(@)
 	cp *.mod ../mod
@@ -111,4 +108,4 @@ module_channel_routing.o: module_UDMAP.o\
 endif
 
 clean:	
-	rm -f *.o *.mod *.stb *~ *.f
+	rm -f *.o *.mod *.stb *~
diff --git a/trunk/NDHMS/Routing/Overland/Makefile b/trunk/NDHMS/Routing/Overland/Makefile
index 8d8d905f2..519915515 100644
--- a/trunk/NDHMS/Routing/Overland/Makefile
+++ b/trunk/NDHMS/Routing/Overland/Makefile
@@ -18,11 +18,11 @@ all: mod
 
 mod:
 	#Build each sub module then build the module that depends on all sub modules	
-	$(COMPILER90) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland_control.F
-	$(COMPILER90) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland_streams_and_lakes.F
-	$(COMPILER90) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland_routing_properties.F
-	$(COMPILER90) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland_mass_balance.F
-	$(COMPILER90) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland.F
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland_control.F
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland_streams_and_lakes.F
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland_routing_properties.F
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland_mass_balance.F
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) $(F90FLAGS) $(LDFLAGS) $(MODFLAGS) -I$(NETCDFINC) module_overland.F
 	ar -r ../../lib/libHYDRO.a module_overland_control.o
 	ar -r ../../lib/libHYDRO.a module_overland_streams_and_lakes.o
 	ar -r ../../lib/libHYDRO.a module_overland_routing_properties.o
diff --git a/trunk/NDHMS/arc/macros.gordon b/trunk/NDHMS/arc/macros.gordon
index f65dd730c..5c5c1aa49 100644
--- a/trunk/NDHMS/arc/macros.gordon
+++ b/trunk/NDHMS/arc/macros.gordon
@@ -22,6 +22,11 @@ else
 HYDRO_D =  $(WRF_HYDRO)
 endif
 
+ifeq ($(WRFIO_NCD_LARGE_FILE_SUPPORT),1)
+WRFIO_NCD_LARGE_FILE_SUPPORT = -DWRFIO_NCD_LARGE_FILE_SUPPORT
+else
+WRFIO_NCD_LARGE_FILE_SUPPORT =
+endif
 
 
 RMD             = rm -f
@@ -31,8 +36,8 @@ BYTESWAPIO      = -convert big_endian
 F90FLAGS        = -w -c -ftz -align all -fno-alias -fp-model precise $(FORMAT_FREE) $(BYTESWAPIO)
 MODFLAG         = -I./ -I../../MPP -I../MPP -I../mod
 LDFLAGS         =
-CPP             = cpp
-CPPFLAGS        = -P -traditional -DMPP_LAND -I../Data_Rec $(HYDRO_D) 
+CPPINVOKE       = -fpp
+CPPFLAGS        = -DMPP_LAND -I../Data_Rec $(HYDRO_D) $(WRFIO_NCD_LARGE_FILE_SUPPORT)
 LIBS            =
 NETCDFINC       = $(NETCDF_INC)
 NETCDFLIB       = -L$(NETCDF_LIB) -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.gordon.debug b/trunk/NDHMS/arc/macros.gordon.debug
index e4cc00313..80940a957 100644
--- a/trunk/NDHMS/arc/macros.gordon.debug
+++ b/trunk/NDHMS/arc/macros.gordon.debug
@@ -32,8 +32,8 @@ F90FLAGS        = -w -c -ftz -align all -fno-alias -fp-model precise $(FORMAT_FR
 F90FLAGS        += -g -traceback
 MODFLAG         = -I./ -I../../MPP -I../MPP -I../mod
 LDFLAGS         =
-CPP             = cpp
-CPPFLAGS        = -C -P -traditional -DMPP_LAND -I../Data_Rec $(HYDRO_D) 
+CPPINVOKE       = -fpp
+CPPFLAGS        = -DMPP_LAND -I../Data_Rec $(HYDRO_D) $(WRFIO_NCD_LARGE_FILE_SUPPORT)
 LIBS            =
 NETCDFINC       = $(NETCDF_INC)
 NETCDFLIB       = -L$(NETCDF_LIB) -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.mpp.IBM.xlf90_r b/trunk/NDHMS/arc/macros.mpp.IBM.xlf90_r
index f6d4ebb0f..b07e965da 100644
--- a/trunk/NDHMS/arc/macros.mpp.IBM.xlf90_r
+++ b/trunk/NDHMS/arc/macros.mpp.IBM.xlf90_r
@@ -30,9 +30,9 @@ F90FLAGS  =     -O2 -qfree=f90 -c -w -qspill=20000 -qmaxmem=64000
 LDFLAGS  =     -O2 -qfree=f90  -w -qspill=20000 -qmaxmem=64000
 MODFLAG	=	-I./ -I ../MPP -I../../MPP -I ../mod
 LDFLAGS	=	
-CPP	=       cpp
+CPPINVOKE	=   -qpreprocess
 LIBS 	=	
-CPPFLAGS	=	-C -P -traditional -DMPP_LAND -I../Data_Rec $(HYDRO_D) 
+CPPFLAGS	=	-DMPP_LAND -I../Data_Rec $(HYDRO_D) $(WRFIO_NCD_LARGE_FILE_SUPPORT)
 NETCDFINC	=	$(NETCDF_INC) 
 NETCDFLIB	=	-L$(NETCDF_LIB) -lnetcdff -lnetcdf
 
diff --git a/trunk/NDHMS/arc/macros.mpp.gfort b/trunk/NDHMS/arc/macros.mpp.gfort
index 6f963f1c9..5802ef388 100644
--- a/trunk/NDHMS/arc/macros.mpp.gfort
+++ b/trunk/NDHMS/arc/macros.mpp.gfort
@@ -53,8 +53,8 @@ COMPILER90=	mpif90
 F90FLAGS  =       -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 
 MODFLAG	=	-I"./" -I"../../MPP" -I"../MPP" -I"../mod"
 LDFLAGS	=	
-CPP	=       cpp
-CPPFLAGS	=        -P -xassembler-with-cpp -traditional -DMPP_LAND -I"../Data_Rec" $(HYDRO_D) $(SPATIAL_SOIL)   $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN) $(PRECIP_DOUBLE)
+CPPINVOKE	=   -cpp
+CPPFLAGS	=   -DMPP_LAND -I"../Data_Rec" $(HYDRO_D) $(SPATIAL_SOIL)  $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN) $(PRECIP_DOUBLE)
 
 LIBS 	=	
 NETCDFINC       =       $(NETCDF_INC)
diff --git a/trunk/NDHMS/arc/macros.mpp.ifort b/trunk/NDHMS/arc/macros.mpp.ifort
index f2ec797e1..8a69a1358 100644
--- a/trunk/NDHMS/arc/macros.mpp.ifort
+++ b/trunk/NDHMS/arc/macros.mpp.ifort
@@ -53,15 +53,15 @@ else
 NCEP_WCOSS =
 endif
 
-RMD	    = rm -f
+RMD	        = rm -f
 COMPILER90  = mpif90
 FORMAT_FREE = -FR
 BYTESWAPIO  = -convert big_endian
 F90FLAGS    = -O2 -g -w -c -ftz -align all -fno-alias -fp-model precise $(FORMAT_FREE) $(BYTESWAPIO)
 MODFLAG	    = -I./ -I ../../MPP -I ../MPP -I ../mod
 LDFLAGS	    =
-CPP	    = cpp
-CPPFLAGS    = -P -traditional -nostdinc -DMPP_LAND -I ../Data_Rec $(HYDRO_D) $(SPATIAL_SOIL)  $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN) $(PRECIP_DOUBLE) $(NCEP_WCOSS)
+CPPINVOKE   = -fpp
+CPPFLAGS    = -DMPP_LAND -I ../Data_Rec $(HYDRO_D) $(SPATIAL_SOIL) $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN) $(PRECIP_DOUBLE) $(NCEP_WCOSS)
 LIBS 	    =	
 NETCDFINC   = $(NETCDF_INC)
 NETCDFLIB   = -L$(NETCDF_LIB) -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.mpp.ifort.luna b/trunk/NDHMS/arc/macros.mpp.ifort.luna
index bc37946cc..d4af6b5c3 100644
--- a/trunk/NDHMS/arc/macros.mpp.ifort.luna
+++ b/trunk/NDHMS/arc/macros.mpp.ifort.luna
@@ -90,8 +90,8 @@ BYTESWAPIO  = -convert big_endian
 F90FLAGS    = -w -c -ftz -align all -fno-alias -fp-model precise $(FORMAT_FREE) $(BYTESWAPIO)
 MODFLAG	    = -I./ -I ../../MPP -I ../MPP -I ../mod
 LDFLAGS	    = $(HDF5_LDFLAGS)
-CPP	    = cpp
-CPPFLAGS    = -P -traditional -DMPP_LAND -I ../Data_Rec $(HYDRO_D) $(SPATIAL_SOIL)  $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN) $(PRECIP_DOUBLE) $(NCEP_WCOSS)
+CPPINVOKE	= -fpp
+CPPFLAGS    = -DMPP_LAND -I ../Data_Rec $(HYDRO_D) $(SPATIAL_SOIL) $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN) $(PRECIP_DOUBLE) $(NCEP_WCOSS)
 LIBS 	    =$(Z_LIB)	
 NETCDFINC   = $(NETCDF_INC)
 NETCDFLIB   = -L$(NETCDF_LIB) -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.theia b/trunk/NDHMS/arc/macros.mpp.ifort.theia
similarity index 97%
rename from trunk/NDHMS/arc/macros.theia
rename to trunk/NDHMS/arc/macros.mpp.ifort.theia
index 164057abd..96d6a0d79 100644
--- a/trunk/NDHMS/arc/macros.theia
+++ b/trunk/NDHMS/arc/macros.mpp.ifort.theia
@@ -79,8 +79,8 @@ F90FLAGS        = -w -c -ftz -align all -fno-alias -fp-model precise $(FORMAT_FR
 #                        byte units)
 MODFLAG         = -I./ -I../../MPP -I../MPP -I../mod
 LDFLAGS         = 
-CPP             = cpp
-CPPFLAGS        = -P -traditional -DMPP_LAND -I../Data_Rec $(HYDRO_D) 
+CPPINVOKE       = -fpp
+CPPFLAGS        = -DMPP_LAND -I../Data_Rec $(HYDRO_D) $(WRFIO_NCD_LARGE_FILE_SUPPORT)
 # -C:                  Do not discard comments.
 # -P:                  Inhibit generation of linemarkers in the output 
 #                       from the preprocessor.
diff --git a/trunk/NDHMS/arc/macros.mpp.linux b/trunk/NDHMS/arc/macros.mpp.linux
index 5bce0844c..238356501 100644
--- a/trunk/NDHMS/arc/macros.mpp.linux
+++ b/trunk/NDHMS/arc/macros.mpp.linux
@@ -55,8 +55,8 @@ F90FLAGS  =     -Mfree -c -byteswapio -O2 -Kieee
 LDFLAGS  =      $(F90FLAGS)
 MODFLAG	=	-I./ -I ../../MPP -I ../MPP -I ../mod 
 LDFLAGS	=	
-CPP	=       cpp
-CPPFLAGS	=       -P -traditional -DMPP_LAND -I../Data_Rec $(HYDRO_D) $(SPATIAL_SOIL)  $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN) $(PRECIP_DOUBLE)
+CPPINVOKE	= -Mpreprocess
+CPPFLAGS	=  -DMPP_LAND -I../Data_Rec $(HYDRO_D) $(SPATIAL_SOIL) $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN) $(PRECIP_DOUBLE)
 LIBS 	=	
 NETCDFINC	=	$(NETCDF_INC) 
 NETCDFLIB	=	-L$(NETCDF_LIB) -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.mpp.mpiifort b/trunk/NDHMS/arc/macros.mpp.mpiifort
index e1793aa67..54cb14175 100644
--- a/trunk/NDHMS/arc/macros.mpp.mpiifort
+++ b/trunk/NDHMS/arc/macros.mpp.mpiifort
@@ -43,8 +43,8 @@ F90FLAGS	= -O2 -g -w -c -ftz -fno-alias -fp-model precise -FR
 # -ftz	: enable flush denormal results to zero
 MODFLAG		= -I./ -I../../MPP -I../MPP -I../mod
 LDFLAGS		= 
-CPP		= cpp
-CPPFLAGS	= -P -traditional -DMPP_LAND -I ../Data_Rec $(HYDRO_D) 
+CPPINVOKE	= -fpp
+CPPFLAGS	= -DMPP_LAND -I ../Data_Rec $(HYDRO_D) $(WRFIO_NCD_LARGE_FILE_SUPPORT)
 LIBS		=	
 NETCDFINC       = $(NETCDF)/include
 NETCDFLIB       = -L$(NETCDF)/lib -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.seq.gfort b/trunk/NDHMS/arc/macros.seq.gfort
index bafd3e7b6..952592ebd 100644
--- a/trunk/NDHMS/arc/macros.seq.gfort
+++ b/trunk/NDHMS/arc/macros.seq.gfort
@@ -35,8 +35,8 @@ COMPILER90=	gfortran
 F90FLAGS  =       -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 
 MODFLAG	=	-I./ -I../mod
 LDFLAGS	=	
-CPP	=       cpp
-CPPFLAGS	=       -C -P -xassembler-with-cpp -traditional -I"../Data_Rec" $(HYDRO_D) $(SPATIAL_SOIL) 
+CPPINVOKE 	=       -cpp
+CPPFLAGS	=       -I"../Data_Rec" $(HYDRO_D) $(SPATIAL_SOIL) $(WRFIO_NCD_LARGE_FILE_SUPPORT)
 LIBS 	=	
 NETCDFINC       =       $(NETCDF_INC)
 NETCDFLIB       =       -L$(NETCDF_LIB) -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.seq.ifort b/trunk/NDHMS/arc/macros.seq.ifort
index 7cd98111b..61ca7836f 100644
--- a/trunk/NDHMS/arc/macros.seq.ifort
+++ b/trunk/NDHMS/arc/macros.seq.ifort
@@ -48,8 +48,8 @@ F90FLAGS  =       -w -c -ftz -align all -fno-alias -fp-model precise -FR -conver
 
 MODFLAG	=	-I./  -I ../mod
 LDFLAGS	=	
-CPP	=       cpp
-CPPFLAGS	=       -C -P -traditional -I ../Data_Rec $(HYDRO_D) $(SPATIAL_SOIL)  $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN)
+CPPINVOKE	=       -fpp
+CPPFLAGS	=       -I ../Data_Rec $(HYDRO_D) $(SPATIAL_SOIL) $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN)
 LIBS 	=	
 NETCDFINC       =       $(NETCDF_INC)
 NETCDFLIB       =       -L$(NETCDF_LIB) -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.seq.linux b/trunk/NDHMS/arc/macros.seq.linux
index 245c8d1ce..7f7ce1524 100644
--- a/trunk/NDHMS/arc/macros.seq.linux
+++ b/trunk/NDHMS/arc/macros.seq.linux
@@ -48,9 +48,8 @@ COMPILER90=	pgf90
 F90FLAGS  =     -Mfree -Mfptrap -c -byteswapio -Ktrap=fp -O2 -Kieee
 LDFLAGS  =      $(F90FLAGS)
 MODFLAG	=	-I./ -I ../mod
-LDFLAGS	=	
-CPP	=       cpp
-CPPFLAGS	=       -C -P -traditional -I ../Data_Rec $(HYDRO_D) $(WRF_HYDRO) $(SPATIAL_SOIL)  $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN)
+CPPINVOKE	= -Mpreprocess
+CPPFLAGS	=       -I ../Data_Rec $(HYDRO_D) $(WRF_HYDRO) $(SPATIAL_SOIL) $(WRF_HYDRO_NUDGING) $(OUTPUT_CHAN_CONN)
 LIBS 	=	
 NETCDFINC       =       $(NETCDF_INC)
 NETCDFLIB       =       -L$(NETCDF_LIB) -lnetcdff -lnetcdf
diff --git a/trunk/NDHMS/arc/macros.theia.debug b/trunk/NDHMS/arc/macros.theia.debug
index 6fecbffa6..adba9b1cc 100644
--- a/trunk/NDHMS/arc/macros.theia.debug
+++ b/trunk/NDHMS/arc/macros.theia.debug
@@ -80,8 +80,8 @@ F90FLAGS        += -g -traceback
 #                        byte units)
 MODFLAG         = -I./ -I../../MPP -I../MPP -I../mod
 LDFLAGS         = 
-CPP             = cpp
-CPPFLAGS        = -P -traditional -DMPP_LAND -I../Data_Rec $(HYDRO_D) 
+CPPINVOKE       = -fpp
+CPPFLAGS        = -DMPP_LAND -I../Data_Rec $(HYDRO_D) $(WRFIO_NCD_LARGE_FILE_SUPPORT)
 # -C:                  Do not discard comments.
 # -P:                  Inhibit generation of linemarkers in the output 
 #                       from the preprocessor.
diff --git a/trunk/NDHMS/nudging/Makefile b/trunk/NDHMS/nudging/Makefile
index e07f482fc..385001418 100644
--- a/trunk/NDHMS/nudging/Makefile
+++ b/trunk/NDHMS/nudging/Makefile
@@ -24,10 +24,7 @@ all:	$(OBJS)
 
 .F.o:
 	@echo ""
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).f
-#	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) $(*).f
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(MODFLAG) -I$(NETCDF_INC) $(*).f
-#	$(RMD) $(*).f
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -o $(@) $(F90FLAGS) $(MODFLAG) -I$(NETCDF_INC) $(*).F
 	@echo ""
 	ar -r ../lib/libHYDRO.a $(@)
 	cp *.mod ../mod
@@ -43,4 +40,4 @@ module_stream_nudging.o: module_nudging_utils.o \
 
 
 clean:
-	rm -f *.o *.mod *.stb *~ *.f
+	rm -f *.o *.mod *.stb *~
diff --git a/trunk/NDHMS/utils/Makefile b/trunk/NDHMS/utils/Makefile
index d30528642..313dd1bb0 100644
--- a/trunk/NDHMS/utils/Makefile
+++ b/trunk/NDHMS/utils/Makefile
@@ -20,8 +20,7 @@ all:	$(OBJS)
 ## The insertion of compile-time constants strangely requires the capital F in the extension.
 .F.o:
 	@echo "Utils Makefile:"
-	$(CPP) $(CPPFLAGS) -I$(NETCDFINC) $(*).F > $(*).F90
-	$(COMPILER90) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I$(NETCDFINC) $(*).F90
+	$(COMPILER90) $(CPPINVOKE) $(CPPFLAGS) -o $(@) $(F90FLAGS) $(LDFLAGS) $(MODFLAG) -I$(NETCDFINC) $(*).F
 	@echo ""
 	ar -r ../lib/libHYDRO.a $(@)
 	cp *.mod ../mod
@@ -31,4 +30,4 @@ all:	$(OBJS)
 #
 
 clean:	
-	rm -f *.o *.mod *.stb *~ *.F90
+	rm -f *.o *.mod *.stb *~