--- MITgcm/tools/genmake2	2012/08/28 21:11:22	1.238
+++ MITgcm/tools/genmake2	2012/09/19 20:46:03	1.241
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.238 2012/08/28 21:11:22 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.241 2012/09/19 20:46:03 utke Exp $
 # $Name:  $
 #
 # Makefile generator for MITgcm UV codes
@@ -174,28 +174,18 @@
 test_for_package_in_cpp_options() {
     cpp_options=$1
     pkg=$2
-    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"
-    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"
-    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg$"
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg$"
-    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg$"
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg$"
+    test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_$pkg\>"
+    test_for_string_in_file $cpp_options "^ *# *undef *\<ALLOW_$pkg\>"
+    test_for_string_in_file $cpp_options "^ *# *define *\<DISABLE_$pkg\>"
+    test_for_string_in_file $cpp_options "^ *# *undef *\<DISABLE_$pkg\>"
 }
 
 # Search for particular CPP #cmds associated with MPI
 # usage: test_for_mpi_in_cpp_eeoptions CPP_file
 test_for_mpi_in_cpp_eeoptions() {
     cpp_options=$1
-    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI[ ]"
-    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI[ ]"
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI[ ]"
-    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI$"
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI$"
-    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI$"
-    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"
+    test_for_string_in_file $cpp_options "^ *# *define *\<ALLOW_USE_MPI\>"
+    test_for_string_in_file $cpp_options "^ *# *undef *\<ALLOW_USE_MPI\>"
 }
 
 # Search for particular string in a file. Return 1 if detected, 0 if not
@@ -203,7 +193,7 @@
 test_for_string_in_file() {
     file=$1
     strng=$2
-    grep -i "$strng" $file > /dev/null 2>&1
+    grep "$strng" $file > /dev/null 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
 	printf "Error: In $file there is an illegal line: "
@@ -1668,7 +1658,7 @@
 
 if test ! "x$MPI" = x ; then
       echo "  Turning on MPI cpp macros"
-      DEFINES="$DEFINES -DALLOW_USE_MPI -DALWAYS_USE_MPI"
+      DEFINES="$DEFINES -DALLOW_USE_MPI"
 fi
 if test ! "x$OMP" = x ; then
       echo "  Add OMPFLAG and turn on OpenMP cpp macros"
@@ -2722,8 +2712,6 @@
 cat >>$MAKEFILE <<EOF
 # Unix ln (link)
 LN = ${LN}
-# C preprocessor
-CPP = cat \$< | ${S64} | ${CPP}
 # Dependency generator
 MAKEDEPEND = ${MAKEDEPEND}
 # Special preprocessor (KAP on DECs, FPP on Crays)
@@ -2906,16 +2894,19 @@
 ## This nullifies any default implicit rules concerning these two file types:
 ## %.o : %.F
 
+# C preprocessing and replacing the _d in constants: 
+CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
+
 .F.$FS:
-	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+	\$(CPPCMD)  > \$@
 .$FS.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
 .F.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
 .F90.$FS90:
-	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+	\$(CPPCMD)  > \$@
 .FF90.f$FS90:
-	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+	\$(CPPCMD)  > \$@
 .$FS90.o:
 	\$(F90C) \$(F90FLAGS) \$(F90OPTIM) -c \$<
 .f$FS90.o:
@@ -2924,11 +2915,11 @@
 .c.o:
 	\$(CC) \$(CFLAGS) \$(DEFINES) \$(INCLUDES) -c \$<
 .flow.flowdir:
-	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+	\$(CPPCMD) > \$@
 
 # Special exceptions that use the ( .F - .p - .$FS - .o ) rule-chain
 .F.p:
-	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
+	\$(CPPCMD) > \$@
 .p.$FS:
 	\$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
 
@@ -2986,7 +2977,7 @@
 	@-rm -f ad_config.template
 	\$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
 
-ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
+ad_input_code.$FS: \$(AD_FILES) \$(AD_FLOW_FILES)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	@-rm -f ad_config.template
@@ -3004,7 +2995,7 @@
 	ls -l ad_input_code_ad.$FS
 	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
-\${EXE_AD}: ad_taf_output.o \$(OBJFILES)
+\$(EXE_AD): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ad_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)
 	\$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_taf_output.o \$(LIBS)
 
 ad_tamc_output.$FS: ad_input_code.$FS
@@ -3034,7 +3025,7 @@
 	@-rm -f ad_config.template
 	\$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
 
-ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
+ftl_input_code.$FS: \$(AD_FILES)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	@-rm -f ad_config.template
@@ -3052,7 +3043,7 @@
 	ls -l ftl_input_code_ftl.$FS
 	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
-\${EXE_FTL}: ftl_taf_output.o \$(OBJFILES)
+\$(EXE_FTL): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES) \$(H_SRC_FILES) \$(F90_SRC_FILES) ftl_taf_output.o \$(OBJFILES) \$(EMBEDDED_FILES)
 	\$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)
 
 ftl_tamc_output.$FS: ftl_input_code.$FS