--- MITgcm/tools/genmake2	2012/08/28 21:11:22	1.238
+++ MITgcm/tools/genmake2	2012/09/20 23:12:47	1.242
@@ -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 1.242 2012/09/20 23:12:47 heimbach 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"
@@ -2492,6 +2482,11 @@
     OAD_DONT_TRANSFORM="/dev/null"
     OAD_KEEP_ORIGINAL="/dev/null"
     OAD_CB2M_FILES="/dev/null"
+    OADTOOLS="$TOOLSDIR/OAD_support"
+    test -f "oadtempflile"  &&  \rm -f "oadtempflile"
+cat >> "oadtempflile" <<EOF
+$OADTOOLS
+EOF
     echo "  looking for dontCompile file:  "
     for i in "." $MODS ; do
 	if test -r $i"/dontCompile" ; then
@@ -2699,6 +2694,7 @@
 EXEDIR      = ${EXEDIR}
 EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
 TOOLSDIR    = ${TOOLSDIR}
+OADTOOLS    = ${OADTOOLS}
 
 #eh3  new defines for the adjoint work
 AUTODIFF    = ${ROOTDIR}/pkg/autodiff
@@ -2722,8 +2718,6 @@
 cat >>$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 +2900,19 @@
 ## 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 +2921,11 @@
 .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 +2983,7 @@
 	@-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)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	@-rm -f ad_config.template
@@ -3004,7 +3001,7 @@
 	ls -l ad_input_code_ad.$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 +3031,7 @@
 	@-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)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	@-rm -f ad_config.template
@@ -3052,7 +3049,7 @@
 	ls -l ftl_input_code_ftl.$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
@@ -3194,16 +3191,16 @@
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(AD_OBJ_FILES_S2) \$(LIBS)
 
 # create sources files modules from header files containing common blocks
-%_mod.FF90 : %.h ../OAD_support/cb2mGetModules.csh ../OAD_support/cb2mGetModules.awk
-	../OAD_support/cb2mGetModules.csh $< ../OAD_support/cb2mGetModules.awk
+%_mod.FF90 : %.h \${OADTOOLS}/cb2mGetModules.csh \${OADTOOLS}/cb2mGetModules.awk
+	\${OADTOOLS}/cb2mGetModules.csh $< \${OADTOOLS}/cb2mGetModules.awk
 
 # create new header files with USE statements for the new modules made above
-%_mod.h : %.h ../OAD_support/cb2mGetHeaders.csh ../OAD_support/cb2mGetHeaders.awk
-	../OAD_support/cb2mGetHeaders.csh $< ../OAD_support/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
+%_mod.h : %.h \${OADTOOLS}/cb2mGetHeaders.csh \${OADTOOLS}/cb2mGetHeaders.awk
+	\${OADTOOLS}/cb2mGetHeaders.csh $< \${OADTOOLS}/cb2mGetHeaders.awk \$(CB2M_F90_SRC_NAMES)
 
 # change the include directives of everybody to refer to  the new header files with the USE statements
-%_cb2m.FF90 : %.F ../OAD_support/cb2mUseModules.bash
-	../OAD_support/cb2mUseModules.bash $< ${MPI}
+%_cb2m.FF90 : %.F \${OADTOOLS}/cb2mUseModules.bash
+	\${OADTOOLS}/cb2mUseModules.bash $< ${MPI}
 
 # makefile debug rule
 small_f: \$(CB2M_F90_PP_SRC_FILES)
@@ -3225,7 +3222,7 @@
 
 # replace stop statements (to avoid the implied unstructured control flow)  with print statements
 ad_input_code_sf.pre.s2p.f90 : ad_input_code_sf.pre.f90
-	cat \$< | sed -f ../OAD_support/stop2print.sed > ad_input_code_sf.pre.s2p.f90
+	cat \$< | sed -f \${OADTOOLS}/stop2print.sed > ad_input_code_sf.pre.s2p.f90
 
 # F -> WHIRL
 ad_input_code_sf.pre.s2p.B: ad_input_code_sf.pre.s2p.f90
@@ -3248,13 +3245,13 @@
 	\${OPEN64ROOT}/whirl2f/whirl2f -FLIST:ftn_file=\$@ -openad \$<
 
 # insert template directives
-ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 ../OAD_support/insertTemplateDir.bash
-	../OAD_support/insertTemplateDir.bash \$< \$@
+ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90: ad_input_code_sf.pre.s2p.xb.x2w.w2f.f$FS90 \${OADTOOLS}/insertTemplateDir.bash
+	\${OADTOOLS}/insertTemplateDir.bash \$< \$@
 
-PPEXTRAS=\$(wildcard ../OAD_support/ad_template.*.F) ../OAD_support/ad_inline.F
+PPEXTRAS=\$(wildcard \${OADTOOLS}/ad_template.*.F) \${OADTOOLS}/ad_inline.F
 # postprocess F'
 postProcess.tag: ad_input_code_sf.pre.s2p.xb.x2w.w2f.td.f$FS90 \$(PPEXTRAS:.F=.f) | w2f__types.f90
-	\${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i ../OAD_support/ad_inline.f \$<
+	\${OPENADFORTTK_BASE}/tools/SourceProcessing/postProcess.py --progress --timing --infoUnitFile w2f__types.f90 --outputFormat=fixed --separateOutput --pathSuffix "" --filenameSuffix "_oad" -m r -i \${OADTOOLS}/ad_inline.f \$<
 	# the target is a placeholder to trigger a single execution of the rule
 	touch \$@
 # put this so make knows about the postprocessing output
@@ -3266,9 +3263,9 @@
 
 # link the support files:
 \$(OPENAD_SUPPORT_F90_SRC_FILES) \$(OPENAD_SUPPORT_C_SRC_FILES):
-	\$(LN) ../OAD_support/\$@ .
+	\$(LN) \${OADTOOLS}/\$@ .
 
-AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.tag \$(PPEXTRAS:.F=.f)
+AD_CLEAN += *_mod.h *_mod.F90 *.FF90 *.mod-whirl temp.sed oad_cp.* postProcess.tag oadtempflile \$(PPEXTRAS:.F=.f)
 
 # ============ end OpenAD specific section ==============