--- MITgcm/tools/genmake2	2014/08/10 16:46:04	1.268
+++ MITgcm/tools/genmake2	2016/01/15 22:08:17	1.278
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.268 2014/08/10 16:46:04 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.278 2016/01/15 22:08:17 jmc Exp $
 # $Name:  $
 #
 # Makefile generator for MITgcm UV codes
@@ -22,14 +22,17 @@
     -oad | --oad
 	  Generate a Makefile for an OpenAD built
 
+    -nocat4ad | -dog4ad | -ncad | -dad
+	  do not concatenate (cat) source code sent to TAF
+	  resulting in compilation of multiple files
+
     -adoptfile NAME | --adoptfile NAME | -adof NAME | --adof NAME
       -adoptfile=NAME | --adoptfile=NAME | -adof=NAME | --adof=NAME
 	  Use "NAME" as the adoptfile.  By default, the file at
 	  "tools/adjoint_options/adjoint_oad" (for OpenAD built) or
 	  "tools/adjoint_options/adjoint_default" will be used.
 
-    -nooptfile | --nooptfile
-      -optfile NAME | --optfile NAME | -of NAME | --of NAME
+    -optfile NAME | --optfile NAME | -of NAME | --of NAME
       -optfile=NAME | --optfile=NAME | -of=NAME | --of=NAME
 	  Use "NAME" as the optfile.  By default, an attempt will be
 	  made to find an appropriate "standard" optfile in the
@@ -1329,6 +1332,7 @@
 AUTODIFF_PKG_USED=f
 OPENAD=
 AD_OPTFILE=
+CAT_SRC_FOR_TAF=1
 TAF=
 AD_TAF_FLAGS=
 FTL_TAF_FLAGS=
@@ -1403,8 +1407,6 @@
 	-help | --help | -h | --h)
 	    usage ;;
 
-	-nooptfile | --nooptfile)
-	    OPTFILE="NONE" ;;
 	-optfile | --optfile | -of | --of)
 	    ac_prev=OPTFILE ;;
 	-optfile=* | --optfile=* | -of=* | --of=*)
@@ -1412,6 +1414,8 @@
 
 	-oad | --oad)
 	    OPENAD="true" ; ALWAYS_USE_F90=1 ;;
+	-nocat4ad | -dog4ad | -ncad | -dad)
+	    CAT_SRC_FOR_TAF=0 ;;
 	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
@@ -1583,7 +1587,7 @@
 
 #TMP=./genmk_$$
 #- try to put temporary files in system-local /tmp dir
-TMP=/tmp/genmk_$$
+TMP=/tmp/genmk_${USER}_$$
 touch $TMP ; retVal=$?
 if [ $retVal -eq 0 ] ; then
   if test ! -r $TMP ; then TMP=./genmk_$$ ; fi
@@ -1957,26 +1961,56 @@
 fi
 rm -f genmake_tcomp*
 
-printf "  Do we have the etime() command using $FC...  "
-cat > genmake_tcomp.$FS <<EOF
+printf "  Do we have the etime() command using $FC... "
+cat > genmake_tcomp_1.$FS <<EOF
       program hello
-      REAL*4 ACTUAL, TARRAY(2)
+      REAL*4 actual, tarray(2)
       EXTERNAL ETIME
       REAL*4 ETIME
-      actual = etime( tarray )
+      actual = ETIME( tarray )
       print *, tarray
       end
 EOF
-$FC $FFLAGS -o genmake_tcomp genmake_tcomp.$FS > genmake_tcomp.log 2>&1
+$FC $FFLAGS -o genmake_tcomp_1 genmake_tcomp_1.$FS > genmake_tcomp.log 2>&1
 RETVAL=$?
 if test "x$RETVAL" = x0 ; then
-    HAVE_ETIME=t
-    DEFINES="$DEFINES -DHAVE_ETIME"
-    echo "yes"
+    HAVE_ETIME='Fct'
+    DEFINES="$DEFINES -DHAVE_ETIME_FCT"
+    echo " yes (${HAVE_ETIME})"
 else
+  cat > genmake_tcomp_2.$FS <<EOF
+      program hello
+      REAL*4 actual, tarray(2)
+      actual = -999.
+      call ETIME( tarray, actual )
+      if ( actual.ge.0. ) then
+        print *, 0, tarray, actual
+      else
+        print *, 1, tarray, actual
+      endif
+      end
+EOF
+  $FC $FFLAGS -o genmake_tcomp_2 genmake_tcomp_2.$FS >> genmake_tcomp.log 2>&1
+  RETVAL=$?
+  if test "x$RETVAL" = x0 ; then
+    echo -n 'c,'
+    ./genmake_tcomp_2 > genmake_tcomp_2.out 2>&1
+    RETVAL=$?
+  fi
+  if test "x$RETVAL" = x0 ; then
+    echo -n 'r:'
+    RETVAL=`cat genmake_tcomp_2.out | $AWK '{print $1}'`
+  fi
+  if test "x$RETVAL" = x0 ; then
+    HAVE_ETIME='SbR'
+    DEFINES="$DEFINES -DHAVE_ETIME_SBR"
+    echo " yes (${HAVE_ETIME})"
+  else
     HAVE_ETIME=
-    echo "no"
+    echo " no"
+  fi
 fi
+#mkdir chk_etime ; cp -p -f genmake_tcomp* chk_etime
 rm -f genmake_tcomp*
 
 printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
@@ -2894,8 +2928,8 @@
 KFLAGS1 = ${KFLAGS1}
 KFLAGS2 = ${KFLAGS2}
 # Optim./debug for FC
-FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
-FOPTIM = ${FOPTIM}
+FFLAGS = ${FFLAGS}
+FOPTIM = ${FOPTIM} ${FEXTRAFLAGS}
 # Optim./debug for FC
 F90FLAGS = ${F90FLAGS}
 F90OPTIM = ${F90OPTIM}
@@ -3122,6 +3156,24 @@
 echo >> $MAKEFILE
 rm -f $TMP.adSrcFiles
 
+if test $CAT_SRC_FOR_TAF = 0 ; then
+cat >>$MAKEFILE <<EOF
+
+# ... Utilities ...
+remove_comments:
+	sed -i.bak -f \$(TOOLSDIR)/remove_comments_sed \$(AD_FILES)
+	@-rm -f \$(AD_FILES:.$FS=.$FS.bak)
+adj_sed:
+	sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_ad.$FS)
+	@-rm -f \$(AD_FILES:.$FS=_ad.$FS.bak)
+ftl_sed:
+	sed -i.bak -f \$(TOOLSDIR)/adjoint_sed \$(AD_FILES:.$FS=_tl.$FS)
+	@-rm -f \$(AD_FILES:.$FS=_tl.$FS.bak)
+adobjfiles: \$(AD_FILES:.$FS=_ad.o)
+ftlobjfiles: \$(AD_FILES:.$FS=_tl.o)
+EOF
+fi
+
 cat >>$MAKEFILE <<EOF
 
 # ... AD ...
@@ -3144,13 +3196,18 @@
 	@\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
 	cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
 
-ad_taf_output.$FS: ad_input_code.$FS
-	@-rm -f ad_input_code_ad.$FS ; echo ''
+adtafonly:
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
 	ls -l ad_input_code_ad.$FS
 	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
-adtafonly:
+EOF
+
+if test $CAT_SRC_FOR_TAF = 1 ; then
+cat >>$MAKEFILE <<EOF
+# ... send 1 file to TAF ...
+ad_taf_output.$FS: ad_input_code.$FS
+	@-rm -f ad_input_code_ad.$FS ; echo ''
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
 	ls -l ad_input_code_ad.$FS
 	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
@@ -3158,20 +3215,48 @@
 \$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
 	\$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
 
-ad_tamc_output.$FS: ad_input_code.$FS
-	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
-	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
+adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
 
-ad_tamc: ad_tamc_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
+EOF
+
+else
+cat >>$MAKEFILE <<EOF
+# ... send multiple files to TAF ...
+ad_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
+	@$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
+	@\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+	@\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
+	@-rm -f \$(AD_FILES:.$FS=_ad.$FS) \$(AD_FILES:.$FS=_ad.o); echo ''
+	\$(MAKE) -f \$(MAKEFILE) remove_comments
+	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) \$(FLOWFILES) \$(AD_FILES)
+	\$(MAKE) -f \$(MAKEFILE) adj_sed
+	cat \$(AD_FILES:.$FS=_ad.$FS) > ad_taf_output.$FS
+
+\$(EXE_AD): \$(SPECIAL_FILES) \$(H_SRC_FILES) ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
+	\$(MAKE) -f \$(MAKEFILE) adobjfiles
+	\$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_ad.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
+
+adobj: ad_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
+	\$(MAKE) -f \$(MAKEFILE) adobjfiles
 
+EOF
+fi
+
+cat >>$MAKEFILE <<EOF
 adonlyfwd:
 	patch < \$(TOOLSDIR)/ad_taf_output.f.onlyfwd.diff
 
 adtrick:
 	patch < \$(TOOLSDIR)/ad_taf_output.f.adtrick.diff
 
-adobj: ad_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o)
+ad_tamc_output.$FS: ad_input_code.$FS
+	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
+	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_tamc_output.$FS
+
+ad_tamc: ad_tamc_output.o \$(OBJFILES)
+	\$(LINK) -o ${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_tamc_output.o \$(LIBS)
 
 # ... FTL ...
 ftlall: ftl_exe_target
@@ -3193,13 +3278,18 @@
 	@\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
 	cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
 
-ftl_taf_output.$FS: ftl_input_code.$FS
-	@-rm -f ftl_input_code_tl.$FS ; echo ''
+ftltafonly:
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
 	ls -l ftl_input_code_tl.$FS
 	cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
-ftltafonly:
+EOF
+
+if test $CAT_SRC_FOR_TAF = 1 ; then
+cat >>$MAKEFILE <<EOF
+# ... send 1 file to TAF ...
+ftl_taf_output.$FS: ftl_input_code.$FS
+	@-rm -f ftl_input_code_tl.$FS ; echo ''
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
 	ls -l ftl_input_code_tl.$FS
 	cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
@@ -3207,6 +3297,31 @@
 \$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
 	\$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) ftl_taf_output.o \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
 
+EOF
+
+else
+cat >>$MAKEFILE <<EOF
+# ... send multiple files to TAF ...
+ftl_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_FILES)
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
+	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
+	@-rm -f ad_config.template
+	@\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
+	@\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
+	@-rm -f \$(AD_FILES:.$FS=_tl.$FS) \$(AD_FILES:.$FS=_tl.o); echo ''
+	\$(MAKE) -f \$(MAKEFILE) remove_comments
+	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) \$(AD_FLOW_FILES) \$(AD_FILES)
+	\$(MAKE) -f \$(MAKEFILE) ftl_sed
+	cat \$(AD_FILES:.$FS=_tl.$FS) > ftl_taf_output.$FS
+
+\$(EXE_FTL): \$(SPECIAL_FILES) \$(H_SRC_FILES) ftl_taf_output.$FS \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(EMBEDDED_FILES)
+	\$(MAKE) -f \$(MAKEFILE) ftlobjfiles
+	\$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(AD_FILES:.$FS=_tl.o) \$(NON_AD_F77_SRC_FILES:.F=.o) \$(F90_SRC_FILES:.F90=.o) \$(C_SRC_FILES:.c=.o) \$(LIBS)
+
+EOF
+fi
+
+cat >>$MAKEFILE <<EOF
 ftl_tamc_output.$FS: ftl_input_code.$FS
 	\$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
 	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_tamc_output.$FS
@@ -3329,6 +3444,7 @@
 OAD_cp.F90 \
 OAD_rev.F90 \
 OAD_tape.F90 \
+OAD_regular_cp.F90 \
 revolve.F90
 
 OPENAD_SUPPORT_C_SRC_FILES = \