--- MITgcm/tools/genmake2	2013/02/23 04:24:42	1.249
+++ MITgcm/tools/genmake2	2013/08/07 16:20:03	1.254
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.249 2013/02/23 04:24:42 utke Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.254 2013/08/07 16:20:03 heimbach Exp $
 # $Name:  $
 #
 # Makefile generator for MITgcm UV codes
@@ -324,15 +324,14 @@
     #
     #    1) a makedepend implementation shipped with the cyrus-imapd
     #       package:  ftp://ftp.andrew.cmu.edu/pub/cyrus-mail/
-    #
-    #    2) a known-buggy xmakedpend shell script
+    #    2) a local tools/xmakedepend shell script
     #
     #  So the choices are, in order:
-    #
     #    1) use the user-specified program
-    #    2) use a system-wide default
-    #    3) locally build and use the cyrus implementation
-    #    4) fall back to the buggy local xmakedpend script
+    #    2) use the local xmakedepend script (get all dependencies, but slower)
+    #    3) use a system-wide default
+    #    4) locally build and use the cyrus makedepend
+    #             (faster, but can miss some dependencies)
     #
     echo >> $LOGFILE
     echo "running: look_for_makedepend()" >> $LOGFILE
@@ -343,7 +342,7 @@
 	    build_cyrus_makedepend
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
-		echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"
+		echo "WARNING: unable to build cyrus-makedepend. Try other 'makedepend'"
 		MAKEDEPEND=
 	    fi
 	else
@@ -356,8 +355,6 @@
 	fi
     fi
     if test "x${MAKEDEPEND}" = x ; then
-	which makedepend > /dev/null 2>&1
-	RV0=$?
 	test -f $MAKEFILE  &&  mv -f $MAKEFILE $MAKEFILE".tst"
 	#  echo 'MAKEFILE="'$MAKEFILE'"'
 	cat <<EOF >> $MAKEFILE
@@ -373,22 +370,39 @@
       stop
       end
 EOF
-	makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
+	$ROOTDIR/tools/xmakedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
 	RV1=$?
+	which makedepend > /dev/null 2>&1
+	RV2=$?
+	if test "x${RV2}" = x0 ; then
+	    makedepend -f $MAKEFILE genmake_tc.f > /dev/null 2>&1
+	    RV3=$? ; loc_msg='not working.'
+	else RV3=$RV2 ; loc_msg='not found.'
+	fi
 	test -f $MAKEFILE  &&  rm -f $MAKEFILE
 	test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
-	if test "x${RV0}${RV1}" = x00 ; then
+	echo "  check makedepend (local: $RV1, system: $RV2, $RV3)"
+	if test "x${RV1}" = x0 ; then
+	    MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+	    echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
+	elif test "x${RV3}" = x0 ; then
+	    echo "    local tools/xmakedepend not working. Use system-default makedepend"
 	    MAKEDEPEND=makedepend
 	    echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
 	else
-	    echo "    system-default makedepend not found. Try to build cyrus-makedepend"
+	    echo "    local tools/xmakedepend not working; system-default makedepend $loc_msg"
+	    echo -n "    Try to build cyrus-makedepend ..."
 	    #  Try to build the cyrus implementation
 	    build_cyrus_makedepend
 	    RETVAL=$?
-	    if test "x$RETVAL" != x0 ; then
-		echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"
-		MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
-		echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
+	    if test "x$RETVAL" = x0 ; then
+		echo "  Works"
+	    else
+		echo "  Fails" ; echo "" >> $LOGFILE
+		echo "ERROR: no working makedepend found ; look_for_makedepend FAILED" | tee -a $LOGFILE
+		echo ""
+		exit -1
+		return
 	    fi
 	fi
     fi
@@ -588,6 +602,81 @@
     fi
 }
 
+#  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
+#  checking for additional included headers (in case of chain of included header)
+mpi_headers_do_local_copy() {
+
+    dBug=0
+    rm -rf ./mpi_headers
+    if test -d $MPIINCLUDEDIR ; then
+
+	#----- check for additional headers (chain of included headers)
+	echo -n '  Check MPI headers ... '
+	listIni=$MPI_HEADER_FILES
+	echo $listIni | grep "\<mpif.h\>" > /dev/null 2>&1
+	outp=$?
+	#- always check mpif.h (the only mpi-header included in standard MITgcm code)
+	if test $outp != 0 ; then listIni="mpif.h $listIni" ; fi
+	if test $dBug = 1 ; then echo "listIni='$listIni'" ; fi
+
+	doCheck=1 ; list2copy='' ; list2check=$listIni
+	while test $doCheck = 1 ; do
+	  newList=''
+	  for i in $list2check ; do
+	    if test -f $MPIINCLUDEDIR/$i ; then
+	      newInc=`grep '^ *include ' $MPIINCLUDEDIR/$i | \
+		sed -e 's/^ *include //' -e 's/\!.*$//' -e "s/'//g"  -e 's/\"//g'`
+	      if test $dBug = 1 ; then echo -n "checking $i : newInc='$newInc'" ; fi
+	      for j in $newInc ; do
+		echo $listIni $list2copy $newList | grep "\<$j\>" > /dev/null 2>&1
+		outp=$?
+	        if test $outp != 0 ; then
+		  if test $dBug = 1 ; then echo -n " ; adding $j" ; fi
+		  newList="$newList $j"
+		fi
+	      done
+	      if test $dBug = 1 ; then echo "" ; fi
+	    fi
+	  done
+	  if test "x$newList" = x ; then doCheck=0
+	  else list2check=$newList ; list2copy="$list2copy $newList"
+	  fi
+	done
+	list2copy="$MPI_HEADER_FILES $list2copy"
+	if test $dBug = 1 ; then echo "list2copy='$list2copy'" ; fi
+
+	#----- create local mpi_headers dir if we have files to copy
+	mkListInc=`echo $list2copy | wc -w`
+	if test $mkListInc != 0 ; then
+	  echo 'create local "./mpi_headers" dir'
+	  mkdir -p ./mpi_headers
+	  INCLUDES="-I./mpi_headers $INCLUDES"
+	  mkListInc=1
+	fi
+	if test "x$LOCAL_MPI_HEADERS" != x ; then mkListInc=0 ; fi
+
+	#----- make local copy and update LOCAL_MPI_HEADERS (if not already set)
+	for i in $list2copy ; do
+	  if test -f $MPIINCLUDEDIR/$i ; then
+	    cp -p $MPIINCLUDEDIR/$i ./mpi_headers
+	    if test $i = 'mpif.h' ; then
+		perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
+	    fi
+	    if test $mkListInc = 2 ; then
+		LOCAL_MPI_HEADERS="$LOCAL_MPI_HEADERS ./mpi_headers/$i"
+	    fi
+	    if test $mkListInc = 1 ; then
+		LOCAL_MPI_HEADERS="./mpi_headers/$i" ; mkListInc=2
+	    fi
+	  fi
+	done
+    else
+	echo "WARNING: MPIINCLUDEDIR='$MPIINCLUDEDIR' is not a directory"
+	echo "WARNING: => skip checking for MPI headers (no ./mpi_headers dir)"
+#	exit -1
+    fi
+}
+
 #  Parse the package dependency information
 get_pdepend_list()  {
 
@@ -1248,6 +1337,11 @@
 SVD_TAMC_FLAGS=
 TAMC_EXTRA=
 
+DIVA=
+MPIINCLUDEDIR=
+MPI_HEADER_FILES=
+LOCAL_MPI_HEADERS=
+
 #  The following state can be set directly by command-line switches
 gm_s1="ROOTDIR STANDARDDIRS MODS PKG_DEPEND PKG_GROUPS DISABLE ENABLE"
 gm_s2="PLATFORM OPTFILE MAKE MAKEFILE MAKEDEPEND FC CC MPI OMP USE_R4"
@@ -1263,7 +1357,7 @@
 #  The following are all related to adjoint/tangent-linear stuff
 gm_s10="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF AD_TAMC_FLAGS AD_TAF_FLAGS"
 gm_s11="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
-gm_s12="TAF_EXTRA TAMC_EXTRA"
+gm_s12="TAF_EXTRA TAMC_EXTRA DIVA MPIINCLUDEDIR MPI_HEADER_FILES"
 
 gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"
 gm_state="$gm_state $gm_s10 $gm_s11 $gm_s12"
@@ -2484,28 +2578,12 @@
     fi
 done
 
-if test ! "x$DIVA" = x ; then
-    echo "  Creating the pseudo-MPI include directory"
-    INCLUDES="-I./mpi_headers $INCLUDES"
-    rm -rf ./mpi_headers
-    mkdir -p ./mpi_headers
-
-    if test "x$MPIINCLUDEDIR" = x ; then
-	if test "x$MPIHOME" = x ; then
-	    MPIHOME='/usr'
-	fi
-	MPIINCLUDEDIR='$MPIHOME/include'
-    fi
-
-    if test -r $MPIINCLUDEDIR/mpif.h ; then
-	for i in $MPI_HEADER_FILES; do
-	    cp -p $MPIINCLUDEDIR/$i ./mpi_headers
-	done
-
-	perl -i -pe 's/MPI_DISPLACEMENT_CURRENT=-1_8/MPI_DISPLACEMENT_CURRENT=-1/g' mpi_headers/mpif.h
-    else
-	echo " We cannot create a copy of mpif.h!"
-#	exit -1
+if test ! "x$DIVA" = x -a ! "x$MPI" = x ; then
+    if test ! "x$MPIINCLUDEDIR" = x ; then
+	#  Do a local copy of MPI headers files (in local dir ./mpi_headers/) after
+	#   checking for additional included headers (in case of chain of included
+	#   header); also set LOCAL_MPI_HEADERS (if not already set)
+        mpi_headers_do_local_copy
     fi
 fi
 
@@ -2537,10 +2615,6 @@
     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
@@ -2892,7 +2966,6 @@
 	@\$(MAKE) -f \$(MAKEFILE) cleanlinks
 	-rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
 	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.log taf_ftl.log
-	-rm -f genmake_warnings genmake_errors make.log
 
 # remove also the executable, files that "genmake2" generates (except Makefile)
 #         and output from a run (plus log files from testreport)
@@ -2901,12 +2974,14 @@
 	-rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
 	-rm -f $LOGFILE genmake_state genmake_*optfile
 	-rm -f SIZE.h.mpi genmake.tr_log make.tr_log
+	-rm -rf mpi_headers mnc_test_*
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f *.txt STD* *diagnostics.log datetime
+	-rm -f *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
+	-rm -f datetime costfinal divided.ctrl snapshot* output_adm.txt.diva_*
 	-rm -f *_MIT_CE_000.opt0000 costfunction*0000
-	-rm -rf mnc_test_*
+	-rm -f oad_cp.[0-9][0-9][0-9].?????
 
 makefile:
 	$THIS_SCRIPT $G2ARGS
@@ -3003,6 +3078,7 @@
 
 TAF_EXTRA      = ${TAF_EXTRA}
 TAMC_EXTRA     = ${TAMC_EXTRA}
+LOCAL_MPI_HEADERS    = ${LOCAL_MPI_HEADERS}
 
 EOF
 
@@ -3042,13 +3118,13 @@
 	@-rm -f ad_config.template
 	\$(MAKE) -f \$(MAKEFILE) \$(EXE_AD)
 
-ad_input_code.$FS: \$(AD_FILES) \$(AD_FLOW_FILES)
+ad_input_code.$FS: \$(F77_SRC_FILES) \$(AD_FLOW_FILES)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	@-rm -f ad_config.template
 	@\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
 	@\$(MAKE) -f \$(MAKEFILE) \$(FLOWFILES)
-	cat \$(FLOWFILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
+	cat \$(FLOWFILES) \$(F77_PP_SRC_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ad_input_code.$FS
 
 ad_taf_output.$FS: ad_input_code.$FS
 	\$(TAF) \$(AD_TAF_FLAGS) \$(TAF_EXTRA) ad_input_code.$FS
@@ -3060,8 +3136,8 @@
 	ls -l ad_input_code_ad.$FS
 	cat ad_input_code_ad.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ad_taf_output.$FS
 
-\$(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)
+\$(EXE_AD): \$(SPECIAL_FILES) \$(F77_SRC_FILES) \$(C_SRC_FILES:.c=.o) \$(H_SRC_FILES) \$(F90_SRC_FILES) ad_taf_output.o \$(EMBEDDED_FILES)
+	\$(LINK) -o \${EXE_AD} \$(FFLAGS) \$(FOPTIM) \$(C_SRC_FILES:.c=.o) ad_taf_output.o \$(LIBS)
 
 ad_tamc_output.$FS: ad_input_code.$FS
 	\$(TAMC) \$(AD_TAMC_FLAGS) \$(TAMC_EXTRA) ad_input_code.$FS
@@ -3090,26 +3166,26 @@
 	@-rm -f ad_config.template
 	\$(MAKE) -f \$(MAKEFILE) \$(EXE_FTL)
 
-ftl_input_code.$FS: \$(AD_FILES)
+ftl_input_code.$FS: \$(F77_SRC_FILES)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template
 	cmp ad_config.template AD_CONFIG.h || cat ad_config.template > AD_CONFIG.h
 	@-rm -f ad_config.template
 	@\$(MAKE) -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
 	@\$(MAKE) -f \$(MAKEFILE) \$(AD_FLOW_FILES)
-	cat \$(AD_FLOW_FILES) \$(AD_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
+	cat \$(AD_FLOW_FILES) \$(F77_PP_SRC_FILES) | sed -f \$(TOOLSDIR)/remove_comments_sed > ftl_input_code.$FS
 
 ftl_taf_output.$FS: ftl_input_code.$FS
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
-	ls -l ftl_input_code_ftl.$FS
-	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
+	ls -l ftl_input_code_tl.$FS
+	cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
 ftltafonly:
 	\$(TAF) \$(FTL_TAF_FLAGS) \$(TAF_EXTRA) ftl_input_code.$FS
-	ls -l ftl_input_code_ftl.$FS
-	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
+	ls -l ftl_input_code_tl.$FS
+	cat ftl_input_code_tl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
-\$(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)
+\$(EXE_FTL): ftl_taf_output.o \$(C_SRC_FILES:.c=.o)
+	\$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(C_SRC_FILES:.c=.o) ftl_taf_output.o \$(LIBS)
 
 ftl_tamc_output.$FS: ftl_input_code.$FS
 	\$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS