--- MITgcm/tools/genmake2	2012/09/25 21:16:29	1.243
+++ MITgcm/tools/genmake2	2013/02/23 04:24:42	1.249
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.243 2012/09/25 21:16:29 utke Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.249 2013/02/23 04:24:42 utke Exp $
 # $Name:  $
 #
 # Makefile generator for MITgcm UV codes
@@ -907,9 +907,9 @@
       program fgennc
 #include "netcdf.inc"
 EOF
-    if test ! "x$MPI" = x ; then
-	echo '#include "mpif.h"' >> genmake_tnc.F
-    fi
+   #if test ! "x$MPI" = x ; then
+   #	echo '#include "mpif.h"' >> genmake_tnc.F
+   #fi
     cat <<EOF >> genmake_tnc.F
       integer iret, ncid, xid
       iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
@@ -1092,6 +1092,45 @@
     echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
 }
 
+check_HAVE_FLUSH()  {
+    if test ! "x$SKIP_CHECK_FLUSH" = x ; then
+	return
+    fi
+    echo >> $LOGFILE
+    echo "running: check_HAVE_FLUSH()" >> $LOGFILE
+    cat <<EOF > genmake_tflsh.$FS
+      program fgenflsh
+      integer iounit
+      character*9 fname
+      iounit = 26
+      fname = 'tmp.tflsh'
+      open(iounit,FILE=fname,STATUS='unknown')
+      write(iounit,*) 'genmake_tflsh: hello'
+      call flush(iounit)
+      close(iounit)
+      end
+EOF
+    echo "===  genmake_tflsh.$FS  >>>" > genmake_tflsh.log
+    cat genmake_tflsh.$FS >> genmake_tflsh.log
+    echo "<<<  genmake_tflsh.$FS  ===" >> genmake_tflsh.log
+
+    echo "$FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS  \ " >> genmake_tflsh.log
+    echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh.o $LIBS" >> genmake_tflsh.log
+    $FC $FFLAGS $FOPTIM -c genmake_tflsh.$FS >> genmake_tflsh.log 2>&1  \
+	&&  $LINK $FFLAGS $FOPTIM -o genmake_tflsh genmake_tflsh.o $LIBS >> genmake_tflsh.log 2>&1
+    RET_COMPILE=$?
+
+    if test "x$RET_COMPILE" = x0 ; then
+	HAVE_FLUSH=t
+	#cat genmake_tflsh.log >> $LOGFILE
+	echo "  check_HAVE_FLUSH: successful" >> $LOGFILE
+    else
+	HAVE_FLUSH=f
+	cat genmake_tflsh.log >> $LOGFILE
+    fi
+    rm -f genmake_tflsh*
+    echo " --> set HAVE_FLUSH='$HAVE_FLUSH'" >> $LOGFILE
+}
 
 ###############################################################################
 #   Sequential part of script starts here
@@ -1149,6 +1188,9 @@
 DEVEL=
 HAVE_TEST_L=
 
+# comment this line out to enable lapack test
+SKIP_LAPACK_CHECK=t
+
 # DEFINES checked by test compilation or command-line
 HAVE_SYSTEM=
 HAVE_FDATE=
@@ -1160,6 +1202,7 @@
 HAVE_ETIME=
 IGNORE_TIME=
 HAVE_LAPACK=
+HAVE_FLUSH=
 
 MODS=
 TOOLSDIR=
@@ -1213,9 +1256,9 @@
 #  The following state is not directly set by command-line switches
 gm_s4="LN S64 LINK PACKAGES INCLUDES FFLAGS FOPTIM"
 gm_s5="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
-gm_s6="TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
-gm_s7="PWD THISHOST THISUSER THISDATE THISVER MACHINE"
-gm_s8="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK"
+gm_s6="PWD TOOLSDIR SOURCEDIRS INCLUDEDIRS EXEDIR EXECUTABLE EXEHOOK"
+gm_s7="THISHOST THISUSER THISDATE THISVER MACHINE FC_NAMEMANGLE"
+gm_s8="HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK HAVE_FLUSH"
 
 #  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"
@@ -1659,6 +1702,8 @@
 if test ! "x$MPI" = x ; then
       echo "  Turning on MPI cpp macros"
       DEFINES="$DEFINES -DALLOW_USE_MPI"
+#- To compile code older than checkpoint63s (2012/09/05), un-comment the following line:
+#     DEFINES="$DEFINES -DALWAYS_USE_MPI"
 fi
 if test ! "x$OMP" = x ; then
       echo "  Add OMPFLAG and turn on OpenMP cpp macros"
@@ -1883,8 +1928,17 @@
 else
     echo "no"
 fi
-DEFINES="$DEFINES $IGNORE_TIME"
 
+printf "  Can we call FLUSH intrinsic subroutine...  "
+check_HAVE_FLUSH
+if test "x$HAVE_FLUSH" = xt ; then
+    DEFINES="$DEFINES -DHAVE_FLUSH"
+    echo "yes"
+else
+    echo "no"
+fi
+
+DEFINES="$DEFINES $IGNORE_TIME"
 if test "x$EMBED_SRC" = xt ; then
     build_embed_encode
 fi
@@ -2715,6 +2769,9 @@
     echo "EMBEDDED_FILES = " >>$MAKEFILE
 fi
 
+# extract default cpp search path so we can pass it to makedepend
+CPPINCLUDES=`cat /dev/null | $CPP -v 2>&1 | awk '/^End of search/{f=0}!/^\#/{if(f){printf " -I%s", $1;}}/^\#include "..." search start/{f=1}'`
+
 cat >>$MAKEFILE <<EOF
 # Unix ln (link)
 LN = ${LN}
@@ -2735,6 +2792,8 @@
 DEFINES = ${DEFINES}
 # Includes for CPP
 INCLUDES = ${INCLUDES}
+# default CPP includes for makedepend
+CPPINCLUDES = ${CPPINCLUDES}
 # Flags for KPP
 KFLAGS1 = ${KFLAGS1}
 KFLAGS2 = ${KFLAGS2}
@@ -2800,7 +2859,7 @@
 
 depend:
 	@\$(MAKE) -f \$(MAKEFILE) links
-	\$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(F77_SRC_FILES)
+	\$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 	-rm -f makedepend.out
 
@@ -2900,7 +2959,7 @@
 ## This nullifies any default implicit rules concerning these two file types:
 ## %.o : %.F
 
-# C preprocessing and replacing the _d in constants: 
+# C preprocessing and replacing the _d in constants:
 CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
 
 .F.$FS:
@@ -3165,7 +3224,8 @@
 OAD_active.F90 \
 OAD_cp.F90 \
 OAD_rev.F90 \
-OAD_tape.F90
+OAD_tape.F90 \
+revolve.F90
 
 OPENAD_SUPPORT_C_SRC_FILES = \
 iaddr.c \