--- MITgcm/tools/genmake2	2012/01/24 14:54:57	1.229
+++ MITgcm/tools/genmake2	2012/08/14 22:10:39	1.233
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.229 2012/01/24 14:54:57 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.233 2012/08/14 22:10:39 jmc Exp $
 # $Name:  $
 #
 # Makefile generator for MITgcm UV codes
@@ -450,7 +450,6 @@
 	    RETVAL=$?
 	    if test "x$RETVAL" = x0 ; then
 		echo "OK"
-		DEFINES="$DEFINES -DHAVE_EMBED_SRC"
 		return 0
 	    fi
 	done
@@ -462,7 +461,6 @@
 	return 1
     fi
     echo "OK"
-    DEFINES="$DEFINES -DHAVE_EMBED_SRC"
 }
 
 #  look for possible C compilers
@@ -784,7 +782,6 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_CLOC=t
-	DEFINES="$DEFINES -DHAVE_CLOC"
     fi
     rm -f genmake_tc*
     echo " --> set HAVE_CLOC='$HAVE_CLOC'" >> $LOGFILE
@@ -846,17 +843,12 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_SIGREG=t
-	DEFINES="$DEFINES -DHAVE_SIGREG"
     fi
     rm -f genmake_tc*
     echo " --> set HAVE_SIGREG='$HAVE_SIGREG'" >> $LOGFILE
 }
 
 check_HAVE_SETRLSTK()  {
-    if test "x$HAVE_SETRLSTK" = xt ; then
-	DEFINES="$DEFINES -DHAVE_SETRLSTK"
-	return
-    fi	
     if test ! "x$HAVE_SETRLSTK" = x ; then
 	return
     fi
@@ -894,7 +886,6 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_SETRLSTK=t
-	DEFINES="$DEFINES -DHAVE_SETRLSTK"
     fi
     rm -f genmake_tc*
     echo " --> set HAVE_SETRLSTK='$HAVE_SETRLSTK'" >> $LOGFILE
@@ -941,7 +932,6 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	HAVE_STAT=t
-	DEFINES="$DEFINES -DHAVE_STAT"
     fi
     rm -f genmake_tc*
     echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE
@@ -1039,6 +1029,109 @@
     echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE
 }
 
+check_lapack_libs()  {
+    if test ! "x$SKIP_LAPACK_CHECK" = x ; then
+	return
+    fi
+    echo >> $LOGFILE
+    echo "running: check_lapack_libs()" >> $LOGFILE
+    cat <<EOF > genmake_tla.F
+      program fgenla
+      integer info 
+      integer ipiv( 2 )
+      double precision ab( 4, 2 ), b( 2 )
+      data ab / 0., 0., 1., 2., 0., 2., 1., 0. /
+      data b / 1., 1. /
+      call dgbsv( 2, 1, 1, 1, ab, 4, ipiv, b, 2, info )
+      IF (info .NE. 0) write(*,*) 'Error:', info
+      write(*,*) b
+      end
+EOF
+    echo "===  genmake_tla.F  >>>" > genmake_tla.log
+    cat genmake_tla.F >> genmake_tla.log
+    echo "<<<  genmake_tla.F  ===" >> genmake_tla.log
+    RET_CPP=f
+    COMM="cat genmake_tla.F | $CPP $DEFINES $INCLUDES"
+    echo "$COMM" >> genmake_tla.log
+    eval $COMM > genmake_tla.$FS 2>/dev/null  &&  RET_CPP=t
+    if test "x$RET_CPP" = xf ; then
+	echo "  WARNING: CPP failed to pre-process the lapack test." \
+	    >> genmake_tla.log
+	echo "    Please check that \$INCLUDES is properly set." \
+	    >> genmake_tla.log
+    fi
+    echo "$FC $FFLAGS $FOPTIM -c genmake_tla.$FS  \ " >> genmake_tla.log
+    echo "  &&  $LINK $FFLAGS $FOPTIM -o genmake_tla.o $LIBS" >> genmake_tla.log
+    $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+	&&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS >> genmake_tla.log 2>&1
+    RET_COMPILE=$?
+    cat genmake_tla.log >> $LOGFILE
+
+    # test program execution not always possible (see check_netcdf_libs)
+    #
+    #test -x ./genmake_tla  &&  ./genmake_tla >> genmake_tla.log 2>&1
+    #RETVAL=$?
+    #if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+
+    if test "x$RET_COMPILE" = x0 ; then
+	HAVE_LAPACK=t
+	echo "check_lapack: successful" >> $LOGFILE
+    else
+	# try again with "-llapack" added to the libs
+	echo "==> try again with added '-llapack'" > genmake_tla.log
+	echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+	echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+	echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack" >> genmake_tla.log
+	cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+	    &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+	    &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack >> genmake_tla.log 2>&1
+	RET_COMPILE=$?
+	echo >> $LOGFILE
+	cat genmake_tla.log >> $LOGFILE
+	if test "x$RET_COMPILE" = x0 ; then
+	    LIBS="$LIBS -llapack"
+	    HAVE_LAPACK=t
+	    echo "check_lapack: successful" >> $LOGFILE
+	else
+	# try again with "-lf77blas -lcblas" added to the libs
+	    echo "==> try again with added '-llapack -lf77blas -lcblas'" > genmake_tla.log
+	    echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+	    echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+	    echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas" >> genmake_tla.log
+	    cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+		&&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+		&&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas >> genmake_tla.log 2>&1
+	    RET_COMPILE=$?
+	    echo >> $LOGFILE
+	    cat genmake_tla.log >> $LOGFILE
+	    if test "x$RET_COMPILE" = x0 ; then
+		LIBS="$LIBS -llapack -lf77blas -lcblas"
+		HAVE_LAPACK=t
+		echo "check_lapack: successful" >> $LOGFILE
+            else
+            # try again with "-latlas" added to the libs
+                echo "==> try again with added '-llapack -lf77blas -lcblas -latlas'" > genmake_tla.log
+                echo "cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS \ " >> genmake_tla.log
+                echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS \ " >> genmake_tla.log
+                echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas" >> genmake_tla.log
+                cat genmake_tla.F | $CPP $DEFINES $INCLUDES > genmake_tla.$FS 2>/dev/null  \
+                    &&  $FC $FFLAGS $FOPTIM -c genmake_tla.$FS >> genmake_tla.log 2>&1  \
+                    &&  $LINK $FFLAGS $FOPTIM -o genmake_tla genmake_tla.o $LIBS -llapack -lf77blas -lcblas -latlas >> genmake_tla.log 2>&1
+                RET_COMPILE=$?
+                echo >> $LOGFILE
+                cat genmake_tla.log >> $LOGFILE
+                if test "x$RET_COMPILE" = x0 ; then
+                    LIBS="$LIBS -llapack -lf77blas -lcblas -latlas"
+                    HAVE_LAPACK=t
+                    echo "check_lapack: successful" >> $LOGFILE
+                fi
+	    fi
+	fi
+    fi
+    rm -f genmake_tla*
+    echo " --> set HAVE_LAPACK='$HAVE_LAPACK'" >> $LOGFILE
+}
+
 
 ###############################################################################
 #   Sequential part of script starts here
@@ -1106,6 +1199,7 @@
 HAVE_NETCDF=
 HAVE_ETIME=
 IGNORE_TIME=
+HAVE_LAPACK=
 
 MODS=
 TOOLSDIR=
@@ -1158,7 +1252,7 @@
 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"
+gm_s8="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME HAVE_LAPACK"
 
 #  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"
@@ -1768,6 +1862,7 @@
 printf "  Can we call simple C routines (here, \"cloc()\") using $FC...  "
 check_HAVE_CLOC
 if test "x$HAVE_CLOC" != x ; then
+    DEFINES="$DEFINES -DHAVE_CLOC"
     echo "yes"
 else
     echo "no"
@@ -1782,6 +1877,7 @@
 printf "  Can we unlimit the stack size using $FC...  "
 check_HAVE_SETRLSTK
 if test "x$HAVE_SETRLSTK" = xt ; then
+    DEFINES="$DEFINES -DHAVE_SETRLSTK"
     echo "yes"
 else
     echo "no"
@@ -1791,6 +1887,7 @@
 printf "  Can we register a signal handler using $FC...  "
 check_HAVE_SIGREG
 if test "x$HAVE_SIGREG" = xt ; then
+    DEFINES="$DEFINES -DHAVE_SIGREG"
     echo "yes"
 else
     echo "no"
@@ -1800,6 +1897,7 @@
 printf "  Can we use stat() through C calls...  "
 check_HAVE_STAT
 if test "x$HAVE_STAT" != x ; then
+    DEFINES="$DEFINES -DHAVE_STAT"
     echo "yes"
 else
     echo "no"
@@ -1809,6 +1907,16 @@
 printf "  Can we create NetCDF-enabled binaries...  "
 check_netcdf_libs
 if test "x$HAVE_NETCDF" != x ; then
+    DEFINES="$DEFINES -DHAVE_NETCDF"
+    echo "yes"
+else
+    echo "no"
+fi
+
+printf "  Can we create LAPACK-enabled binaries...  "
+check_lapack_libs
+if test "x$HAVE_LAPACK" != x ; then
+    DEFINES="$DEFINES -DHAVE_LAPACK"
     echo "yes"
 else
     echo "no"
@@ -1820,6 +1928,7 @@
 fi
 if test "x$EMBED_SRC" = xt ; then
     ENABLE="$ENABLE embed_files"
+#   DEFINES="$DEFINES -DHAVE_EMBED_SRC"
 fi
 
 printf "\n===  Setting defaults  ===\n"
@@ -2125,6 +2234,27 @@
     fi
 fi
 
+#  Check for package RADTRANS: if LAPACK is not available,
+#  then issue a warning that the direct radtrans solver is not available.
+if test "x$HAVE_LAPACK" != xt ; then
+    echo " $PACKAGES " | grep ' radtrans ' > /dev/null 2>&1
+    RETVAL=$?
+    if test "x$RETVAL" = x0 ; then
+	cat <<EOF
+*********************************************************************
+WARNING: the "radtrans" package was enabled but tests failed to
+  compile LAPACK applications.  This means that the direct radtrans
+  solver is not available and compilation will fail if it is enabled.
+  If you want to use the direct solver, please check that:
+
+  1) LAPACK is correctly installed for this compiler and
+  2) the LIBS variable (within the "optfile") specifies the correct
+     LAPACK library to link against.
+*********************************************************************
+EOF
+    fi
+fi
+
 if  test "x${PKG_DEPEND}" != x ; then
   echo "  applying package dependency rules"
   ck=
@@ -2729,14 +2859,14 @@
 	@make -f \$(MAKEFILE) clean
 	@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
+	-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)
 CLEAN:
 	@make -f \$(MAKEFILE) Clean
-	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak
+	-rm -f \$(EXECUTABLE) \$(EXE_AD) \$(EXE_FTL) *.bak
 	-rm -f $LOGFILE genmake_state genmake_*optfile
 	-rm -f SIZE.h.mpi genmake.tr_log make.tr_log
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
@@ -2757,7 +2887,7 @@
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
 AD_CONFIG.h:
 	@echo Creating \$@ ...
-	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > \$@
 FC_NAMEMANGLE.h:
 	@echo Creating \$@ ...
 	echo "$FC_NAMEMANGLE" > \$@
@@ -2871,7 +3001,7 @@
 adtamc: ad_tamc_output.$FS
 
 ad_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES) \$(AD_FLOW_FILES)
-	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ad_config.template
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -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)
@@ -2907,12 +3037,12 @@
 adobj: ad_taf_output.o \$(OBJFILES)
 
 # ... FTL ...
-ftlall: ftl_taf
+ftlall: \$(EXE_FTL)
 ftltaf: ftl_taf_output.$FS
 ftltamc: ftl_tamc_output.$FS
 
 ftl_input_code.$FS: \$(AD_FILES) \$(H_SRC_FILES)
-	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
 	-rm -f ftl_config.template
 	@make -f \$(MAKEFILE) \$(F77_PP_SRC_FILES)
@@ -2929,8 +3059,8 @@
 	ls -l ftl_input_code_ftl.$FS
 	cat ftl_input_code_ftl.$FS | sed -f \$(TOOLSDIR)/adjoint_sed > ftl_taf_output.$FS
 
-ftl_taf: ftl_taf_output.o \$(OBJFILES)
-	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)
+\${EXE_FTL}: ftl_taf_output.o \$(OBJFILES)
+	\$(LINK) -o \${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_taf_output.o \$(LIBS)
 
 ftl_tamc_output.$FS: ftl_input_code.$FS
 	\$(TAMC) \$(FTL_TAMC_FLAGS) \$(TAMC_EXTRA) ftl_input_code.$FS
@@ -2959,7 +3089,7 @@
 	touch ad_taf_output.$FS ftl_taf_output.$FS
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c ad_taf_output.$FS
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c ftl_taf_output.$FS
-	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > ftl_config.template
+	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ftl_config.template
 	cmp ftl_config.template AD_CONFIG.h || cat ftl_config.template > AD_CONFIG.h
 	-rm -f ftl_config.template
 
@@ -3259,7 +3389,7 @@
     fi
 fi
 if test ! -f AD_CONFIG.h ; then
-    $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > AD_CONFIG.h
+    $BASH $TOOLSDIR/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > AD_CONFIG.h
 fi
 
 #  Write the "state" for future records