--- MITgcm/tools/genmake2	2003/11/25 17:22:47	1.49
+++ MITgcm/tools/genmake2	2004/02/16 16:24:41	1.65
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.49 2003/11/25 17:22:47 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.65 2004/02/16 16:24:41 cnh Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -13,30 +13,35 @@
 test_for_package_in_cpp_options() {
     cpp_options=$1
     pkg=$2
-    grep -i "#define.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #define ALLOW_$pkg"
-	exit 99
-    fi
-    grep -i "#undef.*ALLOW_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #undef ALLOW_$pkg"
-	exit 99
-    fi
-    grep -i "#define.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg" || exit 99
+}
+
+# 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" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI" || exit 99
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI" || exit 99
+}
+
+# Search for particular string in a file. Return 1 if detected, 0 if not
+# usage: test_for_string_in_file file string
+test_for_string_in_file() {
+    file=$1
+    strng=$2
+    grep -i "$strng" $file > /dev/null 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #define DISABLE_$pkg"
-	exit 99
+	echo -n "Error: In $file there is an illegal line: "
+        grep -i "$strng" $file
+	return 1
     fi
-    grep -i "#undef.*DISABLE_$pkg" $cpp_options > /dev/null 2>&1
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	echo "Error: In $cpp_options there is an illegal line: #undef DISABLE_$pkg"
-	exit 99
-   fi
+    return 0
 }
 
 # Read the $ROOTDIR/pkg/pkg_groups file and expand any references to
@@ -73,7 +78,9 @@
     tmp1=`uname`"_"`uname -m`
     tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
     tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
-    PLATFORM=`echo $tmp3 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
+    tmp1=`echo $tmp3 | sed -e 's|x86_64|amd64|'`
+    tmp2=`echo $tmp1 | sed -e 's/i[3-6]86/ia32/' | sed -e 's/athlon/ia32/'`
+    PLATFORM=$tmp2
     OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
     echo "  The platform appears to be:  $PLATFORM"
     
@@ -430,6 +437,33 @@
 }
 
 
+check_netcdf_libs()  {
+    cat <<EOF > genmake_tnc.F
+      program fgennc
+#include "netcdf.inc"
+      integer iret, ncid, xid
+      iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      iret = nf_def_dim(ncid, 'X', 11, xid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      iret = nf_close(ncid)
+      IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
+      end
+EOF
+    $CPP genmake_tnc.F > genmake_tnc.f  \
+	&&  $FC $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.f $LIBS >> genmake_tnc.log 2>&1
+    RET_COMPILE=$?
+    test -x ./genmake_tnc  &&  ./genmake_tnc >> genmake_tnc.log 2>&1
+    RETVAL=$?
+    if test "x$RET_COMPILE" = x0 -a "x$RETVAL" = x0 ; then
+	HAVE_NETCDF=t
+    else
+	cat genmake_tnc.log >> genmake_warnings
+    fi
+    rm -f genmake_tnc*
+}
+
+
 #  Set defaults here
 COMMANDL="$0 $@"
 
@@ -438,6 +472,7 @@
 S64=
 KPP=
 FC=
+CPP=
 LINK=
 # DEFINES="-DWORDLENGTH=4"
 DEFINES=
@@ -466,12 +501,13 @@
 HAVE_FDATE=
 FC_NAMEMANGLE=
 HAVE_CLOC=
+HAVE_NETCDF=
 
 MODS=
 TOOLSDIR=
 SOURCEDIRS=
 INCLUDEDIRS=
-STANDARDDIRS=
+STANDARDDIRS="USE_THE_DEFAULT"
 
 PWD=`pwd`
 MAKE=make
@@ -505,7 +541,7 @@
 
 #  The following state can be set directly by command-line switches
 gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE"
-gm_s2="FC IEEE MPI JAM DUMPSTATE STANDARDDIRS"
+gm_s2="FC CPP IEEE MPI JAM DUMPSTATE STANDARDDIRS"
 
 #  The following state is not directly set by command-line switches
 gm_s3="LN S64 KPP LINK PACKAGES MAKEDEPEND PDEPEND PDEFAULT INCLUDES FFLAGS FOPTIM "
@@ -586,7 +622,7 @@
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
 	
-	-adoptfile | --adoptfile | -ad | --ad)
+	-adoptfile | --adoptfile | -adof | --adof)
 	    ac_prev=AD_OPTFILE ;;
 	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
 	    AD_OPTFILE=$ac_optarg ;;
@@ -798,12 +834,21 @@
 if test "x$LINK" = x ; then
     LINK=$FC
 fi
-if test "x$CPP" = x ; then
-    CPP="cpp"
-fi
 if test "x$MAKE" = x ; then
     MAKE="make"
 fi
+if test "x$CPP" = x ; then
+    CPP=cpp
+fi
+#EH3 === UGLY ===
+#  The following an ugly little hack to check for $CPP in /lib/ and it
+#  should eventually be replaced with a more general function that
+#  searches a combo of the user's path and a list of "usual suspects"
+#  to find the correct location for binaries such as $CPP.
+for i in " " "/lib/" ; do
+    echo "#define A a" | $i$CPP > test_cpp 2>&1 && CPP=$i$CPP
+done
+#EH3 === UGLY ===
 echo "#define A a" | $CPP > test_cpp 2>&1
 RETVAL=$?
 if test "x$RETVAL" != x0 ; then
@@ -888,14 +933,16 @@
 else
     echo "no"
 fi
-echo "$FC_NAMEMANGLE" > FC_NAMEMANGLE.h.template
-cmp FC_NAMEMANGLE.h FC_NAMEMANGLE.h.template > /dev/null 2>&1
-RETVAL=$?
-if test "x$RETVAL" != x0 ; then
-    mv -f FC_NAMEMANGLE.h.template FC_NAMEMANGLE.h
-fi
 rm -f genmake_t*
 
+echo -n "  Can we create NetCDF-enabled binaries...  "
+check_netcdf_libs
+if test "x$HAVE_NETCDF" != x ; then
+    echo "yes"
+else
+    echo "no"
+fi
+
 
 printf "\n===  Setting defaults  ===\n"
 echo -n "  Adding MODS directories:  "
@@ -935,7 +982,7 @@
     TOOLSDIR="$ROOTDIR/tools"
 fi
 if test ! -d ${TOOLSDIR} ; then
-    echo "Error: the specified $TOOLSDIR (\"$TOOLSDIR\") does not exist!"
+    echo "Error: the specified TOOLSDIR (\"$TOOLSDIR\") does not exist!"
     exit 1
 fi
 if test "x$S64" = x ; then
@@ -956,11 +1003,25 @@
 	rm -f make_eesupp.errors
     else
 	echo "Error: problem encountered while building source files in eesupp:"
-	cat make_eesupp.errors
+	cat make_eesupp.errors 1>&2
 	exit 1
     fi
 fi
 
+#same for exch2
+if test -r $ROOTDIR"/pkg/exch2/Makefile" ; then
+    echo "  Making source files in exch2 from  templates"
+    ( cd $ROOTDIR"/pkg/exch2/" && $MAKE ) > make_exch2.errors 2>&1
+    RETVAL=$?
+    if test "x${RETVAL}" = x0 ; then
+        rm -f make_exch2.errors
+    else
+        echo "Error: problem encountered while building source files in exch2:"
+        cat make_exch2.errors 1>&2
+        exit 1
+    fi
+fi
+
 printf "\n===  Determining package settings  ===\n"
 if  test "x${PDEPEND}" = x ; then
     tmp=$ROOTDIR"/pkg/pkg_depend"
@@ -1144,6 +1205,32 @@
     fi
 done
 
+#  Build MNC templates and check for ability to build and use NetCDF
+echo $PACKAGES | grep ' mnc ' > /dev/null 2>&1
+RETVAL=$?
+if test "x$RETVAL" = x0 ; then
+    ( cd $ROOTDIR"/pkg/mnc" && $MAKE templates ) > make_mnc.errors 2>&1
+    RETVAL=$?
+    if test "x${RETVAL}" = x0 ; then
+	rm -f make_mnc.errors
+    else
+	echo "Error: problem encountered while building source files in pkg/mnc:"
+	cat make_mnc.errors 1>&2
+	exit 1
+    fi
+    if test "x$HAVE_NETCDF" != xt ; then
+	cat <<EOF
+
+WARNING: the "mnc" package has been enabled but tests failed to 
+  compile and/or execute NetCDF applications.  Please check that:
+
+  1) NetCDF is installed for your compiler and
+  2) the LIBS variable (within the 'optfile") specifies the correct 
+       NetCDF library to link against.
+  
+EOF
+    fi
+fi
 
 # Create a list of #define and #undef to enable/disable packages
 PACKAGES_DOT_H=PACKAGES_CONFIG.h
@@ -1178,9 +1265,8 @@
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
     case $i in 
 	aim_v23)
-	    DEFINES="$DEFINES -DALLOW_AIM"
             ENABLED_PACKAGES="$ENABLED_PACKAGES -DALLOW_AIM"
-	    echo "Warning: ALLOW_AIM is set to enable aim_v23. This is REALLY ugly Jean-Michel :-)"
+	    echo "Warning: ALLOW_AIM is set to enable aim_v23."
 	    ;;
     esac
 #EH3  WARNING :  This is an UGLY HACK that needs to be removed!!!
@@ -1189,51 +1275,60 @@
 
 echo "  Adding STANDARDDIRS"
 BUILDDIR=${BUILDDIR:-.}
-if test "x$STANDARDDIRS" = x ; then
+if test "x$STANDARDDIRS" = xUSE_THE_DEFAULT ; then
     STANDARDDIRS="eesupp model"
 fi
-for d in $STANDARDDIRS ; do
-    adr="$ROOTDIR/$d/src"
-    if test ! -d $adr ; then
-	echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-	echo "  is correct and that you correctly specified the STANDARDDIRS option"
-	exit 1
-    else
-	SOURCEDIRS="$SOURCEDIRS $adr"
-    fi
-    adr="$ROOTDIR/$d/inc"
-    if test ! -d $adr ; then
-	echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
-	echo "  is correct and that you correctly specified the STANDARDDIRS option"
-	exit 1
-    else
-	INCLUDEDIRS="$INCLUDEDIRS $adr"
-    fi
-done
+if test "x$STANDARDDIRS" != x ; then
+    for d in $STANDARDDIRS ; do
+	adr="$ROOTDIR/$d/src"
+	if test ! -d $adr ; then
+	    echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+	    echo "  is correct and that you correctly specified the STANDARDDIRS option"
+	    exit 1
+	else
+	    SOURCEDIRS="$SOURCEDIRS $adr"
+	fi
+	adr="$ROOTDIR/$d/inc"
+	if test ! -d $adr ; then
+	    echo "Error:  directory $adr not found -- please check that ROOTDIR=\"$ROOTDIR\""
+	    echo "  is correct and that you correctly specified the STANDARDDIRS option"
+	    exit 1
+	else
+	    INCLUDEDIRS="$INCLUDEDIRS $adr"
+	fi
+    done
+fi
 
-echo "  Searching for CPP_OPTIONS.h in order to warn about the presence"
-echo "    of \"#define ALLOW_PKGNAME\"-type statements:"
+echo "  Searching for *OPTIONS.h files in order to warn about the presence"
+echo "    of \"#define \"-type statements that are no longer allowed:"
 CPP_OPTIONS=
+CPP_EEOPTIONS=
 spaths=". $INCLUDEDIRS"
+names=`ls -1 "$ROOTDIR/pkg"`
 for i in $spaths ; do
     try="$i/CPP_OPTIONS.h"
-    #  echo -n "    trying $try : "
-    if test -f $try -a -r $try ; then
+    if test -f $try -a -r $try -a "x$CPP_OPTIONS" = x ; then
 	echo "    found CPP_OPTIONS=\"$try\""
 	CPP_OPTIONS="$try"
-	break
+        # New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
+        for n in $names ; do
+            test_for_package_in_cpp_options $CPP_OPTIONS $n
+        done
+    fi
+    try="$i/CPP_EEOPTIONS.h"
+    if test -f $try -a -r $try -a "x$CPP_EEOPTIONS" = x ; then
+	echo "    found CPP_EEOPTIONS=\"$try\""
+        # New safety test: make sure MPI is not determined by CPP_EEOPTIONS.h
+#**** not yet enabled ****
+#        test_for_mpi_in_cpp_eeoptions $try
+#**** not yet enabled ****
+	CPP_EEOPTIONS="$try"
     fi
 done
 if test "x$CPP_OPTIONS" = x ; then
     echo "Error: can't find \"CPP_OPTIONS.h\" in the path list: $spaths"
     exit 1
 fi
-# New safety test: make sure packages are not mentioned in CPP_OPTIONS.h
-names=`ls -1 "$ROOTDIR/pkg"`
-for n in $names ; do
-    test_for_package_in_cpp_options $CPP_OPTIONS $n
-done
-
 
 #  Here, we build the list of files to be "run through" the adjoint
 #  compiler.
@@ -1248,6 +1343,7 @@
     done
 done
 
+
 echo
 echo "===  Creating the Makefile  ==="
 echo "  setting INCLUDES"
@@ -1347,6 +1443,8 @@
 EXE_SVD=$EXECUTABLE"_svd"
 
 cat >>$MAKEFILE <<EOF
+#
+# OPTFILE="$OPTFILE"
 # 
 # BUILDDIR     : Directory where object files are written
 # SOURCEDIRS   : Directories containing the source (.F) files
@@ -1383,6 +1481,9 @@
 ENABLED_PACKAGES = ${ENABLED_PACKAGES}
 DISABLED_PACKAGES = ${DISABLED_PACKAGES}
 
+# These files are created by Makefile
+SPECIAL_FILES = ${PACKAGES_DOT_H} AD_CONFIG.h FC_NAMEMANGLE.h
+
 EOF
 
 #  Note: figure out some way to add Hyades JAM libraries here
@@ -1447,7 +1548,7 @@
 .SUFFIXES: .o .f .p .F .c .F90 .f90
 
 all: \$(EXECUTABLE)
-\$(EXECUTABLE): links \$(OBJFILES)
+\$(EXECUTABLE): \$(SPECIAL_FILES) \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(OBJFILES)
 	@echo Creating \$@ ...
 	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) \$(LIBS)
 depend:
@@ -1455,7 +1556,7 @@
 	\$(MAKEDEPEND) -o .f \$(DEFINES) \$(INCLUDES) \$(SRCFILES)
 	\$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
 
-links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) ${PACKAGES_DOT_H} AD_CONFIG.h
+links: \$(SRCFILES) \$(CSRCFILES) \$(HEADERFILES) \$(F90SRCFILES) \$(SPECIAL_FILES)
 
 small_f: \$(F77FILES) \$(F90FILES)
 
@@ -1468,8 +1569,8 @@
 Clean:
 	@make clean
 	@make cleanlinks
-	-rm -f ${PACKAGES_DOT_H} AD_CONFIG.h
-	-rm -f Makefile.bak genmake_state genmake_*optfile genmake_warnings make.log
+	-rm -f \$(SPECIAL_FILES)
+	-rm -f genmake_state genmake_*optfile genmake_warnings make.log run.log *.bak
 CLEAN:
 	@make Clean
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
@@ -1483,13 +1584,16 @@
 cleanlinks:
 	-find . -type l -exec rm {} \;
 
-# Special targets
+# Special targets ($SPECIAL_FILES) which are create by make
 ${PACKAGES_DOT_H}:
 	@echo Creating \$@ ...
 	@\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bPACKAGES_CONFIG_H "Disabled packages:" \$(DISABLED_PACKAGES) " " "Enabled packages:" \$(ENABLED_PACKAGES) > \$@
 AD_CONFIG.h:
 	@echo Creating \$@ ...
 	@\$(TOOLSDIR)/convert_cpp_cmd2defines "Warning - this file is automatically generated - do NOT edit" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN -UALLOW_ECCO_OPTIMIZATION > \$@
+FC_NAMEMANGLE.h:
+	@echo Creating \$@ ...
+	echo "$FC_NAMEMANGLE" > \$@
 
 # The normal chain of rules is (  .F - .f - .o  )
 .F.f:
@@ -1659,7 +1763,7 @@
 if test ! -f $PACKAGES_DOT_H ; then
     mv -f $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
 else
-    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H
+    cmp $PACKAGES_DOT_H".tmp" $PACKAGES_DOT_H > /dev/null 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	rm -f $PACKAGES_DOT_H".tmp"