--- MITgcm/tools/genmake2	2010/05/23 18:34:43	1.206
+++ MITgcm/tools/genmake2	2010/12/26 01:04:45	1.218
@@ -1,6 +1,7 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.206 2010/05/23 18:34:43 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.218 2010/12/26 01:04:45 jmc Exp $
+# $Name:  $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -8,6 +9,167 @@
 #   modified by aja 01/00
 #   rewritten in bash by eh3 08/03
 
+#  Explain usage
+usage()  {
+cat <<EOF
+
+Usage: "$0" [OPTIONS]
+  where [OPTIONS] can be:
+
+    -help | --help | -h | --h
+          Print this help message and exit.
+
+    -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_default" will be used.
+
+    -nooptfile | --nooptfile
+      -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
+          tools/build_options/ directory.
+
+    -pdepend NAME | --pdepend NAME
+      -pdepend=NAME | --pdepend=NAME
+          Get package dependency information from "NAME".
+
+    -pgroups NAME | --pgroups NAME
+      -pgroups=NAME | --pgroups=NAME
+          Get the package groups information from "NAME".
+
+    -bash NAME
+          Explicitly specify the Bourne or BASH shell to use
+
+    -make NAME | -m NAME
+      --make=NAME | -m=NAME
+          Use "NAME" for the MAKE program. The default is "make" but
+          many platforms, "gmake" is the preferred choice.
+
+    -makefile NAME | -mf NAME
+      --makefile=NAME | -mf=NAME
+          Call the makefile "NAME".  The default is "Makefile".
+
+    -makedepend NAME | -md NAME
+      --makedepend=NAME | -md=NAME
+          Use "NAME" for the MAKEDEPEND program.
+
+    -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
+      -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
+          Specify the location of the MITgcm ROOTDIR as "NAME".
+          By default, genamke will try to find the location by
+          looking in parent directories (up to the 5th parent).
+
+    -mods NAME | --mods NAME | -mo NAME | --mo NAME
+      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
+          Here, "NAME" specifies a list of directories that are
+          used for additional source code.  Files found in the
+          "mods list" are given preference over files of the same
+          name found elsewhere.
+
+    -disable NAME | --disable NAME
+      -disable=NAME | --disable=NAME
+          Here "NAME" specifies a list of packages that we don't
+          want to use.  If this violates package dependencies,
+          genamke will exit with an error message.
+
+    -enable NAME | --enable NAME
+      -enable=NAME | --enable=NAME
+          Here "NAME" specifies a list of packages that we wish
+          to specifically enable.  If this violates package
+          dependencies, genamke will exit with an error message.
+
+    -standarddirs NAME | --standarddirs NAME
+      -standarddirs=NAME | --standarddirs=NAME
+          Here, "NAME" specifies a list of directories to be
+          used as the "standard" code.
+
+    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
+      -fc=NAME | --fc=NAME
+          Use "NAME" as the fortran compiler.  By default, genmake
+          will search for a working compiler by trying a list of
+          "usual suspects" such as g77, f77, etc.
+
+    -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
+          Use "NAME" as the C compiler.  By default, genmake
+          will search for a working compiler by trying a list of
+          "usual suspects" such as gcc, c89, cc, etc.
+
+    -[no]ieee | --[no]ieee
+          Do or don't use IEEE numerics.  Note that this option
+          *only* works if it is supported by the OPTFILE that
+          is being used.
+
+    -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
+          Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
+          *only* works if CPP_EEOPTIONS.h allows this.
+
+    -ignoretime | -ignore_time | --ignoretime | --ignore_time
+          Ignore all the "wall clock" routines entirely.  This will
+          not in any way hurt the model results -- it simply means
+          that the code that checks how long the model spends in
+          various routines will give junk values.
+
+    -ts | --ts
+          Produce timing information per timestep
+    -papis | --papis
+          Produce summary MFlop/s (and IPC) with PAPI per timestep
+    -pcls | --pcls
+          Produce summary MFlop/s etc. with PCL per timestep
+    -foolad | --foolad
+          Fool the AD code generator
+    -papi | --papi
+          Performance analysis with PAPI
+    -pcl | --pcl
+          Performance analysis with PCL
+    -hpmt | --hpmt
+          Performance analysis with the HPM Toolkit
+
+    -gsl | --gsl
+          Use GSL to control floating point rounding and precision
+    -devel | --devel
+          Add additional warning and debugging flags for development
+
+    -mpi | --mpi
+          Include MPI header files and link to MPI libraries
+    -mpi=PATH | --mpi=PATH
+          Include MPI header files and link to MPI libraries using MPI_ROOT
+          set to PATH. i.e. Include files from \$PATH/include, link to libraries
+          from \$PATH/lib and use binaries from \$PATH/bin.
+
+    -omp | --omp
+          Activate OpenMP code + use Compiler option OMPFLAG
+    -omp=OMPFLAG | --omp=OMPFLAG
+          Activate OpenMP code + use Compiler option OMPFLAG
+
+    -es | --es | -embed-source | --embed-source
+          Embed a tarball containing the full source code
+          (including the Makefile, etc.) used to build the
+          executable [off by default]
+
+    -ds | --ds
+          Report genmake internal variables status (DUMPSTATE)
+          to file "genmake_state" (for debug purpose)
+
+  While it is most often a single word, the "NAME" variables specified
+  above can in many cases be a space-delimited string such as:
+
+    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
+    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
+    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'
+
+  which, depending upon your shell, may need to be single-quoted.
+
+  For more detailed genmake documentation, please see:
+
+    http://mitgcm.org/public/devel_HOWTO/
+
+EOF
+
+    exit 1
+}
+
 # Search for particular CPP #cmds associated with packages
 # usage: test_for_package_in_cpp_options CPP_file package_name
 test_for_package_in_cpp_options() {
@@ -56,7 +218,6 @@
 # the package list.
 expand_pkg_groups() {
     new_packages=
-    PKG_GROUPS=$ROOTDIR"/pkg/pkg_groups"
     if test -r $PKG_GROUPS ; then
 	cat $PKG_GROUPS | sed -e 's/#.*$//g' | sed -e 's/:/ : /g' > ./p1.tmp
 	cat ./p1.tmp | $AWK '(NF>2 && $2==":"){ print $0 }' > ./p2.tmp
@@ -67,7 +228,7 @@
 	    if test "x$RETVAL" = x0 ; then
 		matched=1
 		replace=`echo $line | $AWK '{ $1=""; $2=""; print $0 }'`
-		echo "    replacing \"$i\" with: $replace"
+		echo "    replacing \"$i\" with:$replace"
 		new_packages="$new_packages $replace"
 	    else
 		new_packages="$new_packages $i"
@@ -165,7 +326,6 @@
     return
 }
 
-
 look_for_makedepend()  {
 
     #  The "original" makedepend is part of the Imake system that is
@@ -186,6 +346,22 @@
     #    3) locally build and use the cyrus implementation
     #    4) fall back to the buggy local xmakedpend script
     #
+    echo >> $LOGFILE
+    echo "running: look_for_makedepend()" >> $LOGFILE
+    if test "x${MAKEDEPEND}" != x ; then
+	echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
+	RETVAL=$?
+	if test x"$RETVAL" = x0 ; then
+	    build_cyrus_makedepend
+	    RETVAL=$?
+	    if test "x$RETVAL" != x0 ; then
+		echo "WARNING: unable to build cyrus-makedepend. Try 'makedepend'"
+		MAKEDEPEND=
+	    fi
+	else
+	    echo " -->     MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
+	fi
+    fi
     if test "x${MAKEDEPEND}" = x ; then
 	which makedepend > /dev/null 2>&1
 	RV0=$?
@@ -210,29 +386,24 @@
 	test -f $MAKEFILE".tst"  &&  mv -f $MAKEFILE".tst" $MAKEFILE
 	if test "x${RV0}${RV1}" = x00 ; then
 	    MAKEDEPEND=makedepend
+	    echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
 	else
-	    echo "    a system-default makedepend was not found."
-
+	    echo "    system-default makedepend not found. Try to build cyrus-makedepend"
 	    #  Try to build the cyrus implementation
 	    build_cyrus_makedepend
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
+		echo "WARNING: unable to build cyrus-makedepend. Use local xmakedepend"
 		MAKEDEPEND='$(TOOLSDIR)/xmakedepend'
+		echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
 	    fi
-	    rm -f ./genmake_cy_md
-	fi
-    else
-	#  echo "MAKEDEPEND=${MAKEDEPEND}"
-	echo "${MAKEDEPEND}" | grep -i cyrus > /dev/null 2>&1
-	RETVAL=$?
-	if test x"$RETVAL" = x0 ; then
-	    build_cyrus_makedepend
 	fi
     fi
 }
 
-
 build_cyrus_makedepend()  {
+    echo >> $LOGFILE
+    echo "running: build_cyrus_makedepend()" >> $LOGFILE
     rm -f ./genmake_cy_md
     (
 	cd $ROOTDIR/tools/cyrus-imapd-makedepend  \
@@ -249,14 +420,14 @@
     rm -f ./genmake_cy_md
     if test "x$RETVAL" = x0 ; then
 	MAKEDEPEND='$(TOOLSDIR)/cyrus-imapd-makedepend/makedepend'
+ 	echo " --> set MAKEDEPEND=${MAKEDEPEND}" >> $LOGFILE
 	return 0
     else
-	echo "WARNING: unable to build cyrus-imapd-makedepend"
+	echo "WARNING: fail to build cyrus-imapd-makedepend" >> $LOGFILE
 	return 1
     fi
 }
 
-
 build_embed_encode()
 {
     printf "  building the embed-encode utility...  "
@@ -290,55 +461,27 @@
     DEFINES="$DEFINES -DHAVE_EMBED_SRC"
 }
 
-
-# Guess possible config options for this host
-find_possible_configs()  {
-
-    tmp1=`uname`"_"`uname -m`
-    tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
-    tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
-    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/'`
-    tmp3=`echo $tmp2 | sed -e 's/cray sv1/craysv1/'`
-    PLATFORM=$tmp3
-    echo $PLATFORM | grep cygwin > /dev/null 2>&1  &&  PLATFORM=cygwin_ia32
-    OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
-    echo "  The platform appears to be:  $PLATFORM"
-
-    echo "test" > test
-    ln -s ./test link
-    RETVAL=$?
-    if test "x${RETVAL}" = x0 ; then
-	LN="ln -s"
-    else
-	echo "Error: \"ln -s\" does not appear to work on this system!"
-	echo "  For help, please contact <MITgcm-support@mitgcm.org>."
-	exit 1
-    fi
-    rm -f test link
-
-    if test "x$CPP" = x ; then
-	CPP="cpp -traditional -P"
-    fi
-
-    look_for_makedepend
-
-    #================================================================
-    #  look for possible C compilers
-    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
-    p_CC=
-    for c in $tmp ; do
-	rm -f ./genmake_hello.c  ./genmake_hello
-	cat >> genmake_hello.c << EOF
+#  look for possible C compilers
+look_for_C_compilers() {
+    echo >> $LOGFILE
+    echo "running: look_for_C_compilers()" >> $LOGFILE
+    rm -f ./genmake_hello.c  ./genmake_hello
+    cat >> genmake_hello.c << EOF
 #include <stdio.h>
 int main(int argc, char **argv) {
   printf("Hello!\n");
   return 0;
 }
 EOF
-	$c -o genmake_hello genmake_hello.c > /dev/null 2>&1
+    tmp="$MITGCM_CC $CC gcc c89 cc c99 mpicc icc"
+    p_CC=
+    for c in $tmp ; do
+	COMM="$c $CFLAGS -o genmake_hello genmake_hello.c"
+	echo $COMM >> $LOGFILE
+	$COMM >> $LOGFILE 2>&1
 	RETVAL=$?
 	if test "x${RETVAL}" = x0 ; then
+	    echo " $c test successful" >> $LOGFILE
 	    p_CC="$p_CC $c"
 	fi
     done
@@ -354,34 +497,55 @@
 EOF
 	exit 1
     else
-	echo "  The possible C compilers found in your path are:"
-	echo "   "$p_CC
+	echo "  The possible C compilers found in your path are: $p_CC" | tee -a $LOGFILE
 	if test "x$CC" = x ; then
 	    CC=`echo $p_CC | $AWK '{print $1}'`
 	    echo "  Setting C compiler to: "$CC
 	fi
     fi
+    echo " --> set CC='$CC'" >> $LOGFILE
+}
+
+# Guess possible config options for this host
+find_possible_optfile()  {
+
+    echo >> $LOGFILE
+    echo "running: find_possible_optfile()" >> $LOGFILE
+    tmp1=`uname`"_"`uname -m`
+    tmp2=`echo $tmp1 | sed -e 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
+    tmp3=`echo $tmp2 | sed -e 's/power macintosh/ppc/'`
+    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/'`
+    tmp3=`echo $tmp2 | sed -e 's/cray sv1/craysv1/'`
+    PLATFORM=$tmp3
+    echo $PLATFORM | grep cygwin > /dev/null 2>&1  &&  PLATFORM=cygwin_ia32
+    OFLIST=`(cd $ROOTDIR/tools/build_options; ls | grep "^$PLATFORM")`
+    echo "  The platform appears to be:  $PLATFORM" | tee -a $LOGFILE
 
     #================================================================
     #  look for possible FORTRAN compilers
-    tmp="$MITGCM_FC $FC efc g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 gfortran g95"
+    echo "  look for possible FORTRAN compilers" >> $LOGFILE
+    tmp="$MITGCM_FC $FC efc gfortran g77 f77 pgf77 pgf95 ifc ifort f90 f95 mpif77 mpf77 mpxlf95 g95"
     p_FC=
-    for c in $tmp ; do
-	rm -f ./hello.f ./hello
-	cat >> hello.f <<EOF
+    rm -f ./genmake_hello.f
+    cat >> genmake_hello.f <<EOF
       program hello
       do i=1,3
         print *, 'hello world : ', i
       enddo
       end
 EOF
-	$c -o hello hello.f > /dev/null 2>&1
+    for f in $tmp ; do
+	COMM="$f -o genmake_hello genmake_hello.f"
+	echo $COMM >> $LOGFILE
+	$COMM >> $LOGFILE 2>&1
 	RETVAL=$?
 	if test "x${RETVAL}" = x0 ; then
-	    p_FC="$p_FC $c"
+	    echo " $f test successful" >> $LOGFILE
+	    p_FC="$p_FC $f"
 	fi
     done
-    rm -f ./hello.f ./hello
+    rm -f ./genmake_hello.f ./genmake_hello
     if test "x${p_FC}" = x ; then
 	cat 1>&2 <<EOF
 
@@ -394,8 +558,7 @@
 EOF
 	exit 1
     else
-	echo "  The possible FORTRAN compilers found in your path are:"
-	echo "   "$p_FC
+	echo "  The possible FORTRAN compilers found in your path are: $p_FC" | tee -a $LOGFILE
     fi
 
     #  Use the first of the compilers found in the current PATH
@@ -404,7 +567,7 @@
 	for i in $p_FC ; do
 	    OPTFILE=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
 	    if test -r $OPTFILE ; then
-		echo "  Setting OPTFILE to: "$OPTFILE
+		echo "  Setting OPTFILE to: "$OPTFILE | tee -a $LOGFILE
 		break
 	    fi
 	done
@@ -416,17 +579,7 @@
              echo "  I looked for the file "$OPTFILE" but did not find it"
         fi
     fi
-#    echo "  The options file:  $p_OF"
-#    echo "    appears to match so we'll use it."
-#   for i in $p_FC ; do
-#p_OF=$ROOTDIR"/tools/build_options/"$PLATFORM"_"$i
-#if test -r $p_OF ; then
-#    OPTFILE=$p_OF
-#    echo "  The options file:  $p_OF"
-#    echo "    appears to match so we'll use it."
-#    break
-#fi
-#   done
+
     if test "x$OPTFILE" = x ; then
 	cat 1>&2 <<EOF
 
@@ -471,7 +624,6 @@
 # 	fi
 # 	rm -f test.f out
 #     fi
-
 }
 
 #  Parse the package dependency information
@@ -484,170 +636,11 @@
 	> ./.pd_tmp
     RETVAL=$?
     if test ! "x${RETVAL}" = x0 ; then
-      echo "Error: unable to parse package dependencies -- please check PDEPEND=\"$1\""
+      echo "Error: unable to parse package dependencies -- please check PKG_DEPEND=\"$1\""
       exit 1
     fi
     . ./.pd_tmp
     rm -f ./.pd_tmp
-
-}
-
-
-#  Explain usage
-usage()  {
-cat <<EOF
-
-Usage: "$0" [OPTIONS]
-  where [OPTIONS] can be:
-
-    -help | --help | -h | --h
-          Print this help message and exit.
-
-    -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_default" will be used.
-
-    -nooptfile | --nooptfile
-      -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
-          tools/build_options/ directory.
-
-    -pdepend NAME | --pdepend NAME
-      -pdepend=NAME | --pdepend=NAME
-          Get package dependency information from "NAME".
-
-    -pdefault NAME | --pdefault NAME
-      -pdefault=NAME | --pdefault=NAME
-          Get the default package list from "NAME".
-
-    -bash NAME
-          Explicitly specify the Bourne or BASH shell to use
-
-    -make NAME | -m NAME
-      --make=NAME | -m=NAME
-          Use "NAME" for the MAKE program. The default is "make" but
-          many platforms, "gmake" is the preferred choice.
-
-    -makefile NAME | -mf NAME
-      --makefile=NAME | -mf=NAME
-          Call the makefile "NAME".  The default is "Makefile".
-
-    -makedepend NAME | -md NAME
-      --makedepend=NAME | -md=NAME
-          Use "NAME" for the MAKEDEPEND program.
-
-    -rootdir NAME | --rootdir NAME | -rd NAME | --rd NAME
-      -rootdir=NAME | --rootdir=NAME | -rd=NAME | --rd=NAME
-          Specify the location of the MITgcm ROOTDIR as "NAME".
-          By default, genamke will try to find the location by
-          looking in parent directories (up to the 5th parent).
-
-    -mods NAME | --mods NAME | -mo NAME | --mo NAME
-      -mods=NAME | --mods=NAME | -mo=NAME | --mo=NAME
-          Here, "NAME" specifies a list of directories that are
-          used for additional source code.  Files found in the
-          "mods list" are given preference over files of the same
-          name found elsewhere.
-
-    -disable NAME | --disable NAME
-      -disable=NAME | --disable=NAME
-          Here "NAME" specifies a list of packages that we don't
-          want to use.  If this violates package dependencies,
-          genamke will exit with an error message.
-
-    -enable NAME | --enable NAME
-      -enable=NAME | --enable=NAME
-          Here "NAME" specifies a list of packages that we wish
-          to specifically enable.  If this violates package
-          dependencies, genamke will exit with an error message.
-
-    -standarddirs NAME | --standarddirs NAME
-      -standarddirs=NAME | --standarddirs=NAME
-          Here, "NAME" specifies a list of directories to be
-          used as the "standard" code.
-
-    -fortran NAME | --fortran NAME | -fc NAME | --fc NAME
-      -fc=NAME | --fc=NAME
-          Use "NAME" as the fortran compiler.  By default, genmake
-          will search for a working compiler by trying a list of
-          "usual suspects" such as g77, f77, etc.
-
-    -cc NAME | --cc NAME | -cc=NAME | --cc=NAME
-          Use "NAME" as the C compiler.  By default, genmake
-          will search for a working compiler by trying a list of
-          "usual suspects" such as gcc, c89, cc, etc.
-
-    -[no]ieee | --[no]ieee
-          Do or don't use IEEE numerics.  Note that this option
-          *only* works if it is supported by the OPTFILE that
-          is being used.
-
-    -use_real4 | -use_r4 | -ur4 | --use_real4 | --use_r4 | --ur4
-          Use "real*4" type for _RS variable (#undef REAL4_IS_SLOW)
-          *only* works if CPP_EEOPTIONS.h allows this.
-
-    -ignoretime | -ignore_time | --ignoretime | --ignore_time
-          Ignore all the "wall clock" routines entirely.  This will
-          not in any way hurt the model results -- it simply means
-          that the code that checks how long the model spends in
-          various routines will give junk values.
-
-    -ts | --ts
-          Produce timing information per timestep
-    -papis | --papis
-          Produce summary MFlop/s (and IPC) with PAPI per timestep
-    -pcls | --pcls
-          Produce summary MFlop/s etc. with PCL per timestep
-    -foolad | --foolad
-          Fool the AD code generator
-    -papi | --papi
-          Performance analysis with PAPI
-    -pcl | --pcl
-          Performance analysis with PCL
-    -hpmt | --hpmt
-          Performance analysis with the HPM Toolkit
-
-    -gsl | --gsl
-          Use GSL to control floating point rounding and precision
-    -devel | --devel
-          Add additional warning and debugging flags for development
-
-    -mpi | --mpi
-          Include MPI header files and link to MPI libraries
-    -mpi=PATH | --mpi=PATH
-          Include MPI header files and link to MPI libraries using MPI_ROOT
-          set to PATH. i.e. Include files from \$PATH/include, link to libraries
-          from \$PATH/lib and use binaries from \$PATH/bin.
-
-    -omp | --omp
-          Activate OpenMP code + use Compiler option OMPFLAG
-    -omp=OMPFLAG | --omp=OMPFLAG
-          Activate OpenMP code + use Compiler option OMPFLAG
-
-    -es | --es | -embed-source | --embed-source
-          Embed a tarball containing the full source code
-          (including the Makefile, etc.) used to build the
-          executable [off by default]
-
-  While it is most often a single word, the "NAME" variables specified
-  above can in many cases be a space-delimited string such as:
-
-    --enable pkg1   --enable 'pkg1 pkg2'   --enable 'pkg1 pkg2 pkg3'
-    -mods=dir1   -mods='dir1'   -mods='dir1 dir2 dir3'
-    -foptim='-Mvect=cachesize:512000,transform -xtypemap=real:64,double:64,integer:32'
-
-  which, depending upon your shell, may need to be single-quoted.
-
-  For more detailed genmake documentation, please see:
-
-    http://mitgcm.org/public/devel_HOWTO/
-
-EOF
-
-    exit 1
 }
 
 #  Build a CPP macro to automate calling C routines from FORTRAN
@@ -657,21 +650,24 @@
     if test ! "x$FC_NAMEMANGLE" = x ; then
         return 0
     fi
+    echo " running: get_fortran_c_namemangling()" >> $LOGFILE
 
     default_nm="#define FC_NAMEMANGLE(X) X ## _"
 
     cat > genmake_test.c <<EOF
 void tcall( char * string ) { tsub( string ); }
 EOF
-    $MAKE genmake_test.o >> genmake_warnings 2>&1
+    COMM="$CC $CFLAGS -c genmake_test.c"
+    echo ' '$COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_errors
+	cat <<EOF>> $LOGFILE
 
-WARNING: C test compile fails
-WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
-WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+ WARNING: C test compile fails
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
 EOF
 	return 1
     fi
@@ -679,11 +675,11 @@
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
-WARNING: The "nm" command failed.
-WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
-WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
+ WARNING: The "nm" command failed.
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here
 EOF
 	return 1
     fi
@@ -693,15 +689,17 @@
       call tsub( string )
       end
 EOF
-    $FC $FFLAGS -c genmake_tcomp.$FS >> genmake_warnings 2>&1
+    COMM="$FC $FFLAGS -c genmake_tcomp.$FS"
+    echo ' '$COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
-WARNING: FORTRAN test compile fails -- please see "genmake_errors"
-WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
-WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+ WARNING: FORTRAN test compile fails -- please see '$LOGFILE'
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
 EOF
 	return 1
     fi
@@ -709,11 +707,11 @@
     RETVAL=$?
     if test "x$RETVAL" != x0 ; then
 	FC_NAMEMANGLE=$default_nm
-	cat <<EOF>> genmake_warnings
+	cat <<EOF>> $LOGFILE
 
-WARNING: The "nm" command failed.
-WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
-WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
+ WARNING: The "nm" command failed.
+ WARNING: We'll try to use: FC_NAMEMANGLE='$FC_NAMEMANGLE'
+ WARNING: Please contact <MITgcm-support@mitgcm.org> if you need help here.
 EOF
 	return 1
     fi
@@ -739,10 +737,13 @@
 
     #  cleanup the testing files
     rm -f genmake_tcomp.* genmake_test.*
-}
 
+    echo " --> set FC_NAMEMANGLE='$FC_NAMEMANGLE'" >> $LOGFILE
+}
 
 check_HAVE_CLOC()  {
+    echo >> $LOGFILE
+    echo "running: check_HAVE_CLOC()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -760,8 +761,8 @@
 }
 EOF
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -772,23 +773,25 @@
       end
 EOF
     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_F=$?
-    test -x ./genmake_tc  &&  ./genmake_tc >> genmake_warnings 2>&1
+    test -x ./genmake_tc  &&  ./genmake_tc >> $LOGFILE 2>&1
     RETVAL=$?
     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
 }
 
-
 check_HAVE_SIGREG()  {
     if test ! "x$HAVE_SIGREG" = x ; then
 	return
     fi
+    echo >> $LOGFILE
+    echo "running: check_HAVE_SIGREG()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -821,8 +824,8 @@
 }
 EOF
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -832,21 +835,19 @@
       call sigreg(anint)
       end
 EOF
-    echo >> genmake_warnings
-    echo "running: check_HAVE_SIGREG()" >> genmake_warnings
-    cat genmake_tc_2.$FS >> genmake_warnings
+    cat genmake_tc_2.$FS >> $LOGFILE
     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RETVAL=$?
     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"
@@ -855,6 +856,8 @@
     if test ! "x$HAVE_SETRLSTK" = x ; then
 	return
     fi
+    echo >> $LOGFILE
+    echo "running: check_HAVE_SETRLSTK()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -871,8 +874,8 @@
 }
 EOF
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
       program hello
@@ -880,22 +883,22 @@
       call setrlstk()
       end
 EOF
-    echo >> genmake_warnings
-    echo "running: check_HAVE_SETRLSTK()" >> genmake_warnings
-    cat genmake_tc_2.$FS >> genmake_warnings
+    cat genmake_tc_2.$FS >> $LOGFILE
     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-    echo $COMM >> genmake_warnings
-    $COMM >> genmake_warnings 2>&1
+    echo $COMM >> $LOGFILE
+    $COMM >> $LOGFILE 2>&1
     RETVAL=$?
     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
 }
 
-
 check_HAVE_STAT()  {
+    echo >> $LOGFILE
+    echo "running: check_HAVE_STAT()" >> $LOGFILE
     get_fortran_c_namemangling
     cat <<EOF > genmake_tc_1.c
 $FC_NAMEMANGLE
@@ -917,7 +920,7 @@
 }
 EOF
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
-    echo $COMM >> genmake_warnings
+    echo $COMM >> $LOGFILE
     $COMM >> genmake_tc.log 2>&1
     RET_C=$?
     cat <<EOF > genmake_tc_2.$FS
@@ -927,11 +930,9 @@
       print *," HELLO WORLD", nbyte
       end
 EOF
-    echo >> genmake_warnings
-    echo "running: check_HAVE_STAT()" >> genmake_warnings
-    cat genmake_tc_2.$FS >> genmake_warnings
+    cat genmake_tc_2.$FS >> $LOGFILE
     COMM="$FC $FFLAGS -o genmake_tc genmake_tc_2.$FS genmake_tc_1.o"
-    echo $COMM >> genmake_warnings
+    echo $COMM >> $LOGFILE
     $COMM >> genmake_tc.log 2>&1
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
@@ -939,15 +940,15 @@
 	DEFINES="$DEFINES -DHAVE_STAT"
     fi
     rm -f genmake_tc*
+    echo " --> set HAVE_STAT='$HAVE_STAT'" >> $LOGFILE
 }
 
-
 check_netcdf_libs()  {
     if test ! "x$SKIP_NETCDF_CHECK" = x ; then
 	return
     fi
-    echo >> genmake_warnings
-    echo "running: check_netcdf_libs()" >> genmake_warnings
+    echo >> $LOGFILE
+    echo "running: check_netcdf_libs()" >> $LOGFILE
     cat <<EOF > genmake_tnc.F
       program fgennc
 #include "netcdf.inc"
@@ -965,9 +966,9 @@
       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
       end
 EOF
-    echo "===  genmake_tnc.F  ===" > genmake_tnc.log
+    echo "===  genmake_tnc.F  >>>" > genmake_tnc.log
     cat genmake_tnc.F >> genmake_tnc.log
-    echo "===  genmake_tnc.F  ===" >> genmake_tnc.log
+    echo "<<<  genmake_tnc.F  ===" >> genmake_tnc.log
     RET_CPP=f
     COMM="cat genmake_tnc.F | $CPP $DEFINES $INCLUDES"
     echo "$COMM" >> genmake_tnc.log
@@ -983,7 +984,7 @@
     $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
 	&&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS >> genmake_tnc.log 2>&1
     RET_COMPILE=$?
-    cat genmake_tnc.log >> genmake_warnings
+    cat genmake_tnc.log >> $LOGFILE
 
     #EH3  Remove test program execution for machines that either disallow
     #EH3  execution or cannot support it (eg. cross-compilers)
@@ -994,9 +995,10 @@
 
     if test "x$RET_COMPILE" = x0 ; then
 	HAVE_NETCDF=t
+	echo "check_netcdf: successful" >> $LOGFILE
     else
 	# try again with "-lnetcdf" added to the libs
-	echo "try again with added '-lnetcdf'" > genmake_tnc.log
+	echo "==> try again with added '-lnetcdf'" > genmake_tnc.log
 	echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
 	echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
 	echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
@@ -1004,13 +1006,15 @@
 	    &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
 	    &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf >> genmake_tnc.log 2>&1
 	RET_COMPILE=$?
-	cat genmake_tnc.log >> genmake_warnings
+	echo >> $LOGFILE
+	cat genmake_tnc.log >> $LOGFILE
 	if test "x$RET_COMPILE" = x0 ; then
 	    LIBS="$LIBS -lnetcdf"
 	    HAVE_NETCDF=t
+	    echo "check_netcdf: successful" >> $LOGFILE
 	else
 	# try again with "-lnetcdff" added to the libs
-	    echo "try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
+	    echo "==> try again with added '-lnetcdff -lnetcdf'" > genmake_tnc.log
 	    echo "cat genmake_tnc.F | $CPP $DEFINES $INCLUDES > genmake_tnc.$FS \ " >> genmake_tnc.log
 	    echo " &&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS \ " >> genmake_tnc.log
 	    echo " &&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdf" >> genmake_tnc.log
@@ -1018,18 +1022,20 @@
 		&&  $FC $FFLAGS $FOPTIM -c genmake_tnc.$FS >> genmake_tnc.log 2>&1  \
 		&&  $LINK $FFLAGS $FOPTIM -o genmake_tnc genmake_tnc.o $LIBS -lnetcdff -lnetcdf >> genmake_tnc.log 2>&1
 	    RET_COMPILE=$?
-	    cat genmake_tnc.log >> genmake_warnings
+	    echo >> $LOGFILE
+	    cat genmake_tnc.log >> $LOGFILE
 	    if test "x$RET_COMPILE" = x0 ; then
 		LIBS="$LIBS -lnetcdff -lnetcdf"
 		HAVE_NETCDF=t
+		echo "check_netcdf: successful" >> $LOGFILE
 	    fi
 	fi
     fi
     rm -f genmake_tnc*
+    echo " --> set HAVE_NETCDF='$HAVE_NETCDF'" >> $LOGFILE
 }
 
 
-
 ###############################################################################
 #   Sequential part of script starts here
 ###############################################################################
@@ -1051,9 +1057,9 @@
 DISABLE=
 # MAKEFILE=
 # MAKEDEPEND=
-PDEPEND=
-DUMPSTATE=t
-PDEFAULT=
+PKG_DEPEND=
+PKG_GROUPS=
+DUMPSTATE=f
 OPTFILE=
 INCLUDES="-I. $INCLUDES"
 FFLAGS=
@@ -1061,6 +1067,7 @@
 FEXTRAFLAGS=
 USE_EXTENDED_SRC=
 EXTENDED_SRC_FLAG=
+GET_FC_VERSION=
 CFLAGS=
 KFLAGS1=
 KFLAGS2=
@@ -1138,17 +1145,16 @@
 SVD_TAMC_FLAGS=
 TAMC_EXTRA=
 
-
 #  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 USE_R4 TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP DUMPSTATE STANDARDDIRS"
+gm_s1="OPTFILE PKG_DEPEND PKG_GROUPS MAKEFILE MAKEDEPEND PLATFORM ROOTDIR MODS DISABLE ENABLE"
+gm_s2="FC CC IEEE USE_R4 TS PAPIS PCLS PAPI PCL HPMT GSL DEVEL MPI OMP 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 FEXTRAFLAGS"
-gm_s4="CFLAGS KFLAGS1 KFLAGS2 LIBS KPPFILES NOOPTFILES NOOPTFLAGS"
-gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOST THISUSER THISDATE THISVER MACHINE"
+gm_s3="LN S64 LINK MAKE PACKAGES INCLUDES FFLAGS FOPTIM FEXTRAFLAGS"
+gm_s4="CFLAGS LIBS KPP KFLAGS1 KFLAGS2 KPPFILES NOOPTFILES NOOPTFLAGS"
+gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD THISHOST THISUSER THISDATE THISVER MACHINE"
 gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
-gm_s7="HAVE_SYSTEM HAVE_FDATE FC_NAMEMANGLE HAVE_ETIME"
+gm_s7="FC_NAMEMANGLE HAVE_NETCDF HAVE_SYSTEM HAVE_FDATE HAVE_ETIME"
 
 #  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"
@@ -1162,13 +1168,17 @@
 
 GENMAKE :
 
-A program for GENerating MAKEfiles for the MITgcm project.  For a
-quick list of options, use "genmake -h" or for more detail see:
-
-  http://mitgcm.org/devel_HOWTO/
+A program for GENerating MAKEfiles for the MITgcm project.
+   For a quick list of options, use "genmake2 -h"
+or for more detail see the Developer's HOWTO manual at:
+   http://mitgcm.org/public/docs.html
 
 EOF
 
+LOGFILE="genmake.log"
+#- clean-up previous genmake logfiles:
+rm -f genmake_state genmake_*optfile $LOGFILE
+
 echo "===  Processing options files and arguments  ==="
 gm_local="genmake_local"
 printf "  getting local config information:  "
@@ -1215,14 +1225,14 @@
 	    AD_OPTFILE=$ac_optarg ;;
 	
 	-pdepend | --pdepend)
-	    ac_prev=PDEPEND ;;
+	    ac_prev=PKG_DEPEND ;;
 	-pdepend=* | --pdepend=*)
-	    PDEPEND=$ac_optarg ;;
+	    PKG_DEPEND=$ac_optarg ;;
 	
-	-pdefault | --pdefault)
-	    ac_prev=PDEFAULT ;;
-	-pdefault=* | --pdefault=*)
-	    PDEFAULT=$ac_optarg ;;
+	-pgroups | --pgroups)
+	    ac_prev=PKG_GROUPS ;;
+	-pgroups=* | --pgroups=*)
+	    PKG_GROUPS=$ac_optarg ;;
 	
 	-make | --make | -m | --m)
 	    ac_prev=MAKE ;;
@@ -1375,7 +1385,6 @@
 
 done
 
-
 if test -f ./.genmakerc ; then
     echo
     echo "WARNING: genmake2 has detected a copy of the old-style \"./.genmakerc\""
@@ -1396,8 +1405,8 @@
 	for d in . .. ../.. ../../.. ../../../.. ../../../../.. ; do
 	    if [ -d "$d/model" -a -d "$d/eesupp" -a -d "$d/pkg" ]; then
 		ROOTDIR=$d
-		printf "Warning:  ROOTDIR was not specified but there appears to be"
-		echo " a copy of MITgcm at \"$ROOTDIR\" so we'll try it."
+		printf "Warning: ROOTDIR was not specified ;"
+		echo " try using a local copy of MITgcm found at \"$ROOTDIR\""
 		break
 	    fi
 	done
@@ -1434,7 +1443,7 @@
     if test "x$MITGCM_OF" = x ; then
 	echo "Warning: no OPTFILE specified so we'll look for possible settings"
 	printf "\n===  Searching for possible settings for OPTFILE  ===\n"
-	find_possible_configs
+	find_possible_optfile
     else
 	OPTFILE=$MITGCM_OF
     fi
@@ -1449,7 +1458,7 @@
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
-	if test "x$DUMPSTATE" != xf ; then
+	if test "x$DUMPSTATE" = xt ; then
 	    cp -f $OPTFILE "genmake_optfile"
 	fi
     else
@@ -1476,7 +1485,7 @@
 	    echo "--please check that variable syntax is bash-compatible"
 	    exit 1
 	fi
-	if test "x$DUMPSTATE" != xf ; then
+	if test "x$DUMPSTATE" = xt ; then
 	    cp -f $AD_OPTFILE "genmake_ad_optfile"
 	fi
     else
@@ -1504,16 +1513,16 @@
 EOF
     exit 1
 fi
+if test "x$GET_FC_VERSION" != x ; then
+  echo "Get compiler version using: $FC $GET_FC_VERSION" >> $LOGFILE
+  $FC $GET_FC_VERSION >> $LOGFILE 2>&1
+  echo "<-- compiler version ----" >> $LOGFILE
+fi
+
 if test "x$CC" = x ; then
-    CC=cc
-#     cat <<EOF 1>&2
-# Error: no C compiler: please specify using one of the following:
-#   1) within the options file ("CC=...") as specified by "-of=OPTFILE"
-#   2) the "-cc=XXX" command-line option
-#   3) the "./genmake_local" file
-# EOF
-#     exit 1
+    look_for_C_compilers
 fi
+
 if test "x$LINK" = x ; then
     LINK=$FC
 fi
@@ -1521,7 +1530,7 @@
     MAKE="make"
 fi
 if test "x$CPP" = x ; then
-    CPP=cpp
+    CPP="cpp -traditional -P"
 fi
 #EH3 === UGLY ===
 #  The following is an ugly little hack to check for $CPP in /lib/ and
@@ -1548,7 +1557,10 @@
 else
     rm -f test_cpp
 fi
+
 look_for_makedepend
+
+#  Check that soft-link command is set and usable
 if test "x$LN" = x ; then
     LN="ln -s"
 fi
@@ -1558,7 +1570,7 @@
 if test "x$RETVAL" != x0 ; then
     cat <<EOF 1>&2
 
-Error: The command "ln -s" failed -- please specify a working soft-link
+Error: The command "$LN" failed -- please specify a working soft-link
   command in the optfile.
 
 EOF
@@ -1795,7 +1807,6 @@
     ENABLE="$ENABLE embed_files"
 fi
 
-
 printf "\n===  Setting defaults  ===\n"
 printf "  Adding MODS directories: "
 for d in $MODS ; do
@@ -1811,9 +1822,9 @@
 done
 echo
 
-if test "x${PLATFORM}" = x ; then
-    PLATFORM=$p_PLATFORM
-fi
+#if test "x${PLATFORM}" = x ; then
+#    PLATFORM=$p_PLATFORM
+#fi
 
 if test "x${EXEDIR}" = x ; then
     tmp=`echo $PWD | sed -e 's/\// /g' | $AWK '{print $NR}'`
@@ -1883,7 +1894,8 @@
 #  they appear as regular source code
 if test -r $ROOTDIR"/eesupp/src/Makefile" ; then
     echo "  Making source files in eesupp from templates"
-    ( cd $ROOTDIR"/eesupp/src/" && $MAKE ) > make_eesupp.errors 2>&1
+    ( cd $ROOTDIR"/eesupp/src/" && $MAKE clean_old && $MAKE \
+    ) > make_eesupp.errors 2>&1
     RETVAL=$?
     if test "x${RETVAL}" = x0 ; then
 	rm -f make_eesupp.errors
@@ -1898,7 +1910,8 @@
 for pdir in exch2 regrid ; do
     if test -r $ROOTDIR"/pkg/${pdir}/Makefile" ; then
 	echo "  Making source files in pkg/${pdir} from templates"
-	( cd $ROOTDIR"/pkg/"${pdir} && $MAKE ) > make_${pdir}.errors 2>&1
+	( cd $ROOTDIR"/pkg/"${pdir} && $MAKE clean_old && $MAKE \
+	) > make_${pdir}.errors 2>&1
 	RETVAL=$?
 	if test "x${RETVAL}" = x0 ; then
 	    rm -f make_${pdir}.errors
@@ -1911,64 +1924,83 @@
 done
 
 printf "\n===  Determining package settings  ===\n"
-if  test "x${PDEPEND}" = x ; then
+if  test "x${PKG_DEPEND}" = x ; then
     tmp=$ROOTDIR"/pkg/pkg_depend"
-    if test -r $tmp ; then
-	PDEPEND=$tmp
-    else
+    if test -r $tmp ; then PKG_DEPEND=$tmp ; fi
+fi
+if  test "x${PKG_DEPEND}" = x ; then
 	echo "Warning:  No package dependency information was specified."
 	echo "  Please check that ROOTDIR/pkg/pkg_depend exists."
+else
+    if test ! -r ${PKG_DEPEND} ; then
+	echo "Error:  can't read package dependency info from PKG_DEPEND=\"$PKG_DEPEND\""
+	exit 1
     fi
+    echo "  getting package dependency info from  $PKG_DEPEND"
+#  Strip the comments and then convert the dependency file into arrays: PNAME, DNAME
+    get_pdepend_list $PKG_DEPEND
+fi
+
+# A default package groups file "$ROOTDIR/pkg/pkg_groups" is provided
+#  to define the "default_pkg_list" and package groups (for convenience, one
+#  can specify a group of packages using names like "ocean" and "atmosphere").
+if test "x${PKG_GROUPS}" = x ; then
+    tmp=$ROOTDIR"/pkg/pkg_groups"
+    if test -r $tmp ; then PKG_GROUPS=$tmp ; fi
+fi
+if test "x${PKG_GROUPS}" = x ; then
+	echo "Warning:  No package groups information was specified."
+	echo "  Please check that ROOTDIR/pkg/pkg_groups exists."
 else
-    if test ! -r ${PDEPEND} ; then
-	echo "Error:  can't read package dependency info from PDEPEND=\"$PDEPEND\""
+    if test ! -r ${PKG_GROUPS} ; then
+	echo "Error:  can't read package groups info from PKG_GROUPS=\"$PKG_GROUPS\""
 	exit 1
     fi
+    echo "  getting package groups info from      $PKG_GROUPS"
 fi
-echo "  getting package dependency info from  $PDEPEND"
-#  Strip the comments and then convert the dependency file into
-#  two arrays: PNAME, DNAME
-get_pdepend_list $PDEPEND
-
-#  Search for default packages.  Note that a "$ROOTDIR/pkg/pkg_groups"
-#  file has been added so that, for convenience, one can specify
-#  groups of packages using names like "ocean" and "atmosphere".
-echo "  checking default package list:  "
-if test "x${PDEFAULT}" = x ; then
+
+#  Search for packages to compile.
+echo "  checking list of packages to compile:"
+PKG_LIST=
+if test "x${PKG_LIST}" = x ; then
     for i in "." $MODS ; do
 	if test -r $i"/packages.conf" ; then
-		PDEFAULT=$i"/packages.conf"
+		PKG_LIST=$i"/packages.conf"
 		break
 	fi
     done
 fi
-if test "x${PDEFAULT}" = x ; then
-    PDEFAULT="$ROOTDIR/pkg/pkg_default"
-fi
-if test "x${PDEFAULT}" = xNONE ; then
-    echo "    default packages file disabled"
+if test "x${PKG_LIST}" = x ; then
+    pkg_list='default_pkg_list'
+    if test "x${PKG_GROUPS}" = x ; then
+	echo "Error:  need package groups info to expand pkg_list=\"$pkg_list\""
+	exit 1
+    fi
 else
-    if test ! -r $PDEFAULT ; then
-	echo "Warning:  can't read default packages from PDEFAULT=\"$PDEFAULT\""
+    if test ! -r $PKG_LIST ; then
+	echo "Error:  can't read package list from PKG_LIST=\"$PKG_LIST\""
+	exit 1
     else
-	echo "    using PDEFAULT=\"$PDEFAULT\""
+	echo "    using PKG_LIST=\"$PKG_LIST\""
         #  Strip the comments and add all the names
-	def=`cat $PDEFAULT | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
+	pkg_list=`cat $PKG_LIST | sed -e 's/#.*$//g' | $AWK '(NF>0){print $0}'`
 	RETVAL=$?
 	if test "x${RETVAL}" != x0 ; then
-	    printf "Error: can't parse default package list "
-	    echo "-- please check PDEFAULT=\"$PDEFAULT\""
+	    printf "Error: can't parse package list "
+	    echo "-- please check PKG_LIST=\"$PKG_LIST\""
 	    exit 1
 	fi
-	for i in $def ; do
-	    PACKAGES="$PACKAGES $i"
-	done
-	echo "    before group expansion packages are:$PACKAGES"
-	RET=1
-        while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
-	echo "    after group expansion packages are: $PACKAGES"
     fi
 fi
+for i in $pkg_list ; do
+    PACKAGES="$PACKAGES $i"
+done
+echo     "    before group expansion packages are:$PACKAGES"
+if test "x${PKG_GROUPS}" != x ; then
+    RET=1
+    while test $RET = 1 ; do expand_pkg_groups; RET=$?; done
+    echo "    after group expansion packages are: $PACKAGES"
+fi
 
 echo "  applying DISABLE settings"
 echo "" > ./.tmp_pack
@@ -1999,7 +2031,7 @@
 for i in $PACKAGES ; do
     j=`echo $i | sed 's/[-+]//'`
     if test ! -d "$ROOTDIR/pkg/$j" ; then
-	echo "Error: can't find package $i at \"$ROOTDIR/pkg/$i\""
+	echo "Error: dir '$ROOTDIR/pkg/$i' missing for package '$i'"
  	exit 1
     fi
     echo $i >> ./.tmp_pack
@@ -2018,7 +2050,6 @@
 if test "x$HAVE_NETCDF" != xt ; then
     if test "x$mnc_in" = x0 ; then
 	cat <<EOF
-
 *********************************************************************
 WARNING: the "mnc" package was enabled but tests failed to compile
   NetCDF applications.  Please check that:
@@ -2029,7 +2060,6 @@
 
   Due to this failure, the "mnc" package is now DISABLED.
 *********************************************************************
-
 EOF
 	PACKAGES=`echo $PACKAGES | sed -e 's/mnc//g'`
 	DISABLE="$DISABLE mnc"
@@ -2061,7 +2091,6 @@
     RETVAL=$?
     if test "x$RETVAL" = x0 ; then
 	cat <<EOF
-
 *********************************************************************
 WARNING: the "profiles" package was enabled but tests failed to
   compile NetCDF applications.  Please check that:
@@ -2072,7 +2101,6 @@
 
   Due to this failure, the "profiles" package is now DISABLED.
 *********************************************************************
-
 EOF
 	PACKAGES=`echo $PACKAGES | sed -e 's/profiles//g'`
 	DISABLE="$DISABLE profiles"
@@ -2082,9 +2110,10 @@
     fi
 fi
 
-echo "  applying package dependency rules"
-ck=
-while test "x$ck" != xtt ; do
+if  test "x${PKG_DEPEND}" != x ; then
+  echo "  applying package dependency rules"
+  ck=
+  while test "x$ck" != xtt ; do
     i=0
     # rtot=${#PNAME[@]}
     rtot=$nname
@@ -2155,8 +2184,9 @@
 	#i=$(( $i + 1 ))
     done
     ck=$ck"t"
-done
-echo "    packages are: $PACKAGES"
+  done
+  echo "    packages are: $PACKAGES"
+fi
 for i in $PACKAGES ; do
     adr="$ROOTDIR/pkg/$i"
     if test -d $adr ; then
@@ -2272,6 +2302,7 @@
     rm -f ./adSrcFiles.tmp
 fi
 echo "  Creating the list of files for the adjoint compiler."
+touch adSrcFiles.tmp
 for i in $SOURCEDIRS ; do
     list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
     for j in $list_files ; do
@@ -2668,28 +2699,34 @@
 	@printf 'running ... '
 	@\$(EXECUTABLE) > \$@
 
+# remove most of the files that "make" generates
 clean:
 	-rm -rf *.p *.$FS90 *.mod ${RMFILES} work.{pc,pcl} *.template
 	-rm -rf *.o
 	-rm -rf *.$FS *.flowdir
 	-rm -rf *.f$FS90 \$(AD_CLEAN) ad_input*
+
+# remove most of the files that "make" and "make depend" generate
 Clean:
 	@make clean
 	@make cleanlinks
-	-rm -f \$(SPECIAL_FILES)
-	-rm -f genmake_state genmake_*optfile genmake_warnings genmake_errors
-	-rm -f make.log run.log f90mkdepend.log *.bak "$MAKEFILE.old"
+	-rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
 	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.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 Clean
+	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.bak
+	-rm -f $LOGFILE genmake_state genmake_*optfile genmake.tr_log make.tr_log
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f \$(EXECUTABLE) \$(EXE_AD) *.txt STD* *diagnostics.log datetime
+	-rm -f *.txt STD* *diagnostics.log datetime
 	-rm -f *_MIT_CE_000.opt0000 costfunction*0000
 	-rm -rf mnc_test_*
 
-#eh3 Makefile: makefile
 makefile:
 	$THIS_SCRIPT $G2ARGS
 cleanlinks:
@@ -2745,6 +2782,8 @@
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 .$FS.o:
 	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
+.F.o:
+	\$(FC) \$(FFLAGS) \$(FOPTIM) -c \$<
 .F90.$FS90:
 	\$(CPP) \$(DEFINES) \$(INCLUDES) > \$@
 .FF90.f$FS90:
@@ -2879,7 +2918,6 @@
 ftl_tamc: ftl_tamc_output.o \$(OBJFILES)
 	\$(LINK) -o ${EXE_FTL} \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ftl_tamc_output.o \$(LIBS)
 
-
 # ... SVD ...
 svdtaf: ad_taf_output.$FS ftl_taf_output.$FS
 	@echo "--->>> Only ran TAF to generate SVD code!    <<<---"
@@ -3203,9 +3241,8 @@
     $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
 fi
 
-
 #  Write the "state" for future records
-if test "x$DUMPSTATE" != xf ; then
+if test "x$DUMPSTATE" = xt ; then
     printf "" > genmake_state
     for i in $gm_state ; do
 	t1="t2=\$$i"