--- MITgcm/tools/genmake2	2006/01/11 06:02:31	1.141
+++ MITgcm/tools/genmake2	2006/04/07 02:53:55	1.146
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.141 2006/01/11 06:02:31 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.146 2006/04/07 02:53:55 edhill Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -13,20 +13,28 @@
 test_for_package_in_cpp_options() {
     cpp_options=$1
     pkg=$2
-    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
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_$pkg$"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_$pkg$"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*DISABLE_$pkg$"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*DISABLE_$pkg$"
 }
 
 # 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
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI[ ]"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALLOW_USE_MPI$"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALLOW_USE_MPI$"
+    test_for_string_in_file $cpp_options "^[ ]*#define.*ALWAYS_USE_MPI$"
+    test_for_string_in_file $cpp_options "^[ ]*#undef.*ALWAYS_USE_MPI$"
 }
 
 # Search for particular string in a file. Return 1 if detected, 0 if not
@@ -39,7 +47,7 @@
     if test "x${RETVAL}" = x0 ; then
 	printf "Error: In $file there is an illegal line: "
         grep -i "$strng" $file
-	return 1
+	exit 99
     fi
     return 0
 }
@@ -570,6 +578,12 @@
           *only* works if it is supported by the OPTFILE that 
           is being used.
 
+    -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
@@ -2151,6 +2165,24 @@
 echo "  Determining the list of source and include files"
 rm -rf .links.tmp
 mkdir .links.tmp
+touch .links.tmp/foo
+if test ! -r ".links.tmp/foo" ; then
+    echo
+    echo "ERROR : something is wrong with your directory permissions or"
+    echo "   your user file-creation mask (\"umask\") since creating a"
+    echo "   sub-dir, touch-ing a file within it, and then reading it is"
+    echo "   not working.  Please try setting your umask to something"
+    echo "   sane such as:"
+    echo
+    echo "      umask 0002"
+    echo
+    echo "   and please verify that you have the proper permissions for"
+    echo "   creating sub-directories and then reading files created"
+    echo "   within them."
+    echo
+    exit 1
+fi
+rm -f .links.tmp/foo
 echo "# This section creates symbolic links" > srclinks.tmp
 echo "" >> srclinks.tmp
 printf 'SRCFILES = '    > srclist.inc
@@ -2398,7 +2430,8 @@
 	-find \$(EXEDIR) -name "*.meta" -exec rm {} \;
 	-find \$(EXEDIR) -name "*.data" -exec rm {} \;
 	-find \$(EXEDIR) -name "fort.*" -exec rm {} \;
-	-rm -f \$(EXECUTABLE) output.txt STD*
+	-rm -f \$(EXECUTABLE) *.txt STD* *diagnostics.log datetime
+	-rm -rf mnc_test_*
 
 #eh3 Makefile: makefile
 makefile: