--- MITgcm/verification/testreport	2003/10/03 05:12:18	1.9.2.4
+++ MITgcm/verification/testreport	2003/11/26 15:04:42	1.20
@@ -1,6 +1,7 @@
-#!/bin/bash
+#! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.9.2.4 2003/10/03 05:12:18 edhill Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.20 2003/11/26 15:04:42 edhill Exp $
+#  $Name:  $
 #
 
 usage()
@@ -11,17 +12,21 @@
     echo "where possible OPTIONS are:"
     echo "  (-help|-h)               print usage"
     echo "  (-mpi)                   use MPI input files"
+    echo "  (-ieee|-noieee)          if possible, use IEEE compiler flags"
+    echo "                             (DEF=\"noieee\")"
     echo "  (-optfile=|-of=)STRING   list of optfiles to use"
-    echo "  (-a|-addr)STRING         list of email recipients"
+    echo "  (-a|-addr) STRING        list of email recipients"
     echo "                             (DEF=\"edhill@mitgcm.org\")"
-    echo "  (-t|-tdir)STRING         list of test dirs to use"
+    echo "  (-t|-tdir) STRING        list of test dirs to use"
     echo "                             (DEF=\"\" which builds all)"
-    echo "  (-b|-bash)STRING         location of \"bash\" executable"
-    echo "                             (DEF=\"\" for \"/bin/bash\")"
-    echo "  (-c|-command)STRING      command to run"
+    echo "  (-b|-bash) STRING        preferred location of a \"bash\" or"
+    echo "                             Bourne-compatible \"sh\" shell"
+    echo "                             (DEF=\"\" for \"bash\")"
+    echo "  (-command) STRING        command to run"
     echo "                             (DEF=\"make output.txt\")"
-    echo "  (-m|-make)STRING         command to use for \"make\""
+    echo "  (-m|-make) STRING        command to use for \"make\""
     echo "                             (DEF=\"make\")"
+    echo "  (-clean)                 *ONLY* run \"make CLEAN\""
     echo "  (-quick|-q)              same as \"-nogenmake -noclean -nodepend\""
     echo "  (-nogenmake|-ng)         skip the genmake stage"
     echo "  (-noclean|-nc)           skip the \"make clean\" stage"
@@ -41,10 +46,12 @@
     echo -n "building the mpack utility...  "
     if test ! -x "$MPACKDIR/mpack" ; then
 	if test ! -d $MPACKDIR ; then
+	    echo
 	    echo "Error: can't find \"$MPACKDIR\""
 	    echo "  are you sure this program is being run in the correct "
 	    echo "  (that is, \"MITGCM_ROOT\verification\") directory?"
-	    exit 1
+	    echo
+	    HAVE_MPACK=f
 	fi
 	echo -n "building mpack...  "
 	( cd $MPACKDIR && ./configure && $MAKE ) > build_mpack.out 2>&1
@@ -52,8 +59,13 @@
 	if test "x$RETVAL" != x0 ; then
 	    echo
 	    echo "Error building the mpack tools at: $MPACK_DIR"
-	    exit 1
+	    echo
+	    HAVE_MPACK=f
+	else
+	    HAVE_MPACK=t
 	fi
+    else
+	HAVE_MPACK=t
     fi
     echo "OK"
 }
@@ -78,7 +90,7 @@
 	echo testoutput_for_prop: grep "$2" $1/$4/output.txt 1>&2
     fi
     if [ -r $1/$4/output.txt ]; then
-	grep "$2" $1/$4/output.txt | sed 's/.*=//' | nl > tmp1.txt
+	grep "$2" $1/$4/output.txt | sed 's/.*=//' | cat -n > tmp1.txt
 	lncnt=`wc -l tmp1.txt | awk '{print $1}' `
 	if [ $lncnt -lt 3 ]; then
 	    if [ $verbose -gt 0 ]; then
@@ -93,7 +105,7 @@
     if [ $debug -gt 0 ]; then
 	echo testoutput_for_prop: grep "$2" $1/results/output.txt 1>&2
     fi
-    grep "$2" $1/results/output.txt | sed 's/.*=//' | nl > tmp2.txt
+    grep "$2" $1/results/output.txt | sed 's/.*=//' | cat -n > tmp2.txt
     lncnt=`wc -l tmp2.txt | awk '{print $1}' `
     if [ $lncnt -lt 3 ]; then
 	if [ $verbose -gt 0 ]; then
@@ -153,7 +165,6 @@
     if [ $debug -gt 0 ]; then
 	echo testoutput: cg2dres=$cg2dres 1>&2
     fi
-    
     testoutput_for_prop $1 "dynstat_theta_min" "theta minimum" $2; tmin=$?
     testoutput_for_prop $1 "dynstat_theta_max" "theta maximum" $2; tmax=$?
     testoutput_for_prop $1 "dynstat_theta_mean" "theta mean" $2; tmean=$?
@@ -184,11 +195,19 @@
 	GENMAKE2="$BASH ../../../tools/genmake2"
 	(
 	    cd $1;
+	    command="$GENMAKE2  -ds -m $MAKE --mods=../code"
+	    if test "x$OPTFILE" != xNONE ; then
+		command="$command --optfile=$OPTFILE"
+		# echo "  command=\"$command\""
+	    fi
+	    if test "x$IEEE" != x ; then
+		command="$command -ieee"
+	    fi
+	    # echo "command: \"$command\""
 	    printf 'genmake ... ' 1>&2
-            # ../../../tools/genmake -ieee -mods=../code > make.log 2>&1
-	    $GENMAKE2  -ds -m $MAKE --mods=../code "--optfile="$OPTFILE > make.log 2>&1
+	    $command > make.log 2>&1
 	    RETVAL=$?
-	    for i in gm_state gm_optfile gm_local Makefile ; do
+	    for i in genmake_state genmake_optfile genmake_local Makefile ; do
 		if test -r $i ; then
 		    cp $i $CDIR
 		fi
@@ -199,7 +218,7 @@
 		cp make.log $CDIR
 		return 1
 	    else
-		echo "succesful" 1>&2
+		echo "successful" 1>&2
 	    fi
 	)
     fi
@@ -227,7 +246,7 @@
 		    return 1
 		fi
 	    fi
-	    echo succesful 1>&2
+	    echo successful 1>&2
 	    exit 0
 	)
     fi
@@ -250,7 +269,7 @@
 		cp make.log $CDIR"/make.log"
 		return 1
 	    else
-		echo succesful 1>&2
+		echo successful 1>&2
 	    fi
 	)
     fi
@@ -271,7 +290,7 @@
 		cp make.log $CDIR"/make.log"
 		return 1
 	    else
-		echo succesful 1>&2
+		echo successful 1>&2
 	    fi
 	fi
     )
@@ -282,8 +301,16 @@
     # linkdata flag
     #
     # symbolically link data files to run directory
-    if [ $1 -ne 0 ]; then
-	( cd $2 ;  ln -sf ../input/* . )
+    if test "x$1" = x1 ; then
+	(
+	    cd $2
+	    files=`( cd ../input ; ls -1 | grep -v CVS )`
+	    for i in $files ; do
+		if test ! -d "../input/"$i ; then
+		    ln -sf "../input/"$i $i
+		fi
+	    done
+	)
     fi
 }
 
@@ -295,14 +322,18 @@
     #  (where "$COMMAND" is relative to "directory")
     (
 	cd $1
-	printf 'runmodel: ' 1>&2
+	printf 'runmodel ... ' 1>&2
 	# make output.txt
-	$COMMAND
+	$COMMAND >> run.log 2>&1
 	RETVAL=$?
 	if test "x$RETVAL" = x0 ; then
+	    echo successful 1>&2
 	    cp output.txt $CDIR"/output.txt"
 	    return 0
 	else
+	    tail run.log
+	    echo failed 1>&2
+	    cp run.log $CDIR"/run.log"
 	    return 1
 	fi
     )
@@ -383,7 +414,6 @@
  -debug     Produce even more output which will mean nothing to most
  -force     Do "make CLEAN" before compiling. This forces a complete rebuild.
  -clean     Do "make CLEAN" after compiling and testing.
- -noieee    By default, $0 uses the -ieee option for genmake. This turns it off.
  -cleanup   Aggresively removes all model output, executables and object files
             and then exits. Use with care.
 
@@ -416,6 +446,12 @@
 expts=''
 # ieee=1
 
+IEEE=
+if test "x$MITGCM_IEEE" != x ; then
+    IEEE=$MITGCM_IEEE
+fi
+
+
 CLEANUP=f
 QUICK=f
 NOGENMAKE=f
@@ -423,10 +459,11 @@
 NODEPEND=f
 
 BASH=
-OPTFILES=
+OPTFILE=NONE
 ADDRESSES=
 TESTDIRS=
 MPACKDIR="../tools/mpack-1.6"
+HAVE_MPACK=
 MPACK="$MPACKDIR/mpack"
 COMMAND="make output.txt"
 MAKE=make
@@ -452,9 +489,9 @@
 	    usage ;;
 	
 	-optfile | --optfile | -of | --of)
-            ac_prev=OPTFILES ;;
+            ac_prev=OPTFILE ;;
         -optfile=* | --optfile=* | -of=* | --of=*)
-            OPTFILES=$ac_optarg ;;
+            OPTFILE=$ac_optarg ;;
 	
 	-addr | --addr | -a | --a)
             ac_prev=ADDRESSES ;;
@@ -494,9 +531,12 @@
 	    NODEPEND=t ;;
 
 	-mpi) MPI=t ;;
+
+	-ieee) IEEE=true ;;
+	-noieee) IEEE= ;;
+
 	-verbose) verbose=2 ;;
 	-debug) debug=1 ;;
-	-clean) clean=1 ;;
 	-quiet) verbose=0 ;;
 
         -*)
@@ -523,14 +563,8 @@
     TESTDIRS=`scandirs`
 fi
 
-if test "x$OPTFILES" = x ; then
-    OPTFILES=$MITGCM_OF
-fi
-if test "x$OPTFILES" = x ; then
-    echo "Error: please specify an optfile using either the command-line or"
-    echo "  the MITGCM_OF environment variable.  Also, examples are located "
-    echo "  in \$ROOTDIR/tools/build_options"
-    exit 1
+if test "x$OPTFILE" = xNONE -a "x$MITGCM_OF" != x ; then
+    OPTFILE=$MITGCM_OF
 fi
 
 echo "OK"
@@ -555,12 +589,14 @@
 mkdir $DRESULTS
 RETVAL=$?
 if test "x$RETVAL" != x0 ; then
-    echo "Error: can't create results directory \"./$DRESULTS\""
+    echo "ERROR: Can't create results directory \"./$DRESULTS\""
     exit 1
 fi
 SUMMARY="$DRESULTS/summary.txt"
-date > $SUMMARY
-cat << EOF >> $SUMMARY
+echo -n "Start time:  " >> $SUMMARY
+start_date=`date`
+echo $start_date > $SUMMARY
+cat << EOF | tee -a $SUMMARY
                 T           S           U           V
 G D M    c        m  s        m  s        m  s        m  s
 E p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
@@ -571,152 +607,182 @@
 
 NDIR=0
 
-#  For each optfile...
-for OPTFILE in $OPTFILES ; do
-
-    OPTFILE=`pwd`"/$OPTFILE"
-    if test ! -r $OPTFILE ; then
-	echo "Error: can't read optfile \"$OPTFILE\""
-	exit 1
-    fi
-    echo
-    echo "OPTFILE=$OPTFILE" >> $SUMMARY
-    echo >> $SUMMARY
-    
-    #  ...and each test directory...
-    for dir in $TESTDIRS ; do
-
-	#  Cleanup only!
-	if test "x$CLEANUP" = xt ; then
-	    if test -r $dir/build/Makefile ; then
-		( cd $dir/build ; make CLEAN )
-	    fi
-	    if test -r $dir/input/Makefile ; then
-		( cd $dir/input ; make CLEAN )
-	    fi
-	    continue
-	fi
-
-	#  Verify that the testdir exists and contains previous 
-	#  results in the correct location--or skip this directory!
-	if test ! -r $dir"/results/output.txt" ; then
-	    echo
-	    echo "can't read \"$dir/results/output.txt\" -- skipping $dir"
-	    echo
-	    continue
-	fi
-
-	#  Is this an MPI run?
-	if test "x$MPI" = xt ; then
-	    if test ! -r $dir"/code/CPP_EEOPTIONS.h_mpi" -o ! -r $dir"/code/SIZE.h_mpi" ; then
-		echo | tee -a $SUMMARY
-		echo "can't read \"$dir/code/CPP_EEOPTIONS.h_mpi\" or \"$dir/code/SIZE.h_mpi\"" \
-		    | tee -a $SUMMARY
-		continue
-	    else
-		cmp $dir"/code/CPP_EEOPTIONS.h_mpi" $dir"/code/CPP_EEOPTIONS.h"
-		RETVAL=$?
-		if test "x$RETVAL" != x0 ; then
-		    cp $dir"/code/CPP_EEOPTIONS.h_mpi" $dir"/code/CPP_EEOPTIONS.h"
-		fi
-		cmp $dir"/code/SIZE.h_mpi" $dir"/code/SIZE.h"
-		RETVAL=$?
-		if test "x$RETVAL" != x0 ; then
-		    cp $dir"/code/SIZE.h_mpi" $dir"/code/SIZE.h"
-		fi
-	    fi
+of_path=
+if test "x$OPTFILE" != xNONE ; then
+    if test -r $OPTFILE ; then
+	# get the path
+	path=${OPTFILE%/*}
+	if test "x$path" = x ; then
+	    of_path=`pwd`
 	else
-	    if test -r $dir"/code/CPP_EEOPTIONS.h_nompi" ; then
-		cmp $dir"/code/CPP_EEOPTIONS.h_nompi" $dir"/code/CPP_EEOPTIONS.h"
-		RETVAL=$?
-		if test "x$RETVAL" != x0 ; then
-		    cp $dir"/code/CPP_EEOPTIONS.h_nompi" $dir"/code/CPP_EEOPTIONS.h"
-		fi
-	    fi
-            if test -r $dir"/code/SIZE.h_nompi" ; then
-                cmp $dir"/code/SIZE.h_nompi" $dir"/code/SIZE.h"
-		RETVAL=$?
-		if test "x$RETVAL" != x0 ; then
-		    cp $dir"/code/SIZE.h_nompi" $dir"/code/SIZE.h"
-		fi
-            fi
+	    of_path=`( cd $path > /dev/null 2>&1 ; pwd )`
 	fi
-
-	#  Create an output dir for each OPTFILE/tdir combination
-	CDIR=$DRESULTS"/"$DRESULTS"_"$NDIR
-	mkdir $CDIR
-	CDIR=`pwd`"/$CDIR"
-
-	#  ...configue, make, run, and compare the output.
-	echo "-------------------------------------------------------------------------------"
-	echo
-	echo "Experiment:  $dir"
+	file=${OPTFILE##*/}
+	OPTFILE=$of_path/$file
+    else
 	echo
-	unset genmake makedepend make run
-	results='-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --'
+	echo "WARNING: can't read OPTFILE=\"$OPTFILE\" but will try to use it..."
+    fi
+fi
+echo
+echo "OPTFILE=$OPTFILE" >> $SUMMARY
+echo >> $SUMMARY
 
-	if [ -r $dir/build ]; then
-	    seperatebuilddir=1
-	    builddir=build
-	    rundir=build
-	    ( cd $dir/build; ln -sf ../input/* . )
-	else
-	    seperatebuilddir=0
-	    builddir=input
-	    rundir=input
+#  ...and each test directory...
+for dir in $TESTDIRS ; do
+    
+    #  Cleanup only!
+    if test "x$CLEANUP" = xt ; then
+	if test -r $dir/build/Makefile ; then
+	    ( cd $dir/build ; make CLEAN )
 	fi
-
-	if test "x$CLEANUP" = xt ; then
-	    makeclean $dir/$builddir
-	else
-	    genmakemodel $dir/$builddir && genmake=Y \
-		&& makeclean $dir/$builddir \
-		&& makedependmodel $dir/$builddir && makedepend=Y \
-		&& makemodel $dir/$builddir && make=Y \
-		&& linkdata $seperatebuilddir $dir/$rundir \
-		&& runmodel $dir/$builddir && run=Y \
-		&& results=`testoutput $dir $rundir`
+	if test -r $dir/input/Makefile ; then
+	    ( cd $dir/input ; make CLEAN )
 	fi
+	continue
+    fi
 
-	echo
-	formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
-	    ${run:-N} $results
-	echo
-	formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
-	    ${run:-N} $results >> $SUMMARY
-	echo "fresults='" > $CDIR"/summary.txt"
-	formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
-	    ${run:-N} $results >> $CDIR"/summary.txt"
-	echo "'" >> $CDIR"/summary.txt"
-	echo "MACH='$MACH'" >> $CDIR"/summary.txt"
-	echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
-	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	echo "tdir='$dir'" >> $CDIR"/summary.txt"
+    #  Verify that the testdir exists and contains previous 
+    #  results in the correct location--or skip this directory!
+    if test ! -r $dir"/results/output.txt" ; then
+	echo "can't read \"$dir/results/output.txt\" -- skipping $dir"
+	continue
+    fi
 
-	(
-	    cd $DRESULTS
-	    tar -cf $NDIR".tar" $DRESULTS"_"$NDIR > /dev/null 2>&1
-	    gzip $NDIR".tar"
-	)
+    echo "-------------------------------------------------------------------------------"
+    echo
+    echo "Experiment:  $dir"
+    echo
+    unset genmake makedepend make run
+    results='-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --'
 
-	if test "x$ADDRESSES" = xNONE -o "x$ADDRESSES" = x ; then
-	    echo "No mail sent"
-	else
-	    $MPACK -s MITgcm-test -m 1000000 $DRESULTS"/"$NDIR".tar.gz" $ADDRESSES
+    builddir="input"
+    rundir="input"
+    use_seperate_build=0
+    if test -d $dir/build -a -r $dir/build ; then
+	builddir="build"
+	rundir="build"
+	use_seperate_build=1
+	linkdata $use_seperate_build $dir/$rundir
+    fi
+    
+    CODE_DIR=$dir/code
+    BUILD_DIR=$dir/$builddir
+    MPI_FILES="CPP_EEOPTIONS.h_mpi SIZE.h_mpi"
+    NOMPI_FILES="CPP_EEOPTIONS.h_nompi SIZE.h_nompi"
+
+    #  Is this an MPI run?
+    if test "x$MPI" = xt ; then
+	FILES=$MPI_FILES
+	endings="_mpi"
+    else
+	FILES=$NOMPI_FILES
+	endings="_nompi"
+    fi
+    
+    #  Check to see that we have the files
+    have_files=t
+    for i in $FILES ; do
+	if test ! -r $CODE_DIR/$i ; then
+	    echo "Warning: can't read file $CODE_DIR/$i"
+	    have_files=f
+	fi
+    done
+    if test "x$have_files" != xt -a "x$MPI" = xt ; then
+	echo "Skipping $dir due to lack of input files (see above warning)"
+	continue
+    fi
+    
+    #  If we have the $FILES and they differ, copy the $FILES to $BUILD_DIR
+    if test "x$have_files" = xt ; then
+	for i in $FILES ; do
+	    sstr="s|$endings||"
+	    name=`echo $i | sed -e $sstr `
+	    cmp $CODE_DIR/$i $BUILD_DIR/$name > /dev/null 2>&1
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
-		echo "Warning: \"$MPACK\" failed -- please contact <edhill@mitgcm.org>"
-	    else
-		rm -f $DRESULTS"/"$NDIR".tar*"
+		cp $CODE_DIR/$i $BUILD_DIR/$name
 	    fi
-	fi
-
-	NDIR=$(( $NDIR + 1 ))
-	
-    done
+	done
+    fi
+    
+    #  Create an output dir for each OPTFILE/tdir combination
+    rel_CDIR=$DRESULTS"/"$dir
+    mkdir $rel_CDIR
+    CDIR=`pwd`"/$rel_CDIR"
+    
+    if test "x$CLEANUP" = xt ; then
+	makeclean $dir/$builddir
+    else
+	genmakemodel $dir/$builddir && genmake=Y \
+	    && makeclean $dir/$builddir \
+	    && makedependmodel $dir/$builddir && makedepend=Y \
+	    && makemodel $dir/$builddir && make=Y \
+	    && linkdata $use_seperate_build $dir/$rundir \
+	    && runmodel $dir/$rundir && run=Y \
+	    && results=`testoutput $dir $rundir`
+    fi
+    
+    echo
+    formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
+	${run:-N} $results
+    echo
+    formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
+	${run:-N} $results >> $SUMMARY
+    echo "fresults='" > $CDIR"/summary.txt"
+    formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
+	${run:-N} $results >> $CDIR"/summary.txt"
+    echo "'" >> $CDIR"/summary.txt"
+    echo "MACH='$MACH'" >> $CDIR"/summary.txt"
+    echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
+    echo "DATE='$DATE'" >> $CDIR"/summary.txt"
+    echo "tdir='$dir'" >> $CDIR"/summary.txt"
+    
+    echo "-------------------------------------------------------------------------------"
+    
+    NDIR=$(( $NDIR + 1 ))
+    
 done
 
+echo -n "Start time:  " >> $SUMMARY
+echo $start_date >> $SUMMARY
+echo -n "End time:    " >> $SUMMARY
+date >> $SUMMARY
+
+#  If addresses were supplied and mpack built successfully, then try
+#  to send email using mpack.
+if test "x$ADDRESSES" = xNONE -o "x$ADDRESSES" = x ; then
+    echo "No results email was sent."
+else
+    if test "x$HAVE_MPACK" = xt ; then
+	tar -cf $DRESULTS".tar" $DRESULTS > /dev/null 2>&1 \
+	    && gzip $DRESULTS".tar" \
+	    && $MPACK -s MITgcm-test -m 1500000 $DRESULTS".tar.gz" $ADDRESSES
+	RETVAL=$?
+	if test "x$RETVAL" != x0 ; then
+	    echo
+	    echo "Warning: The tar, gzip, & mpack step failed.  Please send email"
+	    echo "  to <MITgcm-support@mitgcm.org> for help.  You may copy the "
+	    echo "  summary of results from the directory \"$DRESULTS\"."
+	    echo
+	else
+	    echo
+	    echo "An email containing results was sent to the following addresses:"
+	    echo "  \"$ADDRESSES\""
+	    echo
+	fi
+	test -f $DRESULTS".tar"  &&  rm -f $DRESULTS".tar"
+	test -f $DRESULTS".tar.gz"  &&  rm -f $DRESULTS".tar.gz"
+    fi
+fi
+
 rm tmp_cmpnum.f a.out
 
-cat $SUMMARY
+if test "x$CLEANUP" != xt ; then
+    cat $SUMMARY
+    if test -e tr.out ; then
+        mv tr.out tr.out.old
+    fi
+    cat $SUMMARY > tr.out
+fi