--- MITgcm/verification/testreport	2007/09/21 19:23:33	1.103
+++ MITgcm/verification/testreport	2007/12/13 18:28:41	1.109
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.103 2007/09/21 19:23:33 jmc Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.109 2007/12/13 18:28:41 jmc Exp $
 #  $Name:  $
 #
 
@@ -15,9 +15,10 @@
     echo "  (-mpi)                   compile and run using MPI"
     echo "  (-ieee|-noieee)          if possible, use IEEE compiler flags"
     echo "                             (DEF=\"-ieee\")"
+    echo "  (-gsl)                   compile with \"-gsl\" flag"
     echo "  (-of=|-optfile=)STRING   list of optfiles to use"
     echo "  (-a|-addr) STRING        list of email recipients"
-    echo "                             (DEF=\"edhill@mitgcm.org\")"
+    echo "                             (DEF=\"\" no email is sent)"
     echo "  (-t|-tdir) STRING        list of group and/or exp. dirs to test"
     echo "                             (recognized groups: basic, tutorials)"
     echo "                             (DEF=\"\" which test all)"
@@ -174,21 +175,6 @@
     return $digits_of_similarity
 }
 
-dashnum()
-{
-    # dashnum n1 n2 n3 ...
-    #
-    #  print numbers using %3i format or "--" if number = 99
-
-    for num in $@ ; do
-	if [ $num = 99 ]; then
-	    printf ' --'
-	else
-	    printf '%3i' $num
-	fi
-    done
-}
-
 check_for_add_mon_output()
 {
     # Check for additional types of monitor output
@@ -342,6 +328,9 @@
 	    if test "x$IEEE" != x ; then
 		command="$command -ieee"
 	    fi
+	    if test "x$GSL" = xt ; then
+		command="$command -gsl"
+	    fi
 	    if test "x$MPI" = xt ; then
 		command="$command -mpi"
 	    fi
@@ -414,6 +403,7 @@
 	    find . -type l -exec rm {} \;
 	    rm -f $EXECUTABLE *.txt STD* *diagnostics.log datetime
 	    rm -rf mnc_test_*
+ 	    rm -f *_MIT_CE_000.opt0000 costfunction*0000
 	    echo successful 1>&2
 	    exit 0
 	)
@@ -542,8 +532,9 @@
 		    if test -h eedata ; then rm -f eedata ; fi
 		fi
 	    fi
+	    prevDir='NONE'
 	    for ldir in $* ; do
-		if test -d "../"$ldir ; then
+		if test -d "../"$ldir -a $ldir != $prevDir ; then
                     printf 'ldir='${ldir} 1>&2
 		    files=`( cd "../"$ldir ; ls -1 | grep -v CVS )`
 		    for i in $files ; do
@@ -559,6 +550,7 @@
 		    fi
 		    printf ' ; ' 1>&2
 		fi
+		prevDir=$ldir
 	    done
 	)
     fi
@@ -575,6 +567,10 @@
 	printf 'runmodel in %s ...' $1 1>&2
 	# make output.txt
 	echo
+	if test -L $EXECUTABLE -a -x "../"$builddir"/"$EXECUTABLE ; then
+	    diff -q $EXECUTABLE "../"$builddir"/"$EXECUTABLE > /dev/null 2>&1
+	    outD=$? ; if test $outD != 0 ; then rm -f $EXECUTABLE ; rm -f run.log ; fi
+	fi
         if test ! -x $EXECUTABLE -a -x "../"$builddir"/"$EXECUTABLE ; then
 	    echo " link" $EXECUTABLE "from dir ../"$builddir > run.log_00
 	    ln -sf "../"$builddir"/"$EXECUTABLE .
@@ -726,14 +722,12 @@
 debug=0
 verbose=1
 clean=0
-expts=''
-# ieee=1
 
 IEEE=true
 if test "x$MITGCM_IEEE" != x ; then
     IEEE=$MITGCM_IEEE
 fi
-
+GSL=f
 
 CLEANUP=f
 QUICK=f
@@ -863,6 +857,7 @@
 
 	-ieee) IEEE=true ;;
 	-noieee) IEEE= ;;
+        -gsl) GSL=t ;;
 
 	-verbose) verbose=2 ;;
 	-debug) debug=1 ;;
@@ -899,12 +894,12 @@
 #- setting for forward or ADM testing
 if test "x$ADM" = xt ; then
     code_dir=code_ad
-    input_dirs='input_ad input'
+    inputdir=input_ad
     ref_outp="output_adm.txt"
     EXECUTABLE="mitgcmuv_ad"
 else
     code_dir=code
-    input_dirs='input'
+    inputdir=input
     ref_outp="output.txt"
     EXECUTABLE="mitgcmuv"
 fi
@@ -1087,15 +1082,25 @@
 #  ...and each test directory...
 for dir in $TESTDIRS ; do
     
+    # set builddir & rundir:
+    builddir="build"
+    if test ! -d $dir/$builddir ; then mkdir $dir/$builddir ; fi
+    rundir="run"
+    if test ! -d $dir/$rundir ; then
+	rundir=$builddir
+    fi
+    CODE_DIR=$dir/$code_dir
+    BUILD_DIR=$dir/$builddir
+
     #  Cleanup only!
     if test "x$CLEANUP" = xt ; then
-	if test -r $dir/build/Makefile ; then
+	if test -r $BUILD_DIR/Makefile ; then
             echo '  ------  clean dir:' $dir/build
-	    ( cd $dir/build ; make CLEAN )
+	    ( cd $BUILD_DIR ; make CLEAN )
 	fi
-	if test -d $dir/run/CVS ; then
-            echo '  ------  clean dir:' $dir/run
-	    run_clean $dir/run
+	if test -d $dir/$rundir/CVS ; then
+            echo '  ------  clean dir:' $dir/$rundir
+	    run_clean $dir/$rundir
 	fi
 	(
 	    cd $dir
@@ -1106,12 +1111,7 @@
 
     #  Verify that the testdir exists and contains previous 
     #  results in the correct location--or skip this directory!
-    fout=
-    if test "x$ADM" = x ; then
-	fout=$dir"/results/"$ref_outp
-    else
-	fout=$dir"/results_ad/"$ref_outp
-    fi
+    fout=$dir"/results/"$ref_outp
     if test ! -r $fout ; then
 	echo "can't read \"$fout\" -- skipping $dir"
 	continue
@@ -1122,15 +1122,6 @@
 
     # Check for additional types of monitor output
 
-    builddir="build"
-    if test ! -d $dir/$builddir ; then mkdir $dir/$builddir ; fi
-    rundir="run"
-    if test ! -d $dir/$rundir ; then
-	rundir=$builddir
-    fi
-    CODE_DIR=$dir/$code_dir
-    BUILD_DIR=$dir/$builddir
-
     if test ! -r $CODE_DIR"/SIZE.h_mpi" -a "x$MPI" = "xt" ; then
 	echo "can't find \"$CODE_DIR/SIZE.h_mpi\" -- skipping $dir"
 	continue
@@ -1142,24 +1133,23 @@
 
     #  Check whether there are "extra runs" for this testdir
     extra_runs=
-    if test "x$ADM" = x ; then
-	ex_run_dirs=`( cd $dir ; echo input.* )`
-	#echo "ex_run_dirs='$ex_run_dirs'"
-	for exd in $ex_run_dirs ; do
-	    name=`echo $exd | sed -e 's/input.//g'`
-	    outf="$dir/results/output.$name.txt"
-            if test -f $outf -a -r $outf ; then
-		if test "x$MULTI_THREAD" = "xt" ; then 
-		    if test -r $dir"/"$exd"/eedata.mth" ; then
-			extra_runs="$extra_runs $name"
-		    #else echo $dir"/"$exd"/eedata.mth: not found"
-		    fi
-		else
+    ex_run_dirs=`( cd $dir ; echo $inputdir.* )`
+    #echo "ex_run_dirs='$ex_run_dirs'"
+    for exd in $ex_run_dirs ; do
+	name=`echo $exd | sed -e "s/$inputdir\.//"`
+	refExOut=`echo $ref_outp | sed "s/\./.${name}./"`
+	outf="$dir/results/$refExOut"
+        if test -f $outf -a -r $outf ; then
+	    if test "x$MULTI_THREAD" = "xt" ; then 
+		if test -r $dir"/"$exd"/eedata.mth" ; then
 		    extra_runs="$extra_runs $name"
+		#else echo $dir"/"$exd"/eedata.mth: not found"
 		fi
+	    else
+		extra_runs="$extra_runs $name"
 	    fi
-	done
-    fi
+	fi
+    done
 
     echo "-------------------------------------------------------------------------------"
     echo
@@ -1188,13 +1178,12 @@
             && symlink_mpifiles $dir $code_dir $builddir \
 	    && makedependmodel $dir/$builddir && makedepend=Y \
 	    && makemodel $dir/$builddir && make=Y \
-	    && linkdata $dir/$rundir $input_dirs \
+	    && linkdata $dir/$rundir $inputdir input \
 	    && runmodel $dir/$rundir && run=Y \
 	    && results=`testoutput_run $dir $rundir $ref_outp`
     fi
     
     echo
-# --> same processing for adjoint & forward test
 	fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
 	echo
  	echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
@@ -1204,19 +1193,26 @@
 	echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
 	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
 	echo "tdir='$dir'" >> $CDIR"/summary.txt"
+	if test "x$ADM" = xt ; then
+	    head -1 $dir/$builddir/taf_ad.log >> $CDIR"/summary.txt"
+	    grep -A3 'Seconds in section "ALL' $dir/$rundir/$OUTPUTFILE \
+				>> $CDIR"/summary.txt"
+	fi
 
 	for ex in $extra_runs ; do
 	    unset run
             results=$EMPTY_RESULTS
+	    #  reference output file
+	    refExOut=`echo $ref_outp | sed "s/\./.${ex}./g"`
 	    #  Create an output dir for each OPTFILE/tdir.ex combination
 	    rel_CDIR=$DRESULTS"/"$dir"."$ex
 	    mkdir $rel_CDIR
 	    CDIR=`pwd`"/$rel_CDIR"
 	    test ! -e "$dir/tr_run.$ex" && mkdir "$dir/tr_run.$ex"
- 	    run_clean $dir/tr_run.$ex
-            linkdata $dir/tr_run.$ex input.$ex input
+	    run_clean $dir/tr_run.$ex
+	    linkdata $dir/tr_run.$ex $inputdir.$ex $inputdir input
 	    runmodel $dir/tr_run.$ex && run=Y \
-		&& results=`testoutput_run $dir tr_run.$ex "output.${ex}.txt"`
+	    && results=`testoutput_run $dir tr_run.$ex $refExOut`
 	    fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
 	    fres="$fres.$ex"
 	    echo
@@ -1227,15 +1223,15 @@
 	    echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
 	    echo "DATE='$DATE'" >> $CDIR"/summary.txt"
 	    echo "tdir='$dir.$ex'" >> $CDIR"/summary.txt"
+            if test "x$ADM" = xt ; then
+	        head -1 $dir/$builddir/taf_ad.log >> $CDIR"/summary.txt"
+	        grep -A3 'Seconds in section "ALL' $dir/tr_run.$ex/$OUTPUTFILE \
+			           >> $CDIR"/summary.txt"
+            fi
 	    if test "x$POSTCLEAN" = xt ; then
 		run_clean $dir/tr_run.$ex
 	    fi
 	done
-# <-- same processing for adjoint & forward test
-    if test "x$ADM" = xt ; then
-	grep -A3 'Seconds in section "ALL' $dir/$rundir/$OUTPUTFILE \
-			   >> $CDIR"/summary.txt"
-    fi
 
     #postclean $dir/$builddir
     if test "x$POSTCLEAN" = xt ; then