--- MITgcm/verification/testreport	2006/07/05 22:39:57	1.83
+++ MITgcm/verification/testreport	2007/01/31 21:28:34	1.90
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.83 2006/07/05 22:39:57 jmc Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.90 2007/01/31 21:28:34 ce107 Exp $
 #  $Name:  $
 #
 
@@ -15,11 +15,14 @@
     echo "  (-mpi)                   compile and run using MPI"
     echo "  (-ieee|-noieee)          if possible, use IEEE compiler flags"
     echo "                             (DEF=\"-ieee\")"
-    echo "  (-optfile=|-of=)STRING   list of optfiles to use"
+    echo "  (-of=|-optfile=)STRING   list of optfiles to use"
     echo "  (-a|-addr) STRING        list of email recipients"
     echo "                             (DEF=\"edhill@mitgcm.org\")"
-    echo "  (-t|-tdir) STRING        list of test dirs to use"
-    echo "                             (DEF=\"\" which builds all)"
+    echo "  (-t|-tdir) STRING        list of group and/or exp. dirs to test"
+    echo "                             (recognized groups: basic, tutorials)"
+    echo "                             (DEF=\"\" which test all)"
+    echo "  (-skd|-skipdir) STRING   list of exp. dirs to skip"
+    echo "                             (DEF=\"\" which test all)"
     echo "  (-b|-bash) STRING        preferred location of a \"bash\" or"
     echo "                             Bourne-compatible \"sh\" shell"
     echo "                             (DEF=\"\" for \"bash\")"
@@ -30,7 +33,7 @@
     echo "                             (DEF=\"make\")"
     echo "  (-odir) STRING           used to build output directory name"
     echo "                             (DEF=\"hostname\")"
-    echo "  (-ptracers|-ptr) STRING  specify which ptracers to test"
+    echo "  (-ptr|-ptracers) STRING  specify which ptracers to test"
     echo "                             (DEF=\"1 2 3 4 5\")"
     echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
     echo "  (-clean)                 *ONLY* run \"make CLEAN\""
@@ -39,6 +42,9 @@
     echo "  (-noclean|-nc)           skip the \"make clean\" stage"
     echo "  (-nodepend|-nd)          skip the \"make depend\" stage"
     echo "  (-deldir|-dd)            on success, delete the output directory"
+    echo "  (-ts)                    provide timing information per timestep"
+    echo "  (-papis)                 provide MFlop/s per timestep using PAPI"
+    echo "  (-pcls)                  provide MFlop/s per timestep using PCL"
     echo
     echo "and where STRING can be a whitespace-delimited list"
     echo "such as:"
@@ -90,14 +96,14 @@
 {
     # testoutput_for_prop dir s1 label subdir extension
     #
-    #  compares files in $dir/$subdir/output.txt and $dir/results/output.txt
+    #  compares files $dir/$subdir/$OUTPUTFILE and $dir/results/output.txt
     #  using search strings s1 and text label 
 
     if [ $debug -gt 0 ]; then
-	echo testoutput_for_prop: grep "$2" $1/$4/output.txt 1>&2
+	echo testoutput_for_prop: grep "$2" $1/$4/$OUTPUTFILE 1>&2
     fi
-    if [ -r $1/$4/output.txt ]; then
-	grep "$2" $1/$4/output.txt | sed 's/.*=//' | cat -n > tmp1.txt
+    if [ -r $1/$4/$OUTPUTFILE ]; then
+	grep "$2" $1/$4/$OUTPUTFILE | sed 's/.*=//' | cat -n > tmp1.txt
 	lncntA=`wc -l tmp1.txt | awk '{print $1}' `
 	if [ $lncntA -lt 3 ]; then
 	    if [ $verbose -gt 0 ]; then
@@ -106,13 +112,13 @@
 	    return 99
 	fi
     else
-	echo testoutput_for_prop: output.txt from model run was not readable 1>&2
+	echo testoutput_for_prop: $OUTPUTFILE from model run was not readable 1>&2
 	return 99
     fi
     if [ $debug -gt 0 ]; then
-	echo testoutput_for_prop: grep "$2" $1/results/output.txt$5 1>&2
+	echo testoutput_for_prop: grep "$2" $1/results/output.$5 1>&2
     fi
-    grep "$2" $1/results/output.txt$5 | sed 's/.*=//' | cat -n > tmp2.txt
+    grep "$2" $1/results/output.$5 | sed 's/.*=//' | cat -n > tmp2.txt
     lncntB=`wc -l tmp2.txt | awk '{print $1}' `
     if [ $lncntB -lt 3 ]; then
 	if [ $verbose -gt 0 ]; then
@@ -128,12 +134,12 @@
     fi
     has_nan=`cat tmp1.txt | grep -i nan | wc -l`
     if [ $has_nan -gt 0  ] ; then
-	echo testoutput_for_prop: output.txt contains $has_nan NaN values  1>&2
+	echo testoutput_for_prop: $OUTPUTFILE contains $has_nan NaN values  1>&2
 	return 99
     fi
     has_inf=`cat tmp1.txt | grep -i inf | wc -l`
     if [ $has_inf -gt 0  ] ; then
-	echo testoutput_for_prop: output.txt contains $has_inf Inf values  1>&2
+	echo testoutput_for_prop: $OUTPUTFILE contains $has_inf Inf values  1>&2
 	return 99
     fi
     if [ $debug -gt 0 ]; then
@@ -183,9 +189,9 @@
 testoutput_ad()
 {
     grep $3 $1/results_ad/output_adm.txt | awk '{print NR " " $5}' > t05.txt
-    grep $3 $1/$2/output_adm.txt | awk '{print NR " " $5}' > t15.txt
+    grep $3 $1/$2/$OUTPUTFILE | awk '{print NR " " $5}' > t15.txt
     grep $3 $1/results_ad/output_adm.txt | awk '{print NR " " $6}' > t06.txt
-    grep $3 $1/$2/output_adm.txt | awk '{print NR " " $6}' > t16.txt
+    grep $3 $1/$2/$OUTPUTFILE | awk '{print NR " " $6}' > t16.txt
     join t05.txt t15.txt > t5.txt
     join t06.txt t16.txt > t6.txt
     echo "-1" >> t5.txt
@@ -315,6 +321,16 @@
 	    if test "x$MPI" = xt ; then
 		command="$command -mpi"
 	    fi
+	    if test "x$TS" = xt ; then
+		command="$command -ts"
+	    fi
+	    if test "x$PAPIS" = xt ; then
+		command="$command -papis"
+	    else 
+	    if test "x$PCLS" = xt ; then
+		command="$command -pcls"
+	    fi
+	    fi
 	    printf 'genmake ... ' 1>&2
 	    $command > make.log 2>&1
 	    RETVAL=$?
@@ -340,7 +356,7 @@
     else
 	(
 	    cd $1;
-	    #if test -e output.txt ; then rm -f output.txt ; fi
+	    #if test -e $OUTPUTFILE ; then rm -f $OUTPUTFILE ; fi
 	    if test -r Makefile ; then
 		printf 'clean build-dir: make Clean ... ' 2>&1
 		$MAKE Clean >> make.log 2>&1
@@ -535,41 +551,48 @@
 	printf 'runmodel in %s ...' $1 1>&2
 	# make output.txt
 	echo
-	rm -f run.log
         if test ! -x $EXECUTABLE -a -x "../"$builddir"/"$EXECUTABLE ; then
-	    echo " link" $EXECUTABLE "from dir ../"$builddir > run.log
+	    echo " link" $EXECUTABLE "from dir ../"$builddir > run.log_00
 	    ln -sf "../"$builddir"/"$EXECUTABLE .
-	else
-            touch run.log
 	fi
         if test ! -x $EXECUTABLE ; then
+		rm -f run.log ; touch run.log
+		if test -f run.log_00 ; then cat run.log_00 >> run.log ; fi
 		echo " no executable:" $EXECUTABLE >> run.log
 		RETVAL=8
+		ENDVAL=-1
 	else
             if test $OUTPUTFILE -ot $EXECUTABLE ; then
+		rm -f run.log ; touch run.log
+		if test -f run.log_00 ; then cat run.log_00 >> run.log ; fi
 		( eval $COMMAND ) >> run.log 2>&1
 		RETVAL=$?
 	    else
-     		echo " $OUTPUTFILE is up to date " >> run.log 2>&1
 		RETVAL=0
+		if test -f run.log ; then
+		    if test -f run.log_00 ; then cat run.log_00 >> run.log ; fi
+     		    echo "---------->> $OUTPUTFILE is up to date " >> run.log 2>&1
+		else 
+		    touch run.log
+		    if test -f run.log_00 ; then cat run.log_00 >> run.log ; fi
+     		    echo "---------->> $OUTPUTFILE is up to date " >> run.log 2>&1
+     		    echo " no previous run.log: assume NORMAL END" >> run.log 2>&1
+		fi
 	    fi
+	    ENDVAL=`cat run.log | grep -v 'ABNORMAL END' | grep -c 'NORMAL END'`
 	fi
-	# echo "COMMAND='$COMMAND'"
-	# echo "pwd='"`pwd`"'"
-	if test "x$RETVAL" = x0 ; then
+	rm -f run.log_00
+	#if test "x$RETVAL" = x0 ; then
+	if [ $RETVAL -eq 0 -a $ENDVAL -gt 0 ] ; then
 	    tail run.log
 	    echo successful 1>&2
 	    # === Reduce the size of the testing emails!
-	    # if test "x$ADM" = x ; then
-	    #   cp output.txt $CDIR"/output.txt"
-	    # else
-	    #   cp output_adm.txt $CDIR"/output_adm.txt"
-	    # fi
+	    #cp $OUTPUTFILE $CDIR"/"$OUTPUTFILE
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 0
 	else
 	    tail run.log
-	    echo failed 1>&2
+	    echo failed '(run:' $RETVAL ' end:' $ENDVAL ')' 1>&2
 	    cp run.log $CDIR"/run.log"
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 1
@@ -643,25 +666,6 @@
     
 }
 
-show_help()
-{
-    cat - << EOF
-$0 [-help] [-quick] [-verbose] dir1 [dir2] [...]
-
- -help|-h      Show this help message
- -quiet     Reduce the amount of output
- -verbose   Produce copious amounts of output
- -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.
- -cleanup   Aggresively removes all model output, executables and object files
-            and then exits. Use with care.
-
-Normal usage:
- $0 *       Configure, compile, run and analyze in all experiment directories
-EOF
-}
-
 scandirs()
 {
     if [ $# -eq 1 ]; then
@@ -701,6 +705,7 @@
 OPTFILE=NONE
 ADDRESSES=
 TESTDIRS=
+SKIPDIRS=
 MPACKDIR="../tools/mpack-1.6"
 HAVE_MPACK=
 MPACK="$MPACKDIR/mpack"
@@ -756,6 +761,11 @@
         -tdir=* | --tdir=*)
             TESTDIRS=$ac_optarg ;;
 
+	-skipdir | --skipdir | -skd | --skd)
+            ac_prev=SKIPDIRS ;;
+        -skipdir=* | --skipdir=*)
+            SKIPDIRS=$ac_optarg ;;
+
 	-bash | --bash | -b | --b)
             ac_prev=BASH ;;
         -bash=* | --bash=*)
@@ -814,6 +824,12 @@
 
 	-deldir | -dd) DELDIR=t ;;
 
+	-ts) TS=t;;
+
+	-papis) PAPIS=t;;
+
+	-pcls) PCL=t;;
+
         -*)
             echo "Error: unrecognized option: "$ac_option
             usage
@@ -836,11 +852,48 @@
 
 if test "x$TESTDIRS" = x ; then
     if test "x$ADM" = xt ; then
-	TESTDIRS=`scandirs results_ad`
+	LIST=`scandirs results_ad`
     else
-	TESTDIRS=`scandirs results`
+	LIST=`scandirs results`
     fi
+else
+    #- expand group of experiments:
+    LIST=" "
+    for xx in $TESTDIRS
+    do
+      case $xx in
+	'basic') LIST=${LIST}" aim.5l_cs hs94.128x64x5 ideal_2D_oce"
+		 LIST=${LIST}" lab_sea tutorial_baroclinic_gyre"
+		 LIST=${LIST}" tutorial_global_oce_latlon tutorial_plume_on_slope"
+		;;
+	'tutorials')
+		 LIST=${LIST}" "`ls | grep 'tutorial_'` ;;
+	*)	 LIST=${LIST}" "$xx ;;
+      esac
+    done 
 fi
+#echo 'LIST='${LIST}'<'
+#- skip dirs, remove duplicate and non-directory:
+TESTDIRS=" "
+count=0
+for xx in $LIST
+do
+    yy=`echo $SKIPDIRS | grep -c $xx`
+    if test $yy = 0 ; then
+	if test -d $xx ; then
+	    yy=`echo $TESTDIRS | grep -c $xx`
+	    if test $yy = 0 ; then TESTDIRS=${TESTDIRS}" "$xx ; fi
+	else count=1 ;
+	    echo ""; echo -n " -- skip \"$xx\" (not a directory !)"
+	fi
+    else
+        if test $count = 1 ; then echo -n ", \"$xx\""
+	else count=1 ; echo "" ;  echo -n " skip: \"$xx\""
+	fi
+    fi
+done 
+if test $count = 1 ; then echo "" ; echo -n " ... " ; fi
+#echo 'TESTDIRS='${TESTDIRS}'<'
 
 if test "x$OPTFILE" = xNONE -a "x$MITGCM_OF" != x ; then
     OPTFILE=$MITGCM_OF
@@ -854,13 +907,12 @@
     OUTPUTFILE="output.txt"
 fi
 
-if test "x$ADM" = xt -a "x$COMMAND" = x ; then
-    COMMAND="./$EXECUTABLE > $OUTPUTFILE"
-fi
-
 if test "x$COMMAND" = x ; then
     COMMAND="./$EXECUTABLE > $OUTPUTFILE"
 fi
+if test "x$MPI" = xt ; then
+    OUTPUTFILE="STDOUT.0000"
+fi
 
 #echo "OK"
 echo "OK (COMMAND= $COMMAND )"
@@ -1034,7 +1086,7 @@
 	#echo "ex_run_dirs='$ex_run_dirs'"
 	for exd in $ex_run_dirs ; do
 	    name=`echo $exd | sed -e 's/input.//g'`
-	    outf="$dir/results/output.txt.$name"
+	    outf="$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
@@ -1077,7 +1129,7 @@
 	    && makemodel $dir/$builddir && make=Y \
 	    && linkdata $dir/$rundir $input_dirs \
 	    && runmodel $dir/$rundir && run=Y \
-	    && results=`testoutput $dir $rundir`
+	    && results=`testoutput $dir $rundir "txt"`
     fi
     
     echo
@@ -1102,7 +1154,7 @@
  	    run_clean $dir/tr_run.$ex
             linkdata $dir/tr_run.$ex input.$ex input
 	    runmodel $dir/tr_run.$ex && run=Y \
-		&& results=`testoutput $dir tr_run.$ex "."$ex`
+		&& results=`testoutput $dir tr_run.$ex ${ex}".txt"`
 	    fres=`printf '%s %s %s %s' ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N}`
 	    fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
 	    fres="$fres.$ex"