--- MITgcm/verification/testreport	2004/11/17 21:38:35	1.48
+++ MITgcm/verification/testreport	2006/06/08 21:39:35	1.80
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.48 2004/11/17 21:38:35 jmc Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.80 2006/06/08 21:39:35 jmc Exp $
 #  $Name:  $
 #
 
@@ -27,6 +27,10 @@
     echo "                             (DEF=\"make output.txt\")"
     echo "  (-m|-make) STRING        command to use for \"make\""
     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 "                             (DEF=\"1 2 3 4 5\")"
     echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
     echo "  (-clean)                 *ONLY* run \"make CLEAN\""
     echo "  (-quick|-q)              same as \"-nogenmake -noclean -nodepend\""
@@ -35,11 +39,15 @@
     echo "  (-nodepend|-nd)          skip the \"make depend\" stage"
     echo "  (-deldir|-dd)            on success, delete the output directory"
     echo
-    echo "and where STRING follows a whitespace-delimited format"
+    echo "and where STRING can be a whitespace-delimited list"
     echo "such as:"
+    echo
     echo "  -t 'exp0 exp2 exp3' "
     echo "  -addr='abc@123.com testing@home.org'"
     echo
+    echo "provided that the expression is properly quoted within the current"
+    echo "shell (note the use of single quotes to protect white space)."
+    echo
     exit 1
 }
 
@@ -89,8 +97,8 @@
     fi
     if [ -r $1/$4/output.txt ]; then
 	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
+	lncntA=`wc -l tmp1.txt | awk '{print $1}' `
+	if [ $lncntA -lt 3 ]; then
 	    if [ $verbose -gt 0 ]; then
 		echo Not enough lines of output when searching for "$2" 1>&2
 	    fi
@@ -104,13 +112,29 @@
 	echo testoutput_for_prop: grep "$2" $1/results/output.txt$5 1>&2
     fi
     grep "$2" $1/results/output.txt$5 | sed 's/.*=//' | cat -n > tmp2.txt
-    lncnt=`wc -l tmp2.txt | awk '{print $1}' `
-    if [ $lncnt -lt 3 ]; then
+    lncntB=`wc -l tmp2.txt | awk '{print $1}' `
+    if [ $lncntB -lt 3 ]; then
 	if [ $verbose -gt 0 ]; then
 	    echo Not enough lines of output when searching for "$2" 1>&2
 	fi
 	return 99
     fi
+    if [ $lncntA -ne $lncntB ]; then
+        if [ $verbose -gt 0 ]; then
+            echo Not same Nb of lines when searching for "$2" ":" $lncntA $lncntB 1>&2
+        fi
+        return 99
+    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
+	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
+	return 99
+    fi
     if [ $debug -gt 0 ]; then
 	echo testoutput_for_prop: join tmp1.txt tmp2.txt 1>&2
     fi
@@ -157,10 +181,10 @@
 
 testoutput_ad()
 {
-    grep $3 $1/results_ad/output.txt_adm | awk '{print NR " " $5}' > t05.txt
-    grep $3 $1/$2/output.txt_adm | awk '{print NR " " $5}' > t15.txt
-    grep $3 $1/results_ad/output.txt_adm | awk '{print NR " " $6}' > t06.txt
-    grep $3 $1/$2/output.txt_adm | awk '{print NR " " $6}' > t16.txt
+    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/results_ad/output_adm.txt | awk '{print NR " " $6}' > t06.txt
+    grep $3 $1/$2/output_adm.txt | awk '{print NR " " $6}' > t16.txt
     join t05.txt t15.txt > t5.txt
     join t06.txt t16.txt > t6.txt
     echo "-1" >> t5.txt
@@ -171,6 +195,31 @@
     rm -f t[01][56].txt t[56].txt
 }
 
+check_for_add_mon_output()
+{
+    # Check for additional types of monitor output
+    if test "x$1" = x ; then
+	return
+    fi
+
+    for ii in $PTRACERS_NUM ; do
+	eval "HAVE_PTR0"$ii"=f"
+    done
+
+    ptr_add="trcstat_ptracerXX_min trcstat_ptracerXX_max"
+    ptr_add="$ptr_add trcstat_ptracerXX_mean trcstat_ptracerXX_sd"
+    for ii in $PTRACERS_NUM ; do
+	for jj in $ptr_add ; do
+	    name=`eval "echo $jj | sed -e 's|XX|0"$ii"|g'"`
+	    tst=`grep $name $1 | wc -l | awk '{print $1}'`
+	    if test ! "x$tst" = x0 ; then
+		eval "HAVE_PTR0"$ii"=t"
+	    fi
+	done
+	#  eval 'echo "HAVE_PTR0'$ii' = $HAVE_PTR0'$ii'"'
+    done
+}
+
 testoutput()
 {
     # testoutput directory subdir extension
@@ -200,8 +249,38 @@
 	testoutput_for_prop $1 "dynstat_vvel_max" "V maximum" $2 $3; vmax=$?
 	testoutput_for_prop $1 "dynstat_vvel_mean" "V mean" $2 $3; vmean=$?
 	testoutput_for_prop $1 "dynstat_vvel_sd" "V s.d." $2 $3; vsd=$?
-	dashnum $cg2dres $tmin $tmax $tmean $tsd $smin $smax $smean $ssd \
-	    $umin $umax $umean $usd $vmin $vmax $vmean $vsd
+
+	#  This is for PTRACERS
+	for ii in $PTRACERS_NUM ; do
+	    eval `echo "p0"$ii"_min=99"`
+	    eval `echo "p0"$ii"_max=99"`
+	    eval `echo "p0"$ii"_mean=99"`
+	    eval `echo "p0"$ii"_sd=99"`
+	    tst=`eval 'echo "$HAVE_PTR0'$ii'"'`
+	    #echo 'tst = '$tst
+	    if test "x$tst" = xt ; then
+		a="trcstat_ptracer0"
+		testoutput_for_prop $1 "$a"$ii"_min"  "p0"$ii"_min"  $2 $3
+		RETVAL=$? ; eval `echo "p0"$ii"_min="$RETVAL`
+		testoutput_for_prop $1 "$a"$ii"_max"  "p0"$ii"_max"  $2 $3
+		RETVAL=$? ; eval `echo "p0"$ii"_max="$RETVAL`
+		testoutput_for_prop $1 "$a"$ii"_mean" "p0"$ii"_mean" $2 $3
+		RETVAL=$? ; eval `echo "p0"$ii"_mean="$RETVAL`
+		testoutput_for_prop $1 "$a"$ii"_sd"   "p0"$ii"_sd"   $2 $3
+		RETVAL=$? ; eval `echo "p0"$ii"_sd="$RETVAL`
+	    fi
+	done
+
+	allargs="$cg2dres $tmin $tmax $tmean $tsd $smin $smax $smean $ssd"
+	allargs="$allargs $umin $umax $umean $usd $vmin $vmax $vmean $vsd"
+	allargs="$allargs $p01_min $p01_max $p01_mean $p01_sd"
+	allargs="$allargs $p02_min $p02_max $p02_mean $p02_sd"
+	allargs="$allargs $p03_min $p03_max $p03_mean $p03_sd"
+	allargs="$allargs $p04_min $p04_max $p04_mean $p04_sd"
+	allargs="$allargs $p05_min $p05_max $p05_mean $p05_sd"
+
+	eval "dashnum $allargs"
+
     else
 	testoutput_ad $1 $2 "precision_grdchk_result"
     fi
@@ -225,7 +304,6 @@
 		command="$command --mods=../code"
 	    else
 		command="$command --mods=../code_ad"
-		command="$command -adof=../../../tools/adjoint_options/adjoint_staf"
 	    fi
 	    if test "x$OPTFILE" != xNONE ; then
 		command="$command --optfile=$OPTFILE"
@@ -233,6 +311,9 @@
 	    if test "x$IEEE" != x ; then
 		command="$command -ieee"
 	    fi
+	    if test "x$MPI" = xt ; then
+		command="$command -mpi"
+	    fi
 	    printf 'genmake ... ' 1>&2
 	    $command > make.log 2>&1
 	    RETVAL=$?
@@ -278,6 +359,20 @@
     fi
 }
 
+postclean()
+{
+    # postclean directory
+    if test "x$POSTCLEAN" = xt ; then
+	(
+	    cd $1;
+	    if test -r Makefile ; then
+		$MAKE CLEAN >> /dev/null 2>&1
+	    fi
+	    exit 0
+	)
+    fi
+}
+
 makedependmodel()
 {
     # makedependmodel directory
@@ -389,23 +484,25 @@
 	    if test "x$ADM" = x ; then
 		files=`( cd ../input ; ls -1 | grep -v CVS )`
 		for i in $files ; do
-		    if test ! -d "../input/"$i ; then
+		    if test ! -d "../input/"$i -a ! -f $i ; then
 			ln -sf "../input/"$i $i
 		    fi
 		done
 	    else
-		files=`( cd ../input ; ls -1 *.bin | grep -v CVS )`
-		for i in $files ; do
-		    if test ! -d "../input/"$i ; then
-			ln -sf "../input/"$i $i
-		    fi
-		done
 		files=`( cd ../input_ad ; ls -1 | grep -v CVS )`
 		for i in $files ; do
 		    if test ! -d "../input_ad/"$i ; then
 			ln -sf "../input_ad/"$i $i
 		    fi
 		done
+		files=`( cd ../input ; ls -1 | grep -v CVS )`
+		for i in $files ; do
+		    if test ! -d "../input/"$i ; then
+		     if test ! -r $i  ; then
+			ln -sf "../input/"$i $i
+		     fi
+		    fi
+		done
 	    fi
 	)
     fi
@@ -419,14 +516,19 @@
     #  (where "$COMMAND" is relative to "directory")
     (
 	cd $1
-	printf 'runmodel ... ' 1>&2
+	printf 'runmodel in %s ...' $1 1>&2
 	# make output.txt
 	echo
 	rm -f run.log
+        if test $OUTPUTFILE -ot $EXECUTABLE ; then
+	   ( eval $COMMAND ) > run.log 2>&1
+	   RETVAL=$?
+	else
+           echo " $OUTPUTFILE is up to date " > run.log 2>&1
+	   RETVAL=0
+	fi
 	# echo "COMMAND='$COMMAND'"
 	# echo "pwd='"`pwd`"'"
-	( eval $COMMAND ) > run.log 2>&1
-	RETVAL=$?
 	if test "x$RETVAL" = x0 ; then
 	    tail run.log
 	    echo successful 1>&2
@@ -434,7 +536,7 @@
 	    # if test "x$ADM" = x ; then
 	    #   cp output.txt $CDIR"/output.txt"
 	    # else
-	    #   cp output.txt_adm $CDIR"/output.txt_adm"
+	    #   cp output_adm.txt $CDIR"/output_adm.txt"
 	    # fi
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 0
@@ -458,23 +560,19 @@
 #include <math.h>
 int main( int argc, char** argv )  {
   int linnum,best,lncnt;
-  double a,b,diff;
-  best = -16;
+  double a,b,abave,relerr;
+  best = -22;
   lncnt = 0;
   while( 1 & (lncnt+=1) < 999 )  {
     scanf("%d", &linnum);
     if (linnum == -1)  break;
     scanf("%lf", &a);  scanf("%lf", &b);
-    diff = 0.5*(fabs(a)+fabs(b));
-    if (diff > 1.e-12) {
-      diff=fabs(a-b)/diff;
-      if (diff > 0.0) {
-        linnum = (int)log10(diff);
-        best = (best > linnum) ? best : linnum;
-      }
-      else {
-        if (best == -16 && diff != 0)  best = -22;
-      }
+    abave = 0.5*(fabs(a)+fabs(b));
+    if (abave > 0.0) {
+      relerr=fabs(a-b)/abave;
+      if (relerr > 0.0) { linnum = (int)rint(log10(relerr)); }
+      else { linnum = -16 ; }
+      best = (best > linnum) ? best : linnum;
     }
   }
   if (lncnt == 999) best=-29;
@@ -482,14 +580,15 @@
   return 0;
 }
 EOF
-    cc -o tmp_cmpnum tmp_cmpnum.c -lm
+    $CC -o tmp_cmpnum tmp_cmpnum.c -lm
 
     if [ -x ./tmp_cmpnum ]; then
 	echo "OK"
 	return 0
     else
 	echo
-	echo "ERROR: failed to compile comparison code" 
+	echo "ERROR: failed to compile comparison code -- please specify" 
+	echo "  a C compiler using the CC environment variable."
 	exit 1
     fi
 }
@@ -569,6 +668,7 @@
 NOGENMAKE=f
 NOCLEAN=f
 NODEPEND=f
+POSTCLEAN=f
 
 BASH=
 OPTFILE=NONE
@@ -578,13 +678,22 @@
 HAVE_MPACK=
 MPACK="$MPACKDIR/mpack"
 COMMAND=
-MAKE=make
+if test "x$MAKE" = x ; then
+    MAKE=make
+fi
+if test "x$CC" = x ; then
+    CC=cc
+fi
 JOBS=
 MPI=f
+OUTDIR=
 DELDIR=
 
 ADM=
 
+# Additional monitor types
+PTRACERS_NUM="1 2 3 4 5"
+
 printf "parsing options...  "
 
 ac_prev=
@@ -634,11 +743,21 @@
 	-make=* | --make=*)
 	    MAKE=$ac_optarg ;;
 
+        -odir | --odir)
+            ac_prev=OUTDIR ;;
+        -odir=* | --odir=*)
+            OUTDIR=$ac_optarg ;;
+
+	-ptracers | --ptracers | -ptr | --ptr)
+	    ac_prev=PTRACERS_NUM ;;
+	-ptracers=* | --ptracers=* | -ptr=* | --ptr=*)
+	    PTRACERS_NUM=$ac_optarg ;;
+
 	-j) ac_prev=JOBS ;;
 	-j=*) JOBS=$ac_optarg ;;
 
 	-clean | --clean)
-	    CLEANUP=t ;;
+	    CLEANUP=t ; DELDIR=t ;;
 
 	-quick | --quick | -q | --q)
 	    QUICK=t ;;
@@ -649,6 +768,9 @@
 	-nodepend | --nodepend | -nd | --nd)
 	    NODEPEND=t ;;
 
+	-postclean | --postclean | -pc | --pc)
+	    POSTCLEAN=t ;;
+
 	-mpi) MPI=t ;;
 
 	-adm | -ad) ADM=t ;;
@@ -690,15 +812,24 @@
     OPTFILE=$MITGCM_OF
 fi
 
+if test "x$ADM" = xt ; then
+    EXECUTABLE="mitgcmuv_ad"
+    OUTPUTFILE="output_adm.txt"
+else
+    EXECUTABLE="mitgcmuv"
+    OUTPUTFILE="output.txt"
+fi
+
 if test "x$ADM" = xt -a "x$COMMAND" = x ; then
-    COMMAND="./mitgcmuv_ad > output.txt_adm 2>&1"
+    COMMAND="./$EXECUTABLE > $OUTPUTFILE"
 fi
 
 if test "x$COMMAND" = x ; then
-    COMMAND="$MAKE output.txt"
+    COMMAND="./$EXECUTABLE > $OUTPUTFILE"
 fi
 
-echo "OK"
+#echo "OK"
+echo "OK (COMMAND= $COMMAND )"
 
 #  create the FORTRAN comparison code
 createcodelet
@@ -715,6 +846,9 @@
 UNAMEA=`uname -a`
 DATE=`date +%Y%m%d`
 BASE="tr_"$MACH"_"$DATE"_"
+if test "x$OUTDIR" != x ; then
+    BASE="tr_"$OUTDIR"_"$DATE"_"
+fi
 DNUM=0
 DRESULTS="$BASE$DNUM"
 while test -e $DRESULTS ; do
@@ -760,14 +894,27 @@
 echo
 echo >> $SUMMARY
 if test "x$ADM" = x ; then
-    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  .
-N n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
-2 d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
-
-EOF
+    line_0="            ----T-----  ----S-----  ----U-----  ----V-----"
+    line_1="G D M    c        m  s        m  s        m  s        m  s"
+    line_2="E p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  ."
+    line_3="N n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d"
+    line_4="2 d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  ."
+    for ii in $PTRACERS_NUM ; do
+	#  tst=`eval 'echo $HAVE_PTR0'$ii`
+	#  if test "x$tst" = xt ; then
+	line_0="$line_0  --PTR 0"$ii"--"
+	line_1="$line_1        m  s"
+	line_2="$line_2  m  m  e  ."
+	line_3="$line_3  i  a  a  d"
+	line_4="$line_4  n  x  n  ."
+	#  fi
+    done
+    echo "$line_0" | tee -a $SUMMARY
+    echo "$line_1" | tee -a $SUMMARY
+    echo "$line_2" | tee -a $SUMMARY
+    echo "$line_3" | tee -a $SUMMARY
+    echo "$line_4" | tee -a $SUMMARY
+    echo " "       | tee -a $SUMMARY
 else
     echo "ADJOINT=true" >> $SUMMARY
     echo >> $SUMMARY
@@ -791,6 +938,10 @@
 	if test -r $dir/input/Makefile ; then
 	    ( cd $dir/input ; make CLEAN )
 	fi
+	(
+	    cd $dir
+	    rm -rf tr_run.*
+	)
 	continue
     fi
 
@@ -800,12 +951,17 @@
     if test "x$ADM" = x ; then
 	fout=$dir"/results/output.txt"
     else
-	fout=$dir"/results_ad/output.txt_adm"
+	fout=$dir"/results_ad/output_adm.txt"
     fi
     if test ! -r $fout ; then
 	echo "can't read \"$fout\" -- skipping $dir"
 	continue
     fi
+    if test "x$ADM" = x ; then
+	check_for_add_mon_output  $fout
+    fi
+
+    # Check for additional types of monitor output
 
     builddir="input"
     rundir="input"
@@ -850,7 +1006,7 @@
     echo "Experiment:  $dir"
     echo
     unset genmake makedepend make run
-    results='-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --'
+    results='-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --'
 
     #  Create an output dir for each OPTFILE/tdir combination
     rel_CDIR=$DRESULTS"/"$dir
@@ -881,26 +1037,34 @@
 	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
 	echo "tdir='$dir'" >> $CDIR"/summary.txt"
 
-	OLD_COMMAND=$COMMAND
-	COMMAND="./mitgcmuv > output.txt"
 	for ex in $extra_runs ; do
-	    test -e "$dir/tr_run.$ex" && rm -rf "$dir/tr_run.$ex"
-	    mkdir "$dir/tr_run.$ex"
-	    links=`( cd "$dir/input" > /dev/null 2>&1 ; ls -1 | grep -v CVS )`
+	    unset run
+	    results='-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --'
+	    #  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"
+	    for ldir in input.$ex input ; do
+		(
+		    cd "$dir/$ldir" > /dev/null 2>&1
+		    ls -1 2>/dev/null \
+			| sed -e 's|^CVS$||g' | sed -e 's|^output.txt$||g'
+		) > tr_exrun_links
+		(
+		    cd "$dir/tr_run.$ex"
+		    cat ../../tr_exrun_links | while read i ; do
+			if test ! "x$i" = x ; then
+			    test ! -r $i  &&  ln -s "../"$ldir"/"$i $i
+			fi
+		    done
+		)
+		test -e tr_exrun_links  &&  rm -f tr_exrun_links
+	    done
+	    ldir=build
 	    (
-		cd "$dir/tr_run.$ex"
-		for i in $links; do
-		    ln -s ../input/$i $i
-		done
-	    )
-	    links=`( cd "$dir/input.$ex" > /dev/null 2>&1 ; ls -1 | grep -v CVS )`
-	    ( 
-		cd "$dir/tr_run.$ex"
-		for i in $links; do
-		    test -e $i  &&  rm -f $i
-		    ln -s ../input.$ex/$i $i
-		done
-		ln -s ../$builddir/mitgcmuv mitgcmuv
+		cd $dir/tr_run.$ex
+		test ! -e mitgcmuv  &&  ln -s "../"$ldir"/"mitgcmuv .
 	    )
 	    runmodel $dir/tr_run.$ex && run=Y \
 		&& results=`testoutput $dir tr_run.$ex "."$ex`
@@ -913,9 +1077,8 @@
 	    echo "MACH='$MACH'" >> $CDIR"/summary.txt"
 	    echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
 	    echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	    echo "tdir='$dir'" >> $CDIR"/summary.txt"
+	    echo "tdir='$dir.$ex'" >> $CDIR"/summary.txt"
 	done
-	COMMAND=$OLD_COMMAND
     else
 	fres=`printf '%s %s %s %s' ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N}`
 	fres=$fres"$results   $dir"
@@ -926,7 +1089,11 @@
 	echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
 	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
 	echo "tdir='$dir'" >> $CDIR"/summary.txt"
+        grep -A3 'Seconds in section "ALL' $dir/$rundir/$OUTPUTFILE \
+			   >> $CDIR"/summary.txt"
     fi
+
+    postclean $dir/$builddir
     
     echo "-------------------------------------------------------------------------------"
     
@@ -968,11 +1135,11 @@
 rm -f tmp_cmpnum.c tmp_cmpnum
 
 if test "x$CLEANUP" != xt ; then
-    cat $SUMMARY
+    cat $SUMMARY | sed 's/ -- -- -- --//g'
     if test -e tr_out.txt ; then
         mv tr_out.txt tr_out.txt.old
     fi
-    cat $SUMMARY > tr_out.txt
+    cat $SUMMARY | sed 's/ -- -- -- --//g' > tr_out.txt
 fi
 
 if test "x$DELDIR" = xt ; then