--- MITgcm/verification/testreport	2007/09/10 21:26:58	1.96
+++ MITgcm/verification/testreport	2010/11/02 22:53:11	1.146
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.96 2007/09/10 21:26:58 jmc Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.146 2010/11/02 22:53:11 jmc Exp $
 #  $Name:  $
 #
 
@@ -11,34 +11,41 @@
     echo
     echo "where possible OPTIONS are:"
     echo "  (-help|-h)               print usage"
-    echo "  (-mth)                   run multi threaded (using eedata.mth)"
+    echo "  (-mth)                   run multi-threaded (using eedata.mth)"
     echo "  (-mpi)                   compile and run using MPI"
-    echo "  (-ieee|-noieee)          if possible, use IEEE compiler flags"
+    echo "  (-ieee/-noieee)          if possible, use IEEE compiler flags"
     echo "                             (DEF=\"-ieee\")"
-    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 group and/or exp. dirs to test"
+    echo "  (-gsl)                   compile with \"-gsl\" flag"
+    echo "  (-use_r4|-ur4)           if allowed, use real*4 type for '_RS' variable"
+    echo "  (-optfile|-of) STRING    list of optfiles to use"
+    echo "  (-addr|-a) STRING        list of email recipients"
+    echo "                             (DEF=\"\" no email is sent)"
+    echo "  (-mpackdir|-mpd) DIR     location of the mpack utility"
+    echo "                             (DEF=\"../tools/mpack-1.6\")"
+    echo "  (-tdir|-t) 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 "  (-skipdir|-skd) STRING   list of exp. dirs to skip"
     echo "                             (DEF=\"\" which test all)"
-    echo "  (-b|-bash) STRING        preferred location of a \"bash\" or"
+    echo "  (-bash|-b) STRING        preferred location of a \"bash\" or"
     echo "                             Bourne-compatible \"sh\" shell"
     echo "                             (DEF=\"\" for \"bash\")"
     echo "  (-adm|-ad)               perform an adjoint run"
-    echo "  (-command) STRING        command to run"
-    echo "                             (DEF=\"make output.txt\")"
-    echo "  (-m|-make) STRING        command to use for \"make\""
+    echo "  (-oad)                   perform an OpenAD adjoint run"
+    echo "  (-command|-c) STRING     command to run"
+    echo "  (-makedepend|-md) STRING command to use for \"makedepend\""
+    echo "  (-make|-m) STRING        command to use for \"make\""
     echo "                             (DEF=\"make\")"
     echo "  (-odir) STRING           used to build output directory name"
     echo "                             (DEF=\"hostname\")"
-    echo "  (-ptr|-ptracers) STRING  specify which ptracers to test"
+    echo "  (-ptracers|-ptr) STRING  specify which ptracers to test"
     echo "                             (DEF=\"1 2 3 4 5\")"
     echo "  (-match) NUMBER          Matching Criteria (number of digits)"
-    echo "                             (DEF=\"12\")"
+    echo "                             (DEF=\"$MATCH_CRIT\")"
     echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
     echo "  (-clean)                 *ONLY* run \"make CLEAN\""
+    echo "  (-norun|-nr)             skip the \"runmodel\" stage (stop after make)"
+    echo "  (-runonly|-ro)           *ONLY* run stage (=\"-quick\" without make)"
     echo "  (-quick|-q)              same as \"-nogenmake -noclean -nodepend\""
     echo "  (-nogenmake|-ng)         skip the genmake stage"
     echo "  (-noclean|-nc)           skip the \"make clean\" stage"
@@ -64,7 +71,8 @@
 build_mpack()
 {
     printf "building the mpack utility...  "
-    if test ! -x "$MPACKDIR/mpack" ; then
+    MPACK="$MPACKDIR/mpack"
+    if test ! -x $MPACK ; then
 	if test ! -d $MPACKDIR ; then
 	    echo
 	    echo "Error: can't find \"$MPACKDIR\""
@@ -73,10 +81,10 @@
 	    echo
 	    HAVE_MPACK=f
 	fi
-	printf "building mpack...  "
 	if test "x$CC" = x ; then
 	    export CC=cc
 	fi
+	printf "building mpack (using CC=$CC)...  "
 	( cd $MPACKDIR && ./configure && $MAKE ) > tr_build_mpack.out 2>&1
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
@@ -87,19 +95,20 @@
 	else
 	    rm -f tr_build_mpack.out
 	    HAVE_MPACK=t
+	    echo "done"
 	fi
     else
 	HAVE_MPACK=t
+	echo "already exist"
     fi
-    echo "OK"
 }
 
 testoutput_var()
 {
-    # testoutput_var dir s1 label subdir extension
+    # testoutput_var dir s1 label subdir reference_output
     #
-    #  compares 1 variable output selected from file $dir/$subdir/$OUTPUTFILE 
-    #     with same output from reference file $dir/results/output.$extension
+    #  compares 1 variable output selected from file $dir/$subdir/$OUTPUTFILE
+    #     with same output from reference file $dir/results/$reference_output
     #  using search strings s1 and text label
 
     if [ $debug -gt 0 ]; then
@@ -108,7 +117,7 @@
     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 [ $lncntA -lt 2 ]; then
 	    if [ $verbose -gt 0 ]; then
 		echo Not enough lines of output when searching for "$2" 1>&2
 	    fi
@@ -119,11 +128,11 @@
 	return 99
     fi
     if [ $debug -gt 0 ]; then
-	echo testoutput_var: grep "$2" $1/results/output.$5 1>&2
+	echo testoutput_var: grep "$2" $1/results/$5 1>&2
     fi
-    grep "$2" $1/results/output.$5 | sed 's/.*=//' | cat -n > tmp2.txt
+    grep "$2" $1/results/$5 | sed 's/.*=//' | cat -n > tmp2.txt
     lncntB=`wc -l tmp2.txt | awk '{print $1}' `
-    if [ $lncntB -lt 3 ]; then
+    if [ $lncntB -lt 2 ]; then
 	if [ $verbose -gt 0 ]; then
 	    echo Not enough lines of output when searching for "$2" 1>&2
 	fi
@@ -161,99 +170,60 @@
     digits_of_similarity=`./tr_cmpnum < tmp4.txt`
     if [ $digits_of_similarity -eq 99 ]; then
 	if [ $verbose -gt 0 ]; then
-	    echo testoutput_var: No comparison was available for \"$2\" 1>&2
+	    echo testoutput_var: No comparison was available for \"$3\" 1>&2
 	fi
 	digits_of_similarity=99
     else
 	if [ $verbose -gt 0 ]; then
-	    echo There were $digits_of_similarity decimal places of similarity for \"$2\" 1>&2
+	    echo There were $digits_of_similarity decimal places of similarity for \"$3\" 1>&2
 	fi
     fi
     rm -f tmp1.txt tmp2.txt tmp3.txt tmp4.txt
-    
-    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
-}
-
-testoutput_ad()
-{
-    grep $3 $1/results_ad/output_adm.txt | awk '{print NR " " $5}' > t05.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/$2/$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
-    echo "-1" >> t6.txt
-    digits_5=`./tr_cmpnum < t5.txt`
-    digits_6=`./tr_cmpnum < t6.txt`
-    dashnum $digits_5 $digits_6
-    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
+    return $digits_of_similarity
 }
 
 testoutput_run()
 {
-    # testoutput_run directory subdir extension
+    # testoutput_run directory subdir reference_output
     #
     #  test output from 1 run in "directory"
-    if test "x$ADM" = x ; then
+# --> same processing for adjoint & forward test
         # default list of output variables to be checked:
         #  1rst : main variable used to decide if it pass or FAIL
         #  others : number of matching digits to be printed in summary.txt
         listChk=$DEF_CHECK_LIST
-	nbDef=`echo $listChk | awk '{print NF-1+3*gsub("+","E")}'`
 	#  load experiment-specific list from file "tr_checklist" (if it exist)
         if test -r $1/$2/tr_checklist ; then listChk=`cat $1/$2/tr_checklist` ; fi
         sVar=`echo $listChk | awk '{print $1}'`
         # remove 1rst var and expand the list: + => min max mean s.d
-        listVar=`echo $listChk | awk '{ for(i=2;i<=NF;i++){if (sub("+","",$i)) \
-            {printf " %s %s %s %s",$i"mn",$i"mx",$i"av",$i"sd"} else {printf " %s",$i} }}'`
+        listVar=`echo $listChk | sed 's/ [a-zA-Z0-9]*+/&mn &mx &av &sd/g' \
+                               | sed 's/+//g' | sed "s/^$sVar//"`
 	if [ $debug -gt 0 ]; then echo "testoutput_run: listVar(I)='$listVar'" 1>&2 ; fi
- 	for ii in 1 2 3 4 5 6 7 8 9 ; do
-	  tst=`eval 'echo "$HAVE_PTR0'$ii'"'`
-	 #echo "-- ptr test=" $tst "number of var=" `echo $listVar | awk '{print NF}'` 1>&2
- 	  if test "x$tst" != xt ; then listVar=`echo "$listVar" | sed "s/ pt$ii..//g"` ; fi
-        done
-        tst=`echo $sVar $listVar | awk '{ for(i=2;i<=NF;i++){t+=($i==$1)}; print t }'`
+        # check for ptracer output in reference_output file :
+        outpref=$1/results/$3
+	ptr_mon="trcstat_ptracerXX_min trcstat_ptracerXX_max"
+	ptr_mon="$ptr_mon trcstat_ptracerXX_mean trcstat_ptracerXX_sd"
+	for ii in $PTRACERS_NUM ; do
+	    ptrfound=0
+	    for jj in $ptr_mon ; do
+		name=`eval "echo $jj | sed -e 's|XX|0"$ii"|g'"`
+		tst=`grep $name $outpref | wc -l | awk '{print $1}'`
+		if test ! "x$tst" = x0 ; then ptrfound=1 ; fi
+	    done
+	    if test $ptrfound = '1' ; then
+		eval "HAVE_PTR0"$ii"=t"
+	    else
+		eval "HAVE_PTR0"$ii"=f"
+	      if test "x$ADM" = x -a "x$OADM" = x; then
+	      # remove this ptr from the list of output variable to check
+	      # echo "-- ptr test=" $tst "number of var=" `echo $listVar | awk '{print NF}'` 1>&2
+		listVar=`echo "$listVar" | sed "s/ pt$ii..//g"`
+	      fi
+	    fi
+	#   eval 'echo "HAVE_PTR0'$ii' = $HAVE_PTR0'$ii'"' 1>&2
+	done
+        tst=`echo $sVar $listVar | awk '{ for(i=2;i<=NF;i++){if($i==$1)t+=1}; print t }'`
         if test $tst != 1 ; then
           if test $tst = 0 ; then echo "==> WARNING: selected var >$sVar< not found" 1>&2
                  else echo "==> WARNING: found selected var >$sVar< $tst times" 1>&2 ; fi
@@ -262,31 +232,33 @@
           listVar=" $sVar "`echo "$listVar " | sed "s/ $sVar / /g"`
         fi
 	if [ $debug -gt 0 ]; then echo "testoutput_run: listVar(M)='$listVar'" 1>&2 ; fi
-	echo "listVar='$listVar'" > $CDIR"/summary.txt"
+	echo "listVar='$listVar'" > $locDIR"/summary.txt"
         allargs=""
         for xx in $listVar
         do
           case $xx in
 	   'PS')  if [ $debug -gt 0 ]
 		  then echo testoutput_run: testoutput_var $1 cg2d_init_res 1>&2 ; fi
-		  testoutput_var $1 "cg2d_init_res" "cg2d init. residual" $2 $3; yy=$?
+		  testoutput_var $1 "cg2d_init_res" "Press. Solver (cg2d)" $2 $3; yy=$?
 		  if [ $debug -gt 0 ] ; then echo testoutput_run: cg2dres=$yy 1>&2 ; fi ;;
- 	   'Tmn') testoutput_var $1 "dynstat_theta_min"  "theta minimum"  $2 $3; yy=$? ;;
- 	   'Tmx') testoutput_var $1 "dynstat_theta_max"  "theta maximum"  $2 $3; yy=$? ;;
- 	   'Tav') testoutput_var $1 "dynstat_theta_mean" "theta mean"	  $2 $3; yy=$? ;;
-	   'Tsd') testoutput_var $1 "dynstat_theta_sd"   "theta s.d."	  $2 $3; yy=$? ;;
-	   'Smn') testoutput_var $1 "dynstat_salt_min"  "salt minimum"	  $2 $3; yy=$? ;;
-	   'Smx') testoutput_var $1 "dynstat_salt_max"  "salt maximum"	  $2 $3; yy=$? ;;
-	   'Sav') testoutput_var $1 "dynstat_salt_mean" "salt mean"	  $2 $3; yy=$? ;;
-	   'Ssd') testoutput_var $1 "dynstat_salt_sd"   "salt s.d."	  $2 $3; yy=$? ;;
+ 	  'Cost') testoutput_var $1 "ADM  precision_derivative_cost" "ADM Cost" $2 $3; yy=$? ;;
+ 	  'Grad') testoutput_var $1 "ADM  precision_derivative_grad" "ADM Grad" $2 $3; yy=$? ;;
+ 	   'Tmn') testoutput_var $1 "dynstat_theta_min"  "Theta minimum"  $2 $3; yy=$? ;;
+ 	   'Tmx') testoutput_var $1 "dynstat_theta_max"  "Theta maximum"  $2 $3; yy=$? ;;
+ 	   'Tav') testoutput_var $1 "dynstat_theta_mean" "Theta mean"	  $2 $3; yy=$? ;;
+	   'Tsd') testoutput_var $1 "dynstat_theta_sd"   "Theta Std.Dev"  $2 $3; yy=$? ;;
+	   'Smn') testoutput_var $1 "dynstat_salt_min"  "Salt minimum"	  $2 $3; yy=$? ;;
+	   'Smx') testoutput_var $1 "dynstat_salt_max"  "Salt maximum"	  $2 $3; yy=$? ;;
+	   'Sav') testoutput_var $1 "dynstat_salt_mean" "Salt mean"	  $2 $3; yy=$? ;;
+	   'Ssd') testoutput_var $1 "dynstat_salt_sd"   "Salt Std.Dev"	  $2 $3; yy=$? ;;
 	   'Umn') testoutput_var $1 "dynstat_uvel_min"  "U minimum"	  $2 $3; yy=$? ;;
 	   'Umx') testoutput_var $1 "dynstat_uvel_max"  "U maximum"	  $2 $3; yy=$? ;;
 	   'Uav') testoutput_var $1 "dynstat_uvel_mean" "U mean"	  $2 $3; yy=$? ;;
-	   'Usd') testoutput_var $1 "dynstat_uvel_sd"   "U s.d."	  $2 $3; yy=$? ;;
+	   'Usd') testoutput_var $1 "dynstat_uvel_sd"   "U Std.Dev"	  $2 $3; yy=$? ;;
 	   'Vmn') testoutput_var $1 "dynstat_vvel_min"  "V minimum"	  $2 $3; yy=$? ;;
 	   'Vmx') testoutput_var $1 "dynstat_vvel_max"  "V maximum"	  $2 $3; yy=$? ;;
 	   'Vav') testoutput_var $1 "dynstat_vvel_mean" "V mean"	  $2 $3; yy=$? ;;
-	   'Vsd') testoutput_var $1 "dynstat_vvel_sd"   "V s.d."	  $2 $3; yy=$? ;;
+	   'Vsd') testoutput_var $1 "dynstat_vvel_sd"   "V Std.Dev"	  $2 $3; yy=$? ;;
 	'pt1mn'|'pt2mn'|'pt3mn'|'pt4mn'|'pt5mn') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
 	   testoutput_var $1 "trcstat_ptracer0"$ii"_min"  "p0"$ii"_min"	  $2 $3; yy=$? ;;
 	'pt1mx'|'pt2mx'|'pt3mx'|'pt4mx'|'pt5mx') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
@@ -294,7 +266,25 @@
 	'pt1av'|'pt2av'|'pt3av'|'pt4av'|'pt5av') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
 	   testoutput_var $1 "trcstat_ptracer0"$ii"_mean" "p0"$ii"_mean" $2 $3; yy=$? ;;
 	'pt1sd'|'pt2sd'|'pt3sd'|'pt4sd'|'pt5sd') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
-	   testoutput_var $1 "trcstat_ptracer0"$ii"_sd"   "p0"$ii"_sd"	  $2 $3; yy=$? ;;
+	   testoutput_var $1 "trcstat_ptracer0"$ii"_sd"   "p0"$ii"_StDv"  $2 $3; yy=$? ;;
+	 'Qntmn') testoutput_var $1 "forcing_qnet_min" "Qnet minimum"  $2 $3; yy=$? ;;
+	 'Qntmx') testoutput_var $1 "forcing_qnet_max" "Qnet maximum"  $2 $3; yy=$? ;;
+	 'Qntav') testoutput_var $1 "forcing_qnet_mean" "Qnet mean"	  $2 $3; yy=$? ;;
+	 'Qntsd') testoutput_var $1 "forcing_qnet_sd"  "Qnet Std.Dev"  $2 $3; yy=$? ;;
+	 'aSImn') testoutput_var $1 "seaice_area_min"   "SIce Area min"	  $2 $3; yy=$? ;;
+	 'aSImx') testoutput_var $1 "seaice_area_max"   "SIce Area max"	  $2 $3; yy=$? ;;
+	 'aSIav') testoutput_var $1 "seaice_area_mean"  "SIce Area mean"  $2 $3; yy=$? ;;
+	 'aSIsd') testoutput_var $1 "seaice_area_sd"    "SIce Area StDv"  $2 $3; yy=$? ;;
+	 'hSImn') testoutput_var $1 "seaice_heff_min"   "SIce Heff min"	  $2 $3; yy=$? ;;
+	 'hSImx') testoutput_var $1 "seaice_heff_max"   "SIce Heff max"	  $2 $3; yy=$? ;;
+	 'hSIav') testoutput_var $1 "seaice_heff_mean"  "SIce Heff mean"  $2 $3; yy=$? ;;
+	 'hSIsd') testoutput_var $1 "seaice_heff_sd"    "SIce Heff StDv"  $2 $3; yy=$? ;;
+	'AthSiG') testoutput_var $1 "thSI_Ice_Area_G" "thSIc Area Global" $2 $3; yy=$? ;;
+	'AthSiS') testoutput_var $1 "thSI_Ice_Area_S" "thSIc Area South"  $2 $3; yy=$? ;;
+	'AthSiN') testoutput_var $1 "thSI_Ice_Area_N" "thSIc Area North"  $2 $3; yy=$? ;;
+	'HthSiG') testoutput_var $1 "thSI_IceH_ave_G" "thSIc H Global"	  $2 $3; yy=$? ;;
+	'HthSiS') testoutput_var $1 "thSI_IceH_ave_S" "thSIc H South"	  $2 $3; yy=$? ;;
+	'HthSiN') testoutput_var $1 "thSI_IceH_ave_N" "thSIc H North"	  $2 $3; yy=$? ;;
               *) yy=99; echo "WARNING: asking for var=$xx : not recognized !" 1>&2 ;;
           esac
           if test $xx = $sVar
@@ -304,17 +294,14 @@
         done
 
 	nbVar=`echo $listVar | awk '{print NF}'`
-        if [ $nbVar -lt $nbDef ] ; then 
+        if [ $nbVar -lt $LEN_CHECK_LIST ] ; then
         #-- fill line (up to standard length) with dot:
-          adNul=`expr $nbDef - $nbVar | awk '{for(i=1;i<=$1;i++){print "."}}'`
+          adNul=`expr $LEN_CHECK_LIST - $nbVar | awk '{for(i=1;i<=$1;i++){print "."}}'`
 	  echo $allargs $adNul
         else
 	  echo $allargs
-        fi 
-
-    else
-	testoutput_ad $1 $2 "precision_grdchk_result"
-    fi
+        fi
+# <-- same processing for adjoint & forward test
 }
 
 genmakemodel()
@@ -331,42 +318,57 @@
 	(
 	    cd $1;
 	    command="$GENMAKE2  -ds -m $MAKE"
-	    if test "x$ADM" = x ; then
-		command="$command --mods=../code"
-	    else
+	    if test "x$MKDEPEND" != x ; then
+		command="$command -makedepend=$MKDEPEND"
+	    fi
+	    if test "x$ADM" = xt ; then
 		command="$command --mods=../code_ad"
+	    elif test "x$OADM" = xt ; then
+		command="$command -adof ../../../tools/adjoint_options/adjoint_oad -mods '../code_oad ../../OpenAD/code_oad_all'"
+	    else
+		command="$command -mods=../code"
 	    fi
 	    if test "x$OPTFILE" != xNONE ; then
-		command="$command --optfile=$OPTFILE"
+		command="$command -optfile=$OPTFILE"
 	    fi
 	    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
+	    if test "x$MULTI_THREAD" = xt ; then
+	    #- run multi-threaded using OpenMP:
+		command="$command -omp"
+	    fi
+	    if test "x$USE_R4" = xt ; then
+		command="$command -use_r4"
+	    fi
 	    if test "x$TS" = xt ; then
 		command="$command -ts"
 	    fi
 	    if test "x$PAPIS" = xt ; then
 		command="$command -papis"
-	    else 
+	    else
 	    if test "x$PCLS" = xt ; then
 		command="$command -pcls"
 	    fi
 	    fi
-	    printf 'genmake ... ' 1>&2
-	    $command > make.log 2>&1
+	    printf 'genmake ... '
+	    eval $command > genmake.tr_log 2>&1
 	    RETVAL=$?
 	    #  Reduce the size of the testing emails!
 	    head -100 Makefile > $CDIR/Makefile_head
 	    if test "x$RETVAL" != x0 ; then
-		tail make.log
-		echo "genmakemodel: genmake failed" 1>&2
-		cp genmake_* make.log $CDIR
+		tail genmake.tr_log
+		echo "genmakemodel: genmake failed"
+		cp genmake_* genmake.tr_log $CDIR
 		return 1
 	    else
-		echo "successful" 1>&2
+		echo "successful"
 	    fi
 	)
     fi
@@ -375,6 +377,7 @@
 makeclean()
 {
     # makeclean directory
+    if test "x$NODEPEND" = xf ; then rm -f $1/make.tr_log ; fi
     if test "x$NOCLEAN" = xt ; then
 	echo "make Clean skipped!"
     else
@@ -382,17 +385,20 @@
 	    cd $1;
 	    #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
+		printf 'clean build-dir: make Clean ... '
+		rm -f Makefile.old
+		$MAKE Clean >> make.tr_log 2>&1
 		RETVAL=$?
 		if test "x$RETVAL" != x0 ; then
-		    tail make.log
-		    echo "makeclean: \"make Clean\" failed" 1>&2
-		    cp make.log $CDIR"/make.log"
+		    tail make.tr_log
+		    echo "makeclean: \"make Clean\" failed"
+		    cp make.tr_log $CDIR"/make.tr_log"
 		    return 1
 		fi
+		echo successful
+	    else
+		echo ''
 	    fi
-	    echo successful 1>&2
 	    exit 0
 	)
     fi
@@ -406,15 +412,16 @@
     else
 	(
 	    cd $1;
-	    printf 'clean run-dir ... ' 2>&1
+	    printf 'clean run-dir ... '
 	    # part of what is done after "make clean" when doing "make CLEAN"
 	    find . -name "*.meta" -exec rm {} \;
 	    find . -name "*.data" -exec rm {} \;
 	    find . -name "fort.*" -exec rm {} \;
 	    find . -type l -exec rm {} \;
-	    rm -f $EXECUTABLE *.txt STD* *diagnostics.log datetime
+	    rm -f $EXECUTABLE $RUNLOG *.txt STD* *diagnostics.log datetime
 	    rm -rf mnc_test_*
-	    echo successful 1>&2
+ 	    rm -f *_MIT_CE_000.opt0000 costfunction*0000
+	    echo successful
 	    exit 0
 	)
     fi
@@ -428,16 +435,16 @@
     else
 	(
 	    cd $1;
-	    printf 'make depend ... ' 1>&2
-	    $MAKE depend >> make.log 2>&1
+	    printf 'make depend ... '
+	    $MAKE depend >> make.tr_log 2>&1
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
-		tail make.log
-		echo "makedependmodel: make depend failed" 1>&2
-		cp make.log $CDIR"/make.log"
+		tail make.tr_log
+		echo "makedependmodel: make depend failed"
+		cp make.tr_log $CDIR"/make.tr_log"
 		return 1
 	    else
-		echo successful 1>&2
+		echo successful
 	    fi
 	)
     fi
@@ -447,28 +454,41 @@
 {
     # makemodel directory
     (
+    if test "x$NOMAKE" = xt ; then
+	cd $1;
+	if test -x $EXECUTABLE ; then
+	    echo "make skipped!"
+	else
+	    echo "no executable!"
+	    return 2
+	fi
+    else
 	cd $1;
 	if test -r Makefile ; then
-	    printf 'make ... ' 1>&2
-	    if test "x$ADM" = x ; then
+	    printf 'make ... '
+	    if test "x$ADM" = xt ; then
+		$MAKE adall >> make.tr_log 2>&1
+	    elif test "x$OADM" = xt ; then
+		$MAKE adAll >> make.tr_log 2>&1
+            else
 		if test "x$JOBS" = x ; then
-		    $MAKE >> make.log 2>&1
+		    $MAKE >> make.tr_log 2>&1
 		else
-		    $MAKE -j $JOBS >> make.log 2>&1
+		    $MAKE -j $JOBS >> make.tr_log 2>&1
 		fi
-	    else
-		$MAKE adall >> make.log 2>&1
 	    fi
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
-		tail make.log
-		echo failed 1>&2
-		cp make.log $CDIR"/make.log"
+		tail make.tr_log
+		echo failed
+		cp make.tr_log $CDIR"/make.tr_log"
+		rm -f $EXECUTABLE
 		return 1
 	    else
-		echo successful 1>&2
+		echo successful
 	    fi
 	fi
+    fi
     )
 }
 
@@ -482,9 +502,9 @@
     code_dir=$2
     BUILD_DIR=$dir/$3
     CODE_DIR=$dir/$code_dir
-    
+
     # These are files that should replace their counter-part when using -mpi
-    MPI_FILES=`(cd $CODE_DIR; find . -name "*_mpi")`
+    MPI_FILES=`(cd $CODE_DIR; find . -name "*_mpi" -print)`
 
     #  Is this an MPI run?
     if test "x$MPI" = xt ; then
@@ -517,7 +537,7 @@
 	    fi
 	done
     fi
-    
+
 }
 
 linkdata()
@@ -528,23 +548,43 @@
     if test -d $1 ; then
 	(
 	    cd $1 ; shift
+	    echo 'linkdata from dirs:' $*
+            inpMPI=`(cd ../$1 ; find . -name "*.mpi" -print | sed 's:^\./::')`
+	    for xx in $inpMPI ; do
+	      if test -r "../"$1"/"$xx ; then
+	        # found 1 _mpi sfx file in 1rst input dir and it is readable
+		yy=`echo $xx | sed 's:\.mpi$::'`
+		if test "x$MPI" = "xt" ; then
+		# mpi test: remove symbolic link & link _mpi sfx file
+		    if test -h $yy ; then rm -f $yy ; fi
+		    if test ! -r $yy ; then
+			ln -sf "../"$1"/"$xx $yy ;
+			printf " $xx" 1>&2
+		    fi
+		else
+		# not mpi test: remove symbolic link
+		    if test -h $yy ; then rm -f $yy ; fi
+		fi
+	      fi
+	    done
 	    if test -r "../"$1"/eedata.mth" ; then
 	    # found eedata.mth in 1rst input dir and it is readable
 		if test "x$MULTI_THREAD" = "xt" ; then
 		# multi-threaded test: remove symbolic link & link eedata.mth
 		    if test -h eedata ; then rm -f eedata ; fi
-		    if test ! -r eedata ; then 
+		    if test ! -r eedata ; then
 			ln -sf "../"$1"/eedata.mth" eedata ;
-			printf 'eedata.mth ' 1>&2
+			printf ' eedata.mth' 1>&2
 		    fi
 		else
 		# not multi-threaded test: remove eedata symbolic link
 		    if test -h eedata ; then rm -f eedata ; fi
 		fi
 	    fi
+	    prevDir='NONE'
 	    for ldir in $* ; do
-		if test -d "../"$ldir ; then
-                    printf 'ldir='${ldir} 1>&2
+		if test -d "../"$ldir -a $ldir != $prevDir ; then
+                    printf " ldir=${ldir}:" 1>&2
 		    files=`( cd "../"$ldir ; ls -1 | grep -v CVS )`
 		    for i in $files ; do
 			if test ! -d "../"$ldir/$i ; then
@@ -554,11 +594,14 @@
 			    fi
 			fi
 		    done
+		    printf ' ;' 1>&2
 		    if test -x "../"$ldir"/"prepare_run ; then
-			"../"$ldir"/"prepare_run
+			"../"$ldir"/"prepare_run 1>&2
+		    else
+			echo '' 1>&2
 		    fi
-		    printf ' ; ' 1>&2
 		fi
+		prevDir=$ldir
 	    done
 	)
     fi
@@ -568,56 +611,69 @@
 {
     # runmodel directory
     #
-    #  runs "$COMMAND in "directory" 
+    #  runs "$COMMAND in "directory"
     #  (where "$COMMAND" is relative to "directory")
     (
 	cd $1
-	printf 'runmodel in %s ...' $1 1>&2
-	# make output.txt
-	echo
+	printf 'runmodel in %s ... ' $1
+	if test -L $EXECUTABLE ; then
+	  if test -x "../"$builddir"/"$EXECUTABLE ; then
+	    diff -q $EXECUTABLE "../"$builddir"/"$EXECUTABLE > /dev/null 2>&1
+	    outD=$? ; if test $outD != 0 ; then rm -f $EXECUTABLE ; fi
+	  else rm -f $EXECUTABLE
+	  fi
+	fi
         if test ! -x $EXECUTABLE -a -x "../"$builddir"/"$EXECUTABLE ; then
-	    echo " link" $EXECUTABLE "from dir ../"$builddir > run.log_00
+	    echo " link" $EXECUTABLE "from dir ../"$builddir > run.log_tmp
 	    ln -sf "../"$builddir"/"$EXECUTABLE .
 	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
+		rm -f $RUNLOG ; touch $RUNLOG
+		if test -f run.log_tmp ; then cat run.log_tmp >> $RUNLOG ; fi
+		echo " no executable:" $EXECUTABLE >> $RUNLOG
 		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
+            if test ! -f $OUTPUTFILE -o $OUTPUTFILE -ot $EXECUTABLE ; then
+              # output do not exist or is older than executable:
+		rm -f $RUNLOG ; touch $RUNLOG
+		if test -f run.log_tmp ; then cat run.log_tmp >> $RUNLOG ; fi
+		( eval $COMMAND ) >> $RUNLOG 2>&1
 		RETVAL=$?
 	    else
 		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
+		if test -f $RUNLOG ; then
+		    if test -f run.log_tmp ; then cat run.log_tmp >> $RUNLOG ; fi
+     		    echo "---------->> $OUTPUTFILE is up to date " >> $RUNLOG 2>&1
+		else
+		    touch $RUNLOG
+		    if test -f run.log_tmp ; then cat run.log_tmp >> $RUNLOG ; fi
+     		    echo "---------->> $OUTPUTFILE is up to date " >> $RUNLOG 2>&1
+     		    echo " no previous $RUNLOG: assume NORMAL END" >> $RUNLOG 2>&1
 		fi
 	    fi
-	    ENDVAL=`cat run.log | grep -v 'ABNORMAL END' | grep -c 'NORMAL END'`
+	    ENDVAL=`cat $RUNLOG | grep -v 'ABNORMAL END' | grep -c 'NORMAL END'`
 	fi
-	rm -f run.log_00
-	#if test "x$RETVAL" = x0 ; then
+	rm -f run.log_tmp
 	if [ $RETVAL -eq 0 -a $ENDVAL -gt 0 ] ; then
-	    tail run.log
-	    echo successful 1>&2
+	    echo successful
+	    printf '=> output from running in %s :\n' $1 1>&2
+	    tail $RUNLOG | sed 's/^.*/> &/g' 1>&2
 	    # === Reduce the size of the testing emails!
 	    #cp $OUTPUTFILE $CDIR"/"$OUTPUTFILE
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 0
+	elif [ $RETVAL -ne 0 -a $ENDVAL -gt 0 ] ; then
+	    #-- for some weird cases (run is finihed but with error code)
+	    echo 'finished with error (run:' $RETVAL ' end:' $ENDVAL ')'
+	    printf '=> output from running in %s :\n' $1 1>&2
+	    tail $RUNLOG | sed 's/^.*/> &/g' 1>&2
+	    return 0
 	else
-	    tail run.log
-	    echo failed '(run:' $RETVAL ' end:' $ENDVAL ')' 1>&2
-	    cp run.log $CDIR"/run.log"
+	    echo 'failed (run:' $RETVAL ' end:' $ENDVAL ')'
+	    printf '=> output from running in %s :\n' $1 1>&2
+	    tail $RUNLOG | sed 's/^.*/> &/g' 1>&2
+	    cp $RUNLOG $CDIR"/"$RUNLOG
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 1
 	fi
@@ -628,7 +684,7 @@
 {
     # create codelet for comparing model output
 
-    printf "creating the comparison code...  "
+    printf "creating the comparison code (using CC=$CC)...  "
     cat > tr_cmpnum.c <<EOF
 #include <stdio.h>
 #include <math.h>
@@ -668,7 +724,7 @@
 	return 0
     else
 	echo
-	echo "ERROR: failed to compile comparison code -- please specify" 
+	echo "ERROR: failed to compile comparison code -- please specify"
 	echo "  a C compiler using the CC environment variable."
 	exit 1
     fi
@@ -684,9 +740,10 @@
     listPrt=$@
     listRes=`echo $listPrt | sed 's/>//' | sed 's/<//'`
     xx=`echo $listPrt | sed 's/.*>//' | sed 's/<.*//' | awk '{print $1}'`
+    printf '%3s' $listPrt
+#   line below does not work on hp-ux_ia64 : do those substitutions later on
 #   printf '%3s' $listPrt | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</'
-    printf '%3s' $listPrt | sed 's/ 99/ --/g' | sed 's/  > / /' | sed 's/  < / /'
-    
+
     if [ $xx = '..' ]; then
 	printf ' N/O '
     elif [ $xx = '--' ]; then
@@ -702,14 +759,14 @@
     fi
     printf '  %s' $nm
     printf '\n'
-    
+
 }
 
 scandirs()
 {
     if [ $# -eq 1 ]; then
  	for arg in * ; do
- 	    test -d $arg/$1 && echo $arg
+ 	    test -f $arg/$1 && echo $arg
  	done
     else
  	echo $*
@@ -717,6 +774,35 @@
 }
 
 
+check_eedata()
+{
+    # check_eedata size.h eedata
+    if [ $# -eq 2 ] ; then
+      if test -f $1 -a -f $2 ; then
+      sx=`grep "^     & *nSx *=" $1 | sed "s/^     & *nSx *=//" | sed 's/, *$//'`
+      nx=`grep "^ *nTx *=" $2 | tail -1 | sed 's/^ *nTx *= *//' | sed "s/, *$//"`
+      if test "x$nx" = x ; then
+	rx=10
+      else
+	rx=`expr $sx % $nx`
+      fi
+      sy=`grep "^     & *nSy *=" $1 | sed "s/^     & *nSy *=//" | sed 's/, *$//'`
+      ny=`grep "^ *nTy *=" $2 | tail -1 | sed 's/^ *nTy *= *//' | sed "s/, *$//"`
+      if test "x$ny" = x ; then
+	ry=20
+      else
+	ry=`expr $sy % $ny`
+      fi
+      echo `expr $rx + $ry`
+    else
+      echo '-1'
+      fi
+    else
+      echo '-2'
+    fi
+
+}
+
 ###############################################################################
 
 
@@ -724,17 +810,17 @@
 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
+NORUN=f
 QUICK=f
+NOMAKE=f
 NOGENMAKE=f
 NOCLEAN=f
 NODEPEND=f
@@ -747,8 +833,9 @@
 SKIPDIRS=
 MPACKDIR="../tools/mpack-1.6"
 HAVE_MPACK=
-MPACK="$MPACKDIR/mpack"
+MPACK=
 COMMAND=
+MKDEPEND=
 if test "x$MAKE" = x ; then
     MAKE=make
 fi
@@ -760,10 +847,12 @@
 MULTI_THREAD=f
 OUTDIR=
 DELDIR=
+USE_R4=
 
 ADM=
+OADM=
 
-# Additional monitor types
+# list of pTracers to check for monitor output
 PTRACERS_NUM="1 2 3 4 5"
 
 MATCH_CRIT=13
@@ -781,7 +870,7 @@
     fi
 
     ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
-    
+
     case $ac_option in
 	
 	-help | --help | -h | --h)
@@ -794,32 +883,41 @@
 	
 	-addr | --addr | -a | --a)
             ac_prev=ADDRESSES ;;
-        -addr=* | --addr=*)
+        -addr=* | --addr=* | -a=* | --a=*)
             ADDRESSES=$ac_optarg ;;
+        -mpackdir | --mpackdir | -mpd | --mpd)
+            ac_prev=MPACKDIR ;;
+        -mpackdir=* | --mpackdir=* | -mpd=* | --mpd=*)
+            MPACKDIR=$ac_optarg ;;
 
 	-tdir | --tdir | -t | --t)
             ac_prev=TESTDIRS ;;
-        -tdir=* | --tdir=*)
+        -tdir=* | --tdir=* | -t=* | --t=*)
             TESTDIRS=$ac_optarg ;;
 
 	-skipdir | --skipdir | -skd | --skd)
             ac_prev=SKIPDIRS ;;
-        -skipdir=* | --skipdir=*)
+        -skipdir=* | --skipdir=* | -skd=* | --skd=*)
             SKIPDIRS=$ac_optarg ;;
 
 	-bash | --bash | -b | --b)
             ac_prev=BASH ;;
-        -bash=* | --bash=*)
+        -bash=* | --bash=* | -b=* | --b=*)
             BASH=$ac_optarg ;;
 
 	-command | --command | -c | --c)
 	    ac_prev=COMMAND ;;
-	-command=* | --command=*)
+	-command=* | --command=* | -c=* | --c=*)
 	    COMMAND=$ac_optarg ;;
 
+	-makedepend | --makedepend | -md | --md)
+	    ac_prev=MKDEPEND ;;
+	-makedepend=* | --makedepend=* | -md=* | --md=*)
+	    MKDEPEND=$ac_optarg ;;
+
 	-make | --make | -m | --m)
 	    ac_prev=MAKE ;;
-	-make=* | --make=*)
+	-make=* | --make=* | -m=* | --m=*)
 	    MAKE=$ac_optarg ;;
 
         -odir | --odir)
@@ -835,12 +933,16 @@
 	-match | --match ) ac_prev=MATCH_CRIT ;;
 	-match=* | --match=* ) MATCH_CRIT=$ac_optarg ;;
 
-	-j) ac_prev=JOBS ;;
-	-j=*) JOBS=$ac_optarg ;;
+	-j | --j) ac_prev=JOBS ;;
+	-j=* | --j=*) JOBS=$ac_optarg ;;
 
 	-clean | --clean)
 	    CLEANUP=t ; DELDIR=t ;;
 
+	-norun | --norun | -nr | --nr)
+	    NORUN=t ;;
+	-runonly | --runonly | -ro | --ro)
+	    QUICK=t ; NOMAKE=t ;;
 	-quick | --quick | -q | --q)
 	    QUICK=t ;;
 	-nogenmake | --nogenmake | -ng | --ng)
@@ -859,8 +961,11 @@
 
 	-adm | -ad) ADM=t ;;
 
+	-oad) OADM=t; NODEPEND=t ;;
+
 	-ieee) IEEE=true ;;
 	-noieee) IEEE= ;;
+        -gsl) GSL=t ;;
 
 	-verbose) verbose=2 ;;
 	-debug) debug=1 ;;
@@ -868,24 +973,24 @@
 
 	-deldir | -dd) DELDIR=t ;;
 
-	-ts) TS=t;;
+	-use_r4|-ur4) USE_R4=t ;;
 
+	-ts) TS=t;;
 	-papis) PAPIS=t;;
-
 	-pcls) PCL=t;;
 
         -*)
             echo "Error: unrecognized option: "$ac_option
             usage
             ;;
-        
+
         *)
             echo "Error: unrecognized argument: "$ac_option
             usage
             ;;
-        
+
      esac
-     
+
 done
 
 if test "x$QUICK" = xt ; then
@@ -894,12 +999,30 @@
     NODEPEND=t
 fi
 
+#- setting for forward or ADM testing
+if test "x$ADM" = xt ; then
+    code_dir=code_ad
+    inputdir=input_ad
+    ref_outp="output_adm.txt"
+    EXECUTABLE="mitgcmuv_ad"
+elif test "x$OADM" = xt ; then
+    code_dir=code_oad
+    inputdir=input_oad
+    ref_outp="output_oadm.txt"
+    EXECUTABLE="mitgcmuv_ad"
+else
+    code_dir=code
+    inputdir=input
+    ref_outp="output.txt"
+    EXECUTABLE="mitgcmuv"
+fi
+
+xx=`echo $TESTDIRS | awk '{print $1}'`
 if test "x$TESTDIRS" = x ; then
-    if test "x$ADM" = xt ; then
-	LIST=`scandirs results_ad`
-    else
-	LIST=`scandirs results`
-    fi
+    LIST=`scandirs results/$ref_outp`
+elif test $xx = 'start_from' ; then
+    xx=`echo $TESTDIRS | awk '{print $2}'`
+    LIST=`scandirs results/$ref_outp | sed -n "/$xx/,$ p"`
 else
     #- expand group of experiments:
     LIST=" "
@@ -914,7 +1037,7 @@
 		 LIST=${LIST}" "`ls | grep 'tutorial_'` ;;
 	*)	 LIST=${LIST}" "$xx ;;
       esac
-    done 
+    done
 fi
 #echo 'LIST='${LIST}'<'
 #- skip dirs, remove duplicate and non-directory:
@@ -935,7 +1058,7 @@
 	else count=1 ; echo "" ;  echo -n " skip: \"$xx\""
 	fi
     fi
-done 
+done
 if test $count = 1 ; then echo "" ; echo -n " ... " ; fi
 #echo 'TESTDIRS='${TESTDIRS}'<'
 
@@ -943,14 +1066,8 @@
     OPTFILE=$MITGCM_OF
 fi
 
-if test "x$ADM" = xt ; then
-    EXECUTABLE="mitgcmuv_ad"
-    OUTPUTFILE="output_adm.txt"
-else
-    EXECUTABLE="mitgcmuv"
-    OUTPUTFILE="output.txt"
-fi
-
+RUNLOG="run.tr_log"
+OUTPUTFILE=$ref_outp
 if test "x$COMMAND" = x ; then
     COMMAND="./$EXECUTABLE > $OUTPUTFILE"
 fi
@@ -958,38 +1075,54 @@
     OUTPUTFILE="STDOUT.0000"
 fi
 
-#echo "OK"
 echo "OK (COMMAND= $COMMAND )"
 
 # set the Default List of output variables to be checked:
 #  (use default or load experiment-specific list from file "tr_checklist")
 # content : 1rst = main variable used to decide if it pass or FAIL
 #         others = number of matching digits to be printed in summary.txt
-if test "x$ADM" != xt ; then
+if test "x$ADM" = x -a "x$OADM" = x; then
     DEF_CHECK_LIST='PS PS T+ S+ U+ V+ pt1+ pt2+ pt3+ pt4+ pt5+'
     EMPTY_RESULTS='.. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. ..'
-    nbDef=`echo $DEF_CHECK_LIST | awk '{print NF-1+3*gsub("+","E")}'`
+    LEN_CHECK_LIST=`echo $DEF_CHECK_LIST | sed 's/ [a-zA-Z0-9]*+/&mn &mx &av &sd/g' | awk '{print NF-1}'`
     ii=`echo $EMPTY_RESULTS | awk '{print NF}'`
-    EMPTY_RESULTS=$EMPTY_RESULTS`expr $nbDef - $ii | awk 'BEGIN{FS=":"}{for(i=1;i<=$1;i++){printf "  ."}}'`
+    EMPTY_RESULTS=$EMPTY_RESULTS`expr $LEN_CHECK_LIST - $ii | awk 'BEGIN{FS=":"}{for(i=1;i<=$1;i++){printf "  ."}}'`
+else
+    DEF_CHECK_LIST='Grad Cost Grad'
+    EMPTY_RESULTS='.. ..'
+    LEN_CHECK_LIST=`echo $DEF_CHECK_LIST | sed 's/ [a-zA-Z0-9]*+/&mn &mx &av &sd/g' | awk '{print NF-1}'`
 fi
 
 #  create the FORTRAN comparison code
-createcodelet
+if test -x tr_cmpnum ; then
+    echo "skipping comparison code build"
+else
+    createcodelet
+fi
 
-#  build the mpack utility
-if test "x$ADDRESSES" = xNONE -o "x$ADDRESSES" = x ; then
+#  build the mpack utility (if ADDRESSES = NONE, do it to test the build)
+if test "x$ADDRESSES" = x ; then
     echo "skipping mpack build"
 else
     build_mpack
 fi
 
 #  Create a uniquely named directory to store results
+CMDLINE=$0
+for xx in "$@" ; do nw=`echo $xx | wc -w`
+    if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
+                        else CMDLINE="$CMDLINE '$xx'" ; fi
+done
+#for xx in "$@" ; do CMDLINE="$CMDLINE '$xx'" ; done
 MACH=`hostname`
 UNAMEA=`uname -a`
 DATE=`date +%Y%m%d`
 BASE="tr_"$MACH"_"$DATE"_"
 if test "x$OUTDIR" != x ; then
     BASE="tr_"$OUTDIR"_"$DATE"_"
+else
+    short_name=`hostname | sed 's/\..*$//'`
+    BASE="tr_"$short_name"_"$DATE"_"
 fi
 DNUM=0
 DRESULTS="$BASE$DNUM"
@@ -1004,9 +1137,10 @@
     exit 1
 fi
 SUMMARY="$DRESULTS/summary.txt"
-printf "Start time:  " >> $SUMMARY
 start_date=`date`
 echo $start_date > $SUMMARY
+echo 'run:' $CMDLINE >> $SUMMARY
+echo 'on :' $UNAMEA  >> $SUMMARY
 
 of_path=
 if test "x$OPTFILE" != xNONE ; then
@@ -1035,25 +1169,21 @@
 fi
 echo
 echo >> $SUMMARY
-if test "x$ADM" = x ; then
-    if [ $MATCH_CRIT -lt 10 ] ; 
-    then line_0="default  "$MATCH_CRIT ; 
+if test "x$ADM" = x -a "x$OADM" = x; then
+    if [ $MATCH_CRIT -lt 10 ] ;
+    then line_0="default  "$MATCH_CRIT ;
     else line_0="default "$MATCH_CRIT ; fi
        line_0="$line_0  ----T-----  ----S-----  ----U-----  ----V-----"
-#   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
@@ -1064,6 +1194,10 @@
 else
     echo "ADJOINT=true" >> $SUMMARY
     echo >> $SUMMARY
+    if [ $MATCH_CRIT -lt 10 ] ;
+    then line_0="default     "$MATCH_CRIT ;
+    else line_0="default    "$MATCH_CRIT ; fi
+    echo "$line_0" | tee -a $SUMMARY
     cat << EOF | tee -a $SUMMARY
 G D M    C  G
 E p a R  o  r
@@ -1072,63 +1206,53 @@
 
 EOF
 fi
+echo "-------------------------------------------------------------------------------"
 
 #  ...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"
+    pfxdir="tr_$rundir"
+    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
-            echo '  ------  clean dir:' $dir/build
-	    ( cd $dir/build ; make CLEAN )
-	fi
-	if test -d $dir/run/CVS ; then
-            echo '  ------  clean dir:' $dir/run
-	    run_clean $dir/run
-	fi
-	(
-	    cd $dir
-	    rm -rf tr_run.*
+	echo -n '  --- dir:' $BUILD_DIR ': '
+	makeclean $BUILD_DIR
+	(   cd $BUILD_DIR
+	    rm -f $EXECUTABLE *.bak
+	    rm -f genmake_state genmake_*optfile genmake.log
+	    rm -f genmake.tr_log make.tr_log
 	)
+	if test -d $dir/$rundir/CVS ; then
+            echo -n '  --- dir:' $dir/$rundir ': '
+	    run_clean $dir/$rundir
+	fi
+	trdir=`( cd $dir ; find . -type d -name "$pfxdir.*" -print | sed 's/^.\///')`
+	ttd=`echo $trdir | wc -w`
+	if test $ttd != 0 ; then
+	    echo '  --- rm dir:' $trdir
+	    ( cd $dir ; rm -rf $trdir )
+	fi
 	continue
     fi
 
-    #  Verify that the testdir exists and contains previous 
+    #  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/output.txt"
-    else
-	fout=$dir"/results_ad/output_adm.txt"
-    fi
+    fout=$dir"/results/"$ref_outp
     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="build"
-    if test ! -d $dir/$builddir ; then mkdir $dir/$builddir ; fi
-    rundir="run"
-   #rundir=$builddir
-    if test ! -d $dir/$rundir ; then
-	rundir=$builddir
-    fi
-    
-    if test "x$ADM" = x ; then
-	code_dir=code
-	CODE_DIR=$dir/code
-        input_dirs='input'
-    else
-	code_dir=code_ad
-	CODE_DIR=$dir/code_ad
-        input_dirs='input_ad input'
-    fi
-    BUILD_DIR=$dir/$builddir
+    # Check for specific files for particular type of run
 
     if test ! -r $CODE_DIR"/SIZE.h_mpi" -a "x$MPI" = "xt" ; then
 	echo "can't find \"$CODE_DIR/SIZE.h_mpi\" -- skipping $dir"
@@ -1138,31 +1262,47 @@
 	echo "can't find \"$dir/input/eedata.mth\" -- skipping $dir"
 	continue
     fi
+    if test "x$MPI" = "xt" -a "x$MULTI_THREAD" = "xt" ; then
+      retv=`check_eedata $CODE_DIR"/SIZE.h_mpi" $dir"/input/eedata.mth"`
+      if test $retv != 0 ; then
+	echo "input/eedata.mth tiling misfit -- skipping $dir"
+	continue
+      fi
+    fi
 
     #  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
+    if test "x$NORUN" = xf ; then
+	ex_run_dirs=`( cd $dir ; echo $inputdir.* )`
+    fi
+    #echo "ex_run_dirs='$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
+	      if test "x$MPI" = "xt" ; then
+		retv=`check_eedata $CODE_DIR"/SIZE.h_mpi" $dir"/"$exd"/eedata.mth"`
+		if test $retv = 0 ; then
 		    extra_runs="$extra_runs $name"
+		else
+		    echo $exd"/eedata.mth tiling misfit -- skipping $dir"
 		fi
+	      else
+		extra_runs="$extra_runs $name"
+	      fi
+	    #else echo $dir"/"$exd"/eedata.mth: not found"
 	    fi
-	done
-    fi
+	  else
+	    extra_runs="$extra_runs $name"
+	  fi
+	fi
+    done
 
-    echo "-------------------------------------------------------------------------------"
     echo
-    if test "x$extra_runs" = "x" ; then 
+    if test "x$extra_runs" = "x" ; then
        echo "Experiment:  $dir"
     else
        echo "Experiment:  $dir ; extra_runs=$extra_runs"
@@ -1172,92 +1312,99 @@
     results=$EMPTY_RESULTS
 
     #  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
-	echo '====>>> this is to check that we never go through this part <<< ==='
-	makeclean $dir/$builddir \
-	    && run_clean $dir/$rundir
+    locDIR=$DRESULTS"/"$dir
+    mkdir $locDIR
+    CDIR=`pwd`"/$locDIR"
+
+    if test "x$NORUN" = xt ; then
+	    run=N
+	genmakemodel $dir/$builddir && genmake=Y \
+	    && makeclean $dir/$builddir \
+            && symlink_mpifiles $dir $code_dir $builddir \
+	    && makedependmodel $dir/$builddir && makedepend=Y \
+	    && makemodel $dir/$builddir && make=Y
     else
 	genmakemodel $dir/$builddir && genmake=Y \
 	    && makeclean $dir/$builddir \
-	    && run_clean $dir/$rundir \
             && symlink_mpifiles $dir $code_dir $builddir \
 	    && makedependmodel $dir/$builddir && makedepend=Y \
 	    && makemodel $dir/$builddir && make=Y \
-	    && linkdata $dir/$rundir $input_dirs \
+	    && run_clean $dir/$rundir \
+	    && linkdata $dir/$rundir $inputdir \
 	    && runmodel $dir/$rundir && run=Y \
-	    && results=`testoutput_run $dir $rundir "txt"`
+	    && results=`testoutput_run $dir $rundir $ref_outp`
     fi
-    
-    echo
-    if test "x$ADM" = x ; then
+    #echo "results='$results'"
+
 	fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
-	echo
-	echo "$fres" >> $SUMMARY
-        touch $CDIR"/summary.txt"
-	echo "fresults='$fres'" >> $CDIR"/summary.txt"
-	echo "MACH='$MACH'" >> $CDIR"/summary.txt"
-	echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
-	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	echo "tdir='$dir'" >> $CDIR"/summary.txt"
+	echo 1>&2
+ 	echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
+	touch $locDIR"/summary.txt"
+	echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $locDIR"/summary.txt"
+	echo "MACH='$MACH'" >> $locDIR"/summary.txt"
+	echo "UNAMEA='$UNAMEA'" >> $locDIR"/summary.txt"
+	echo "DATE='$DATE'" >> $locDIR"/summary.txt"
+	echo "tdir='$dir'" >> $locDIR"/summary.txt"
+	if test "x$ADM" = xt ; then
+	    head -1 $dir/$builddir/taf_ad.log >> $locDIR"/summary.txt"
+	    grep -A3 'Seconds in section "ALL' $dir/$rundir/$OUTPUTFILE \
+				>> $locDIR"/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
-	    runmodel $dir/tr_run.$ex && run=Y \
-		&& results=`testoutput_run $dir tr_run.$ex ${ex}".txt"`
-	    fres=`printf '%s %s %s %s' ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N}`
+	    locDIR=$DRESULTS"/"$dir"."$ex
+	    mkdir $locDIR
+	    CDIR=`pwd`"/$locDIR"
+	    test ! -e "$dir/$pfxdir.$ex" && mkdir "$dir/$pfxdir.$ex"
+	    run_clean $dir/$pfxdir.$ex
+	    linkdata $dir/$pfxdir.$ex $inputdir.$ex $inputdir
+	    runmodel $dir/$pfxdir.$ex && run=Y \
+	    && results=`testoutput_run $dir $pfxdir.$ex $refExOut`
 	    fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
 	    fres="$fres.$ex"
-	    echo
-	    echo "$fres" >> $SUMMARY
-            touch $CDIR"/summary.txt"
-	    echo "fresults='$fres'" >> $CDIR"/summary.txt"
-	    echo "MACH='$MACH'" >> $CDIR"/summary.txt"
-	    echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
-	    echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	    echo "tdir='$dir.$ex'" >> $CDIR"/summary.txt"
+	    echo 1>&2
+	    echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
+	    touch $locDIR"/summary.txt"
+	    echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $locDIR"/summary.txt"
+	    echo "MACH='$MACH'" >> $locDIR"/summary.txt"
+	    echo "UNAMEA='$UNAMEA'" >> $locDIR"/summary.txt"
+	    echo "DATE='$DATE'" >> $locDIR"/summary.txt"
+	    echo "tdir='$dir.$ex'" >> $locDIR"/summary.txt"
+            if test "x$ADM" = xt ; then
+	        head -1 $dir/$builddir/taf_ad.log >> $locDIR"/summary.txt"
+	        grep -A3 'Seconds in section "ALL' $dir/$pfxdir.$ex/$OUTPUTFILE \
+			           >> $locDIR"/summary.txt"
+            fi
 	    if test "x$POSTCLEAN" = xt ; then
- 		run_clean $dir/tr_run.$ex
+		run_clean $dir/$pfxdir.$ex
 	    fi
 	done
-    else
-	fres=`printf '%s %s %s %s' ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N}`
-	fres=$fres"$results   $dir"
-	echo
-	echo "$fres" >> $SUMMARY
-        touch $CDIR"/summary.txt"
-	echo "fresults='$fres'" >> $CDIR"/summary.txt"
-	echo "MACH='$MACH'" >> $CDIR"/summary.txt"
-	echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
-	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	echo "tdir='$dir'" >> $CDIR"/summary.txt"
-        grep -A3 'Seconds in section "ALL' $dir/$rundir/$OUTPUTFILE \
-			   >> $CDIR"/summary.txt"
-    fi
 
+    if test -f $DRESULTS"/"genmake_state ; then : ; else
+	if test -f $dir/$builddir/Makefile ; then
+	    mkOpt=`grep '^# OPTFILE=' $dir/$builddir/Makefile 2>/dev/null | head -1 | sed 's/^# //'`
+	    echo "from '$dir/$builddir/Makefile', extract:" > $DRESULTS/genmake_state
+	    sed -n '/^# executed by:/,+1 p' $dir/$builddir/Makefile >> $DRESULTS/genmake_state
+	    echo $mkOpt >> $DRESULTS/genmake_state
+	fi
+    fi
     #postclean $dir/$builddir
     if test "x$POSTCLEAN" = xt ; then
  	makeclean $dir/$builddir \
  	    && run_clean $dir/$rundir
     fi
-    
+
     echo "-------------------------------------------------------------------------------"
-    
+
 done
 
 printf "Start time:  " >> $SUMMARY
-echo $start_date >> $SUMMARY
+echo "$start_date" >> $SUMMARY
 printf "End time:    " >> $SUMMARY
 date >> $SUMMARY
 
@@ -1282,20 +1429,22 @@
 	    echo "An email containing results was sent to the following addresses:"
 	    echo "  \"$ADDRESSES\""
 	    echo
+	    test -f $DRESULTS".tar"  &&  rm -f $DRESULTS".tar"
+	    test -f $DRESULTS".tar.gz"  &&  rm -f $DRESULTS".tar.gz"
 	fi
-	test -f $DRESULTS".tar"  &&  rm -f $DRESULTS".tar"
-	test -f $DRESULTS".tar.gz"  &&  rm -f $DRESULTS".tar.gz"
     fi
 fi
 
-rm -f tr_cmpnum.c tr_cmpnum
+if test "x$QUICK" = xf -a "x$NORUN" = xf ; then
+    rm -f tr_cmpnum.c tr_cmpnum
+fi
 
 if test "x$CLEANUP" != xt ; then
-    cat $SUMMARY | sed 's/  \.  \.  \.  \.  \.  \.  \.  \.  \.  \.  \.  \.//'
+    cat $SUMMARY | sed 's/ \.  \.  \.  \.  \.  \.  \.  \.  \.  \.  \.  \. //'
     if test -e tr_out.txt ; then
         mv tr_out.txt tr_out.txt.old
     fi
-    cat $SUMMARY | sed '11,$ s/  \.//g' > tr_out.txt
+    cat $SUMMARY | sed '/^[YN] [YN] [YN] [YN]/ s/ \. //g' > tr_out.txt
 fi
 
 if test "x$DELDIR" = xt ; then