--- MITgcm/verification/testreport	2008/03/12 02:20:04	1.113
+++ MITgcm/verification/testreport	2016/05/20 19:34:38	1.208
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.113 2008/03/12 02:20:04 jmc Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.208 2016/05/20 19:34:38 jmc Exp $
 #  $Name:  $
 #
 
@@ -11,45 +11,66 @@
     echo
     echo "where possible OPTIONS are:"
     echo "  (-help|-h)               print usage"
-    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 "                             (DEF=\"-ieee\")"
+    echo " ---- type of test : ----"
+    echo "  (-tlm)                   perform a Tangent Linear run"
+    echo "  (-adm|-ad)               perform an adjoint run"
+    echo "  (-oad)                   perform an OpenAD adjoint run"
+    echo "  (-mth)                   run multi-threaded (using eedata.mth)"
+    echo "  (-mpi)                   use MPI to compile and run on 2 processors"
+    echo "  (-MPI)  NUMBER           use MPI to compile and run on max NUMBER procs"
+    echo "  (-mfile|-mf) STRING      MPI: file with list of possible machines to run on"
+    echo "  (-command|-c) STRING     command to run (e.g., if non-standard MPI setting)"
+    echo "                            DEF='mitgcmuv' or ='mpirun -np TR_NPROC mitgcmuv'"
+    echo " ---- testing options : ----"
+    echo "  (-optfile|-of) STRING    optfile to use"
+    echo "  (-fast)                  use optfile default for compiler flags (no '-ieee')"
+    echo "                            DEF=off => use IEEE numerics option (if available)"
+    echo "  (-devel)                 use optfile developement flags (if available)"
     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=\"\" no email is sent)"
-    echo "  (-mpd|-mpackdir) DIR     location of the mpack utility"
-    echo "                             (DEF=\"../tools/mpack-1.6\")"
-    echo "  (-t|-tdir) STRING        list of group and/or exp. dirs to test"
+    echo "  (-use_r4|-ur4)           if allowed, use real*4 type for '_RS' variable"
+    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 "                             (if list= 'start_from THIS_EXP' then"
+    echo "                              test THIS_EXP + all the following)"
+    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 "                             Bourne-compatible \"sh\" shell"
+    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 " ---- system options : ----"
+    echo "  (-bash|-b) STRING        preferred location of a \"bash\" or \"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 "  (-ef) STRING             used as genmake2 \"-extra_flag\" argument"
+    echo "  (-ncad)                  use genmake2 option \"-nocat4ad\" (-ncad)"
+    echo "  (-small_f)               make target small_f before making target all"
+    echo "  (-makedepend|-md) STRING command to use for \"makedepend\""
+    echo "  (-make|-m) STRING        command to use for \"make\""
     echo "                             (DEF=\"make\")"
+    echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
+    echo " ---- output options : ----"
+    echo "  (-match) NUMBER          Matching Criteria (number of digits)"
+    echo "                             (DEF=\"$MATCH_CRIT\")"
     echo "  (-odir) STRING           used to build output directory name"
     echo "                             (DEF=\"hostname\")"
-    echo "  (-ptr|-ptracers) STRING  specify which ptracers to test"
-    echo "                             (DEF=\"1 2 3 4 5\")"
-    echo "  (-match) NUMBER          Matching Criteria (number of digits)"
-    echo "                             (DEF=\"12\")"
-    echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
-    echo "  (-clean)                 *ONLY* run \"make CLEAN\""
+    echo "  (-addr|-a) STRING        list of email recipients"
+    echo "                             (DEF=\"\" no email is sent)"
+    echo "  (-send)       STRING     sending command (instead of using mpack)"
+    echo "  (-savdir|-sd) STRING     location to save output tar file to send (DEF='$SAVDIR')"
+    echo "  (-mpackdir|-mpd) DIR     location of the mpack utility"
+    echo "                             (DEF=\"../tools/mpack-1.6\")"
+    echo " -- do only some parts: --"
+    echo "  (-clean)                 *ONLY* run \"make CLEAN\" & clean run-dir"
+    echo "  (-norun|-nr)             skip the \"runmodel\" stage (stop after make)"
+    echo "  (-obj)                   only produces objects (=norun & no executable)"
+    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"
     echo "  (-nodepend|-nd)          skip the \"make depend\" stage"
+    echo "  (-postclean|-pc)         after each exp. test, clean build-dir & run-dir"
+    echo "  (-deloutp|-do)           delete output files after successful run"
     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:"
@@ -103,67 +124,66 @@
 {
     # testoutput_var dir s1 label subdir reference_output
     #
-    #  compares 1 variable output selected from file $dir/$subdir/$OUTPUTFILE 
-    #     with same output from reference file $dir/results/$reference_output
+    #  compares 1 variable output selected from file $dir/$subdir/$OUTPUTFILE
+    #     with same output from reference file $dir/$reference_output
     #  using search strings s1 and text label
 
     if [ $debug -gt 0 ]; then
 	echo testoutput_var: grep "$2" $1/$4/$OUTPUTFILE 1>&2
     fi
     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}' `
+	grep "$2" $1/$4/$OUTPUTFILE | sed 's/.*=//' | nl > ${TMP}a.txt
+	lncntA=`wc -l ${TMP}a.txt | awk '{print $1}' `
 	if [ $lncntA -lt 2 ]; then
 	    if [ $verbose -gt 0 ]; then
 		echo Not enough lines of output when searching for "$2" 1>&2
 	    fi
-	    return 99
+	    rm -f ${TMP}a.txt ; return 99
 	fi
     else
 	echo testoutput_var: $OUTPUTFILE from model run was not readable 1>&2
 	return 99
     fi
     if [ $debug -gt 0 ]; then
-	echo testoutput_var: grep "$2" $1/results/$5 1>&2
+	echo testoutput_var: grep "$2" $1/$5 1>&2
     fi
-    grep "$2" $1/results/$5 | sed 's/.*=//' | cat -n > tmp2.txt
-    lncntB=`wc -l tmp2.txt | awk '{print $1}' `
+    grep "$2" $1/$5 | sed 's/.*=//' | nl > ${TMP}b.txt
+    lncntB=`wc -l ${TMP}b.txt | awk '{print $1}' `
     if [ $lncntB -lt 2 ]; then
 	if [ $verbose -gt 0 ]; then
 	    echo Not enough lines of output when searching for "$2" 1>&2
 	fi
-	return 99
+	rm -f ${TMP}a.txt ${TMP}b.txt ; 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
+	if [ $verbose -gt 0 ]; then
+	    echo Not same Nb of lines when searching for "$2" ":" $lncntA $lncntB 1>&2
+	fi
+	rm -f ${TMP}a.txt ${TMP}b.txt ; return 99
     fi
-    has_nan=`cat tmp1.txt | grep -i nan | wc -l`
+    has_nan=`cat ${TMP}a.txt | grep -i nan | wc -l`
     if [ $has_nan -gt 0  ] ; then
 	echo testoutput_var: $OUTPUTFILE contains $has_nan NaN values  1>&2
-	return 99
+	rm -f ${TMP}a.txt ${TMP}b.txt ; return 99
     fi
-    has_inf=`cat tmp1.txt | grep -i inf | wc -l`
+    has_inf=`cat ${TMP}a.txt | grep -i inf | wc -l`
     if [ $has_inf -gt 0  ] ; then
 	echo testoutput_var: $OUTPUTFILE contains $has_inf Inf values  1>&2
-	return 99
+	rm -f ${TMP}a.txt ${TMP}b.txt ; return 99
     fi
     if [ $debug -gt 0 ]; then
-	echo testoutput_var: join tmp1.txt tmp2.txt 1>&2
+	echo testoutput_var: join ${TMP}a.txt ${TMP}b.txt 1>&2
     fi
-    join tmp1.txt tmp2.txt | awk '{print $1 " " $2 " " $3}' > tmp3.txt
+    # On the SGI O3K (*not* the O2K), "cat -n" inserts a ":" after the line number
+    join ${TMP}a.txt ${TMP}b.txt | awk '{print $1 " " $2 " " $3}' | sed -e 's|:||g' > ${TMP}c.txt
     if [ $debug -gt 0 ]; then
 	echo testoutput_var: compare_lines 1>&2
     fi
     if [ $verbose -gt 1 ]; then
-	cat tmp3.txt 1>&2
+	cat ${TMP}c.txt 1>&2
     fi
-    echo "-1" >> tmp3.txt
-    # On the SGI O3K (*not* the O2K), "cat -n" inserts a ":" after the line number
-    cat tmp3.txt | sed -e 's|:||g' > tmp4.txt
-    digits_of_similarity=`./tr_cmpnum < tmp4.txt`
+    echo "-1" >> ${TMP}c.txt
+    digits_of_similarity=`./tr_cmpnum < ${TMP}c.txt`
     if [ $digits_of_similarity -eq 99 ]; then
 	if [ $verbose -gt 0 ]; then
 	    echo testoutput_var: No comparison was available for \"$3\" 1>&2
@@ -174,34 +194,9 @@
 	    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
-}
+    rm -f ${TMP}a.txt ${TMP}b.txt ${TMP}c.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()
@@ -210,100 +205,162 @@
     #
     #  test output from 1 run in "directory"
 # --> 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=$DEF_CHECK_LIST
+	# default list of output variables to be checked:
+	#  1rst : main variable used to decide if it pass or FAIL
+	#  others : number of matching digits to be printed in summary.txt
+	listChk=$DEF_CHECK_LIST
 	#  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 $listChk | sed 's/ [a-zA-Z0-9]*+/&mn &mx &av &sd/g' \
-                               | sed 's/+//g' | sed "s/^$sVar//"`
+	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 $listChk | sed 's/ [a-zA-Z0-9]*+/&mn &mx &av &sd/g' \
+			       | sed 's/+//g' | sed "s/^$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 }'`
-        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
-          echo "==> WARNING: in checked list:" $listVar 1>&2
-        #- put it back once:
-          listVar=" $sVar "`echo "$listVar " | sed "s/ $sVar / /g"`
-        fi
+	# set ref.outp file-name and, if compressed, uncompress it into subdir
+	refoutp=results/$3
+	if test ! -r $1/results/$3 ; then
+	  if test -r $1/results/${3}.gz ; then
+	    tmpNam1=$3
+	    tmpNam2=`echo $tmpNam1 | sed 's/\..*\././'`
+	    if test "x$tmpNam1" = "x$tmpNam2" ; then
+		tmpNam1=`echo $tmpNam2 | sed 's/\./.std./'`
+	    fi
+	    refoutp=$2/$tmpNam1
+	    if [ $debug -gt 0 ]; then
+		echo "testoutput_run: gunzip 'results/$3.gz' into '$refoutp'" 1>&2
+	    fi
+	    gzip -cd $1/results/${3}.gz > $1/$refoutp
+	  else
+	    echo "missing reference output file '$3' (.gz) in '$1/results/'"
+	  fi
+	fi
+	# check for ptracer output in reference_output file :
+	if test $KIND = 0 ; then
+	  ptr_mon="trcstat_ptracerXX_min trcstat_ptracerXX_max"
+	  ptr_mon="$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 $1/$refoutp | 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"
+	      # 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$ii..//g"`
+	    fi
+	  # eval 'echo "HAVE_PTR0'$ii' = $HAVE_PTR0'$ii'"' 1>&2
+	  done
+	fi
+	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
+	  echo "==> WARNING: in checked list:" $listVar 1>&2
+	#- put it back once:
+	  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"
-        allargs=""
-        for xx in $listVar
-        do
-          case $xx in
+	echo "listVar='$listVar'" >> $locDIR"/summary.txt"
+	#---
+	allargs=""
+	for xx in $listVar
+	do
+         #ii=`echo $xx | sed 's/^pt[0-9][0-9]*..$/XXX/'`	#- any ptr number
+          ii=`echo $xx | sed 's/^pt[1-9]..$/XXX/'`		#- 1 to 9 ptr number
+          if test $ii != 'XXX' ; then
+          #- all except ptracer stats:
+	    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" "Press. Solver (cg2d)" $2 $3; yy=$?
+		  testoutput_var $1 "cg2d_init_res" "Press. Solver (cg2d)" $2 $refoutp ; yy=$?
 		  if [ $debug -gt 0 ] ; then echo testoutput_run: cg2dres=$yy 1>&2 ; fi ;;
- 	  '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 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 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 $xx | sed 's/pt//' | sed 's/..$//'`
-	   testoutput_var $1 "trcstat_ptracer0"$ii"_max"  "p0"$ii"_max"	  $2 $3; yy=$? ;;
-	'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"_StDv"  $2 $3; yy=$? ;;
-	 'Qntmn') testoutput_var $1 "extforcing_qnet_min" "Qnet minimum"  $2 $3; yy=$? ;;
-	 'Qntmx') testoutput_var $1 "extforcing_qnet_max" "Qnet maximum"  $2 $3; yy=$? ;;
-	 'Qntav') testoutput_var $1 "extforcing_qnet_mean" "Qnet mean"	  $2 $3; yy=$? ;;
-	 'Qntsd') testoutput_var $1 "extforcing_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 Hell max"	  $2 $3; yy=$? ;;
-	 'hSIav') testoutput_var $1 "seaice_heff_mean"  "SIce Hell mean"  $2 $3; yy=$? ;;
-	 'hSIsd') testoutput_var $1 "seaice_heff_sd"    "SIce Hell 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 = $sVar
-          then allargs="$allargs > $yy <"
-          else allargs="$allargs $yy"
+	  'Cost') testoutput_var $1 "ADM  ref_cost_function" "ADM CostFct" $2 $refoutp ; yy=$? ;;
+	 'AdGrd') testoutput_var $1 "ADM  adjoint_gradient"  "ADM Ad Grad" $2 $refoutp ; yy=$? ;;
+	 'FDGrd') testoutput_var $1 "ADM  finite-diff_grad"  "ADM FD Grad" $2 $refoutp ; yy=$? ;;
+	'tlmCst') testoutput_var $1 "TLM  ref_cost_function" "TLM CostFct" $2 $refoutp ; yy=$? ;;
+	'tlmGrd') testoutput_var $1 "TLM  tangent-lin_grad"  "TLM TL Grad" $2 $refoutp ; yy=$? ;;
+	'fwdGrd') testoutput_var $1 "TLM  finite-diff_grad"  "TLM FD Grad" $2 $refoutp ; yy=$? ;;
+	   'Tmn') testoutput_var $1 "dynstat_theta_min"  "Theta minimum"  $2 $refoutp ; yy=$? ;;
+	   'Tmx') testoutput_var $1 "dynstat_theta_max"  "Theta maximum"  $2 $refoutp ; yy=$? ;;
+	   'Tav') testoutput_var $1 "dynstat_theta_mean" "Theta mean"	  $2 $refoutp ; yy=$? ;;
+	   'Tsd') testoutput_var $1 "dynstat_theta_sd"   "Theta Std.Dev"  $2 $refoutp ; yy=$? ;;
+	   'Smn') testoutput_var $1 "dynstat_salt_min"  "Salt minimum"	  $2 $refoutp ; yy=$? ;;
+	   'Smx') testoutput_var $1 "dynstat_salt_max"  "Salt maximum"	  $2 $refoutp ; yy=$? ;;
+	   'Sav') testoutput_var $1 "dynstat_salt_mean" "Salt mean"	  $2 $refoutp ; yy=$? ;;
+	   'Ssd') testoutput_var $1 "dynstat_salt_sd"   "Salt Std.Dev"	  $2 $refoutp ; yy=$? ;;
+	   'Umn') testoutput_var $1 "dynstat_uvel_min"  "U minimum"	  $2 $refoutp ; yy=$? ;;
+	   'Umx') testoutput_var $1 "dynstat_uvel_max"  "U maximum"	  $2 $refoutp ; yy=$? ;;
+	   'Uav') testoutput_var $1 "dynstat_uvel_mean" "U mean"	  $2 $refoutp ; yy=$? ;;
+	   'Usd') testoutput_var $1 "dynstat_uvel_sd"   "U Std.Dev"	  $2 $refoutp ; yy=$? ;;
+	   'Vmn') testoutput_var $1 "dynstat_vvel_min"  "V minimum"	  $2 $refoutp ; yy=$? ;;
+	   'Vmx') testoutput_var $1 "dynstat_vvel_max"  "V maximum"	  $2 $refoutp ; yy=$? ;;
+	   'Vav') testoutput_var $1 "dynstat_vvel_mean" "V mean"	  $2 $refoutp ; yy=$? ;;
+	   'Vsd') testoutput_var $1 "dynstat_vvel_sd"   "V Std.Dev"	  $2 $refoutp ; yy=$? ;;
+	 'Qntmn') testoutput_var $1 "forcing_qnet_min" "Qnet minimum"  $2 $refoutp ; yy=$? ;;
+	 'Qntmx') testoutput_var $1 "forcing_qnet_max" "Qnet maximum"  $2 $refoutp ; yy=$? ;;
+	 'Qntav') testoutput_var $1 "forcing_qnet_mean" "Qnet mean"	  $2 $refoutp ; yy=$? ;;
+	 'Qntsd') testoutput_var $1 "forcing_qnet_sd"  "Qnet Std.Dev"  $2 $refoutp ; yy=$? ;;
+	 'aSImn') testoutput_var $1 "seaice_area_min"   "SIce Area min"	  $2 $refoutp ; yy=$? ;;
+	 'aSImx') testoutput_var $1 "seaice_area_max"   "SIce Area max"	  $2 $refoutp ; yy=$? ;;
+	 'aSIav') testoutput_var $1 "seaice_area_mean"  "SIce Area mean"  $2 $refoutp ; yy=$? ;;
+	 'aSIsd') testoutput_var $1 "seaice_area_sd"    "SIce Area StDv"  $2 $refoutp ; yy=$? ;;
+	 'hSImn') testoutput_var $1 "seaice_heff_min"   "SIce Heff min"	  $2 $refoutp ; yy=$? ;;
+	 'hSImx') testoutput_var $1 "seaice_heff_max"   "SIce Heff max"	  $2 $refoutp ; yy=$? ;;
+	 'hSIav') testoutput_var $1 "seaice_heff_mean"  "SIce Heff mean"  $2 $refoutp ; yy=$? ;;
+	 'hSIsd') testoutput_var $1 "seaice_heff_sd"    "SIce Heff StDv"  $2 $refoutp ; yy=$? ;;
+	 'uSImn') testoutput_var $1 "seaice_uice_min"   "SIce Uice min"	  $2 $refoutp ; yy=$? ;;
+	 'uSImx') testoutput_var $1 "seaice_uice_max"   "SIce Uice max"	  $2 $refoutp ; yy=$? ;;
+	 'uSIav') testoutput_var $1 "seaice_uice_mean"  "SIce Uice mean"  $2 $refoutp ; yy=$? ;;
+	 'uSIsd') testoutput_var $1 "seaice_uice_sd"    "SIce Uice StDv"  $2 $refoutp ; yy=$? ;;
+	 'vSImn') testoutput_var $1 "seaice_vice_min"   "SIce Vice min"	  $2 $refoutp ; yy=$? ;;
+	 'vSImx') testoutput_var $1 "seaice_vice_max"   "SIce Vice max"	  $2 $refoutp ; yy=$? ;;
+	 'vSIav') testoutput_var $1 "seaice_vice_mean"  "SIce Vice mean"  $2 $refoutp ; yy=$? ;;
+	 'vSIsd') testoutput_var $1 "seaice_vice_sd"    "SIce Vice StDv"  $2 $refoutp ; yy=$? ;;
+	'AthSiG') testoutput_var $1 "thSI_Ice_Area_G" "thSIc Area Global" $2 $refoutp ; yy=$? ;;
+	'AthSiS') testoutput_var $1 "thSI_Ice_Area_S" "thSIc Area South"  $2 $refoutp ; yy=$? ;;
+	'AthSiN') testoutput_var $1 "thSI_Ice_Area_N" "thSIc Area North"  $2 $refoutp ; yy=$? ;;
+	'HthSiG') testoutput_var $1 "thSI_IceH_ave_G" "thSIc H Glob-ave"  $2 $refoutp ; yy=$? ;;
+	'HthSiS') testoutput_var $1 "thSI_IceH_ave_S" "thSIc H South-av"  $2 $refoutp ; yy=$? ;;
+	'HthSiN') testoutput_var $1 "thSI_IceH_ave_N" "thSIc H North-av"  $2 $refoutp ; yy=$? ;;
+	'HthMxS') testoutput_var $1 "thSI_IceH_max_S" "thSIc H South-max" $2 $refoutp ; yy=$? ;;
+	'HthMxN') testoutput_var $1 "thSI_IceH_max_N" "thSIc H North-max" $2 $refoutp ; yy=$? ;;
+	 'sbo_M') testoutput_var $1 "sbo_mass"          "SBO mass"	  $2 $refoutp ; yy=$? ;;
+	 'sboFW') testoutput_var $1 "sbo_mass_fw"       "SBO m-FW"	  $2 $refoutp ; yy=$? ;;
+	 'sboAc') testoutput_var $1 "sbo_zoamc"         "SBO AM-C"	  $2 $refoutp ; yy=$? ;;
+	 'sboAp') testoutput_var $1 "sbo_zoamp"         "SBO AM-P"	  $2 $refoutp ; yy=$? ;;
+	'StrmIc') testoutput_var $1 "STREAMICE_FP_ERR" "StreamIce Solver" $2 $refoutp ; yy=$? ;;
+	      *) yy=99; echo "WARNING: asking for var=$xx : not recognized !" 1>&2 ;;
+	    esac
+          else
+          #- ptracers stats:
+            nn=`echo $xx | sed 's/pt//' | sed 's/..$//'`
+            ii=`echo $xx | sed 's/^pt[0-9]*//'`
+	    case $ii in
+	    'mn') testoutput_var $1 "trcstat_ptracer0"$nn"_min"  "p0"$nn"_min"  $2 $refoutp ; yy=$? ;;
+	    'mx') testoutput_var $1 "trcstat_ptracer0"$nn"_max"  "p0"$nn"_max"  $2 $refoutp ; yy=$? ;;
+	    'av') testoutput_var $1 "trcstat_ptracer0"$nn"_mean" "p0"$nn"_mean" $2 $refoutp ; yy=$? ;;
+	    'sd') testoutput_var $1 "trcstat_ptracer0"$nn"_sd"   "p0"$nn"_StDv" $2 $refoutp ; yy=$? ;;
+	    esac
           fi
-        done
+	  if test $xx = $sVar
+	  then allargs="$allargs > $yy <"
+	  else allargs="$allargs $yy"
+	  fi
+	done
 
 	nbVar=`echo $listVar | awk '{print NF}'`
-        if [ $nbVar -lt $LEN_CHECK_LIST ] ; then 
-        #-- fill line (up to standard length) with dot:
-          adNul=`expr $LEN_CHECK_LIST - $nbVar | awk '{for(i=1;i<=$1;i++){print "."}}'`
+	if [ $nbVar -lt $LEN_CHECK_LIST ] ; then
+	#-- fill line (up to standard length) with dot:
+	  adNul=`expr $LEN_CHECK_LIST - $nbVar | awk '{for(i=1;i<=$1;i++){print "."}}'`
 	  echo $allargs $adNul
-        else
+	else
 	  echo $allargs
-        fi 
+        fi
 # <-- same processing for adjoint & forward test
 }
 
@@ -321,45 +378,64 @@
 	(
 	    cd $1;
 	    command="$GENMAKE2  -ds -m $MAKE"
-	    if test "x$ADM" = x ; then
-		command="$command --mods=../code"
+	    if test "x$MKDEPEND" != x ; then
+		command="$command -makedepend=$MKDEPEND"
+	    fi
+	    if test $KIND = 4 ; then
+		command="$command -oad -mods=../$code_dir"
 	    else
-		command="$command --mods=../code_ad"
+		command="$command -mods=../$code_dir"
 	    fi
 	    if test "x$OPTFILE" != xNONE ; then
-		command="$command --optfile=$OPTFILE"
+		command="$command -optfile=$OPTFILE"
 	    fi
-	    if test "x$IEEE" != x ; then
+	    if test $OptLev = 1 ; then
 		command="$command -ieee"
 	    fi
+	    if test $OptLev = 0 ; then
+		command="$command -devel"
+	    fi
 	    if test "x$GSL" = xt ; then
 		command="$command -gsl"
 	    fi
-	    if test "x$MPI" = xt ; then
+	    if test "x$MPI" != x0 ; 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="$command -use_r4"
+	    fi
+	    if test "x$EXTRFLG" != x ; then
+		command="$command -extra_flag $EXTRFLG"
+	    fi
+	    if test "x$NOCATAD" = xt ; then
+		command="$command -nocat4ad"
+	    fi
 	    if test "x$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.log genmake_* genmake.tr_log $CDIR
 		return 1
 	    else
-		echo "successful" 1>&2
+		echo "successful"
 	    fi
 	)
     fi
@@ -368,6 +444,7 @@
 makeclean()
 {
     # makeclean directory
+    if test "x$NOGENMAKE" = xf ; then rm -f $1/make.tr_log ; fi
     if test "x$NOCLEAN" = xt ; then
 	echo "make Clean skipped!"
     else
@@ -375,17 +452,19 @@
 	    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 ... '
+		$MAKE Clean >> make.tr_log 2>&1
 		RETVAL=$?
 		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 genmake.log genmake.tr_log $CDIR
 		    return 1
 		fi
+		echo successful
+	    else
+		echo ''
 	    fi
-	    echo successful 1>&2
 	    exit 0
 	)
     fi
@@ -397,20 +476,23 @@
     if test "x$NOCLEAN" = xt ; then
 	echo "run_clean skipped!"
     else
-	(
-	    cd $1;
-	    printf 'clean run-dir ... ' 2>&1
-	    # 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 -rf mnc_test_*
- 	    rm -f *_MIT_CE_000.opt0000 costfunction*0000
-	    echo successful 1>&2
-	    exit 0
-	)
+      (
+	cd $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 {} \;
+	#- should remove executable only if sym-link (already done above)
+	rm -f $RUNLOG *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
+	rm -f datetime costfinal divided.ctrl snapshot* output_adm.*.diva_*
+	rm -f *_MIT_CE_000.opt0000 costfunction*0000
+	rm -f oad_cp.[0-9][0-9][0-9].?????
+	rm -rf mnc_test_*
+	echo successful
+	exit 0
+      )
     fi
 }
 
@@ -422,16 +504,16 @@
     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 genmake.log genmake.tr_log $CDIR
 		return 1
 	    else
-		echo successful 1>&2
+		echo successful
 	    fi
 	)
     fi
@@ -441,31 +523,155 @@
 {
     # makemodel directory
     (
+    mk_fail=0
+    if test "x$NOMAKE" = xt ; then
+	cd $1;
+	if test -x $EXECUTABLE ; then
+	    echo "make skipped!"
+	else
+	    echo "no executable!"
+	    mk_fail=3
+	fi
+    else
 	cd $1;
 	if test -r Makefile ; then
-	    printf 'make ... ' 1>&2
-	    if test "x$ADM" = x ; then
-		if test "x$JOBS" = x ; then
-		    $MAKE >> make.log 2>&1
+	    if test "x$MKSMALLF" = xt ; then
+		printf 'make small_f ... '
+		$MAKE_CMD small_f >> make.tr_log 2>&1
+		RETVAL=$?
+		if test "x$RETVAL" != x0 ; then
+		    tail make.tr_log
+		    echo failed
+		    cp genmake.log genmake.tr_log $CDIR
+		    tail -$NBLINES_MKLOG make.tr_log > $CDIR"/make.tr_log_tail"
+		    rm -f $EXECUTABLE
+		    mk_fail=1
 		else
-		    $MAKE -j $JOBS >> make.log 2>&1
+		    echo successful
 		fi
-	    else
-		$MAKE adall >> make.log 2>&1
 	    fi
+	    printf 'make ... '
+	    $MAKE_CMD $TARG >> make.tr_log 2>&1
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
-		tail make.log
-		echo failed 1>&2
-		cp make.log $CDIR"/make.log"
-		return 1
+		tail make.tr_log
+		echo failed
+		cp genmake.log genmake.tr_log $CDIR
+		tail -$NBLINES_MKLOG make.tr_log > $CDIR"/make.tr_log_tail"
+		rm -f $EXECUTABLE
+		mk_fail=1
 	    else
-		echo successful 1>&2
+		echo successful
 	    fi
+	else
+	    echo "no Makefile !"
+	    mk_fail=2
+	fi
+    fi
+    if test $KIND = 1 -a -f taf_ftl.log ; then
+	head -1 taf_ftl.log >> $CDIR"/summary.txt"
+    fi
+    if test $KIND = 2 -a -f taf_ad.log ; then
+	head -1 taf_ad.log >> $CDIR"/summary.txt"
+	nerr=`grep -c 'TAF *.* ERROR ' taf_ad.log`
+	nwar=`grep -c 'TAF RECOMPUTATION *.* WARNING ' taf_ad.log`
+	if test -f taf_output ; then
+	    n2er=`grep -c 'TAF *.* ERROR ' taf_output`
+	    n3er=`grep -c '\*ERROR\* ' taf_output`
+	    nerr=`expr $nerr + $n2er + $n3er`
 	fi
+	echo " TAF reports $nerr Errors and $nwar Recomputation Warnings" \
+				>> $CDIR"/summary.txt"
+    fi
+    if test $mk_fail != 0 ; then return $mk_fail ; fi
     )
 }
 
+mk_mpi_size()
+{
+    # mk_mpi_size input_file output_file proc_Nb threads_Nb_X threads_Nb_Y
+    #
+    #  make new SIZE.h (=output_file) from SIZE.h_mpi (=input_file)
+    #     for an MPI build with no more than proc_Nb processors ;
+    #  ensure that enough tiles per proc (nSx,nSy) remain for the given
+    #     number of threads (nTx,nTy) ;
+    #  return the effective number of processors.
+
+    inp=$1
+    out=$2
+    np=$3
+    tx=$4
+    ty=$5
+    tmp=TTT.$$
+
+    # dirX : select with direction to favor in MPI process repartition
+    #   dirX=1 : prefer to put more proc in X direction
+    #   dirX=0 : prefer to put more proc in Y direction
+    dirX=0
+
+    px=`grep "^     & *nPx *=" $inp | sed "s/^     & *nPx *= *//" | sed 's/, *$//'`
+    py=`grep "^     & *nPy *=" $inp | sed "s/^     & *nPy *= *//" | sed 's/, *$//'`
+    sx=`grep "^     & *nSx *=" $inp | sed "s/^     & *nSx *= *//" | sed 's/, *$//'`
+    sy=`grep "^     & *nSy *=" $inp | sed "s/^     & *nSy *= *//" | sed 's/, *$//'`
+
+    #- for each direction, assume # of threads is a multiple of total number of tiles
+    nx=$px
+    if [ `expr $sx % $tx` -ne 0 -a `expr $sx \* $px % $tx` -eq 0 ] ; then
+	nx=`expr $sx \* $px / $tx`
+	if [ $verbose -gt 1 ]; then
+	    echo " change px from $px to $nx to accommodate $tx threads"
+	fi
+    fi
+    ny=$py
+    if [ `expr $sy % $ty` -ne 0 -a `expr $sy \* $py % $ty` -eq 0 ] ; then
+	ny=`expr $sy \* $py / $ty`
+	if [ $verbose -gt 1 ]; then
+	    echo " change py from $py to $ny to accommodate $ty threads"
+	fi
+    fi
+    #- find the largest divisor of input_file proc Nb, but not larger than $np
+    pp=0
+    i=1
+    while [ $i -le $nx ] ; do
+      if [ `expr $nx % $i` -eq 0 ] ; then
+	j=1
+	while [ $j -le $ny ] ; do
+	  if [ `expr $ny % $j` -eq 0 ] ; then
+	    ij=`expr $i \* $j`
+	    if [ $ij -gt $pp ] ; then
+		flag=1
+	    elif [ $ij -eq $pp ] ; then
+		flag=$dirX
+	    else
+		flag=0
+	    fi
+	    if test $flag = 1 ; then
+	      if [ $ij -le $np ] ; then
+		ix=$i ; jy=$j ; pp=$ij
+		#echo "  ix,jy= $ix,$jy"
+	      fi
+	    fi
+	  fi
+	  j=`expr $j + 1`
+	done
+      fi
+      i=`expr $i + 1`
+    done
+
+    #- create new SIZE.h type file:
+    sx=`expr $sx \* $px / $ix`
+    sy=`expr $sy \* $py / $jy`
+    if [ $verbose -gt 1 ]; then
+	echo " px,py,np= $px,$py,$np : New MPI size: px,py= $ix,$jy : sx,sy= $sx,$sy"
+    fi
+    sed "/^     \& *nPx *=/s/[0-9]*,/$ix,/" $inp > $tmp
+    sed "/^     \& *nPy *=/s/[0-9]*,/$jy,/" $tmp > $out
+    sed "/^     \& *nSx *=/s/[0-9]*,/$sx,/" $out > $tmp
+    sed "/^     \& *nSy *=/s/[0-9]*,/$sy,/" $tmp > $out
+    rm -f $tmp
+    return $pp
+}
+
 symlink_mpifiles()
 {
     # Put special links so that MPI specific files are used
@@ -474,44 +680,44 @@
 
     dir=$1
     code_dir=$2
-    BUILD_DIR=$dir/$3
-    CODE_DIR=$dir/$code_dir
-    
+    build_dir=$dir/$3
+
     # These are files that should replace their counter-part when using -mpi
-    MPI_FILES=`(cd $CODE_DIR; find . -name "*_mpi" -print)`
+    MPI_FILES=`(cd $dir/$code_dir; find . -name "*_mpi" -print)`
 
-    #  Is this an MPI run?
-    if test "x$MPI" = xt ; then
-	# YES: We symbolically link these files to the build
-	# dir so long as there is no real file in place
-	for ii in $MPI_FILES ; do
-	    i=`echo $ii | sed 's:^\./::'`
-	    name=`echo $i | sed 's:_mpi::' `
-	    cmp $CODE_DIR/$i $BUILD_DIR/$name > /dev/null 2>&1
-	    RETVAL=$?
-	    if test "x$RETVAL" != x0 ; then
-		if ! test -f $BUILD_DIR/$i ; then
-	            #echo Linking $name to $i
-		    (cd $BUILD_DIR; ln -sf ../$code_dir/$i $name)
-		fi
-	    fi
-	done
-    else
-        # NO: We undo any _mpi symbolically linked files
-	for ii in $MPI_FILES ; do
-	    i=`echo $ii | sed 's:^\./::'`
-	    name=`echo $i | sed 's:_mpi::' `
-	    if test -L $BUILD_DIR/$name ; then
-		cmp $BUILD_DIR/$name "../$code_dir/$name"_mpi > /dev/null 2>&1
+    for ii in $MPI_FILES ; do
+	i=`echo $ii | sed 's:^\./::'`
+	name=`echo $i | sed 's:_mpi::'`
+	file="../$code_dir/$i"
+	if test $name = 'SIZE.h' ; then file="SIZE.h.mpi" ; fi
+
+	#  Is this an MPI run?
+	if test "x$MPI" = x0 ; then
+	    # NO: We undo any _mpi symbolically linked files
+	    if test -L $build_dir/$name ; then
+		( cd $build_dir ; cmp $name $file > /dev/null 2>&1 )
 		RETVAL=$?
 		if test "x$RETVAL" = x0 ; then
-		    #echo Un-linking $name from $linktarg
-		    rm -f $BUILD_DIR/$name
+		    if [ $verbose -gt 1 ]; then
+			echo "  Un-linking $name from ../$code_dir" ; fi
+		    rm -f $build_dir/$name
 		fi
 	    fi
-	done
-    fi
-    
+	else
+	    # YES: We symbolically link these files to the build
+	    # dir so long as there is no real file in place
+	    ( cd $build_dir ; cmp $name $file > /dev/null 2>&1 )
+	    RETVAL=$?
+	    if [ $verbose -gt 1 ]; then echo "  cmp $name $file returns: $RETVAL" ; fi
+	    if test "x$RETVAL" != x0 ; then
+		if test -h $build_dir/$name ; then rm -f $build_dir/$name ; fi
+		if test ! -r $build_dir/$name ; then
+		    if [ $verbose -gt 1 ]; then echo "  Linking $name to $file" ; fi
+		    (cd $build_dir; ln -sf $file $name)
+		fi
+	    fi
+	fi
+    done
 }
 
 linkdata()
@@ -522,14 +728,33 @@
     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" = "x0" ; then
+		    # not mpi test: remove symbolic link
+		    if test -h $yy ; then rm -f $yy ; fi
+		else
+		    # 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
+		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
@@ -539,7 +764,7 @@
 	    prevDir='NONE'
 	    for ldir in $* ; do
 		if test -d "../"$ldir -a $ldir != $prevDir ; then
-                    printf 'ldir='${ldir} 1>&2
+		    printf " ldir=${ldir}:" 1>&2
 		    files=`( cd "../"$ldir ; ls -1 | grep -v CVS )`
 		    for i in $files ; do
 			if test ! -d "../"$ldir/$i ; then
@@ -549,10 +774,12 @@
 			    fi
 			fi
 		    done
+		    printf ' ;' 1>&2
 		    if test -x "../"$ldir"/"prepare_run ; then
-			"../"$ldir"/"prepare_run
+			"../"$ldir"/"prepare_run 1>&2
+		    else
+			echo '' 1>&2
 		    fi
-		    printf ' ; ' 1>&2
 		fi
 		prevDir=$ldir
 	    done
@@ -564,62 +791,107 @@
 {
     # runmodel directory
     #
-    #  runs "$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
-	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
+	printf 'runmodel in %s ... ' $1
+	if test "x$MPI" != x0 ; then
+	    #- adjust the MPI run command with the right number of Procs
+	    #echo '' ; echo "  COMMAND='$COMMAND'"
+	    COMMAND=`echo $COMMAND | sed "s/ TR_NPROC/ $LOC_NPROC/"`
+	    if test "x$MPI_MFILE" != x ; then
+	      COMMAND=`echo $COMMAND | sed "s/ TR_MFILE / ..\/..\/$LOC_MFILE /"`
+	    fi
+	    #echo "  COMMAND='$COMMAND'"
+	fi
+	if test -L $EXECUTABLE ; then
+	  if test -x "../"$builddir"/"$EXECUTABLE ; then
+	    cmp $EXECUTABLE "../"$builddir"/"$EXECUTABLE > /dev/null 2>&1
+	    outD=$? ; if test "x$outD" != x0 ; 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
+	if test ! -x $EXECUTABLE -a -x "../"$builddir"/"$EXECUTABLE ; then
+	    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
-		RETVAL=8
-		ENDVAL=-1
+	if test ! -x $EXECUTABLE ; then
+	    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 ! -f $OUTPUTFILE -o $OUTPUTFILE -ot $EXECUTABLE ; then
-              # output do not exist or is older than executable:
-		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
-		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
+	  if test ! -f $OUTPUTFILE -o $OUTPUTFILE -ot $EXECUTABLE ; then
+	    # output do not exist or is older than executable:
+	    rm -f $OUTPUTFILE $RUNLOG ; touch $RUNLOG
+	    if test -f run.log_tmp ; then cat run.log_tmp >> $RUNLOG ; fi
+	#- Divided Adjoint Run:
+	#  get the number of additional runs (add_DIVA_runs) from file "run_ADM_DIVA"
+	    if test $KIND = 2 -a -f run_ADM_DIVA ; then
+	      adm_diva_nb=`sed -n '/^ *add_DIVA_runs\>.*=/p' run_ADM_DIVA | sed 's/ //g'`
+	      echo " Divided Adjoint Run: $adm_diva_nb" >> $RUNLOG
+	      eval "let $adm_diva_nb"
+	      if [ $add_DIVA_runs -ge 1 ] ; then
+		rm -f costf* divided.ctrl snapshot*
+		echo -n "(add_DIVA_runs=$add_DIVA_runs) ... "
+		for ii in `seq 1 $add_DIVA_runs` ; do
+		  ( eval $COMMAND ) >> $RUNLOG 2>&1
+		  echo " additional DIVA run # $ii : done" >> $RUNLOG
+		  mv -f $OUTPUTFILE ${OUTPUTFILE}.diva_${ii}
+		done
+	      fi
 	    fi
-	    ENDVAL=`cat run.log | grep -v 'ABNORMAL END' | grep -c 'NORMAL END'`
+	#- special DIVA processing ends here
+	    ( eval $COMMAND ) >> $RUNLOG 2>&1
+	    RETVAL=$?
+	    ENDVAL=`tail $OUTPUTFILE | grep -c 'PROGRAM MAIN: Execution ended Normally'`
+	    if [ $POSTCLEAN -eq 1 -a $ENDVAL -gt 0 ] ; then
+		find . -name "*.meta" -exec rm {} \;
+		find . -name "*.data" -exec rm {} \;
+		rm -rf mnc_test_*
+	    fi
+	  else
+	    RETVAL=0
+	    ENDVAL=`tail $OUTPUTFILE | grep -c 'PROGRAM MAIN: Execution ended Normally'`
+	    touch $RUNLOG
+	    if test -f run.log_tmp ; then cat run.log_tmp >> $RUNLOG ; fi
+	    echo "---------->> $OUTPUTFILE is up to date " >> $RUNLOG 2>&1
+	  fi
+	fi
+	rm -f run.log_tmp
+	#- in all cases where OutputFile exists, report SIZE and time
+	if test -f $OUTPUTFILE ; then
+	  grep '(PID\.TID 0000\.0001)      n.. =' $OUTPUTFILE \
+		| sed 's/(PID.TID 0000.0001)   //' >> $CDIR"/summary.txt"
+#	  grep -A3 'Seconds in section "ALL' $OUTPUTFILE \
+#		| sed 's/(PID.TID 0000.0001)   //' >> $CDIR"/summary.txt"
+#         some implementations of grep cannot do contextual searches so we
+#         replace the above with a sed command
+	  cat $OUTPUTFILE | sed -n '/Seconds in section "ALL/{N
+	  N
+	  N
+	  p
+	  }' | sed 's/(PID.TID 0000.0001)   //' >> $CDIR"/summary.txt"
 	fi
-	rm -f run.log_00
-	#if test "x$RETVAL" = x0 ; then
+	if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	if [ $RETVAL -eq 0 -a $ENDVAL -gt 0 ] ; then
-	    tail run.log
-	    echo successful 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
+	    echo successful
+	    printf '=> output from running in %s :\n' $1 1>&2
+	    tail $RUNLOG | sed 's/^.*/> &/g' 1>&2
+	    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"
-            if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
+	    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
 	    return 1
 	fi
     )
@@ -669,7 +941,7 @@
 	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
@@ -688,7 +960,7 @@
     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/  < /</'
-    
+
     if [ $xx = '..' ]; then
 	printf ' N/O '
     elif [ $xx = '--' ]; then
@@ -703,15 +975,23 @@
 	fi
     fi
     printf '  %s' $nm
+    if test $KIND = 2 ; then
+	#-- apppend taf repport summary:
+	tafrep=`grep -c '^ TAF reports ' $CDIR/summary.txt`
+	if test $tafrep = 1 ; then
+	    grep '^ TAF reports ' $CDIR/summary.txt | awk '{printf "  (e=%i, w=%i)",$3,$6}'
+	fi
+    fi
     printf '\n'
-    
+
 }
 
 scandirs()
 {
     if [ $# -eq 1 ]; then
  	for arg in * ; do
- 	    test -f $arg/$1 && echo $arg
+ 	   #test -f $arg/$1 && echo $arg
+ 	    test -f $arg/$1 -o -f $arg/$1.gz && echo $arg
  	done
     else
  	echo $*
@@ -719,26 +999,65 @@
 }
 
 
+check_eedata()
+{
+    # check_eedata eedata size.h
+    if [ $# -eq 2 ] ; then
+     if test -f $1 -a -f $2 ; then
+      nx=`grep "^ *nTx *=" $1 | tail -1 | sed 's/^ *nTx *= *//' | sed "s/, *$//"`
+      sx=`grep "^     & *nSx *=" $2 | sed "s/^     & *nSx *=//" | sed 's/, *$//'`
+      if test "x$nx" = x ; then
+	rx=10
+      else
+	rx=`expr $sx % $nx`
+      fi
+      ny=`grep "^ *nTy *=" $1 | tail -1 | sed 's/^ *nTy *= *//' | sed "s/, *$//"`
+      sy=`grep "^     & *nSy *=" $2 | sed "s/^     & *nSy *=//" | sed 's/, *$//'`
+      if test "x$ny" = x ; then
+	ry=20
+      else
+	ry=`expr $sy % $ny`
+      fi
+      echo `expr $rx + $ry`
+     else
+      echo '-1'
+     fi
+    elif [ $# -eq 1 ] ; then
+     if test -f $1 ; then
+      nx=`grep "^ *nTx *=" $1 | tail -1 | sed 's/^ *nTx *= *//' | sed "s/, *$//"`
+      if test "x$nx" = x ; then nx=1 ; fi
+      ny=`grep "^ *nTy *=" $1 | tail -1 | sed 's/^ *nTy *= *//' | sed "s/, *$//"`
+      if test "x$ny" = x ; then ny=1 ; fi
+     #echo $nx $ny
+      echo $nx
+     else
+      echo '-1'
+     fi
+    else
+      echo '-2'
+    fi
+
+}
+
 ###############################################################################
 
 
 #  Default properties
 debug=0
 verbose=1
-clean=0
+NBLINES_MKLOG=16000
 
-IEEE=true
-if test "x$MITGCM_IEEE" != x ; then
-    IEEE=$MITGCM_IEEE
-fi
+OptLev=1
 GSL=f
 
 CLEANUP=f
+NORUN=f
 QUICK=f
+NOMAKE=f
 NOGENMAKE=f
 NOCLEAN=f
 NODEPEND=f
-POSTCLEAN=f
+POSTCLEAN=0
 
 BASH=
 OPTFILE=NONE
@@ -748,25 +1067,38 @@
 MPACKDIR="../tools/mpack-1.6"
 HAVE_MPACK=
 MPACK=
+SENDCMD=
+SAVDIR='.'
 COMMAND=
+MKDEPEND=
 if test "x$MAKE" = x ; then
     MAKE=make
 fi
+MAKE_CMD=
 if test "x$CC" = x ; then
     CC=cc
 fi
 JOBS=
-MPI=f
+TARG=
+MPI=0
+MPI_MFILE=
 MULTI_THREAD=f
 OUTDIR=
 DELDIR=
+USE_R4=
+EXTRFLG=
+NOCATAD=
+MKSMALLF=
+
+#- type of testing (KIND):
+#   KIND=0 : forward (= default) ;  KIND=1 : Tangent Linear with TAF ;
+#   KIND=2 : Adjoint with TAF ;     KIND=4 : Adjoint with OpenAD
+KIND=0
 
-ADM=
-
-# Additional monitor types
+# list of pTracers to check for monitor output
 PTRACERS_NUM="1 2 3 4 5"
 
-MATCH_CRIT=13
+MATCH_CRIT=10
 
 printf "parsing options...  "
 
@@ -781,91 +1113,100 @@
     fi
 
     ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
-    
+
     case $ac_option in
 	
-	-help | --help | -h | --h)
-	    usage ;;
-	
-	-optfile | --optfile | -of | --of)
-            ac_prev=OPTFILE ;;
-        -optfile=* | --optfile=* | -of=* | --of=*)
-            OPTFILE=$ac_optarg ;;
-	
-	-addr | --addr | -a | --a)
-            ac_prev=ADDRESSES ;;
-        -addr=* | --addr=*)
-            ADDRESSES=$ac_optarg ;;
-        -mpackdir | --mpackdir | -mpd | --mpd)
-            ac_prev=MPACKDIR ;;
-        -mpackdir=* | --mpackdir=* | -mpd=* | --mpd=*)
-            MPACKDIR=$ac_optarg ;;
-
-	-tdir | --tdir | -t | --t)
-            ac_prev=TESTDIRS ;;
-        -tdir=* | --tdir=*)
-            TESTDIRS=$ac_optarg ;;
-
-	-skipdir | --skipdir | -skd | --skd)
-            ac_prev=SKIPDIRS ;;
-        -skipdir=* | --skipdir=*)
-            SKIPDIRS=$ac_optarg ;;
-
-	-bash | --bash | -b | --b)
-            ac_prev=BASH ;;
-        -bash=* | --bash=*)
-            BASH=$ac_optarg ;;
-
-	-command | --command | -c | --c)
-	    ac_prev=COMMAND ;;
-	-command=* | --command=*)
-	    COMMAND=$ac_optarg ;;
-
-	-make | --make | -m | --m)
-	    ac_prev=MAKE ;;
-	-make=* | --make=*)
-	    MAKE=$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 ;;
+	-help | --help | -h | --h) usage ;;
+
+	-optfile | --optfile | -of | --of) ac_prev=OPTFILE ;;
+	-optfile=* | --optfile=* | -of=* | --of=*) OPTFILE=$ac_optarg ;;
+
+	-addr | --addr | -a | --a) ac_prev=ADDRESSES ;;
+	-addr=* | --addr=* | -a=* | --a=*) ADDRESSES=$ac_optarg ;;
+	-mpackdir | --mpackdir | -mpd | --mpd) ac_prev=MPACKDIR ;;
+	-mpackdir=* | --mpackdir=* | -mpd=* | --mpd=*) MPACKDIR=$ac_optarg ;;
+
+	-send | --send ) ac_prev=SENDCMD ;;
+	-send=* | --send=* ) SENDCMD=$ac_optarg ;;
+	-savdir | --savdir | -sd | --sd ) ac_prev=SAVDIR ;;
+	-savdir=* | --savdir=* | -sd=* | --sd=* ) SAVDIR=$ac_optarg ;;
+
+	-tdir | --tdir | -t | --t) ac_prev=TESTDIRS ;;
+	-tdir=* | --tdir=* | -t=* | --t=*) TESTDIRS=$ac_optarg ;;
+	-skipdir | --skipdir | -skd | --skd) ac_prev=SKIPDIRS ;;
+	-skipdir=* | --skipdir=* | -skd=* | --skd=*) SKIPDIRS=$ac_optarg ;;
+
+	-bash | --bash | -b | --b) ac_prev=BASH ;;
+	-bash=* | --bash=* | -b=* | --b=*) BASH=$ac_optarg ;;
+
+	-command | --command | -c | --c) ac_prev=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=* | -m=* | --m=*) MAKE=$ac_optarg ;;
+
+	-repl_mk | --repl_mk ) ac_prev=MAKE_CMD ;;
+	-repl_mk=* | --repl_mk=*) MAKE_CMD=$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 ;;
 
 	-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 ;;
+	-ef | --ef) ac_prev=EXTRFLG ;;
+	-ef=* | --ef=*) EXTRFLG=$ac_optarg ;;
 
-	-quick | --quick | -q | --q)
-	    QUICK=t ;;
-	-nogenmake | --nogenmake | -ng | --ng)
-	    NOGENMAKE=t ;;
-	-noclean | --noclean | -nc | --nc)
-	    NOCLEAN=t ;;
-	-nodepend | --nodepend | -nd | --nd)
-	    NODEPEND=t ;;
+	-clean | --clean) CLEANUP=t ; DELDIR=t ;;
 
-	-postclean | --postclean | -pc | --pc)
-	    POSTCLEAN=t ;;
+	-norun | --norun | -nr | --nr) NORUN=t ;;
+	-obj | --obj ) TARG='obj' ; NORUN=t ;;
+	-runonly | --runonly | -ro | --ro) QUICK=t ; NOMAKE=t ;;
+	-quick | --quick | -q | --q) QUICK=t ;;
+	-nogenmake | --nogenmake | -ng | --ng) NOGENMAKE=t ;;
+	-noclean | --noclean | -nc | --nc) NOCLEAN=t ;;
+	-nodepend | --nodepend | -nd | --nd) NODEPEND=t ;;
+
+	-postclean | --postclean | -pc | --pc) POSTCLEAN=2 ;;
+	-deloutp | --deloutp | -do | --do) POSTCLEAN=1 ;;
+
+	-mpi | --mpi) MPI=2 ;;
+	-MPI | --MPI) ac_prev=MPI ;;
+	-MPI=* | --MPI=*) MPI=$ac_optarg ;;
 
-	-mpi) MPI=t ;;
+	-mfile | --mfile | -mf | --mf) ac_prev=MPI_MFILE ;;
+	-mfile=* | --mfile=* | -mf=* | --mf=*) MPI_MFILE=$ac_optarg ;;
 
 	-mth) MULTI_THREAD=t ;;
 
-	-adm | -ad) ADM=t ;;
-
-	-ieee) IEEE=true ;;
-	-noieee) IEEE= ;;
-        -gsl) GSL=t ;;
+	-tlm) if test $KIND = 0 ; then KIND=1 ; else
+		echo "Error: '-tlm', '-adm' and '-oad' are exclusive" ; usage
+	      fi ;;
+	-adm | -ad) if test $KIND = 0 ; then KIND=2 ; else
+		echo "Error: '-tlm', '-adm' and '-oad' are exclusive" ; usage
+	      fi ;;
+	-oad) if test $KIND = 0 ; then KIND=4 ; NODEPEND=t ; else
+		echo "Error: '-tlm', '-adm' and '-oad' are exclusive" ; usage
+	      fi ;;
+	-ncad) NOCATAD=t ;;
+	-small_f) MKSMALLF=t ;;
+
+	-ieee)   echo "Warning: ignore option '-ieee' (already the default)"
+		 printf " ... " ;;
+	-noieee) echo "Warning: will use option '-fast' instead of '-noieee' (obsolete)"
+		 printf " ... " ; OptLev=`expr $OptLev \* 2` ;;
+	-fast)  OptLev=`expr $OptLev \* 2` ;;
+	-devel) OptLev=0 ;;
+	-gsl) GSL=t ;;
 
 	-verbose) verbose=2 ;;
 	-debug) debug=1 ;;
@@ -873,24 +1214,19 @@
 
 	-deldir | -dd) DELDIR=t ;;
 
-	-ts) TS=t;;
+	-use_r4|-ur4) USE_R4=t ;;
 
+	-ts) TS=t;;
 	-papis) PAPIS=t;;
+	-pcls) PCLS=t;;
 
-	-pcls) PCL=t;;
+	-*) echo "Error: unrecognized option: "$ac_option
+	    usage ;;
+	*)  echo "Error: unrecognized argument: "$ac_option
+	    usage ;;
 
-        -*)
-            echo "Error: unrecognized option: "$ac_option
-            usage
-            ;;
-        
-        *)
-            echo "Error: unrecognized argument: "$ac_option
-            usage
-            ;;
-        
      esac
-     
+
 done
 
 if test "x$QUICK" = xt ; then
@@ -898,22 +1234,58 @@
     NOCLEAN=t
     NODEPEND=t
 fi
+if test "x$MAKE_CMD" = x ; then MAKE_CMD=$MAKE ; fi
+
+#- check length of MPI machine file:
+if test "x$MPI" != x0 -a "x$MPI_MFILE" != x ; then
+    if test -r $MPI_MFILE ; then
+	nl=`wc -l $MPI_MFILE | awk '{print $1}'`
+	if [ $nl -lt $MPI ] ; then
+	  echo "Error: need at least $MPI nodes (currently only $nl) in MPI_MFILE=$MPI_FILE"
+	  usage
+	fi
+	if [ $verbose -gt 1 ]; then
+	    echo " MPI_MFILE=$MPI_MFILE : $nl procs for MPI=$MPI run"
+	fi
+    else
+	  echo "Error: cannot access MPI_MFILE=$MPI_FILE"
+	  usage
+    fi
+fi
 
 #- setting for forward or ADM testing
-if test "x$ADM" = xt ; then
+if test $KIND = 1 ; then
+    TARG=ftlall
+    code_dir=code_ad
+    inputdir=input_ad
+    ref_outp="output_tlm.txt"
+    EXECUTABLE="mitgcmuv_ftl"
+elif test $KIND = 2 ; then
+    if test "x$TARG" = xobj ; then TARG=adobj ; else TARG=adall ; fi
     code_dir=code_ad
     inputdir=input_ad
     ref_outp="output_adm.txt"
     EXECUTABLE="mitgcmuv_ad"
+elif test $KIND = 4 ; then
+    TARG=adAll
+    code_dir=code_oad
+    inputdir=input_oad
+    ref_outp="output_oadm.txt"
+    EXECUTABLE="mitgcmuv_ad"
 else
     code_dir=code
     inputdir=input
     ref_outp="output.txt"
     EXECUTABLE="mitgcmuv"
 fi
+if test "x$JOBS" != x ; then TARG="-j $JOBS $TARG" ; fi
 
+xx=`echo $TESTDIRS | awk '{print $1}'`
 if test "x$TESTDIRS" = x ; then
     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=" "
@@ -928,7 +1300,7 @@
 		 LIST=${LIST}" "`ls | grep 'tutorial_'` ;;
 	*)	 LIST=${LIST}" "$xx ;;
       esac
-    done 
+    done
 fi
 #echo 'LIST='${LIST}'<'
 #- skip dirs, remove duplicate and non-directory:
@@ -945,63 +1317,94 @@
 	    echo ""; echo -n " -- skip \"$xx\" (not a directory !)"
 	fi
     else
-        if test $count = 1 ; then echo -n ", \"$xx\""
+	if test $count = 1 ; then echo -n ", \"$xx\""
 	else count=1 ; echo "" ;  echo -n " skip: \"$xx\""
 	fi
     fi
-done 
+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=$MITGCM_OF
+LOC_MFILE='tr_mpi_mfile'
+RUNLOG="run.tr_log"
+if test "x$MPI" = x0 ; then
+  OUTPUTFILE=$ref_outp
+  if test "x$COMMAND" = x ; then COMMAND="./$EXECUTABLE > $OUTPUTFILE" ; fi
+else
+  OUTPUTFILE="STDOUT.0000"
+  if test "x$COMMAND" = x ; then COMMAND="mpirun -np TR_NPROC ./$EXECUTABLE" ; fi
 fi
 
-OUTPUTFILE=$ref_outp
-if test "x$COMMAND" = x ; then
-    COMMAND="./$EXECUTABLE > $OUTPUTFILE"
-fi
-if test "x$MPI" = xt ; then
-    OUTPUTFILE="STDOUT.0000"
-fi
+echo "OK (COMMAND='$COMMAND')"
 
-echo "OK (COMMAND= $COMMAND )"
+#TMP=./tr_$$
+#- try to put temporary files in system-local /tmp dir
+TMP=/tmp/tr_${USER}_$$
+touch $TMP ; retVal=$?
+if [ $retVal -eq 0 ] ; then
+  if test ! -r $TMP ; then TMP=./tr_$$ ; fi
+else
+  TMP=./tr_$$
+fi
+rm -f $TMP
+if [ $verbose -gt 1 ]; then echo " temp files: $TMP" ; fi
 
 # 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" = x ; then
+if test $KIND = 1 ; then
+    DEF_CHECK_LIST='tlmGrd tlmCst tlmGrd fwdGrd'
+    EMPTY_RESULTS='.. .. ..'
+    LEN_CHECK_LIST=`echo $DEF_CHECK_LIST | sed 's/ [a-zA-Z0-9]*+/&mn &mx &av &sd/g' | awk '{print NF-1}'`
+elif test $KIND = 2 -o $KIND = 4 ; then
+    DEF_CHECK_LIST='AdGrd Cost AdGrd FDGrd'
+    EMPTY_RESULTS='.. .. ..'
+    LEN_CHECK_LIST=`echo $DEF_CHECK_LIST | sed 's/ [a-zA-Z0-9]*+/&mn &mx &av &sd/g' | awk '{print NF-1}'`
+else
     DEF_CHECK_LIST='PS PS T+ S+ U+ V+ pt1+ pt2+ pt3+ pt4+ pt5+'
     EMPTY_RESULTS='.. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. ..'
     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 $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$CLEANUP" = xt -o -x tr_cmpnum ; then
+    echo "skipping comparison code build"
+else
+    createcodelet
+fi
 
 #  build the mpack utility (if ADDRESSES = NONE, do it to test the build)
-if test "x$ADDRESSES" = x ; then
+if test "x$ADDRESSES" = x -o "x$SENDCMD" != x ; then
     echo "skipping mpack build"
 else
     build_mpack
+    if test "x$HAVE_MPACK" = xt ; then SENDCMD=$MPACK ; fi
 fi
 
 #  Create a uniquely named directory to store results
 CMDLINE=$0
-for xx in "$@" ; do CMDLINE="$CMDLINE '$xx'" ; done
+for xx in "$@" ; do nw=`echo $xx | wc -w`
+    if test $nw = '1' ; then CMDLINE="$CMDLINE $xx" ; else
+      nb=`echo $xx | grep -c '='`
+      if test $nb = 0 ; then CMDLINE="$CMDLINE '$xx'"
+      else yy=`echo "$xx'" | sed "s/=/='/"` ;
+			     CMDLINE="$CMDLINE $yy" ; fi
+    fi
+done
 MACH=`hostname`
 UNAMEA=`uname -a`
 DATE=`date +%Y%m%d`
 BASE="tr_"$MACH"_"$DATE"_"
 if test "x$OUTDIR" != x ; then
     BASE="tr_"$OUTDIR"_"$DATE"_"
+else
+   #short_name=`hostname -s | tr '[:upper:]' '[:lower:]'`
+   # hostname -s is not universal (does work on AIX system)
+    short_name=`hostname | sed 's/\..*$//' | tr '[:upper:]' '[:lower:]'`
+    BASE="tr_"$short_name"_"$DATE"_"
 fi
 DNUM=0
 DRESULTS="$BASE$DNUM"
@@ -1037,66 +1440,73 @@
 	echo >> $SUMMARY
 	echo "  OPTFILE=$OPTFILE" >> $SUMMARY
     else
-	echo | tee $SUMMARY
-	echo "ERROR: can't read OPTFILE=\"$OPTFILE\"" | tee $SUMMARY
+	echo | tee -a $SUMMARY
+	echo "ERROR: can't read OPTFILE=\"$OPTFILE\"" | tee -a $SUMMARY
 	exit 1
     fi
 else
     echo >> $SUMMARY
-    echo "No \"OPTFILE\" was explicitly specified by testreport," >> $SUMMARY
-    echo "   so the genmake default will be used." >> $SUMMARY
+    echo "No \"OPTFILE\" was specified ; genmake2 found and uses:" >> $SUMMARY
+    #-note: to be filled later after 1rst run
 fi
 echo
 echo >> $SUMMARY
-if test "x$ADM" = x ; then
-    if [ $MATCH_CRIT -lt 10 ] ; 
-    then line_0="default  "$MATCH_CRIT ; 
-    else line_0="default "$MATCH_CRIT ; fi
+if test $KIND = 0 ; then
+    line_0=`printf '%s %2i' 'default' $MATCH_CRIT`
        line_0="$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_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
+else
+    line_0=`printf '%s %2i' 'default   ' $MATCH_CRIT`
+  if test $KIND = 1 ; then
+   #echo "TANGLIN=true" >> $SUMMARY
+    echo "TangLin generated by TAF" >> $SUMMARY
+  elif test $KIND = 3 ; then
+    echo "TangLin generated by OpenAD" >> $SUMMARY
+  elif test $KIND = 2 ; then
+   #echo "ADJOINT=true" >> $SUMMARY
+    echo "Adjoint generated by TAF" >> $SUMMARY
+  else
+    echo "Adjoint generated by OpenAD" >> $SUMMARY
+  fi
+  if test $KIND = 1 -o $KIND = 3 ; then
+    line_1="G D M    C  T  F"
+    line_2="e p a R  o  L  D"
+  else
+    line_1="G D M    C  A  F"
+    line_2="e p a R  o  d  D"
+  fi
+    line_3="n n k u  s  G  G"
+    line_4="2 d e n  t  r  r"
+    echo >> $SUMMARY
+fi
+if test "x$CLEANUP" != xt ; then
     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
-    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
-N n k u  s  a
-2 d e n  t  d
-
-EOF
+    echo ""        | tee -a $SUMMARY
 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
@@ -1105,35 +1515,39 @@
 
     #  Cleanup only!
     if test "x$CLEANUP" = xt ; then
-	if test -r $BUILD_DIR/Makefile ; then
-            echo '  ------  clean dir:' $dir/build
-	    ( cd $BUILD_DIR ; make CLEAN )
-	fi
+	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 SIZE.h.mpi genmake.tr_log make.tr_log
+	    rm -rf mpi_headers
+	)
 	if test -d $dir/$rundir/CVS ; then
-            echo '  ------  clean dir:' $dir/$rundir
+	    echo -n '  --- dir:' $dir/$rundir ': '
 	    run_clean $dir/$rundir
 	fi
-	(
-	    cd $dir
-	    rm -rf tr_run.*
-	)
+	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=$dir"/results/"$ref_outp
-    if test ! -r $fout ; then
+   #if test ! -r $fout ; then
+    if test ! -r $fout -a ! -r ${fout}.gz ; then
 	echo "can't read \"$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
+    # Check for specific files for particular type of run
 
-    if test ! -r $CODE_DIR"/SIZE.h_mpi" -a "x$MPI" = "xt" ; then
+    if test ! -r $CODE_DIR"/SIZE.h_mpi"  -a "x$MPI" != "x0" ; then
 	echo "can't find \"$CODE_DIR/SIZE.h_mpi\" -- skipping $dir"
 	continue
     fi
@@ -1142,120 +1556,216 @@
 	continue
     fi
 
+    if test "x$MPI" != "x0" ; then
+	ntx=1 ; nty=1
+	if test "x$MULTI_THREAD" = "xt" ; then
+	  ff=$dir"/input/eedata.mth"
+	  ntx=`grep "^ *nTx *=" $ff | tail -1 | sed 's/^ *nTx *= *//' | sed "s/, *$//"`
+	  nty=`grep "^ *nTy *=" $ff | tail -1 | sed 's/^ *nTy *= *//' | sed "s/, *$//"`
+	  if test "x$ntx" = x ; then ntx=1 ; fi
+	  if test "x$nty" = x ; then nty=1 ; fi
+	fi
+	#- create new SIZE.h with no more than '$MPI' Procs
+	mk_mpi_size $CODE_DIR"/SIZE.h_mpi" $BUILD_DIR"/tr_size.mpi" $MPI $ntx $nty
+	LOC_NPROC=$?
+	(   cd $BUILD_DIR
+	    if test -r SIZE.h.mpi ; then
+		cmp tr_size.mpi SIZE.h.mpi > /dev/null 2>&1 ; RETVAL=$?
+	    else RETVAL=1
+	    fi
+	    if test "x$RETVAL" = x0 ; then
+		rm -f tr_size.mpi
+	    else
+		rm -f SIZE.h.mpi ; mv tr_size.mpi SIZE.h.mpi
+	    fi
+	)
+	if test "x$MPI_MFILE" != x ; then
+	    #- create new MPI machine-file with the right number of Procs
+	    rm -f $LOC_MFILE
+	    cat $MPI_MFILE | sort | uniq | head -$LOC_NPROC > $LOC_MFILE
+	    nl=`wc -l $LOC_MFILE | awk '{print $1}'`
+	    if [ $nl -lt $LOC_NPROC ] ; then
+		rm -f $LOC_MFILE
+		cat $MPI_MFILE | head -$LOC_NPROC > $LOC_MFILE
+		#sed -n "1,$LOC_NPROC p" $MPI_MFILE > $LOC_MFILE
+	    fi
+	    if [ $verbose -gt 1 ]; then
+		nl=`wc -l $LOC_MFILE | awk '{print $1}'`
+		echo " new LOC_MFILE=$LOC_MFILE : $nl procs for LOC_NPROC=$LOC_NPROC"
+	    fi
+	fi
+	if test "x$MULTI_THREAD" = "xt" ; then
+	    retv=`check_eedata $dir"/input/eedata.mth" $BUILD_DIR"/SIZE.h.mpi"`
+	    if test $retv != 0 ; then
+		echo "input/eedata.mth tiling misfit -- skipping $dir"
+		continue
+	    fi
+	fi
+    fi
+
     #  Check whether there are "extra runs" for this testdir
     extra_runs=
-    ex_run_dirs=`( cd $dir ; echo $inputdir.* )`
+    if test "x$NORUN" = xf ; then
+	ex_run_dirs=`( cd $dir ; ls -d $inputdir.* 2> /dev/null )`
+    fi
     #echo "ex_run_dirs='$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 -r $outf -o -r ${outf}.gz ; then
+	  if test "x$MULTI_THREAD" = "xt" ; then
+	    if test -r $dir"/"$exd"/eedata.mth" ; then
+	      if test "x$MPI" = "x0" ; then
+		extra_runs="$extra_runs $name"
+	      else
+		retv=`check_eedata $dir"/"$exd"/eedata.mth" $BUILD_DIR"/SIZE.h.mpi"`
+		if test $retv = 0 ; then
 		    extra_runs="$extra_runs $name"
-		#else echo $dir"/"$exd"/eedata.mth: not found"
+		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
+	  else
+	    extra_runs="$extra_runs $name"
+	  fi
 	fi
     done
 
-    echo "-------------------------------------------------------------------------------"
     echo
-    if test "x$extra_runs" = "x" ; then 
-       echo "Experiment:  $dir"
+    if test "x$extra_runs" = "x" ; then
+	echo "Experiment:  $dir"
     else
-       echo "Experiment:  $dir ; extra_runs=$extra_runs"
+	echo "Experiment:  $dir ; extra_runs=$extra_runs"
     fi
     echo
     unset genmake makedepend make run
     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
+    #  Create an output dir & summary.txt file for each tested experiment (tdir)
+    locDIR=$DRESULTS"/"$dir
+    mkdir $locDIR
+    #- report to this experiment local summary file ---
+    echo "DATE='$DATE' ; tdir='$dir'" > $locDIR"/summary.txt"
+    echo "MACH='$MACH'" >> $locDIR"/summary.txt"
+    echo "UNAMEA='$UNAMEA'" >> $locDIR"/summary.txt"
+    CDIR=`pwd`"/$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 \
+	    && symlink_mpifiles $dir $code_dir $builddir \
 	    && makedependmodel $dir/$builddir && makedepend=Y \
 	    && makemodel $dir/$builddir && make=Y \
-	    && linkdata $dir/$rundir $inputdir input \
+	    && run_clean $dir/$rundir \
+	    && linkdata $dir/$rundir $inputdir \
 	    && runmodel $dir/$rundir && run=Y \
 	    && results=`testoutput_run $dir $rundir $ref_outp`
     fi
-    
-    echo
+    #echo "results='$results'"
+
 	fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
-	echo
- 	echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
-	touch $CDIR"/summary.txt"
-	echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $CDIR"/summary.txt"
-	echo "MACH='$MACH'" >> $CDIR"/summary.txt"
-	echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
-	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	echo "tdir='$dir'" >> $CDIR"/summary.txt"
-	if test "x$ADM" = xt ; then
-	    head -1 $dir/$builddir/taf_ad.log >> $CDIR"/summary.txt"
-	    grep -A3 'Seconds in section "ALL' $dir/$rundir/$OUTPUTFILE \
-				>> $CDIR"/summary.txt"
-	fi
+	echo 1>&2
+	echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
+	echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $locDIR"/summary.txt"
 
 	for ex in $extra_runs ; do
 	    unset run
-            results=$EMPTY_RESULTS
+	    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 $inputdir.$ex $inputdir input
-	    runmodel $dir/tr_run.$ex && run=Y \
-	    && results=`testoutput_run $dir tr_run.$ex $refExOut`
-	    fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
-	    fres="$fres.$ex"
-	    echo
+	    #  Create an output dir & summary.txt file for each extra run (tdir.ex)
+	    locDIR=$DRESULTS"/"$dir"."$ex
+	    mkdir $locDIR
+	    #- report to this experiment local summary file ---
+	    echo "DATE='$DATE' ; tdir='$dir.$ex'" > $locDIR"/summary.txt"
+	    #echo "MACH='$MACH'" >> $locDIR"/summary.txt"
+	    #echo "UNAMEA='$UNAMEA'" >> $locDIR"/summary.txt"
+	    CDIR=`pwd`"/$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 $dir.$ex ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
+	    echo 1>&2
 	    echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
-	    touch $CDIR"/summary.txt"
-	    echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $CDIR"/summary.txt"
-	    echo "MACH='$MACH'" >> $CDIR"/summary.txt"
-	    echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
-	    echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	    echo "tdir='$dir.$ex'" >> $CDIR"/summary.txt"
-            if test "x$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
+	    echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $locDIR"/summary.txt"
+	    if test "x$POSTCLEAN" = x2 ; then
+		run_clean $dir/$pfxdir.$ex
 	    fi
 	done
 
+    if test ! -f $DRESULTS"/"genmake_state ; then
+	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
+# bsd-sed cannot do the above code
+	    cat $dir/$builddir/Makefile | \
+		sed -n '/^# executed by:/{N
+                                          p
+                                          }' >> $DRESULTS/genmake_state
+	    echo " $mkOpt" >> $DRESULTS/genmake_state
+	    if test "x$OPTFILE" = xNONE ; then
+		eval $mkOpt
+#		sed "/^No \"OPTFILE\" was specified ; genmake2/a\  OPTFILE=${OPTFILE}"\
+#			$SUMMARY > tmp.tr_log
+# bsd-sed requires a newline after "a\":
+		sed "/^No \"OPTFILE\" was specified ; genmake2/a\\
+                         OPTFILE=${OPTFILE}" $SUMMARY > tmp.tr_log
+		RETVAL=$?
+		if test "x$RETVAL" = x0 ; then
+		    cp -f tmp.tr_log $SUMMARY
+		fi
+		rm -f tmp.tr_log
+	    fi
+	    gmkLog=$dir/$builddir/genmake.log
+	    if test -r $gmkLog ; then
+		grep '^Get compiler version using:' $gmkLog > /dev/null 2>&1
+		RETVAL=$?
+		if test "x$RETVAL" = x0 ; then
+		  echo -n "from '$gmkLog', " >> $DRESULTS/genmake_state
+		  echo "extract compiler version:"   >> $DRESULTS/genmake_state
+		  sed -n '/Get compiler version/,/<-- compiler version/p' \
+		     $gmkLog | grep -v '^... compiler version ' > tmp.tr_log
+		  sed -n '1p' tmp.tr_log >> $DRESULTS/genmake_state
+		  sed -n '2,/^$/p' tmp.tr_log | sed '/^$/d' | sed 's/^./ &/' \
+					 >> $DRESULTS/genmake_state
+		  rm -f tmp.tr_log
+		fi
+	    fi
+	    gmkLog=$dir/$builddir/genmake_state
+	    if test -r $gmkLog ; then
+		echo -n "from '$gmkLog', "      >> $DRESULTS/genmake_state
+		echo "get genmake settings:"    >> $DRESULTS/genmake_state
+		sed -n '/^HAVE_/p' $gmkLog | sed 's/^./ &/' \
+						>> $DRESULTS/genmake_state
+	    fi
+	fi
+    fi
     #postclean $dir/$builddir
-    if test "x$POSTCLEAN" = xt ; then
- 	makeclean $dir/$builddir \
- 	    && run_clean $dir/$rundir
+    if test "x$POSTCLEAN" = x2 ; then
+	makeclean $dir/$builddir \
+	    && run_clean $dir/$rundir
     fi
-    
+    if test "x$MPI" != x0 -a "x$MPI_MFILE" != x ; then rm -f $LOC_MFILE ; fi
+
     echo "-------------------------------------------------------------------------------"
-    
+
 done
 
 printf "Start time:  " >> $SUMMARY
-echo $start_date >> $SUMMARY
+echo "$start_date" >> $SUMMARY
 printf "End time:    " >> $SUMMARY
 date >> $SUMMARY
 
@@ -1264,10 +1774,13 @@
 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 3555000 $DRESULTS".tar.gz" $ADDRESSES
+    if test "x$SENDCMD" != x ; then
+	if [ $verbose -gt 1 ]; then
+	   echo " run: $SENDCMD -s MITgcm-test -m 3555000 ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES"
+	fi
+	tar -cf ${SAVDIR}/${DRESULTS}".tar" $DRESULTS > /dev/null 2>&1 \
+	    && gzip ${SAVDIR}/${DRESULTS}".tar" \
+	    && $SENDCMD -s MITgcm-test -m 3555000 ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
 	    echo
@@ -1280,18 +1793,20 @@
 	    echo "An email containing results was sent to the following addresses:"
 	    echo "  \"$ADDRESSES\""
 	    echo
+	    test -f ${SAVDIR}/${DRESULTS}".tar" &&  rm -f ${SAVDIR}/${DRESULTS}".tar"
+	    test -f ${SAVDIR}/${DRESULTS}".tar.gz" &&  rm -f ${SAVDIR}/${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/ \.  \.  \.  \.  \.  \.  \.  \.  \.  \.  \.  \. //'
     if test -e tr_out.txt ; then
-        mv tr_out.txt tr_out.txt.old
+	mv tr_out.txt tr_out.txt.old
     fi
     cat $SUMMARY | sed '/^[YN] [YN] [YN] [YN]/ s/ \. //g' > tr_out.txt
 fi
@@ -1299,4 +1814,4 @@
 if test "x$DELDIR" = xt ; then
     rm -rf $DRESULTS
 fi
-
+echo "======== End of testreport execution ========"