--- MITgcm/verification/testreport	2003/09/16 17:46:52	1.8
+++ MITgcm/verification/testreport	2010/01/14 23:17:42	1.132
@@ -1,6 +1,7 @@
-#!/bin/bash
+#! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.8 2003/09/16 17:46:52 edhill Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.132 2010/01/14 23:17:42 jmc Exp $
+#  $Name:  $
 #
 
 usage()
@@ -10,234 +11,433 @@
     echo
     echo "where possible OPTIONS are:"
     echo "  (-help|-h)               print usage"
-    echo "  (-mpi)                   use MPI input files"
-    echo "  (-optfile=|-of=)STRING   list of optfiles to use"
-    echo "  (-a|-addr)STRING         list of email recipients"
-    echo "                             (DEF=\"edhill@mitgcm.org\")"
-    echo "  (-t|-tdir)STRING         list of test dirs to use"
-    echo "                             (DEF=\"\" which builds all)"
-    echo "  (-b|-bash)STRING         location of \"bash\" executable"
-    echo "                             (DEF=\"\" for \"/bin/bash\")"
-    echo "  (-c|-command)STRING      command to run"
+    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 "  (-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 "                             (recognized groups: basic, tutorials)"
+    echo "                             (DEF=\"\" which test all)"
+    echo "  (-skd|-skipdir) STRING   list of exp. dirs to skip"
+    echo "                             (DEF=\"\" which test all)"
+    echo "  (-b|-bash) STRING        preferred location of a \"bash\" or"
+    echo "                             Bourne-compatible \"sh\" shell"
+    echo "                             (DEF=\"\" for \"bash\")"
+    echo "  (-adm|-ad)               perform an adjoint run"
+    echo "  (-oad)                   perform an OpenAD adjoint run"
+    echo "  (-command) STRING        command to run"
     echo "                             (DEF=\"make output.txt\")"
-    echo "  (-m|-make)STRING         command to use for \"make\""
+    echo "  (-m|-make) STRING        command to use for \"make\""
     echo "                             (DEF=\"make\")"
+    echo "  (-odir) STRING           used to build output directory name"
+    echo "                             (DEF=\"hostname\")"
+    echo "  (-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 "  (-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 "  (-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 follows a whitespace-delimited format"
+    echo "and where STRING can be a whitespace-delimited list"
     echo "such as:"
+    echo
     echo "  -t 'exp0 exp2 exp3' "
     echo "  -addr='abc@123.com testing@home.org'"
     echo
+    echo "provided that the expression is properly quoted within the current"
+    echo "shell (note the use of single quotes to protect white space)."
+    echo
     exit 1
 }
 
 #  build the mpack utility
 build_mpack()
 {
-    echo -n "building the mpack utility...  "
-    if test ! -x "$MPACKDIR/mpack" ; then
+    printf "building the mpack utility...  "
+    MPACK="$MPACKDIR/mpack"
+    if test ! -x $MPACK ; then
 	if test ! -d $MPACKDIR ; then
+	    echo
 	    echo "Error: can't find \"$MPACKDIR\""
 	    echo "  are you sure this program is being run in the correct "
 	    echo "  (that is, \"MITGCM_ROOT\verification\") directory?"
-	    exit 1
+	    echo
+	    HAVE_MPACK=f
+	fi
+	if test "x$CC" = x ; then
+	    export CC=cc
 	fi
-	echo -n "building mpack...  "
-	( cd $MPACKDIR && ./configure && $MAKE ) > build_mpack.out 2>&1
+	printf "building mpack (using CC=$CC)...  "
+	( cd $MPACKDIR && ./configure && $MAKE ) > tr_build_mpack.out 2>&1
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
 	    echo
 	    echo "Error building the mpack tools at: $MPACK_DIR"
-	    exit 1
+	    echo
+	    HAVE_MPACK=f
+	else
+	    rm -f tr_build_mpack.out
+	    HAVE_MPACK=t
+	    echo "done"
 	fi
+    else
+	HAVE_MPACK=t
+	echo "already exist"
     fi
-    echo "OK"
-}
-
-compare_lines()
-{
-    # use codelet to compare lines
-    if [ $verbose -gt 1 ]; then
-	cat tmp3.txt 1>&2
-    fi
-    return `./a.out < tmp3.txt`
 }
 
-testoutput_for_prop()
+testoutput_var()
 {
-    # testoutput_for_prop dir s1 label subdir
+    # testoutput_var dir s1 label subdir reference_output
     #
-    #  compares files in $dir/$subdir/output.txt and $dir/results/output.txt
-    #  using search strings s1 and text label 
+    #  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
-	echo testoutput_for_prop: grep "$2" $1/$4/output.txt 1>&2
+	echo testoutput_var: grep "$2" $1/$4/$OUTPUTFILE 1>&2
     fi
-    if [ -r $1/$4/output.txt ]; then
-	grep "$2" $1/$4/output.txt | sed 's/.*=//' | nl > tmp1.txt
-	lncnt=`wc -l tmp1.txt | awk '{print $1}' `
-	if [ $lncnt -lt 3 ]; then
+    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 2 ]; then
 	    if [ $verbose -gt 0 ]; then
 		echo Not enough lines of output when searching for "$2" 1>&2
 	    fi
 	    return 99
 	fi
     else
-	echo testoutput_for_prop: output.txt from model run was not readable 1>&2
+	echo testoutput_var: $OUTPUTFILE from model run was not readable 1>&2
 	return 99
     fi
     if [ $debug -gt 0 ]; then
-	echo testoutput_for_prop: grep "$2" $1/results/output.txt 1>&2
+	echo testoutput_var: grep "$2" $1/results/$5 1>&2
     fi
-    grep "$2" $1/results/output.txt | sed 's/.*=//' | nl > tmp2.txt
-    lncnt=`wc -l tmp2.txt | awk '{print $1}' `
-    if [ $lncnt -lt 3 ]; then
+    grep "$2" $1/results/$5 | sed 's/.*=//' | cat -n > tmp2.txt
+    lncntB=`wc -l tmp2.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
     fi
+    if [ $lncntA -ne $lncntB ]; then
+        if [ $verbose -gt 0 ]; then
+            echo Not same Nb of lines when searching for "$2" ":" $lncntA $lncntB 1>&2
+        fi
+        return 99
+    fi
+    has_nan=`cat tmp1.txt | grep -i nan | wc -l`
+    if [ $has_nan -gt 0  ] ; then
+	echo testoutput_var: $OUTPUTFILE contains $has_nan NaN values  1>&2
+	return 99
+    fi
+    has_inf=`cat tmp1.txt | grep -i inf | wc -l`
+    if [ $has_inf -gt 0  ] ; then
+	echo testoutput_var: $OUTPUTFILE contains $has_inf Inf values  1>&2
+	return 99
+    fi
     if [ $debug -gt 0 ]; then
-	echo testoutput_for_prop: join tmp1.txt tmp2.txt 1>&2
+	echo testoutput_var: join tmp1.txt tmp2.txt 1>&2
     fi
     join tmp1.txt tmp2.txt | awk '{print $1 " " $2 " " $3}' > tmp3.txt
     if [ $debug -gt 0 ]; then
-	echo testoutput_for_prop: compare_lines 1>&2
+	echo testoutput_var: compare_lines 1>&2
+    fi
+    if [ $verbose -gt 1 ]; then
+	cat tmp3.txt 1>&2
     fi
-    compare_lines
-    digits_of_similarity=$?
+    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`
     if [ $digits_of_similarity -eq 99 ]; then
 	if [ $verbose -gt 0 ]; then
-	    echo testoutput_for_prop: 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 tmp1.txt tmp2.txt tmp3.txt
+    rm -f tmp1.txt tmp2.txt tmp3.txt tmp4.txt
     
     return $digits_of_similarity
 }
 
-dashnum()
+testoutput_run()
 {
-    # dashnum n1 n2 n3 ...
+    # testoutput_run directory subdir reference_output
     #
-    #  print numbers using %3i format or "--" if number = 99
+    #  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
+	#  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 [ $debug -gt 0 ]; then echo "testoutput_run: listVar(I)='$listVar'" 1>&2 ; fi
+        # 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
+          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
+	   '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 $3; yy=$?
+		  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 "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 = $sVar
+          then allargs="$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 "."}}'`
+	  echo $allargs $adNul
+        else
+	  echo $allargs
+        fi 
+# <-- same processing for adjoint & forward test
+}
 
-    for num in $@ ; do
-	if [ $num = 99 ]; then
-	    printf ' --'
+genmakemodel()
+{
+    # genmakemodel directory
+    if test "x$NOGENMAKE" = xt ; then
+	echo "genmake skipped!"
+    else
+	if test "x$BASH" = x ; then
+	    GENMAKE2="../../../tools/genmake2"
 	else
-	    printf '%3i' $num
+	    GENMAKE2="$BASH ../../../tools/genmake2 -bash $BASH"
 	fi
-    done
+	(
+	    cd $1;
+	    command="$GENMAKE2  -ds -m $MAKE"
+	    if test "x$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=$OPTFILE"
+	    fi
+	    if test "x$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="$command -omp"
+	    fi
+	    if test "x$TS" = xt ; then
+		command="$command -ts"
+	    fi
+	    if test "x$PAPIS" = xt ; then
+		command="$command -papis"
+	    else 
+	    if test "x$PCLS" = xt ; then
+		command="$command -pcls"
+	    fi
+	    fi
+	    printf 'genmake ... ' 1>&2
+	    # $command > make.log 2>&1
+	    eval $command > make.log 2>&1
+	    RETVAL=$?
+	    #  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
+		return 1
+	    else
+		echo "successful" 1>&2
+	    fi
+	)
+    fi
 }
 
-testoutput()
+makeclean()
 {
-    # testoutput diretory subdir
-    #
-    #  test output in "directory"
-
-    if [ $debug -gt 0 ]; then
-	echo testoutput: testoutput_for_prop $1 cg2d_init_res 1>&2
-    fi
-    testoutput_for_prop $1 "cg2d_init_res" "cg2d init. residual" $2; cg2dres=$?
-    if [ $debug -gt 0 ]; then
-	echo testoutput: cg2dres=$cg2dres 1>&2
+    # makeclean directory
+    if test "x$NOCLEAN" = xt ; then
+	echo "make Clean skipped!"
+    else
+	(
+	    cd $1;
+	    #if test -e $OUTPUTFILE ; then rm -f $OUTPUTFILE ; fi
+	    if test -r Makefile ; then
+		printf 'clean build-dir: make Clean ... ' 2>&1
+		$MAKE Clean >> make.log 2>&1
+		RETVAL=$?
+		if test "x$RETVAL" != x0 ; then
+		    tail make.log
+		    echo "makeclean: \"make Clean\" failed" 1>&2
+		    cp make.log $CDIR"/make.log"
+		    return 1
+		fi
+		echo successful 1>&2
+	    else
+		echo ''
+	    fi
+	    exit 0
+	)
     fi
-    
-    testoutput_for_prop $1 "dynstat_theta_min" "theta minimum" $2; tmin=$?
-    testoutput_for_prop $1 "dynstat_theta_max" "theta maximum" $2; tmax=$?
-    testoutput_for_prop $1 "dynstat_theta_mean" "theta mean" $2; tmean=$?
-    testoutput_for_prop $1 "dynstat_theta_sd" "theta s.d." $2; tsd=$?
-    testoutput_for_prop $1 "dynstat_salt_min" "salt minimum" $2; smin=$?
-    testoutput_for_prop $1 "dynstat_salt_max" "salt maximum" $2; smax=$?
-    testoutput_for_prop $1 "dynstat_salt_mean" "salt mean" $2; smean=$?
-    testoutput_for_prop $1 "dynstat_salt_sd" "salt s.d." $2; ssd=$?
-    testoutput_for_prop $1 "dynstat_uvel_min" "U minimum" $2; umin=$?
-    testoutput_for_prop $1 "dynstat_uvel_max" "U maximum" $2; umax=$?
-    testoutput_for_prop $1 "dynstat_uvel_mean" "U mean" $2; umean=$?
-    testoutput_for_prop $1 "dynstat_uvel_sd" "U s.d." $2; usd=$?
-    testoutput_for_prop $1 "dynstat_vvel_min" "V minimum" $2; vmin=$?
-    testoutput_for_prop $1 "dynstat_vvel_max" "V maximum" $2; vmax=$?
-    testoutput_for_prop $1 "dynstat_vvel_mean" "V mean" $2; vmean=$?
-    testoutput_for_prop $1 "dynstat_vvel_sd" "V s.d." $2; vsd=$?
-    
-    dashnum $cg2dres $tmin $tmax $tmean $tsd $smin $smax $smean $ssd \
-        $umin $umax $umean $usd $vmin $vmax $vmean $vsd
 }
 
-genmakemodel()
+run_clean()
 {
-    # genmakemodel directory
-    GENMAKE2="$BASH ../../../tools/genmake2"
-    (
-	cd $1;
-	printf 'genmake ... ' 1>&2
-        # ../../../tools/genmake -ieee -mods=../code > make.log 2>&1
-	$GENMAKE2  -ds --mods=../code "--optfile="$OPTFILE > make.log 2>&1
-	RETVAL=$?
-	for i in gm_state gm_optfile gm_local Makefile ; do
-	    if test -r $i ; then
-		cp $i $CDIR
-	    fi
-	done
-	if test "x$RETVAL" != x0 ; then
-	    tail make.log
-	    echo "genmakemodel: genmake failed" 1>&2
-	    cp make.log $CDIR
-	    return 1
-	else
-	    echo "succesful" 1>&2
-	fi
-    )
+    # run_clean directory
+    if test "x$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
+	)
+    fi
 }
 
-makeclean()
+makedependmodel()
 {
-    # makeclean directory
-    (
-	cd $1;
-	if test -e output.txt ; then
-	    rm -f output.txt
-	fi
-	printf 'make CLEAN ... ' 2>&1
-	if test -r Makefile ; then
-	    $MAKE CLEAN >> make.log 2>&1
+    # makedependmodel directory
+    if test "x$NODEPEND" = xt ; then
+	echo "make depend skipped!"
+    else
+	(
+	    cd $1;
+	    printf 'make depend ... ' 1>&2
+	    $MAKE depend >> make.log 2>&1
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
 		tail make.log
-		echo "makeclean: \"make CLEAN\" failed" 1>&2
+		echo "makedependmodel: make depend failed" 1>&2
 		cp make.log $CDIR"/make.log"
 		return 1
+	    else
+		echo successful 1>&2
 	    fi
-	fi
-	echo succesful 1>&2
-	exit 0
-    )
-}
-
-makedependmodel()
-{
-    # makedependmodel directory
-    (
-	cd $1;
-	printf 'make depend ... ' 1>&2
-	$MAKE depend >> make.log 2>&1
-	RETVAL=$?
-	if test "x$RETVAL" != x0 ; then
-	    tail make.log
-	    echo "makedependmodel: make depend failed" 1>&2
-	    cp make.log $CDIR"/make.log"
-	    return 1
-	else
-	    echo succesful 1>&2
-	fi
-    )
+	)
+    fi
 }
 
 makemodel()
@@ -247,27 +447,140 @@
 	cd $1;
 	if test -r Makefile ; then
 	    printf 'make ... ' 1>&2
-	    $MAKE >> make.log 2>&1
+	    if test "x$ADM" = xt ; then
+		$MAKE adall >> make.log 2>&1
+	    elif test "x$OADM" = xt ; then
+		$MAKE adAll >> make.log 2>&1
+            else
+		if test "x$JOBS" = x ; then
+		    $MAKE >> make.log 2>&1
+		else
+		    $MAKE -j $JOBS >> make.log 2>&1
+		fi
+	    fi
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
 		tail make.log
 		echo failed 1>&2
 		cp make.log $CDIR"/make.log"
+		rm -f $EXECUTABLE
 		return 1
 	    else
-		echo succesful 1>&2
+		echo successful 1>&2
 	    fi
 	fi
     )
 }
 
+symlink_mpifiles()
+{
+    # Put special links so that MPI specific files are used
+    # This MUST be invoked between makeclean and makelinks because
+    # the Makefile will link to non-mpi files by default
+
+    dir=$1
+    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 $CODE_DIR; find . -name "*_mpi" -print)`
+
+    #  Is this an MPI run?
+    if test "x$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
+		RETVAL=$?
+		if test "x$RETVAL" = x0 ; then
+		    #echo Un-linking $name from $linktarg
+		    rm -f $BUILD_DIR/$name
+		fi
+	    fi
+	done
+    fi
+    
+}
+
 linkdata()
 {
-    # linkdata flag
+    # linkdata run_dir input_dir_1 input_dir_2 ...
     #
     # symbolically link data files to run directory
-    if [ $1 -ne 0 ]; then
-	( cd $2 ;  ln -sf ../input/* . )
+    if test -d $1 ; then
+	(
+	    cd $1 ; shift
+            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 
+			ln -sf "../"$1"/eedata.mth" eedata ;
+			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 -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
+			    if test ! -r $i  ; then
+				printf ' '$i 1>&2
+				ln -sf "../"$ldir"/"$i $i
+			    fi
+			fi
+		    done
+		    if test -x "../"$ldir"/"prepare_run ; then
+			"../"$ldir"/"prepare_run
+		    fi
+		    printf ' ; ' 1>&2
+		fi
+		prevDir=$ldir
+	    done
+	)
     fi
 }
 
@@ -275,18 +588,66 @@
 {
     # runmodel directory
     #
-    #  runs "$COMMAND" in "directory" 
+    #  runs "$COMMAND in "directory" 
     #  (where "$COMMAND" is relative to "directory")
     (
 	cd $1
-	printf 'runmodel: ' 1>&2
+	printf 'runmodel in %s ...' $1 1>&2
 	# make output.txt
-	$COMMAND
-	RETVAL=$?
-	if test "x$RETVAL" = x0 ; then
-	    cp output.txt $CDIR"/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 ; fi
+	fi
+        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 $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 $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 $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 $RUNLOG | grep -v 'ABNORMAL END' | grep -c 'NORMAL END'`
+	fi
+	rm -f run.log_tmp
+	if [ $RETVAL -eq 0 -a $ENDVAL -gt 0 ] ; then
+	    tail $RUNLOG
+	    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
+	    return 0
+	elif [ $RETVAL -ne 0 -a $ENDVAL -gt 0 ] ; then
+	    #-- for some weird cases (run is finihed but with error code)
+	    tail $RUNLOG
+	    echo finished with error '(run:' $RETVAL ' end:' $ENDVAL ')' 1>&2
 	    return 0
 	else
+	    tail $RUNLOG
+	    echo failed '(run:' $RETVAL ' end:' $ENDVAL ')' 1>&2
+	    cp $RUNLOG $CDIR"/"$RUNLOG
+            if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 1
 	fi
     )
@@ -296,39 +657,48 @@
 {
     # create codelet for comparing model output
 
-    echo -n "creating the comparison code...  "
-    cat > tmp_cmpnum.f <<EOFA
-      program cmpnum
-      implicit none
-      real*8 a,b,diff
-      integer linnum,best
-      best=-16
-  99  read(*,*,end=70,err=60) linnum,a,b
-      diff=0.5*(abs(a)+abs(b))
-c     print *,a,b,diff,abs(a-b)/diff
-      if (diff.gt.1.e-12) then
-        diff=abs(a-b)/diff
-        if (diff.gt.0.) then
-c         print *,int(log10(diff)),diff
-          linnum=int(log10(diff))
-          best=max(best,linnum)
-        endif
-      else
-        if (best.eq.-16.and.diff.ne.0.) best=-22
-      endif
-      goto 99
-  60  stop 'cmpnum: An error occured reading a,b'
-  70  print *,-best
-      end
-EOFA
+    printf "creating the comparison code (using CC=$CC)...  "
+    cat > tr_cmpnum.c <<EOF
+#include <stdio.h>
+#include <math.h>
+int main( int argc, char** argv )  {
+  int linnum,cmplin,best,lncnt;
+  double a,b,abave,relerr;
+  best = -22;
+  lncnt = 0;
+  while( 1 & ( (lncnt+=1) < 999 ) )  {
+    scanf("%d", &linnum);
+    if (linnum == -1)  break;
+    scanf("%lf", &a);  scanf("%lf", &b);
+    abave = 0.5*(fabs(a)+fabs(b));
+    if ( abave == abave ) {
+      if (abave > 0.0) {
+        relerr=fabs(a-b)/abave;
+        if (relerr > 0.0) { cmplin = (int)rint(log10(relerr)); }
+        else { cmplin = -16 ; }
+        best = (best > cmplin) ? best : cmplin; }
+      else { cmplin = -22 ; }
+   /* printf("%d ; %lf ; %lf\n",cmplin,a,b); */
+      }
+   else {
+   /* printf("%lf ; %lf ; %lf\n",abave,a,b); */
+      break; }
+  }
+  if (lncnt == 999) best=-29;
+  if (linnum != -1) best=-99;
+  printf("%d\n", -best);
+  return 0;
+}
+EOF
+    $CC -o tr_cmpnum tr_cmpnum.c -lm
 
-    f77 tmp_cmpnum.f
-    if [ -x ./a.out ]; then
+    if [ -x ./tr_cmpnum ]; then
 	echo "OK"
 	return 0
     else
 	echo
-	echo "createcodelet: failed to compile codelet" 
+	echo "ERROR: failed to compile comparison code -- please specify" 
+	echo "  a C compiler using the CC environment variable."
 	exit 1
     fi
 }
@@ -340,12 +710,21 @@
     nm=$1
     printf '%s %s %s %s' $2 $3 $4 $5
     shift; shift; shift; shift; shift;
-    printf '%3s' $@
+    listPrt=$@
+    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/  < /</'
     
-    if [ $1 = '--' ]; then
+    if [ $xx = '..' ]; then
+	printf ' N/O '
+    elif [ $xx = '--' ]; then
+	printf ' N/O '
+    elif [ $xx = 99 ]; then
 	printf ' N/O '
     else
-	if [ $1 -gt 12 ]; then
+	if [ $xx -ge $MATCH_CRIT ]; then
 	    printf ' pass'
 	else
 	    printf ' FAIL'
@@ -356,62 +735,98 @@
     
 }
 
-show_help()
+scandirs()
 {
-    cat - << EOF
-$0 [-help] [-quick] [-verbose] dir1 [dir2] [...]
- -help      Show this help message
- -quick     Skip "genmake" and "make depend" if the Makefile exists
- -quiet     Reduce the amount of output
- -verbose   Produce copious amounts of output
- -debug     Produce even more output which will mean nothing to most
- -force     Do "make CLEAN" before compiling. This forces a complete rebuild.
- -clean     Do "make CLEAN" after compiling and testing.
- -noieee    By default, $0 uses the -ieee option for genmake. This turns it off.
- -cleanup   Aggresively removes all model output, executables and object files
-            and then exits. Use with care.
-
-Normal usage:
- $0 *       Configure, compile, run and analyze in all experiment directories
-EOF
+    if [ $# -eq 1 ]; then
+ 	for arg in * ; do
+ 	    test -f $arg/$1 && echo $arg
+ 	done
+    else
+ 	echo $*
+    fi
 }
 
-scandirs()
+
+check_eedata()
 {
-    if [ $# -eq 0 ]; then
-	for arg in * ; do
-	    test -d $arg/input && echo $arg
-	done
+    # 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 $*
+      echo '-1'
+      fi
+    else
+      echo '-2'
     fi
-}
 
+}
 
 ###############################################################################
-###############################################################################
-###############################################################################
 
 
 #  Default properties
 debug=0
 verbose=1
 clean=0
-expts=''
-# ieee=1
-# quick=0
+
+IEEE=true
+if test "x$MITGCM_IEEE" != x ; then
+    IEEE=$MITGCM_IEEE
+fi
+GSL=f
+
+CLEANUP=f
+QUICK=f
+NOGENMAKE=f
+NOCLEAN=f
+NODEPEND=f
+POSTCLEAN=f
 
 BASH=
-OPTFILES=
-ADDRESSES=edhill@mitgcm.org
+OPTFILE=NONE
+ADDRESSES=
 TESTDIRS=
+SKIPDIRS=
 MPACKDIR="../tools/mpack-1.6"
-MPACK="$MPACKDIR/mpack"
-COMMAND="make output.txt"
-MAKE=make
+HAVE_MPACK=
+MPACK=
+COMMAND=
+if test "x$MAKE" = x ; then
+    MAKE=make
+fi
+if test "x$CC" = x ; then
+    CC=cc
+fi
+JOBS=
 MPI=f
+MULTI_THREAD=f
+OUTDIR=
+DELDIR=
 
-echo -n "parsing options...  "
+ADM=
+OADM=
+
+# list of pTracers to check for monitor output
+PTRACERS_NUM="1 2 3 4 5"
+
+MATCH_CRIT=13
+
+printf "parsing options...  "
 
 ac_prev=
 for ac_option ; do
@@ -431,20 +846,29 @@
 	    usage ;;
 	
 	-optfile | --optfile | -of | --of)
-            ac_prev=OPTFILES ;;
+            ac_prev=OPTFILE ;;
         -optfile=* | --optfile=* | -of=* | --of=*)
-            OPTFILES=$ac_optarg ;;
+            OPTFILE=$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=$ac_optarg ;;
+
 	-bash | --bash | -b | --b)
             ac_prev=BASH ;;
         -bash=* | --bash=*)
@@ -460,12 +884,61 @@
 	-make=* | --make=*)
 	    MAKE=$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 ;;
+
+	-match | --match ) ac_prev=MATCH_CRIT ;;
+	-match=* | --match=* ) MATCH_CRIT=$ac_optarg ;;
+
+	-j) ac_prev=JOBS ;;
+	-j=*) JOBS=$ac_optarg ;;
+
+	-clean | --clean)
+	    CLEANUP=t ; DELDIR=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=t ;;
+
 	-mpi) MPI=t ;;
+
+	-mth) MULTI_THREAD=t ;;
+
+	-adm | -ad) ADM=t ;;
+
+	-oad) OADM=t; NODEPEND=t ;;
+
+	-ieee) IEEE=true ;;
+	-noieee) IEEE= ;;
+        -gsl) GSL=t ;;
+
 	-verbose) verbose=2 ;;
 	-debug) debug=1 ;;
-	-clean) clean=1 ;;
 	-quiet) verbose=0 ;;
 
+	-deldir | -dd) DELDIR=t ;;
+
+	-ts) TS=t;;
+
+	-papis) PAPIS=t;;
+
+	-pcls) PCL=t;;
+
         -*)
             echo "Error: unrecognized option: "$ac_option
             usage
@@ -480,23 +953,129 @@
      
 done
 
+if test "x$QUICK" = xt ; then
+    NOGENMAKE=t
+    NOCLEAN=t
+    NODEPEND=t
+fi
+
+#- setting for forward or ADM testing
+if test "x$ADM" = xt ; then
+    code_dir=code_ad
+    inputdir=input_ad
+    ref_outp="output_adm.txt"
+    EXECUTABLE="mitgcmuv_ad"
+elif test "x$OADM" = xt ; then
+    code_dir=code_oad
+    inputdir=input_oad
+    ref_outp="output_oadm.txt"
+    EXECUTABLE="mitgcmuv_ad"
+else
+    code_dir=code
+    inputdir=input
+    ref_outp="output.txt"
+    EXECUTABLE="mitgcmuv"
+fi
+
 if test "x$TESTDIRS" = x ; then
-    TESTDIRS=`scandirs`
+    LIST=`scandirs results/$ref_outp`
+else
+    #- expand group of experiments:
+    LIST=" "
+    for xx in $TESTDIRS
+    do
+      case $xx in
+	'basic') LIST=${LIST}" aim.5l_cs hs94.128x64x5 ideal_2D_oce"
+		 LIST=${LIST}" lab_sea tutorial_baroclinic_gyre"
+		 LIST=${LIST}" tutorial_global_oce_latlon tutorial_plume_on_slope"
+		;;
+	'tutorials')
+		 LIST=${LIST}" "`ls | grep 'tutorial_'` ;;
+	*)	 LIST=${LIST}" "$xx ;;
+      esac
+    done 
 fi
+#echo 'LIST='${LIST}'<'
+#- skip dirs, remove duplicate and non-directory:
+TESTDIRS=" "
+count=0
+for xx in $LIST
+do
+    yy=`echo $SKIPDIRS | grep -c $xx`
+    if test $yy = 0 ; then
+	if test -d $xx ; then
+	    yy=`echo $TESTDIRS | grep -c $xx`
+	    if test $yy = 0 ; then TESTDIRS=${TESTDIRS}" "$xx ; fi
+	else count=1 ;
+	    echo ""; echo -n " -- skip \"$xx\" (not a directory !)"
+	fi
+    else
+        if test $count = 1 ; then echo -n ", \"$xx\""
+	else count=1 ; echo "" ;  echo -n " skip: \"$xx\""
+	fi
+    fi
+done 
+if test $count = 1 ; then echo "" ; echo -n " ... " ; fi
+#echo 'TESTDIRS='${TESTDIRS}'<'
+
+if test "x$OPTFILE" = xNONE -a "x$MITGCM_OF" != x ; then
+    OPTFILE=$MITGCM_OF
+fi
+
+RUNLOG="run.log"
+OUTPUTFILE=$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"
+# 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$ADM" = x -a "x$OADM" = x; then
+    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
 
-#  build the mpack utility
-build_mpack
+#  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=$MACH"_"$DATE"_"
+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"
 while test -e $DRESULTS ; do
@@ -506,132 +1085,302 @@
 mkdir $DRESULTS
 RETVAL=$?
 if test "x$RETVAL" != x0 ; then
-    echo "Error: can't create results directory \"./$DRESULTS\""
+    echo "ERROR: Can't create results directory \"./$DRESULTS\""
     exit 1
 fi
 SUMMARY="$DRESULTS/summary.txt"
-date > $SUMMARY
-cat << EOF >> $SUMMARY
-                T           S           U           V
-G D M    c        m  s        m  s        m  s        m  s
-E p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
-N n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
-2 d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
+start_date=`date`
+echo $start_date > $SUMMARY
+echo 'run:' $CMDLINE >> $SUMMARY
+echo 'on :' $UNAMEA  >> $SUMMARY
+
+of_path=
+if test "x$OPTFILE" != xNONE ; then
+    if test -r $OPTFILE ; then
+	# get the path
+	path=${OPTFILE%/*}
+	if test "x$path" = x ; then
+	    of_path=`pwd`
+	else
+	    of_path=`( cd $path > /dev/null 2>&1 ; pwd )`
+	fi
+	file=${OPTFILE##*/}
+	OPTFILE=$of_path/$file
+	cp $OPTFILE $DRESULTS
+	echo >> $SUMMARY
+	echo "  OPTFILE=$OPTFILE" >> $SUMMARY
+    else
+	echo | tee $SUMMARY
+	echo "ERROR: can't read OPTFILE=\"$OPTFILE\"" | tee $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
+fi
+echo
+echo >> $SUMMARY
+if test "x$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 $PTRACERS_NUM ; do
+	line_0="$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="$line_4  n  x  n  ."
+    done
+    echo "$line_0" | tee -a $SUMMARY
+    echo "$line_1" | tee -a $SUMMARY
+    echo "$line_2" | tee -a $SUMMARY
+    echo "$line_3" | tee -a $SUMMARY
+    echo "$line_4" | tee -a $SUMMARY
+    echo " "       | tee -a $SUMMARY
+else
+    echo "ADJOINT=true" >> $SUMMARY
+    echo >> $SUMMARY
+    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
+fi
 
-NDIR=0
+#  ...and each test directory...
+for dir in $TESTDIRS ; do
+    
+    # set builddir & rundir:
+    builddir="build"
+    if test ! -d $dir/$builddir ; then mkdir $dir/$builddir ; fi
+    rundir="run"
+    if test ! -d $dir/$rundir ; then
+	rundir=$builddir
+    fi
+    CODE_DIR=$dir/$code_dir
+    BUILD_DIR=$dir/$builddir
 
-#  For each optfile...
-for OPTFILE in $OPTFILES ; do
+    #  Cleanup only!
+    if test "x$CLEANUP" = xt ; then
+	echo -n '  --- dir:' $BUILD_DIR ': '
+	makeclean $BUILD_DIR
+        rm -f $BUILD_DIR/$EXECUTABLE
+	if test -d $dir/$rundir/CVS ; then
+            echo -n '  --- dir:' $dir/$rundir ': '
+	    run_clean $dir/$rundir
+	fi
+	trdir=`( cd $dir ; find . -type d -name "tr_run.*" -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
 
-    OPTFILE=`pwd`"/$OPTFILE"
-    if test ! -r $OPTFILE ; then
-	echo "Error: can't read optfile \"$OPTFILE\""
-	exit 1
+    #  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 $fout ; then
+	echo "can't read \"$fout\" -- skipping $dir"
+	continue
     fi
-    echo
-    echo "OPTFILE=$OPTFILE" >> $SUMMARY
-    echo >> $SUMMARY
-    
-    #  ...and each test directory...
-    for dir in $TESTDIRS ; do
 
-	#  Verify that the testdir exists and contains previous 
-	#  results in the correct location--or skip this directory!
-	if test ! -r $dir"/results/output.txt" ; then
-	    echo | tee -a $SUMMARY
-	    echo "can't read \"$dir/results/output.txt\" -- skipping $dir" \
-		| tee -a $SUMMARY
-	    continue
-	fi
-
-	#  Is this an MPI run?
-	if test "x$MPI" = xt ; then
-	    if test ! -r $dir"/code/CPP_EEOPTIONS.h_mpi" -o ! -r $dir"/code/SIZE.h_mpi" ; then
-		echo | tee -a $SUMMARY
-		echo "can't read \"$dir/code/CPP_EEOPTIONS.h_mpi\" or \"$dir/code/SIZE.h_mpi\"" \
-		    | tee -a $SUMMARY
-		continue
-	    else
-		cp $dir"/code/CPP_EEOPTIONS.h_mpi" $dir"/code/CPP_EEOPTIONS.h"
-		cp $dir"/code/SIZE.h_mpi" $dir"/code/SIZE.h"
-	    fi
-	else
-	    if test -r $dir"/code/CPP_EEOPTIONS.h_nompi" ; then
-		cp $dir"/code/CPP_EEOPTIONS.h_nompi" $dir"/code/CPP_EEOPTIONS.h"
-	    fi
-            if test -r $dir"/code/SIZE.h_nompi" ; then
-                cp $dir"/code/SIZE.h_nompi" $dir"/code/SIZE.h"
-            fi
-	fi
+    # Check for specific files for particular type of run
 
-	#  Create an output dir for each OPTFILE/tdir combination
-	CDIR=$DRESULTS"/"$DRESULTS"_"$NDIR
-	mkdir $CDIR
-	CDIR=`pwd`"/$CDIR"
+    if test ! -r $CODE_DIR"/SIZE.h_mpi" -a "x$MPI" = "xt" ; then
+	echo "can't find \"$CODE_DIR/SIZE.h_mpi\" -- skipping $dir"
+	continue
+    fi
+    if test ! -r $dir"/input/eedata.mth" -a "x$MULTI_THREAD" = "xt" ; then
+	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
 
-	#  ...configue, make, run, and compare the output.
-	echo "-------------------------------------------------------------------------------"
-	echo
-	echo "Experiment:  $dir"
-	echo
-	unset genmake makedepend make run
-	results='-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --'
-	( cd $dir/input; rm -f *.{o,f,c,F} *.[f,F]90 work* output.txt Make* make.log; )
-	if [ -r $dir/build ]; then
-	    seperatebuilddir=1
-	    builddir=build
-	    rundir=build
-	    ( cd $dir/build; ln -sf ../input/* . )
-	else
-	    seperatebuilddir=0
-	    builddir=input
-	    rundir=input
+    #  Check whether there are "extra runs" for this testdir
+    extra_runs=
+    ex_run_dirs=`( cd $dir ; echo $inputdir.* )`
+    #echo "ex_run_dirs='$ex_run_dirs'"
+    for exd in $ex_run_dirs ; do
+	name=`echo $exd | sed -e "s/$inputdir\.//"`
+	refExOut=`echo $ref_outp | sed "s/\./.${name}./"`
+	outf="$dir/results/$refExOut"
+        if test -f $outf -a -r $outf ; then
+	  if test "x$MULTI_THREAD" = "xt" ; then 
+	    if test -r $dir"/"$exd"/eedata.mth" ; then
+	      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
+	  else
+	    extra_runs="$extra_runs $name"
+	  fi
 	fi
+    done
 
+    echo "-------------------------------------------------------------------------------"
+    echo
+    if test "x$extra_runs" = "x" ; then 
+       echo "Experiment:  $dir"
+    else
+       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
+    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 $seperatebuilddir $dir/$rundir \
-	    && runmodel $dir/$builddir && run=Y \
-	    && results=`testoutput $dir $rundir`
-	echo
-	formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
-	    ${run:-N} $results
+	    && linkdata $dir/$rundir $inputdir input \
+	    && runmodel $dir/$rundir && run=Y \
+	    && results=`testoutput_run $dir $rundir $ref_outp`
+    fi
+    
+    echo
+	fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
 	echo
-	formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
-	    ${run:-N} $results >> $SUMMARY
-	echo "fresults='" > $CDIR"/summary.txt"
-	formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} \
-	    ${run:-N} $results >> $CDIR"/summary.txt"
-	echo "'" >> $CDIR"/summary.txt"
+ 	echo "$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
 
-	(
-	    cd $DRESULTS
-	    tar -cf $NDIR".tar" $DRESULTS"_"$NDIR > /dev/null 2>&1
-	    gzip $NDIR".tar"
-	)
+	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 $inputdir.$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.$ex"
+	    echo
+	    echo "$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
+	    fi
+	done
+
+    #postclean $dir/$builddir
+    if test "x$POSTCLEAN" = xt ; then
+ 	makeclean $dir/$builddir \
+ 	    && run_clean $dir/$rundir
+    fi
+    
+    echo "-------------------------------------------------------------------------------"
+    
+done
 
-	$MPACK -s MITgcm-test -m 1000000 $DRESULTS"/"$NDIR".tar.gz" $ADDRESSES
+printf "Start time:  " >> $SUMMARY
+echo "$start_date" >> $SUMMARY
+printf "End time:    " >> $SUMMARY
+date >> $SUMMARY
+
+#  If addresses were supplied and mpack built successfully, then try
+#  to send email using mpack.
+if test "x$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" $ADDRESSES
 	RETVAL=$?
 	if test "x$RETVAL" != x0 ; then
-	    echo "Warning: \"$MPACK\" failed -- please contact <edhill@mitgcm.org>"
+	    echo
+	    echo "Warning: The tar, gzip, & mpack step failed.  Please send email"
+	    echo "  to <MITgcm-support@mitgcm.org> for help.  You may copy the "
+	    echo "  summary of results from the directory \"$DRESULTS\"."
+	    echo
 	else
-	    rm -f $DRESULTS"/"$NDIR".tar*"
+	    echo
+	    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
+    fi
+fi
 
-	NDIR=$(( $NDIR + 1 ))
-	
-    done
-done
+rm -f tr_cmpnum.c tr_cmpnum
 
-rm tmp_cmpnum.f a.out
+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
+    fi
+    cat $SUMMARY | sed '/^[YN] [YN] [YN] [YN]/ s/ \. //g' > tr_out.txt
+fi
 
-cat $SUMMARY
+if test "x$DELDIR" = xt ; then
+    rm -rf $DRESULTS
+fi