/[MITgcm]/MITgcm/verification/testreport

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-revision 1.163 by jmc,
Wed May 18 22:03:57 2011 UTC
+revision 1.212 by jmc,
Sun Mar 12 16:34:11 2017 UTC
 Line 11 
 usage()
      echo
      echo "where possible OPTIONS are:"
      echo "  (-help|-h)               print usage"
+     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 "  (-ieee/-noieee)          if possible, use IEEE compiler flags"
+     echo "  (-command|-c) STRING     command to run (e.g., if non-standard MPI setting)"
-     echo "                             (DEF=\"-ieee\")"
+     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 "  (-use_r4|-ur4)           if allowed, use real*4 type for '_RS' variable"
-     echo "  (-optfile|-of) STRING    list of optfiles to use"
-     echo "  (-addr|-a) STRING        list of email recipients"
-     echo "                             (DEF=\"\" no email is sent)"
-     echo "  (-mpackdir|-mpd) DIR     location of the mpack utility"
-     echo "                             (DEF=\"../tools/mpack-1.6\")"
      echo "  (-tdir|-t) STRING        list of group and/or exp. dirs to test"
      echo "                             (recognized groups: basic, tutorials)"
      echo "                             (DEF=\"\" which test all)"
-Line 31 
 usage()
+Line 35 
 usage()
      echo "                              test THIS_EXP + all the following)"
      echo "  (-skipdir|-skd) STRING   list of exp. dirs to skip"
      echo "                             (DEF=\"\" which test all)"
-     echo "  (-bash|-b) STRING        preferred location of a \"bash\" or"
+     echo "  (-ts)                    provide timing information per timestep"
-     echo "                             Bourne-compatible \"sh\" shell"
+     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 "  (-ef) STRING             used as genmake2 \"-extra_flag\" argument"
-     echo "  (-oad)                   perform an OpenAD adjoint run"
+     echo "  (-ncad)                  use genmake2 option \"-nocat4ad\" (-ncad)"
-     echo "  (-command|-c) STRING     command to run"
+     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 "  (-odir) STRING           used to build output directory name"
+     echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
-     echo "                             (DEF=\"hostname\")"
+     echo " ---- output options : ----"
- #   echo "  (-ptracers|-ptr) STRING  specify which ptracers to test"
- #   echo "                             (DEF=\"1 2 3 4 5\")"
      echo "  (-match) NUMBER          Matching Criteria (number of digits)"
      echo "                             (DEF=\"$MATCH_CRIT\")"
-     echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
+     echo "  (-odir) STRING           used to build output directory name"
+     echo "                             (DEF=\"hostname\")"
+     echo "  (-addr|-a) STRING        list of email recipients"
+     echo "                             (DEF=\"\" no email is sent)"
+     echo "  (-send)       STRING     sending command (instead of using mpack)"
+     echo "  (-savdir|-sd) STRING     location to save output tar file to send (DEF='$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 "  (-src)                   only produces small '*.f' src files (not even obj)"
+     echo "                            + with: '-adm/-tlm', also makes taf outp src code"
      echo "  (-runonly|-ro)           *ONLY* run stage (=\"-quick\" without make)"
      echo "  (-quick|-q)              same as \"-nogenmake -noclean -nodepend\""
      echo "  (-nogenmake|-ng)         skip the genmake stage"
-Line 57 
 usage()
+Line 73 
 usage()
      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:"
-Line 114 
 testoutput_var()
+Line 127 
 testoutput_var()
      # 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
+     #     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
+         grep "$2" $1/$4/$OUTPUTFILE | sed 's/.*=//' | nl > ${TMP}a.txt
-         lncntA=`wc -l tmp1.txt | awk '{print $1}' `
+         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
+     grep "$2" $1/$5 | sed 's/.*=//' | nl > ${TMP}b.txt
-     lncntB=`wc -l tmp2.txt | awk '{print $1}' `
+     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
+         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
+     echo "-1" >> ${TMP}c.txt
-     # On the SGI O3K (*not* the O2K), "cat -n" inserts a ":" after the line number
+     digits_of_similarity=`./tr_cmpnum < ${TMP}c.txt`
-     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_var: No comparison was available for \"$3\" 1>&2
-Line 184 
 testoutput_var()
+Line 196 
 testoutput_var()
              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
+     rm -f ${TMP}a.txt ${TMP}b.txt ${TMP}c.txt
      return $digits_of_similarity
  }
-Line 195 
 testoutput_run()
+Line 207 
 testoutput_run()
      #
      #  test output from 1 run in "directory"
  # --> same processing for adjoint & forward test
          # default list of output variables to be checked:
          #  1rst : main variable used to decide if it pass or FAIL
          #  others : number of matching digits to be printed in summary.txt
          listChk=$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 :
+         # set ref.outp file-name and, if compressed, uncompress it into subdir
-         outpref=$1/results/$3
+         refoutp=results/$3
-         ptr_mon="trcstat_ptracerXX_min trcstat_ptracerXX_max"
+         if test ! -r $1/results/$3 ; then
-         ptr_mon="$ptr_mon trcstat_ptracerXX_mean trcstat_ptracerXX_sd"
+           if test -r $1/results/${3}.gz ; then
-         for ii in $PTRACERS_NUM ; do
+             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 $outpref | wc -l | awk '{print $1}'`
+                 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"$ii"=f"
-               if test "x$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
+           # eval 'echo "HAVE_PTR0'$ii' = $HAVE_PTR0'$ii'"' 1>&2
-         done
+           done
-         tst=`echo $sVar $listVar | awk '{ for(i=2;i<=NF;i++){if($i==$1)t+=1}; print t }'`
+         fi
-         if test $tst != 1 ; then
+         tst=`echo $sVar $listVar | awk '{ for(i=2;i<=NF;i++){if($i==$1)t+=1}; print t }'`
-           if test $tst = 0 ; then echo "==> WARNING: selected var >$sVar< not found" 1>&2
+         if test $tst != 1 ; then
-                  else echo "==> WARNING: found selected var >$sVar< $tst times" 1>&2 ; fi
+           if test $tst = 0 ; then echo "==> WARNING: selected var >$sVar< not found" 1>&2
-           echo "==> WARNING: in checked list:" $listVar 1>&2
+                  else echo "==> WARNING: found selected var >$sVar< $tst times" 1>&2 ; fi
-         #- put it back once:
+           echo "==> WARNING: in checked list:" $listVar 1>&2
-           listVar=" $sVar "`echo "$listVar " | sed "s/ $sVar / /g"`
+         #- put it back once:
-         fi
+           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'" >> $locDIR"/summary.txt"
          #---
          allargs=""
          for xx in $listVar
          do
-           case $xx in
+          #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 $3; yy=$? ;;
+           'Cost') testoutput_var $1 "ADM  ref_cost_function" "ADM CostFct" $2 $refoutp ; yy=$? ;;
-           'Grad') testoutput_var $1 "ADM  precision_derivative_grad" "ADM Grad" $2 $3; yy=$? ;;
+          'AdGrd') testoutput_var $1 "ADM  adjoint_gradient"  "ADM Ad Grad" $2 $refoutp ; yy=$? ;;
-            'Tmn') testoutput_var $1 "dynstat_theta_min"  "Theta minimum"  $2 $3; yy=$? ;;
+          'FDGrd') testoutput_var $1 "ADM  finite-diff_grad"  "ADM FD Grad" $2 $refoutp ; yy=$? ;;
-            'Tmx') testoutput_var $1 "dynstat_theta_max"  "Theta maximum"  $2 $3; yy=$? ;;
+         'tlmCst') testoutput_var $1 "TLM  ref_cost_function" "TLM CostFct" $2 $refoutp ; yy=$? ;;
-            'Tav') testoutput_var $1 "dynstat_theta_mean" "Theta mean"     $2 $3; yy=$? ;;
+         'tlmGrd') testoutput_var $1 "TLM  tangent-lin_grad"  "TLM TL Grad" $2 $refoutp ; yy=$? ;;
-            'Tsd') testoutput_var $1 "dynstat_theta_sd"   "Theta Std.Dev"  $2 $3; yy=$? ;;
+         'fwdGrd') testoutput_var $1 "TLM  finite-diff_grad"  "TLM FD Grad" $2 $refoutp ; yy=$? ;;
-            'Smn') testoutput_var $1 "dynstat_salt_min"  "Salt minimum"    $2 $3; yy=$? ;;
+            'Tmn') testoutput_var $1 "dynstat_theta_min"  "Theta minimum"  $2 $refoutp ; yy=$? ;;
-            'Smx') testoutput_var $1 "dynstat_salt_max"  "Salt maximum"    $2 $3; yy=$? ;;
+            'Tmx') testoutput_var $1 "dynstat_theta_max"  "Theta maximum"  $2 $refoutp ; yy=$? ;;
-            'Sav') testoutput_var $1 "dynstat_salt_mean" "Salt mean"       $2 $3; yy=$? ;;
+            'Tav') testoutput_var $1 "dynstat_theta_mean" "Theta mean"     $2 $refoutp ; yy=$? ;;
-            'Ssd') testoutput_var $1 "dynstat_salt_sd"   "Salt Std.Dev"    $2 $3; yy=$? ;;
+            'Tsd') testoutput_var $1 "dynstat_theta_sd"   "Theta Std.Dev"  $2 $refoutp ; yy=$? ;;
-            'Umn') testoutput_var $1 "dynstat_uvel_min"  "U minimum"       $2 $3; yy=$? ;;
+            'Smn') testoutput_var $1 "dynstat_salt_min"  "Salt minimum"    $2 $refoutp ; yy=$? ;;
-            'Umx') testoutput_var $1 "dynstat_uvel_max"  "U maximum"       $2 $3; yy=$? ;;
+            'Smx') testoutput_var $1 "dynstat_salt_max"  "Salt maximum"    $2 $refoutp ; yy=$? ;;
-            'Uav') testoutput_var $1 "dynstat_uvel_mean" "U mean"          $2 $3; yy=$? ;;
+            'Sav') testoutput_var $1 "dynstat_salt_mean" "Salt mean"       $2 $refoutp ; yy=$? ;;
-            'Usd') testoutput_var $1 "dynstat_uvel_sd"   "U Std.Dev"       $2 $3; yy=$? ;;
+            'Ssd') testoutput_var $1 "dynstat_salt_sd"   "Salt Std.Dev"    $2 $refoutp ; yy=$? ;;
-            'Vmn') testoutput_var $1 "dynstat_vvel_min"  "V minimum"       $2 $3; yy=$? ;;
+            'Umn') testoutput_var $1 "dynstat_uvel_min"  "U minimum"       $2 $refoutp ; yy=$? ;;
-            'Vmx') testoutput_var $1 "dynstat_vvel_max"  "V maximum"       $2 $3; yy=$? ;;
+            'Umx') testoutput_var $1 "dynstat_uvel_max"  "U maximum"       $2 $refoutp ; yy=$? ;;
-            'Vav') testoutput_var $1 "dynstat_vvel_mean" "V mean"          $2 $3; yy=$? ;;
+            'Uav') testoutput_var $1 "dynstat_uvel_mean" "U mean"          $2 $refoutp ; yy=$? ;;
-            'Vsd') testoutput_var $1 "dynstat_vvel_sd"   "V Std.Dev"       $2 $3; yy=$? ;;
+            'Usd') testoutput_var $1 "dynstat_uvel_sd"   "U Std.Dev"       $2 $refoutp ; yy=$? ;;
-         'pt1mn'|'pt2mn'|'pt3mn'|'pt4mn'|'pt5mn') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
+            'Vmn') testoutput_var $1 "dynstat_vvel_min"  "V minimum"       $2 $refoutp ; yy=$? ;;
-            testoutput_var $1 "trcstat_ptracer0"$ii"_min"  "p0"$ii"_min"   $2 $3; yy=$? ;;
+            'Vmx') testoutput_var $1 "dynstat_vvel_max"  "V maximum"       $2 $refoutp ; yy=$? ;;
-         'pt1mx'|'pt2mx'|'pt3mx'|'pt4mx'|'pt5mx') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
+            'Vav') testoutput_var $1 "dynstat_vvel_mean" "V mean"          $2 $refoutp ; yy=$? ;;
-            testoutput_var $1 "trcstat_ptracer0"$ii"_max"  "p0"$ii"_max"   $2 $3; yy=$? ;;
+            'Vsd') testoutput_var $1 "dynstat_vvel_sd"   "V Std.Dev"       $2 $refoutp ; yy=$? ;;
-         'pt1av'|'pt2av'|'pt3av'|'pt4av'|'pt5av') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
+          'Qntmn') testoutput_var $1 "forcing_qnet_min" "Qnet minimum"  $2 $refoutp ; yy=$? ;;
-            testoutput_var $1 "trcstat_ptracer0"$ii"_mean" "p0"$ii"_mean" $2 $3; yy=$? ;;
+          'Qntmx') testoutput_var $1 "forcing_qnet_max" "Qnet maximum"  $2 $refoutp ; yy=$? ;;
-         'pt1sd'|'pt2sd'|'pt3sd'|'pt4sd'|'pt5sd') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
+          'Qntav') testoutput_var $1 "forcing_qnet_mean" "Qnet mean"       $2 $refoutp ; yy=$? ;;
-            testoutput_var $1 "trcstat_ptracer0"$ii"_sd"   "p0"$ii"_StDv"  $2 $3; yy=$? ;;
+          'Qntsd') testoutput_var $1 "forcing_qnet_sd"  "Qnet Std.Dev"  $2 $refoutp ; yy=$? ;;
-          'Qntmn') testoutput_var $1 "forcing_qnet_min" "Qnet minimum"  $2 $3; yy=$? ;;
+          'aSImn') testoutput_var $1 "seaice_area_min"   "SIce Area min"   $2 $refoutp ; yy=$? ;;
-          'Qntmx') testoutput_var $1 "forcing_qnet_max" "Qnet maximum"  $2 $3; yy=$? ;;
+          'aSImx') testoutput_var $1 "seaice_area_max"   "SIce Area max"   $2 $refoutp ; yy=$? ;;
-          'Qntav') testoutput_var $1 "forcing_qnet_mean" "Qnet mean"       $2 $3; yy=$? ;;
+          'aSIav') testoutput_var $1 "seaice_area_mean"  "SIce Area mean"  $2 $refoutp ; yy=$? ;;
-          'Qntsd') testoutput_var $1 "forcing_qnet_sd"  "Qnet Std.Dev"  $2 $3; yy=$? ;;
+          'aSIsd') testoutput_var $1 "seaice_area_sd"    "SIce Area StDv"  $2 $refoutp ; yy=$? ;;
-          'aSImn') testoutput_var $1 "seaice_area_min"   "SIce Area min"   $2 $3; yy=$? ;;
+          'hSImn') testoutput_var $1 "seaice_heff_min"   "SIce Heff min"   $2 $refoutp ; yy=$? ;;
-          'aSImx') testoutput_var $1 "seaice_area_max"   "SIce Area max"   $2 $3; yy=$? ;;
+          'hSImx') testoutput_var $1 "seaice_heff_max"   "SIce Heff max"   $2 $refoutp ; yy=$? ;;
-          'aSIav') testoutput_var $1 "seaice_area_mean"  "SIce Area mean"  $2 $3; yy=$? ;;
+          'hSIav') testoutput_var $1 "seaice_heff_mean"  "SIce Heff mean"  $2 $refoutp ; yy=$? ;;
-          'aSIsd') testoutput_var $1 "seaice_area_sd"    "SIce Area StDv"  $2 $3; yy=$? ;;
+          'hSIsd') testoutput_var $1 "seaice_heff_sd"    "SIce Heff StDv"  $2 $refoutp ; yy=$? ;;
-          'hSImn') testoutput_var $1 "seaice_heff_min"   "SIce Heff min"   $2 $3; yy=$? ;;
+          'uSImn') testoutput_var $1 "seaice_uice_min"   "SIce Uice min"   $2 $refoutp ; yy=$? ;;
-          'hSImx') testoutput_var $1 "seaice_heff_max"   "SIce Heff max"   $2 $3; yy=$? ;;
+          'uSImx') testoutput_var $1 "seaice_uice_max"   "SIce Uice max"   $2 $refoutp ; yy=$? ;;
-          'hSIav') testoutput_var $1 "seaice_heff_mean"  "SIce Heff mean"  $2 $3; yy=$? ;;
+          'uSIav') testoutput_var $1 "seaice_uice_mean"  "SIce Uice mean"  $2 $refoutp ; yy=$? ;;
-          'hSIsd') testoutput_var $1 "seaice_heff_sd"    "SIce Heff StDv"  $2 $3; yy=$? ;;
+          'uSIsd') testoutput_var $1 "seaice_uice_sd"    "SIce Uice StDv"  $2 $refoutp ; yy=$? ;;
-         'AthSiG') testoutput_var $1 "thSI_Ice_Area_G" "thSIc Area Global" $2 $3; yy=$? ;;
+          'vSImn') testoutput_var $1 "seaice_vice_min"   "SIce Vice min"   $2 $refoutp ; yy=$? ;;
-         'AthSiS') testoutput_var $1 "thSI_Ice_Area_S" "thSIc Area South"  $2 $3; yy=$? ;;
+          'vSImx') testoutput_var $1 "seaice_vice_max"   "SIce Vice max"   $2 $refoutp ; yy=$? ;;
-         'AthSiN') testoutput_var $1 "thSI_Ice_Area_N" "thSIc Area North"  $2 $3; yy=$? ;;
+          'vSIav') testoutput_var $1 "seaice_vice_mean"  "SIce Vice mean"  $2 $refoutp ; yy=$? ;;
-         'HthSiG') testoutput_var $1 "thSI_IceH_ave_G" "thSIc H Global"    $2 $3; yy=$? ;;
+          'vSIsd') testoutput_var $1 "seaice_vice_sd"    "SIce Vice StDv"  $2 $refoutp ; yy=$? ;;
-         'HthSiS') testoutput_var $1 "thSI_IceH_ave_S" "thSIc H South"     $2 $3; yy=$? ;;
+         'AthSiG') testoutput_var $1 "thSI_Ice_Area_G" "thSIc Area Global" $2 $refoutp ; yy=$? ;;
-         'HthSiN') testoutput_var $1 "thSI_IceH_ave_N" "thSIc H North"     $2 $3; yy=$? ;;
+         'AthSiS') testoutput_var $1 "thSI_Ice_Area_S" "thSIc Area South"  $2 $refoutp ; yy=$? ;;
-               *) yy=99; echo "WARNING: asking for var=$xx : not recognized !" 1>&2 ;;
+         'AthSiN') testoutput_var $1 "thSI_Ice_Area_N" "thSIc Area North"  $2 $refoutp ; yy=$? ;;
-           esac
+         'HthSiG') testoutput_var $1 "thSI_IceH_ave_G" "thSIc H Glob-ave"  $2 $refoutp ; yy=$? ;;
-           if test $xx = $sVar
+         'HthSiS') testoutput_var $1 "thSI_IceH_ave_S" "thSIc H South-av"  $2 $refoutp ; yy=$? ;;
-           then allargs="$allargs > $yy <"
+         'HthSiN') testoutput_var $1 "thSI_IceH_ave_N" "thSIc H North-av"  $2 $refoutp ; yy=$? ;;
-           else allargs="$allargs $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 "."}}'`
            echo $allargs $adNul
          else
            echo $allargs
          fi
  # <-- same processing for adjoint & forward test
-Line 328 
 genmakemodel()
+Line 383 
 genmakemodel()
              if test "x$MKDEPEND" != x ; then
                  command="$command -makedepend=$MKDEPEND"
              fi
-             if test "x$ADM" = xt ; then
+             if test $KIND = 4 ; then
-                 command="$command --mods=../code_ad"
+                 command="$command -oad -mods=../$code_dir"
-             elif test "x$OADM" = xt ; then
-                 command="$command -adof ../../../tools/adjoint_options/adjoint_oad -mods '../code_oad ../../OpenAD/code_oad_all'"
              else
-                 command="$command -mods=../code"
+                 command="$command -mods=../$code_dir"
              fi
              if test "x$OPTFILE" != xNONE ; then
                  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
-Line 354 
 genmakemodel()
+Line 410 
 genmakemodel()
              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="$command -ts"
              fi
-Line 384 
 genmakemodel()
+Line 446 
 genmakemodel()
  makeclean()
  {
      # makeclean directory
-     if test "x$NODEPEND" = xf ; then rm -f $1/make.tr_log ; fi
+     if test "x$NOGENMAKE" = xf ; then rm -f $1/make.tr_log ; fi
      if test "x$NOCLEAN" = xt ; then
          echo "make Clean skipped!"
      else
-Line 416 
 run_clean()
+Line 478 
 run_clean()
      if test "x$NOCLEAN" = xt ; then
          echo "run_clean skipped!"
      else
-         (
+       (
-             cd $1;
+         cd $1;
-             printf 'clean run-dir ... '
+         printf 'clean run-dir ... '
-             # part of what is done after "make clean" when doing "make CLEAN"
+         # part of what is done after "make clean" when doing "make CLEAN"
-             find . -name "*.meta" -exec rm {} \;
+         find . -name "*.meta" -exec rm {} \;
-             find . -name "*.data" -exec rm {} \;
+         find . -name "*.data" -exec rm {} \;
-             find . -name "fort.*" -exec rm {} \;
+         find . -name "fort.*" -exec rm {} \;
-             find . -type l -exec rm {} \;
+         find . -type l -exec rm {} \;
-             #- should remove executable only if sym-link (alredy done above)
+         #- should remove executable only if sym-link (already done above)
-             rm -f $RUNLOG *.txt STD* *diagnostics.log datetime
+         rm -f $RUNLOG *.txt STDOUT.* STDERR.* *diagnostics.log *.[0-9][0-9][0-9][0-9].log
-             rm -rf mnc_test_*
+         rm -f datetime costfinal divided.ctrl snapshot* output_adm.*.diva_*
-             rm -f *_MIT_CE_000.opt0000 costfunction*0000
+         rm -f *_MIT_CE_000.opt0000 costfunction*0000
-             echo successful
+         rm -f oad_cp.[0-9][0-9][0-9].?????
-             exit 0
+         rm -rf mnc_test_*
-         )
+         echo successful
+         exit 0
+       )
      fi
  }
-Line 473 
 makemodel()
+Line 537 
 makemodel()
      else
          cd $1;
          if test -r Makefile ; then
-             printf 'make ... '
+             if test "x$MKSMALLF" = xt ; then
-             if test "x$ADM" = xt ; then
+                 printf 'make small_f ... '
-                 $MAKE adall >> make.tr_log 2>&1
+                 $MAKE_CMD small_f >> make.tr_log 2>&1
-             elif test "x$OADM" = xt ; then
+                 RETVAL=$?
-                 $MAKE adAll >> make.tr_log 2>&1
+                 if test "x$RETVAL" != x0 ; then
-             else
+                     tail make.tr_log
-                 if test "x$JOBS" = x ; then
+                     echo failed
-                     $MAKE >> make.tr_log 2>&1
+                     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.tr_log 2>&1
+                     echo successful
                  fi
              fi
+             printf "make $TARG ... "
+             $MAKE_CMD $TARG >> make.tr_log 2>&1
              RETVAL=$?
              if test "x$RETVAL" != x0 ; then
                  tail make.tr_log
-Line 501 
 makemodel()
+Line 570 
 makemodel()
              mk_fail=2
          fi
      fi
-     if test "x$ADM" = xt -a -f taf_ad.log ; then
+     if test $KIND = 1 -a -f taf_ftl.log ; then
-             head -1 taf_ad.log >> $CDIR"/summary.txt"
+         head -1 taf_ftl.log >> $CDIR"/summary.txt"
-             nerr=`grep -c 'TAF *.* ERROR ' taf_ad.log`
+     fi
-             nwar=`grep -c 'TAF RECOMPUTATION *.* WARNING ' taf_ad.log`
+     if test $KIND = 2 -a -f taf_ad.log ; then
-             echo " TAF reports $nerr Errors and $nwar Recomputation Warnings" \
+         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
-Line 514 
 makemodel()
+Line 591 
 makemodel()
  mk_mpi_size()
  {
-     # mk_mpi_size input_file output_file proc_Nb prefer_to_split_X
+     # 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)
+     #  make new SIZE.h (=output_file) from SIZE.h_mpi (=input_file)
      #     for an MPI build with no more than proc_Nb processors ;
-     # return the effective number of 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
-     dirX=$4
+     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 $px ] ; do
+     while [ $i -le $nx ] ; do
-       if [ `expr $px % $i` -eq 0 ] ; then
+       if [ `expr $nx % $i` -eq 0 ] ; then
          j=1
-         while [ $j -le $py ] ; do
+         while [ $j -le $ny ] ; do
-           if [ `expr $py % $j` -eq 0 ] ; then
+           if [ `expr $ny % $j` -eq 0 ] ; then
              ij=`expr $i \* $j`
              if [ $ij -gt $pp ] ; then
                  flag=1
-Line 631 
 linkdata()
+Line 731 
 linkdata()
          (
              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
-Line 666 
 linkdata()
+Line 766 
 linkdata()
              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
-Line 701 
 runmodel()
+Line 801 
 runmodel()
          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 /"`
+             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
-Line 714 
 runmodel()
+Line 814 
 runmodel()
            else 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 $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
+         #- special DIVA processing ends here
              ( eval $COMMAND ) >> $RUNLOG 2>&1
              RETVAL=$?
              ENDVAL=`tail $OUTPUTFILE | grep -c 'PROGRAM MAIN: Execution ended Normally'`
-Line 742 
 runmodel()
+Line 859 
 runmodel()
              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 AD time)
+         #- 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"
+                 | sed 's/(PID.TID 0000.0001)   //' >> $CDIR"/summary.txt"
-           if test "x$ADM" = xt ; then
+ #         grep -A3 'Seconds in section "ALL' $OUTPUTFILE \
-             grep -A3 'Seconds in section "ALL' $OUTPUTFILE >> $CDIR"/summary.txt"
+ #               | sed 's/(PID.TID 0000.0001)   //' >> $CDIR"/summary.txt"
-           fi
+ #         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
          if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
          if [ $RETVAL -eq 0 -a $ENDVAL -gt 0 ] ; then
-Line 854 
 formatresults()
+Line 977 
 formatresults()
          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'
  }
-Line 862 
 scandirs()
+Line 992 
 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 $*
-Line 918 
 debug=0
+Line 1049 
 debug=0
  verbose=1
  NBLINES_MKLOG=16000
- IEEE=true
+ OptLev=1
- if test "x$MITGCM_IEEE" != x ; then
-     IEEE=$MITGCM_IEEE
- fi
  GSL=f
  CLEANUP=f
-Line 941 
 SKIPDIRS=
+Line 1069 
 SKIPDIRS=
  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=
+ TARG=
  MPI=0
  MPI_MFILE=
  MULTI_THREAD=f
  OUTDIR=
  DELDIR=
  USE_R4=
+ EXTRFLG=
- ADM=
+ NOCATAD=
- OADM=
+ 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
  # list of pTracers to check for monitor output
  PTRACERS_NUM="1 2 3 4 5"
-Line 991 
 for ac_option ; do
+Line 1128 
 for ac_option ; do
          -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 ;;
-Line 1008 
 for ac_option ; do
+Line 1150 
 for ac_option ; do
          -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 ;;
-Line 1020 
 for ac_option ; do
+Line 1165 
 for ac_option ; do
          -j | --j) ac_prev=JOBS ;;
          -j=* | --j=*) JOBS=$ac_optarg ;;
+         -ef | --ef) ac_prev=EXTRFLG ;;
+         -ef=* | --ef=*) EXTRFLG=$ac_optarg ;;
          -clean | --clean) CLEANUP=t ; DELDIR=t ;;
          -norun | --norun | -nr | --nr) NORUN=t ;;
+         -obj | --obj ) TARG='obj' ; NORUN=t ;;
+         -src | --src ) TARG='small_f' ; NORUN=t ;;
          -runonly | --runonly | -ro | --ro) QUICK=t ; NOMAKE=t ;;
          -quick | --quick | -q | --q) QUICK=t ;;
          -nogenmake | --nogenmake | -ng | --ng) NOGENMAKE=t ;;
-Line 1041 
 for ac_option ; do
+Line 1191 
 for ac_option ; do
          -mth) MULTI_THREAD=t ;;
-         -adm | -ad) ADM=t ;;
+         -tlm) if test $KIND = 0 ; then KIND=1 ; else
-         -oad) OADM=t; NODEPEND=t ;;
+                 echo "Error: '-tlm', '-adm' and '-oad' are exclusive" ; usage
+               fi ;;
-         -ieee) IEEE=true ;;
+         -adm | -ad) if test $KIND = 0 ; then KIND=2 ; else
-         -noieee) IEEE= ;;
+                 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 ;;
-Line 1058 
 for ac_option ; do
+Line 1221 
 for ac_option ; do
          -ts) TS=t;;
          -papis) PAPIS=t;;
-         -pcls) PCL=t;;
+         -pcls) PCLS=t;;
          -*) echo "Error: unrecognized option: "$ac_option
              usage ;;
-Line 1074 
 if test "x$QUICK" = xt ; then
+Line 1237 
 if test "x$QUICK" = xt ; then
      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
+     if test "x$TARG" = xsmall_f ; then TARG=ftltaf ; else TARG=ftlall ; fi
+     code_dir=code_ad
+     inputdir=input_ad
+     ref_outp="output_tlm.txt"
+     EXECUTABLE="mitgcmuv_ftl"
+ elif test $KIND = 2 ; then
+     if test "x$TARG" = x        ; then TARG=adall ; fi
+     if test "x$TARG" = xobj     ; then TARG=adobj ; fi
+     if test "x$TARG" = xsmall_f ; then TARG=adtaf ; fi
      code_dir=code_ad
      inputdir=input_ad
      ref_outp="output_adm.txt"
      EXECUTABLE="mitgcmuv_ad"
- elif test "x$OADM" = xt ; then
+ elif test $KIND = 4 ; then
+     TARG=adAll
      code_dir=code_oad
      inputdir=input_oad
      ref_outp="output_oadm.txt"
-Line 1109 
 else
+Line 1283 
 else
      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
-Line 1147 
 do
+Line 1322 
 do
              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
-Line 1155 
 done
+Line 1330 
 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
  LOC_MFILE='tr_mpi_mfile'
  RUNLOG="run.tr_log"
- OUTPUTFILE=$ref_outp
+ if test "x$MPI" = x0 ; then
- if test "x$COMMAND" = x ; then
+   OUTPUTFILE=$ref_outp
-     COMMAND="./$EXECUTABLE > $OUTPUTFILE"
+   if test "x$COMMAND" = x ; then COMMAND="./$EXECUTABLE > $OUTPUTFILE" ; fi
- fi
+ else
- if test "x$MPI" != x0 ; then
+   OUTPUTFILE="STDOUT.0000"
-     OUTPUTFILE="STDOUT.0000"
+   if test "x$COMMAND" = x ; then COMMAND="mpirun -np TR_NPROC ./$EXECUTABLE" ; fi
  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 -a "x$OADM" = 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 $DEF_CHECK_LIST | sed 's/ [a-zA-Z0-9]*+/&mn &mx &av &sd/g' | awk '{print NF-1}'`
  fi
  #  create the FORTRAN comparison code
- if test -x tr_cmpnum ; then
+ if test "x$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 nw=`echo $xx | wc -w`
-     if test $nw = '1' ; then CMDLINE="$CMDLINE $xx"
+     if test $nw = '1' ; then CMDLINE="$CMDLINE $xx" ; else
-                         else CMDLINE="$CMDLINE '$xx'" ; fi
+       nb=`echo $xx | grep -c '='`
+       if test $nb = 0 ; then CMDLINE="$CMDLINE '$xx'"
+       else yy=`echo "$xx'" | sed "s/=/='/"` ;
+                              CMDLINE="$CMDLINE $yy" ; fi
+     fi
  done
- #for xx in "$@" ; do CMDLINE="$CMDLINE '$xx'" ; done
  MACH=`hostname`
  UNAMEA=`uname -a`
  DATE=`date +%Y%m%d`
-Line 1215 
 BASE="tr_"$MACH"_"$DATE"_"
+Line 1406 
 BASE="tr_"$MACH"_"$DATE"_"
  if test "x$OUTDIR" != x ; then
      BASE="tr_"$OUTDIR"_"$DATE"_"
  else
-     short_name=`hostname | sed 's/\..*$//'`
+    #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"_"$DATE"_"
  fi
  DNUM=0
-Line 1252 
 if test "x$OPTFILE" != xNONE ; then
+Line 1445 
 if test "x$OPTFILE" != xNONE ; then
          echo >> $SUMMARY
          echo "  OPTFILE=$OPTFILE" >> $SUMMARY
      else
-         echo | tee $SUMMARY
+         echo | tee -a $SUMMARY
-         echo "ERROR: can't read OPTFILE=\"$OPTFILE\"" | tee $SUMMARY
+         echo "ERROR: can't read OPTFILE=\"$OPTFILE\"" | tee -a $SUMMARY
          exit 1
      fi
  else
-Line 1263 
 else
+Line 1456 
 else
  fi
  echo
  echo >> $SUMMARY
- if test "x$ADM" = x -a "x$OADM" = x; then
+ if test $KIND = 0 ; then
-     if [ $MATCH_CRIT -lt 10 ] ;
+     line_0=`printf '%s %2i' 'default' $MATCH_CRIT`
-     then line_0="default  "$MATCH_CRIT ;
-     else line_0="default "$MATCH_CRIT ; fi
         line_0="$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_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_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"$ii"--"
-Line 1279 
 if test "x$ADM" = x -a "x$OADM" = x; the
+Line 1470 
 if test "x$ADM" = x -a "x$OADM" = x; the
          line_3="$line_3  i  a  a  d"
          line_4="$line_4  n  x  n  ."
      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
+     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
-d e n  t  d
- EOF
  fi
  echo "-------------------------------------------------------------------------------"
-Line 1324 
 for dir in $TESTDIRS ; do
+Line 1526 
 for dir in $TESTDIRS ; do
              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 -n '  --- dir:' $dir/$rundir ': '
              run_clean $dir/$rundir
          fi
          trdir=`( cd $dir ; find . -type d -name "$pfxdir.*" -print | sed 's/^.\///')`
-Line 1341 
 for dir in $TESTDIRS ; do
+Line 1544 
 for dir in $TESTDIRS ; do
      #  Verify that the testdir exists and contains previous
      #  results in the correct location--or skip this directory!
      fout=$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
-Line 1358 
 for dir in $TESTDIRS ; do
+Line 1562 
 for dir in $TESTDIRS ; do
      fi
      if test "x$MPI" != "x0" ; then
-         prefer_X=0
+         ntx=1 ; nty=1
          if test "x$MULTI_THREAD" = "xt" ; then
-             retv=`check_eedata $dir"/input/eedata.mth"`
+           ff=$dir"/input/eedata.mth"
-             if test $retv = 1 ; then prefer_X=1 ; fi
+           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 $prefer_X
+         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
-Line 1404 
 for dir in $TESTDIRS ; do
+Line 1611 
 for dir in $TESTDIRS ; do
      #  Check whether there are "extra runs" for this testdir
      extra_runs=
      if test "x$NORUN" = xf ; then
-         ex_run_dirs=`( cd $dir ; echo $inputdir.* )`
+         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 -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
-Line 1434 
 for dir in $TESTDIRS ; do
+Line 1641 
 for dir in $TESTDIRS ; do
      echo
      if test "x$extra_runs" = "x" ; then
-        echo "Experiment:  $dir"
+         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
-Line 1455 
 for dir in $TESTDIRS ; do
+Line 1662 
 for dir in $TESTDIRS ; do
              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
+             echo
      else
          genmakemodel $dir/$builddir && genmake=Y \
              && makeclean $dir/$builddir \
              && symlink_mpifiles $dir $code_dir $builddir \
              && makedependmodel $dir/$builddir && makedepend=Y \
              && makemodel $dir/$builddir && make=Y \
              && run_clean $dir/$rundir \
              && linkdata $dir/$rundir $inputdir \
              && runmodel $dir/$rundir && run=Y \
              && results=`testoutput_run $dir $rundir $ref_outp`
+             echo 1>&2
      fi
      #echo "results='$results'"
          fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
-         echo 1>&2
+         echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
-         echo "$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
              #  reference output file
              refExOut=`echo $ref_outp | sed "s/\./.${ex}./g"`
              #  Create an output dir & summary.txt file for each extra run (tdir.ex)
-Line 1494 
 for dir in $TESTDIRS ; do
+Line 1702 
 for dir in $TESTDIRS ; do
              linkdata $dir/$pfxdir.$ex $inputdir.$ex $inputdir
              runmodel $dir/$pfxdir.$ex && run=Y \
              && results=`testoutput_run $dir $pfxdir.$ex $refExOut`
-             fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
-             fres="$fres.$ex"
              echo 1>&2
+             fres=`formatresults $dir.$ex ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
              echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
              echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $locDIR"/summary.txt"
              if test "x$POSTCLEAN" = x2 ; then
-Line 1504 
 for dir in $TESTDIRS ; do
+Line 1712 
 for dir in $TESTDIRS ; do
              fi
          done
-     if test -f $DRESULTS"/"genmake_state ; then : ; else
+     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
+ #           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}"\
+ #               sed "/^No \"OPTFILE\" was specified ; genmake2/a\  OPTFILE=${OPTFILE}"\
-                         $SUMMARY > tr_0.tmp_log
+ #                       $SUMMARY > tmp.tr_log
+ # bsd-sed requires a newline after "a\":
+                 sed "/^No \"OPTFILE\" was specified ; genmake2/a\\
+                          OPTFILE=${OPTFILE}" $SUMMARY > tmp.tr_log
                  RETVAL=$?
-                 if test "x$RETVAL" = x0 ; then rm -f $SUMMARY
+                 if test "x$RETVAL" = x0 ; then
-                         cp tr_0.tmp_log $SUMMARY
+                     cp -f tmp.tr_log $SUMMARY
-                 else rm -f tr_0.tmp_log
                  fi
+                 rm -f tmp.tr_log
              fi
              gmkLog=$dir/$builddir/genmake.log
-             grep '^Get compiler version using:' $gmkLog > /dev/null 2>&1
+             if test -r $gmkLog ; then
-             RETVAL=$?
+                 grep '^Get compiler version using:' $gmkLog > /dev/null 2>&1
-             if test "x$RETVAL" = x0 ; then
+                 RETVAL=$?
-                 echo "from '$gmkLog', extract compiler version:" >> $DRESULTS/genmake_state
+                 if test "x$RETVAL" = x0 ; then
-                 sed -n '/Get compiler version/,/<-- compiler version/p' $gmkLog \
+                   echo -n "from '$gmkLog', " >> $DRESULTS/genmake_state
-                        | grep -v '^... compiler version ' > tr_1.tmp_log
+                   echo "extract compiler version:"   >> $DRESULTS/genmake_state
-                 sed -n '1,/^$/p' tr_1.tmp_log | sed '/^$/d' | sed 's/^./ &/' \
+                   sed -n '/Get compiler version/,/<-- compiler version/p' \
-                         >> $DRESULTS/genmake_state
+                      $gmkLog | grep -v '^... compiler version ' > tmp.tr_log
-                 rm -f tr_1.tmp_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" = 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
-Line 1554 
 date >> $SUMMARY
+Line 1781 
 date >> $SUMMARY
  if test "x$ADDRESSES" = xNONE -o "x$ADDRESSES" = x ; then
      echo "No results email was sent."
  else
-     if test "x$HAVE_MPACK" = xt ; then
+     if test "x$SENDCMD" != x ; then
-         tar -cf $DRESULTS".tar" $DRESULTS > /dev/null 2>&1 \
+         SendOpt='' ; headCMD=`echo $SENDCMD | awk '{print $1}'`
-             && gzip $DRESULTS".tar" \
+         if test $headCMD != 'scp' ; then SendOpt='-s MITgcm-test -m 3555000' ; fi
-             && $MPACK -s MITgcm-test -m 3555000 $DRESULTS".tar.gz" $ADDRESSES
+         if [ $verbose -gt 1 ]; then
+            echo " run: $SENDCMD $SendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES"
+         fi
+         tar -cf ${SAVDIR}/${DRESULTS}".tar" $DRESULTS > /dev/null 2>&1 \
+             && gzip ${SAVDIR}/${DRESULTS}".tar" \
+             && $SENDCMD $SendOpt ${SAVDIR}/${DRESULTS}".tar.gz" $ADDRESSES
          RETVAL=$?
          if test "x$RETVAL" != x0 ; then
              echo
-             echo "Warning: The tar, gzip, & mpack step failed.  Please send email"
+             echo "Warning: The tar, gzip, & $SENDCMD step failed.  Please send email"
              echo "  to <MITgcm-support@mitgcm.org> for help.  You may copy the "
              echo "  summary of results from the directory \"$DRESULTS\"."
              echo
-Line 1570 
 else
+Line 1802 
 else
              echo "An email containing results was sent to the following addresses:"
              echo "  \"$ADDRESSES\""
              echo
-             test -f $DRESULTS".tar"  &&  rm -f $DRESULTS".tar"
+             test -f ${SAVDIR}/${DRESULTS}".tar" &&  rm -f ${SAVDIR}/${DRESULTS}".tar"
-             test -f $DRESULTS".tar.gz"  &&  rm -f $DRESULTS".tar.gz"
+             test -f ${SAVDIR}/${DRESULTS}".tar.gz" &&  rm -f ${SAVDIR}/${DRESULTS}".tar.gz"
          fi
      fi
  fi
-Line 1583 
 fi
+Line 1815 
 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
      fi
      cat $SUMMARY | sed '/^[YN] [YN] [YN] [YN]/ s/ \. //g' > tr_out.txt
  fi
-Line 1591 
 fi
+Line 1823 
 fi
  if test "x$DELDIR" = xt ; then
      rm -rf $DRESULTS
  fi
+ echo "======== End of testreport execution ========"

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+Added in v.1.212

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