--- MITgcm/verification/testreport	2009/01/29 21:45:43	1.120
+++ MITgcm/verification/testreport	2010/10/07 20:59:39	1.142
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.120 2009/01/29 21:45:43 utke Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.142 2010/10/07 20:59:39 jmc Exp $
 #  $Name:  $
 #
 
@@ -11,38 +11,41 @@
     echo
     echo "where possible OPTIONS are:"
     echo "  (-help|-h)               print usage"
-    echo "  (-mth)                   run multi threaded (using eedata.mth)"
+    echo "  (-mth)                   run multi-threaded (using eedata.mth)"
     echo "  (-mpi)                   compile and run using MPI"
-    echo "  (-ieee|-noieee)          if possible, use IEEE compiler flags"
+    echo "  (-ieee/-noieee)          if possible, use IEEE compiler flags"
     echo "                             (DEF=\"-ieee\")"
     echo "  (-gsl)                   compile with \"-gsl\" flag"
-    echo "  (-of=|-optfile=)STRING   list of optfiles to use"
-    echo "  (-a|-addr) STRING        list of email recipients"
+    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 "  (-mpd|-mpackdir) DIR     location of the mpack utility"
+    echo "  (-mpackdir|-mpd) 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 "  (-tdir|-t) STRING        list of group and/or exp. dirs to test"
     echo "                             (recognized groups: basic, tutorials)"
     echo "                             (DEF=\"\" which test all)"
-    echo "  (-skd|-skipdir) STRING   list of exp. dirs to skip"
+    echo "  (-skipdir|-skd) STRING   list of exp. dirs to skip"
     echo "                             (DEF=\"\" which test all)"
-    echo "  (-b|-bash) STRING        preferred location of a \"bash\" or"
+    echo "  (-bash|-b) STRING        preferred location of a \"bash\" or"
     echo "                             Bourne-compatible \"sh\" shell"
     echo "                             (DEF=\"\" for \"bash\")"
     echo "  (-adm|-ad)               perform an adjoint run"
     echo "  (-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 "  (-command|-c) STRING     command to run"
+    echo "  (-makedepend|-md) STRING command to use for \"makedepend\""
+    echo "  (-make|-m) STRING        command to use for \"make\""
     echo "                             (DEF=\"make\")"
     echo "  (-odir) STRING           used to build output directory name"
     echo "                             (DEF=\"hostname\")"
-    echo "  (-ptr|-ptracers) STRING  specify which ptracers to test"
+    echo "  (-ptracers|-ptr) STRING  specify which ptracers to test"
     echo "                             (DEF=\"1 2 3 4 5\")"
     echo "  (-match) NUMBER          Matching Criteria (number of digits)"
-    echo "                             (DEF=\"12\")"
+    echo "                             (DEF=\"$MATCH_CRIT\")"
     echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
     echo "  (-clean)                 *ONLY* run \"make CLEAN\""
+    echo "  (-norun|-nr)             skip the \"runmodel\" stage (stop after make)"
+    echo "  (-runonly|-ro)           *ONLY* run stage (=\"-quick\" without make)"
     echo "  (-quick|-q)              same as \"-nogenmake -noclean -nodepend\""
     echo "  (-nogenmake|-ng)         skip the genmake stage"
     echo "  (-noclean|-nc)           skip the \"make clean\" stage"
@@ -104,7 +107,7 @@
 {
     # testoutput_var dir s1 label subdir reference_output
     #
-    #  compares 1 variable output selected from file $dir/$subdir/$OUTPUTFILE 
+    #  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
 
@@ -176,7 +179,7 @@
 	fi
     fi
     rm -f tmp1.txt tmp2.txt tmp3.txt tmp4.txt
-    
+
     return $digits_of_similarity
 }
 
@@ -229,7 +232,7 @@
           listVar=" $sVar "`echo "$listVar " | sed "s/ $sVar / /g"`
         fi
 	if [ $debug -gt 0 ]; then echo "testoutput_run: listVar(M)='$listVar'" 1>&2 ; fi
-	echo "listVar='$listVar'" > $CDIR"/summary.txt"
+	echo "listVar='$listVar'" > $locDIR"/summary.txt"
         allargs=""
         for xx in $listVar
         do
@@ -264,18 +267,18 @@
 	   testoutput_var $1 "trcstat_ptracer0"$ii"_mean" "p0"$ii"_mean" $2 $3; yy=$? ;;
 	'pt1sd'|'pt2sd'|'pt3sd'|'pt4sd'|'pt5sd') ii=`echo $xx | sed 's/pt//' | sed 's/..$//'`
 	   testoutput_var $1 "trcstat_ptracer0"$ii"_sd"   "p0"$ii"_StDv"  $2 $3; yy=$? ;;
-	 'Qntmn') testoutput_var $1 "extforcing_qnet_min" "Qnet minimum"  $2 $3; yy=$? ;;
-	 'Qntmx') testoutput_var $1 "extforcing_qnet_max" "Qnet maximum"  $2 $3; yy=$? ;;
-	 'Qntav') testoutput_var $1 "extforcing_qnet_mean" "Qnet mean"	  $2 $3; yy=$? ;;
-	 'Qntsd') testoutput_var $1 "extforcing_qnet_sd"  "Qnet Std.Dev"  $2 $3; yy=$? ;;
+	 '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 Hell max"	  $2 $3; yy=$? ;;
-	 'hSIav') testoutput_var $1 "seaice_heff_mean"  "SIce Hell mean"  $2 $3; yy=$? ;;
-	 'hSIsd') testoutput_var $1 "seaice_heff_sd"    "SIce Hell StDv"  $2 $3; yy=$? ;;
+	 '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 $3; yy=$? ;;
@@ -291,13 +294,13 @@
         done
 
 	nbVar=`echo $listVar | awk '{print NF}'`
-        if [ $nbVar -lt $LEN_CHECK_LIST ] ; then 
+        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 
+        fi
 # <-- same processing for adjoint & forward test
 }
 
@@ -315,15 +318,18 @@
 	(
 	    cd $1;
 	    command="$GENMAKE2  -ds -m $MAKE"
+	    if test "x$MKDEPEND" != x ; then
+		command="$command -makedepend=$MKDEPEND"
+	    fi
 	    if test "x$ADM" = xt ; then
 		command="$command --mods=../code_ad"
 	    elif test "x$OADM" = xt ; then
 		command="$command -adof ../../../tools/adjoint_options/adjoint_oad -mods '../code_oad ../../OpenAD/code_oad_all'"
 	    else
-		command="$command --mods=../code"
+		command="$command -mods=../code"
 	    fi
 	    if test "x$OPTFILE" != xNONE ; then
-		command="$command --optfile=$OPTFILE"
+		command="$command -optfile=$OPTFILE"
 	    fi
 	    if test "x$IEEE" != x ; then
 		command="$command -ieee"
@@ -334,29 +340,35 @@
 	    if test "x$MPI" = xt ; then
 		command="$command -mpi"
 	    fi
+	    if test "x$MULTI_THREAD" = xt ; then
+	    #- run multi-threaded using OpenMP:
+		command="$command -omp"
+	    fi
+	    if test "x$USE_R4" = xt ; then
+		command="$command -use_r4"
+	    fi
 	    if test "x$TS" = xt ; then
 		command="$command -ts"
 	    fi
 	    if test "x$PAPIS" = xt ; then
 		command="$command -papis"
-	    else 
+	    else
 	    if test "x$PCLS" = xt ; then
 		command="$command -pcls"
 	    fi
 	    fi
-	    printf 'genmake ... ' 1>&2
-	    # $command > make.log 2>&1
+	    printf 'genmake ... '
 	    eval $command > make.log 2>&1
 	    RETVAL=$?
 	    #  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
+		echo "genmakemodel: genmake failed"
 		cp genmake_* make.log $CDIR
 		return 1
 	    else
-		echo "successful" 1>&2
+		echo "successful"
 	    fi
 	)
     fi
@@ -372,17 +384,19 @@
 	    cd $1;
 	    #if test -e $OUTPUTFILE ; then rm -f $OUTPUTFILE ; fi
 	    if test -r Makefile ; then
-		printf 'clean build-dir: make Clean ... ' 2>&1
+		printf 'clean build-dir: make Clean ... '
 		$MAKE Clean >> make.log 2>&1
 		RETVAL=$?
 		if test "x$RETVAL" != x0 ; then
 		    tail make.log
-		    echo "makeclean: \"make Clean\" failed" 1>&2
+		    echo "makeclean: \"make Clean\" failed"
 		    cp make.log $CDIR"/make.log"
 		    return 1
 		fi
+		echo successful
+	    else
+		echo ''
 	    fi
-	    echo successful 1>&2
 	    exit 0
 	)
     fi
@@ -396,7 +410,7 @@
     else
 	(
 	    cd $1;
-	    printf 'clean run-dir ... ' 2>&1
+	    printf 'clean run-dir ... '
 	    # part of what is done after "make clean" when doing "make CLEAN"
 	    find . -name "*.meta" -exec rm {} \;
 	    find . -name "*.data" -exec rm {} \;
@@ -405,7 +419,7 @@
 	    rm -f $EXECUTABLE *.txt STD* *diagnostics.log datetime
 	    rm -rf mnc_test_*
  	    rm -f *_MIT_CE_000.opt0000 costfunction*0000
-	    echo successful 1>&2
+	    echo successful
 	    exit 0
 	)
     fi
@@ -419,16 +433,16 @@
     else
 	(
 	    cd $1;
-	    printf 'make depend ... ' 1>&2
+	    printf 'make depend ... '
 	    $MAKE depend >> make.log 2>&1
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
 		tail make.log
-		echo "makedependmodel: make depend failed" 1>&2
+		echo "makedependmodel: make depend failed"
 		cp make.log $CDIR"/make.log"
 		return 1
 	    else
-		echo successful 1>&2
+		echo successful
 	    fi
 	)
     fi
@@ -438,9 +452,18 @@
 {
     # makemodel directory
     (
+    if test "x$NOMAKE" = xt ; then
+	cd $1;
+	if test -x $EXECUTABLE ; then
+	    echo "make skipped!"
+	else
+	    echo "no executable!"
+	    return 2
+	fi
+    else
 	cd $1;
 	if test -r Makefile ; then
-	    printf 'make ... ' 1>&2
+	    printf 'make ... '
 	    if test "x$ADM" = xt ; then
 		$MAKE adall >> make.log 2>&1
 	    elif test "x$OADM" = xt ; then
@@ -455,13 +478,15 @@
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
 		tail make.log
-		echo failed 1>&2
+		echo failed
 		cp make.log $CDIR"/make.log"
+		rm -f $EXECUTABLE
 		return 1
 	    else
-		echo successful 1>&2
+		echo successful
 	    fi
 	fi
+    fi
     )
 }
 
@@ -475,7 +500,7 @@
     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)`
 
@@ -510,7 +535,7 @@
 	    fi
 	done
     fi
-    
+
 }
 
 linkdata()
@@ -521,14 +546,33 @@
     if test -d $1 ; then
 	(
 	    cd $1 ; shift
+	    echo 'linkdata from dirs:' $*
+            inpMPI=`(cd ../$1 ; find . -name "*.mpi" -print | sed 's:^\./::')`
+	    for xx in $inpMPI ; do
+	      if test -r "../"$1"/"$xx ; then
+	        # found 1 _mpi sfx file in 1rst input dir and it is readable
+		yy=`echo $xx | sed 's:\.mpi$::'`
+		if test "x$MPI" = "xt" ; then
+		# mpi test: remove symbolic link & link _mpi sfx file
+		    if test -h $yy ; then rm -f $yy ; fi
+		    if test ! -r $yy ; then
+			ln -sf "../"$1"/"$xx $yy ;
+			printf " $xx" 1>&2
+		    fi
+		else
+		# not mpi test: remove symbolic link
+		    if test -h $yy ; then rm -f $yy ; fi
+		fi
+	      fi
+	    done
 	    if test -r "../"$1"/eedata.mth" ; then
 	    # found eedata.mth in 1rst input dir and it is readable
 		if test "x$MULTI_THREAD" = "xt" ; then
 		# multi-threaded test: remove symbolic link & link eedata.mth
 		    if test -h eedata ; then rm -f eedata ; fi
-		    if test ! -r eedata ; then 
+		    if test ! -r eedata ; then
 			ln -sf "../"$1"/eedata.mth" eedata ;
-			printf 'eedata.mth ' 1>&2
+			printf ' eedata.mth' 1>&2
 		    fi
 		else
 		# not multi-threaded test: remove eedata symbolic link
@@ -538,7 +582,7 @@
 	    prevDir='NONE'
 	    for ldir in $* ; do
 		if test -d "../"$ldir -a $ldir != $prevDir ; then
-                    printf 'ldir='${ldir} 1>&2
+                    printf " ldir=${ldir}:" 1>&2
 		    files=`( cd "../"$ldir ; ls -1 | grep -v CVS )`
 		    for i in $files ; do
 			if test ! -d "../"$ldir/$i ; then
@@ -548,10 +592,12 @@
 			    fi
 			fi
 		    done
+		    printf ' ;' 1>&2
 		    if test -x "../"$ldir"/"prepare_run ; then
-			"../"$ldir"/"prepare_run
+			"../"$ldir"/"prepare_run 1>&2
+		    else
+			echo '' 1>&2
 		    fi
-		    printf ' ; ' 1>&2
 		fi
 		prevDir=$ldir
 	    done
@@ -563,16 +609,17 @@
 {
     # runmodel directory
     #
-    #  runs "$COMMAND in "directory" 
+    #  runs "$COMMAND in "directory"
     #  (where "$COMMAND" is relative to "directory")
     (
 	cd $1
-	printf 'runmodel in %s ...' $1 1>&2
-	# make output.txt
-	echo
-	if test -L $EXECUTABLE -a -x "../"$builddir"/"$EXECUTABLE ; then
+	printf 'runmodel in %s ... ' $1
+	if test -L $EXECUTABLE ; then
+	  if test -x "../"$builddir"/"$EXECUTABLE ; then
 	    diff -q $EXECUTABLE "../"$builddir"/"$EXECUTABLE > /dev/null 2>&1
 	    outD=$? ; if test $outD != 0 ; then rm -f $EXECUTABLE ; fi
+	  else rm -f $EXECUTABLE
+	  fi
 	fi
         if test ! -x $EXECUTABLE -a -x "../"$builddir"/"$EXECUTABLE ; then
 	    echo " link" $EXECUTABLE "from dir ../"$builddir > run.log_tmp
@@ -596,7 +643,7 @@
 		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 
+		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
@@ -606,17 +653,24 @@
 	    ENDVAL=`cat $RUNLOG | grep -v 'ABNORMAL END' | grep -c 'NORMAL END'`
 	fi
 	rm -f run.log_tmp
-	#if test "x$RETVAL" = x0 ; then
 	if [ $RETVAL -eq 0 -a $ENDVAL -gt 0 ] ; then
-	    tail $RUNLOG
-	    echo successful 1>&2
+	    echo successful
+	    printf '=> output from running in %s :\n' $1 1>&2
+	    tail $RUNLOG | sed 's/^.*/> &/g' 1>&2
 	    # === Reduce the size of the testing emails!
 	    #cp $OUTPUTFILE $CDIR"/"$OUTPUTFILE
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 0
+	elif [ $RETVAL -ne 0 -a $ENDVAL -gt 0 ] ; then
+	    #-- for some weird cases (run is finihed but with error code)
+	    echo 'finished with error (run:' $RETVAL ' end:' $ENDVAL ')'
+	    printf '=> output from running in %s :\n' $1 1>&2
+	    tail $RUNLOG | sed 's/^.*/> &/g' 1>&2
+	    return 0
 	else
-	    tail $RUNLOG
-	    echo failed '(run:' $RETVAL ' end:' $ENDVAL ')' 1>&2
+	    echo 'failed (run:' $RETVAL ' end:' $ENDVAL ')'
+	    printf '=> output from running in %s :\n' $1 1>&2
+	    tail $RUNLOG | sed 's/^.*/> &/g' 1>&2
 	    cp $RUNLOG $CDIR"/"$RUNLOG
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 1
@@ -668,7 +722,7 @@
 	return 0
     else
 	echo
-	echo "ERROR: failed to compile comparison code -- please specify" 
+	echo "ERROR: failed to compile comparison code -- please specify"
 	echo "  a C compiler using the CC environment variable."
 	exit 1
     fi
@@ -687,7 +741,7 @@
     printf '%3s' $listPrt
 #   line below does not work on hp-ux_ia64 : do those substitutions later on
 #   printf '%3s' $listPrt | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</'
-    
+
     if [ $xx = '..' ]; then
 	printf ' N/O '
     elif [ $xx = '--' ]; then
@@ -703,7 +757,7 @@
     fi
     printf '  %s' $nm
     printf '\n'
-    
+
 }
 
 scandirs()
@@ -718,6 +772,35 @@
 }
 
 
+check_eedata()
+{
+    # check_eedata size.h eedata
+    if [ $# -eq 2 ] ; then
+      if test -f $1 -a -f $2 ; then
+      sx=`grep "^     & *nSx *=" $1 | sed "s/^     & *nSx *=//" | sed 's/, *$//'`
+      nx=`grep "^ *nTx *=" $2 | tail -1 | sed 's/^ *nTx *= *//' | sed "s/, *$//"`
+      if test "x$nx" = x ; then
+	rx=10
+      else
+	rx=`expr $sx % $nx`
+      fi
+      sy=`grep "^     & *nSy *=" $1 | sed "s/^     & *nSy *=//" | sed 's/, *$//'`
+      ny=`grep "^ *nTy *=" $2 | tail -1 | sed 's/^ *nTy *= *//' | sed "s/, *$//"`
+      if test "x$ny" = x ; then
+	ry=20
+      else
+	ry=`expr $sy % $ny`
+      fi
+      echo `expr $rx + $ry`
+    else
+      echo '-1'
+      fi
+    else
+      echo '-2'
+    fi
+
+}
+
 ###############################################################################
 
 
@@ -733,7 +816,9 @@
 GSL=f
 
 CLEANUP=f
+NORUN=f
 QUICK=f
+NOMAKE=f
 NOGENMAKE=f
 NOCLEAN=f
 NODEPEND=f
@@ -748,6 +833,7 @@
 HAVE_MPACK=
 MPACK=
 COMMAND=
+MKDEPEND=
 if test "x$MAKE" = x ; then
     MAKE=make
 fi
@@ -759,6 +845,7 @@
 MULTI_THREAD=f
 OUTDIR=
 DELDIR=
+USE_R4=
 
 ADM=
 OADM=
@@ -781,7 +868,7 @@
     fi
 
     ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
-    
+
     case $ac_option in
 	
 	-help | --help | -h | --h)
@@ -794,7 +881,7 @@
 	
 	-addr | --addr | -a | --a)
             ac_prev=ADDRESSES ;;
-        -addr=* | --addr=*)
+        -addr=* | --addr=* | -a=* | --a=*)
             ADDRESSES=$ac_optarg ;;
         -mpackdir | --mpackdir | -mpd | --mpd)
             ac_prev=MPACKDIR ;;
@@ -803,27 +890,32 @@
 
 	-tdir | --tdir | -t | --t)
             ac_prev=TESTDIRS ;;
-        -tdir=* | --tdir=*)
+        -tdir=* | --tdir=* | -t=* | --t=*)
             TESTDIRS=$ac_optarg ;;
 
 	-skipdir | --skipdir | -skd | --skd)
             ac_prev=SKIPDIRS ;;
-        -skipdir=* | --skipdir=*)
+        -skipdir=* | --skipdir=* | -skd=* | --skd=*)
             SKIPDIRS=$ac_optarg ;;
 
 	-bash | --bash | -b | --b)
             ac_prev=BASH ;;
-        -bash=* | --bash=*)
+        -bash=* | --bash=* | -b=* | --b=*)
             BASH=$ac_optarg ;;
 
 	-command | --command | -c | --c)
 	    ac_prev=COMMAND ;;
-	-command=* | --command=*)
+	-command=* | --command=* | -c=* | --c=*)
 	    COMMAND=$ac_optarg ;;
 
+	-makedepend | --makedepend | -md | --md)
+	    ac_prev=MKDEPEND ;;
+	-makedepend=* | --makedepend=* | -md=* | --md=*)
+	    MKDEPEND=$ac_optarg ;;
+
 	-make | --make | -m | --m)
 	    ac_prev=MAKE ;;
-	-make=* | --make=*)
+	-make=* | --make=* | -m=* | --m=*)
 	    MAKE=$ac_optarg ;;
 
         -odir | --odir)
@@ -839,12 +931,16 @@
 	-match | --match ) ac_prev=MATCH_CRIT ;;
 	-match=* | --match=* ) MATCH_CRIT=$ac_optarg ;;
 
-	-j) ac_prev=JOBS ;;
-	-j=*) JOBS=$ac_optarg ;;
+	-j | --j) ac_prev=JOBS ;;
+	-j=* | --j=*) JOBS=$ac_optarg ;;
 
 	-clean | --clean)
 	    CLEANUP=t ; DELDIR=t ;;
 
+	-norun | --norun | -nr | --nr)
+	    NORUN=t ;;
+	-runonly | --runonly | -ro | --ro)
+	    QUICK=t ; NOMAKE=t ;;
 	-quick | --quick | -q | --q)
 	    QUICK=t ;;
 	-nogenmake | --nogenmake | -ng | --ng)
@@ -875,24 +971,24 @@
 
 	-deldir | -dd) DELDIR=t ;;
 
-	-ts) TS=t;;
+	-use_r4|-ur4) USE_R4=t ;;
 
+	-ts) TS=t;;
 	-papis) PAPIS=t;;
-
 	-pcls) PCL=t;;
 
         -*)
             echo "Error: unrecognized option: "$ac_option
             usage
             ;;
-        
+
         *)
             echo "Error: unrecognized argument: "$ac_option
             usage
             ;;
-        
+
      esac
-     
+
 done
 
 if test "x$QUICK" = xt ; then
@@ -919,8 +1015,12 @@
     EXECUTABLE="mitgcmuv"
 fi
 
+xx=`echo $TESTDIRS | awk '{print $1}'`
 if test "x$TESTDIRS" = x ; then
     LIST=`scandirs results/$ref_outp`
+elif test $xx = 'start_from' ; then
+    xx=`echo $TESTDIRS | awk '{print $2}'`
+    LIST=`scandirs results/$ref_outp | sed -n "/$xx/,$ p"`
 else
     #- expand group of experiments:
     LIST=" "
@@ -935,7 +1035,7 @@
 		 LIST=${LIST}" "`ls | grep 'tutorial_'` ;;
 	*)	 LIST=${LIST}" "$xx ;;
       esac
-    done 
+    done
 fi
 #echo 'LIST='${LIST}'<'
 #- skip dirs, remove duplicate and non-directory:
@@ -956,7 +1056,7 @@
 	else count=1 ; echo "" ;  echo -n " skip: \"$xx\""
 	fi
     fi
-done 
+done
 if test $count = 1 ; then echo "" ; echo -n " ... " ; fi
 #echo 'TESTDIRS='${TESTDIRS}'<'
 
@@ -992,7 +1092,11 @@
 fi
 
 #  create the FORTRAN comparison code
-createcodelet
+if test -x tr_cmpnum ; then
+    echo "skipping comparison code build"
+else
+    createcodelet
+fi
 
 #  build the mpack utility (if ADDRESSES = NONE, do it to test the build)
 if test "x$ADDRESSES" = x ; then
@@ -1014,6 +1118,9 @@
 BASE="tr_"$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"
@@ -1061,11 +1168,10 @@
 echo
 echo >> $SUMMARY
 if test "x$ADM" = x -a "x$OADM" = x; then
-    if [ $MATCH_CRIT -lt 10 ] ; 
-    then line_0="default  "$MATCH_CRIT ; 
+    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"
@@ -1086,8 +1192,8 @@
 else
     echo "ADJOINT=true" >> $SUMMARY
     echo >> $SUMMARY
-    if [ $MATCH_CRIT -lt 10 ] ; 
-    then line_0="default     "$MATCH_CRIT ; 
+    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
@@ -1098,10 +1204,11 @@
 
 EOF
 fi
+echo "-------------------------------------------------------------------------------"
 
 #  ...and each test directory...
 for dir in $TESTDIRS ; do
-    
+
     # set builddir & rundir:
     builddir="build"
     if test ! -d $dir/$builddir ; then mkdir $dir/$builddir ; fi
@@ -1114,22 +1221,23 @@
 
     #  Cleanup only!
     if test "x$CLEANUP" = xt ; then
-	if test -r $BUILD_DIR/Makefile ; then
-            echo '  ------  clean dir:' $dir/$builddir
-	    ( cd $BUILD_DIR ; make CLEAN )
-	fi
+	echo -n '  --- dir:' $BUILD_DIR ': '
+	makeclean $BUILD_DIR
+        rm -f $BUILD_DIR/$EXECUTABLE
 	if test -d $dir/$rundir/CVS ; then
-            echo '  ------  clean dir:' $dir/$rundir
+            echo -n '  --- dir:' $dir/$rundir ': '
 	    run_clean $dir/$rundir
 	fi
-	(
-	    cd $dir
-	    rm -rf tr_run.*
-	)
+	trdir=`( cd $dir ; find . -type d -name "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
 
-    #  Verify that the testdir exists and contains previous 
+    #  Verify that the testdir exists and contains previous
     #  results in the correct location--or skip this directory!
     fout=$dir"/results/"$ref_outp
     if test ! -r $fout ; then
@@ -1147,30 +1255,47 @@
 	echo "can't find \"$dir/input/eedata.mth\" -- skipping $dir"
 	continue
     fi
+    if test "x$MPI" = "xt" -a "x$MULTI_THREAD" = "xt" ; then
+      retv=`check_eedata $CODE_DIR"/SIZE.h_mpi" $dir"/input/eedata.mth"`
+      if test $retv != 0 ; then
+	echo "input/eedata.mth tiling misfit -- skipping $dir"
+	continue
+      fi
+    fi
 
     #  Check whether there are "extra runs" for this testdir
     extra_runs=
-    ex_run_dirs=`( cd $dir ; echo $inputdir.* )`
+    if test "x$NORUN" = xf ; then
+	ex_run_dirs=`( cd $dir ; echo $inputdir.* )`
+    fi
     #echo "ex_run_dirs='$ex_run_dirs'"
     for exd in $ex_run_dirs ; do
 	name=`echo $exd | sed -e "s/$inputdir\.//"`
 	refExOut=`echo $ref_outp | sed "s/\./.${name}./"`
 	outf="$dir/results/$refExOut"
         if test -f $outf -a -r $outf ; then
-	    if test "x$MULTI_THREAD" = "xt" ; then 
-		if test -r $dir"/"$exd"/eedata.mth" ; then
+	  if test "x$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 $dir"/"$exd"/eedata.mth: not found"
+		else
+		    echo $exd"/eedata.mth tiling misfit -- skipping $dir"
 		fi
-	    else
+	      else
 		extra_runs="$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$extra_runs" = "x" ; then 
+    if test "x$extra_runs" = "x" ; then
        echo "Experiment:  $dir"
     else
        echo "Experiment:  $dir ; extra_runs=$extra_runs"
@@ -1180,40 +1305,43 @@
     results=$EMPTY_RESULTS
 
     #  Create an output dir for each OPTFILE/tdir combination
-    rel_CDIR=$DRESULTS"/"$dir
-    mkdir $rel_CDIR
-    CDIR=`pwd`"/$rel_CDIR"
-    
-    if test "x$CLEANUP" = xt ; then
-	echo '====>>> this is to check that we never go through this part <<< ==='
-	makeclean $dir/$builddir \
-	    && run_clean $dir/$rundir
+    locDIR=$DRESULTS"/"$dir
+    mkdir $locDIR
+    CDIR=`pwd`"/$locDIR"
+
+    if test "x$NORUN" = xt ; then
+	    run=N
+	genmakemodel $dir/$builddir && genmake=Y \
+	    && makeclean $dir/$builddir \
+            && symlink_mpifiles $dir $code_dir $builddir \
+	    && makedependmodel $dir/$builddir && makedepend=Y \
+	    && makemodel $dir/$builddir && make=Y
     else
 	genmakemodel $dir/$builddir && genmake=Y \
 	    && makeclean $dir/$builddir \
-	    && run_clean $dir/$rundir \
             && symlink_mpifiles $dir $code_dir $builddir \
 	    && makedependmodel $dir/$builddir && makedepend=Y \
 	    && makemodel $dir/$builddir && make=Y \
-	    && linkdata $dir/$rundir $inputdir input \
+	    && run_clean $dir/$rundir \
+	    && linkdata $dir/$rundir $inputdir \
 	    && runmodel $dir/$rundir && run=Y \
 	    && results=`testoutput_run $dir $rundir $ref_outp`
     fi
-    
-    echo
+    #echo "results='$results'"
+
 	fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
-	echo
+	echo 1>&2
  	echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
-	touch $CDIR"/summary.txt"
-	echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $CDIR"/summary.txt"
-	echo "MACH='$MACH'" >> $CDIR"/summary.txt"
-	echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
-	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	echo "tdir='$dir'" >> $CDIR"/summary.txt"
+	touch $locDIR"/summary.txt"
+	echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $locDIR"/summary.txt"
+	echo "MACH='$MACH'" >> $locDIR"/summary.txt"
+	echo "UNAMEA='$UNAMEA'" >> $locDIR"/summary.txt"
+	echo "DATE='$DATE'" >> $locDIR"/summary.txt"
+	echo "tdir='$dir'" >> $locDIR"/summary.txt"
 	if test "x$ADM" = xt ; then
-	    head -1 $dir/$builddir/taf_ad.log >> $CDIR"/summary.txt"
+	    head -1 $dir/$builddir/taf_ad.log >> $locDIR"/summary.txt"
 	    grep -A3 'Seconds in section "ALL' $dir/$rundir/$OUTPUTFILE \
-				>> $CDIR"/summary.txt"
+				>> $locDIR"/summary.txt"
 	fi
 
 	for ex in $extra_runs ; do
@@ -1222,42 +1350,50 @@
 	    #  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"
+	    locDIR=$DRESULTS"/"$dir"."$ex
+	    mkdir $locDIR
+	    CDIR=`pwd`"/$locDIR"
 	    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
+	    linkdata $dir/tr_run.$ex $inputdir.$ex $inputdir
 	    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.$ex"
-	    echo
+	    echo 1>&2
 	    echo "$fres" | sed 's/ 99/ --/g' | sed 's/  > />/' | sed 's/  < /</' >> $SUMMARY
-	    touch $CDIR"/summary.txt"
-	    echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $CDIR"/summary.txt"
-	    echo "MACH='$MACH'" >> $CDIR"/summary.txt"
-	    echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
-	    echo "DATE='$DATE'" >> $CDIR"/summary.txt"
-	    echo "tdir='$dir.$ex'" >> $CDIR"/summary.txt"
+	    touch $locDIR"/summary.txt"
+	    echo "fresults='$fres'" | sed 's/ 99/ --/g' >> $locDIR"/summary.txt"
+	    echo "MACH='$MACH'" >> $locDIR"/summary.txt"
+	    echo "UNAMEA='$UNAMEA'" >> $locDIR"/summary.txt"
+	    echo "DATE='$DATE'" >> $locDIR"/summary.txt"
+	    echo "tdir='$dir.$ex'" >> $locDIR"/summary.txt"
             if test "x$ADM" = xt ; then
-	        head -1 $dir/$builddir/taf_ad.log >> $CDIR"/summary.txt"
+	        head -1 $dir/$builddir/taf_ad.log >> $locDIR"/summary.txt"
 	        grep -A3 'Seconds in section "ALL' $dir/tr_run.$ex/$OUTPUTFILE \
-			           >> $CDIR"/summary.txt"
+			           >> $locDIR"/summary.txt"
             fi
 	    if test "x$POSTCLEAN" = xt ; then
 		run_clean $dir/tr_run.$ex
 	    fi
 	done
 
+    if test -f $DRESULTS"/"genmake_state ; then : ; else
+	if test -f $dir/$builddir/Makefile ; then
+	    mkOpt=`grep '^# OPTFILE=' $dir/$builddir/Makefile 2>/dev/null | head -1 | sed 's/^# //'`
+	    echo "from '$dir/$builddir/Makefile', extract:" > $DRESULTS/genmake_state
+	    sed -n '/^# executed by:/,+1 p' $dir/$builddir/Makefile >> $DRESULTS/genmake_state
+	    echo $mkOpt >> $DRESULTS/genmake_state
+	fi
+    fi
     #postclean $dir/$builddir
     if test "x$POSTCLEAN" = xt ; then
  	makeclean $dir/$builddir \
  	    && run_clean $dir/$rundir
     fi
-    
+
     echo "-------------------------------------------------------------------------------"
-    
+
 done
 
 printf "Start time:  " >> $SUMMARY
@@ -1286,13 +1422,15 @@
 	    echo "An email containing results was sent to the following addresses:"
 	    echo "  \"$ADDRESSES\""
 	    echo
+	    test -f $DRESULTS".tar"  &&  rm -f $DRESULTS".tar"
+	    test -f $DRESULTS".tar.gz"  &&  rm -f $DRESULTS".tar.gz"
 	fi
-	test -f $DRESULTS".tar"  &&  rm -f $DRESULTS".tar"
-	test -f $DRESULTS".tar.gz"  &&  rm -f $DRESULTS".tar.gz"
     fi
 fi
 
-rm -f tr_cmpnum.c tr_cmpnum
+if test "x$QUICK" = xf -a "x$NORUN" = xf ; then
+    rm -f tr_cmpnum.c tr_cmpnum
+fi
 
 if test "x$CLEANUP" != xt ; then
     cat $SUMMARY | sed 's/ \.  \.  \.  \.  \.  \.  \.  \.  \.  \.  \.  \. //'