--- MITgcm/verification/testreport	2006/03/20 21:50:36	1.77
+++ MITgcm/verification/testreport	2007/01/31 21:28:34	1.90
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.77 2006/03/20 21:50:36 jmc Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.90 2007/01/31 21:28:34 ce107 Exp $
 #  $Name:  $
 #
 
@@ -11,14 +11,18 @@
     echo
     echo "where possible OPTIONS are:"
     echo "  (-help|-h)               print usage"
-    echo "  (-mpi)                   use MPI input files"
+    echo "  (-mth)                   run multi threaded (using eedata.mth)"
+    echo "  (-mpi)                   compile and run using MPI"
     echo "  (-ieee|-noieee)          if possible, use IEEE compiler flags"
     echo "                             (DEF=\"-ieee\")"
-    echo "  (-optfile=|-of=)STRING   list of optfiles to use"
+    echo "  (-of=|-optfile=)STRING   list of optfiles to use"
     echo "  (-a|-addr) STRING        list of email recipients"
     echo "                             (DEF=\"edhill@mitgcm.org\")"
-    echo "  (-t|-tdir) STRING        list of test dirs to use"
-    echo "                             (DEF=\"\" which builds all)"
+    echo "  (-t|-tdir) STRING        list of group and/or exp. dirs to test"
+    echo "                             (recognized groups: basic, tutorials)"
+    echo "                             (DEF=\"\" which test all)"
+    echo "  (-skd|-skipdir) STRING   list of exp. dirs to skip"
+    echo "                             (DEF=\"\" which test all)"
     echo "  (-b|-bash) STRING        preferred location of a \"bash\" or"
     echo "                             Bourne-compatible \"sh\" shell"
     echo "                             (DEF=\"\" for \"bash\")"
@@ -29,7 +33,7 @@
     echo "                             (DEF=\"make\")"
     echo "  (-odir) STRING           used to build output directory name"
     echo "                             (DEF=\"hostname\")"
-    echo "  (-ptracers|-ptr) STRING  specify which ptracers to test"
+    echo "  (-ptr|-ptracers) STRING  specify which ptracers to test"
     echo "                             (DEF=\"1 2 3 4 5\")"
     echo "  (-j) JOBS                use \"make -j JOBS\" for parallel builds"
     echo "  (-clean)                 *ONLY* run \"make CLEAN\""
@@ -38,6 +42,9 @@
     echo "  (-noclean|-nc)           skip the \"make clean\" stage"
     echo "  (-nodepend|-nd)          skip the \"make depend\" stage"
     echo "  (-deldir|-dd)            on success, delete the output directory"
+    echo "  (-ts)                    provide timing information per timestep"
+    echo "  (-papis)                 provide MFlop/s per timestep using PAPI"
+    echo "  (-pcls)                  provide MFlop/s per timestep using PCL"
     echo
     echo "and where STRING can be a whitespace-delimited list"
     echo "such as:"
@@ -89,14 +96,14 @@
 {
     # testoutput_for_prop dir s1 label subdir extension
     #
-    #  compares files in $dir/$subdir/output.txt and $dir/results/output.txt
+    #  compares files $dir/$subdir/$OUTPUTFILE and $dir/results/output.txt
     #  using search strings s1 and text label 
 
     if [ $debug -gt 0 ]; then
-	echo testoutput_for_prop: grep "$2" $1/$4/output.txt 1>&2
+	echo testoutput_for_prop: grep "$2" $1/$4/$OUTPUTFILE 1>&2
     fi
-    if [ -r $1/$4/output.txt ]; then
-	grep "$2" $1/$4/output.txt | sed 's/.*=//' | cat -n > tmp1.txt
+    if [ -r $1/$4/$OUTPUTFILE ]; then
+	grep "$2" $1/$4/$OUTPUTFILE | sed 's/.*=//' | cat -n > tmp1.txt
 	lncntA=`wc -l tmp1.txt | awk '{print $1}' `
 	if [ $lncntA -lt 3 ]; then
 	    if [ $verbose -gt 0 ]; then
@@ -105,13 +112,13 @@
 	    return 99
 	fi
     else
-	echo testoutput_for_prop: output.txt from model run was not readable 1>&2
+	echo testoutput_for_prop: $OUTPUTFILE from model run was not readable 1>&2
 	return 99
     fi
     if [ $debug -gt 0 ]; then
-	echo testoutput_for_prop: grep "$2" $1/results/output.txt$5 1>&2
+	echo testoutput_for_prop: grep "$2" $1/results/output.$5 1>&2
     fi
-    grep "$2" $1/results/output.txt$5 | sed 's/.*=//' | cat -n > tmp2.txt
+    grep "$2" $1/results/output.$5 | sed 's/.*=//' | cat -n > tmp2.txt
     lncntB=`wc -l tmp2.txt | awk '{print $1}' `
     if [ $lncntB -lt 3 ]; then
 	if [ $verbose -gt 0 ]; then
@@ -127,12 +134,12 @@
     fi
     has_nan=`cat tmp1.txt | grep -i nan | wc -l`
     if [ $has_nan -gt 0  ] ; then
-	echo testoutput_for_prop: output.txt contains $has_nan NaN values  1>&2
+	echo testoutput_for_prop: $OUTPUTFILE contains $has_nan NaN values  1>&2
 	return 99
     fi
     has_inf=`cat tmp1.txt | grep -i inf | wc -l`
     if [ $has_inf -gt 0  ] ; then
-	echo testoutput_for_prop: output.txt contains $has_inf Inf values  1>&2
+	echo testoutput_for_prop: $OUTPUTFILE contains $has_inf Inf values  1>&2
 	return 99
     fi
     if [ $debug -gt 0 ]; then
@@ -181,10 +188,10 @@
 
 testoutput_ad()
 {
-    grep $3 $1/results_ad/output.txt_adm | awk '{print NR " " $5}' > t05.txt
-    grep $3 $1/$2/output.txt_adm | awk '{print NR " " $5}' > t15.txt
-    grep $3 $1/results_ad/output.txt_adm | awk '{print NR " " $6}' > t06.txt
-    grep $3 $1/$2/output.txt_adm | awk '{print NR " " $6}' > t16.txt
+    grep $3 $1/results_ad/output_adm.txt | awk '{print NR " " $5}' > t05.txt
+    grep $3 $1/$2/$OUTPUTFILE | awk '{print NR " " $5}' > t15.txt
+    grep $3 $1/results_ad/output_adm.txt | awk '{print NR " " $6}' > t06.txt
+    grep $3 $1/$2/$OUTPUTFILE | awk '{print NR " " $6}' > t16.txt
     join t05.txt t15.txt > t5.txt
     join t06.txt t16.txt > t6.txt
     echo "-1" >> t5.txt
@@ -304,7 +311,6 @@
 		command="$command --mods=../code"
 	    else
 		command="$command --mods=../code_ad"
-		command="$command -adof=../../../tools/adjoint_options/adjoint_staf"
 	    fi
 	    if test "x$OPTFILE" != xNONE ; then
 		command="$command --optfile=$OPTFILE"
@@ -315,6 +321,16 @@
 	    if test "x$MPI" = xt ; then
 		command="$command -mpi"
 	    fi
+	    if test "x$TS" = xt ; then
+		command="$command -ts"
+	    fi
+	    if test "x$PAPIS" = xt ; then
+		command="$command -papis"
+	    else 
+	    if test "x$PCLS" = xt ; then
+		command="$command -pcls"
+	    fi
+	    fi
 	    printf 'genmake ... ' 1>&2
 	    $command > make.log 2>&1
 	    RETVAL=$?
@@ -336,20 +352,18 @@
 {
     # makeclean directory
     if test "x$NOCLEAN" = xt ; then
-	echo "make CLEAN skipped!"
+	echo "make Clean skipped!"
     else
 	(
 	    cd $1;
-	    if test -e output.txt ; then
-		rm -f output.txt
-	    fi
-	    printf 'make CLEAN ... ' 2>&1
+	    #if test -e $OUTPUTFILE ; then rm -f $OUTPUTFILE ; fi
 	    if test -r Makefile ; then
-		$MAKE CLEAN >> make.log 2>&1
+		printf 'clean build-dir: make Clean ... ' 2>&1
+		$MAKE Clean >> make.log 2>&1
 		RETVAL=$?
 		if test "x$RETVAL" != x0 ; then
 		    tail make.log
-		    echo "makeclean: \"make CLEAN\" failed" 1>&2
+		    echo "makeclean: \"make Clean\" failed" 1>&2
 		    cp make.log $CDIR"/make.log"
 		    return 1
 		fi
@@ -360,15 +374,23 @@
     fi
 }
 
-postclean()
+run_clean()
 {
-    # postclean directory
-    if test "x$POSTCLEAN" = xt ; then
+    # run_clean directory
+    if test "x$NOCLEAN" = xt ; then
+	echo "run_clean skipped!"
+    else
 	(
 	    cd $1;
-	    if test -r Makefile ; then
-		$MAKE CLEAN >> /dev/null 2>&1
-	    fi
+	    printf 'clean run-dir ... ' 2>&1
+	    # part of what is done after "make clean" when doing "make CLEAN"
+	    find . -name "*.meta" -exec rm {} \;
+	    find . -name "*.data" -exec rm {} \;
+	    find . -name "fort.*" -exec rm {} \;
+	    find . -type l -exec rm {} \;
+	    rm -f $EXECUTABLE *.txt STD* *diagnostics.log datetime
+	    rm -rf mnc_test_*
+	    echo successful 1>&2
 	    exit 0
 	)
     fi
@@ -476,33 +498,44 @@
 
 linkdata()
 {
-    # linkdata flag
+    # linkdata run_dir input_dir_1 input_dir_2 ...
     #
     # symbolically link data files to run directory
-    if test "x$1" = x1 ; then
+    if test -d $1 ; then
 	(
-	    cd $2
-	    if test "x$ADM" = x ; then
-		files=`( cd ../input ; ls -1 | grep -v CVS )`
-		for i in $files ; do
-		    if test ! -d "../input/"$i -a ! -f $i ; then
-			ln -sf "../input/"$i $i
+	    cd $1 ; shift
+	    if test -r "../"$1"/eedata.mth" ; then
+	    # found eedata.mth in 1rst input dir and it is readable
+		if test "x$MULTI_THREAD" = "xt" ; then
+		# multi-threaded test: remove symbolic link & link eedata.mth
+		    if test -h eedata ; then rm -f eedata ; fi
+		    if test ! -r eedata ; then 
+			ln -sf "../"$1"/eedata.mth" eedata ;
+			printf 'eedata.mth ' 1>&2
 		    fi
-		done
-	    else
-		files=`( cd ../input ; ls -1 *.bin | grep -v CVS )`
-		for i in $files ; do
-		    if test ! -d "../input/"$i ; then
-			ln -sf "../input/"$i $i
-		    fi
-		done
-		files=`( cd ../input_ad ; ls -1 | grep -v CVS )`
-		for i in $files ; do
-		    if test ! -d "../input_ad/"$i ; then
-			ln -sf "../input_ad/"$i $i
-		    fi
-		done
+		else
+		# not multi-threaded test: remove eedata symbolic link
+		    if test -h eedata ; then rm -f eedata ; fi
+		fi
 	    fi
+	    for ldir in $* ; do
+		if test -d "../"$ldir ; then
+                    printf 'ldir='${ldir} 1>&2
+		    files=`( cd "../"$ldir ; ls -1 | grep -v CVS )`
+		    for i in $files ; do
+			if test ! -d "../"$ldir/$i ; then
+			    if test ! -r $i  ; then
+				printf ' '$i 1>&2
+				ln -sf "../"$ldir"/"$i $i
+			    fi
+			fi
+		    done
+		    if test -x "../"$ldir"/"prepare_run ; then
+			"../"$ldir"/"prepare_run
+		    fi
+		    printf ' ; ' 1>&2
+		fi
+	    done
 	)
     fi
 }
@@ -518,30 +551,48 @@
 	printf 'runmodel in %s ...' $1 1>&2
 	# make output.txt
 	echo
-	rm -f run.log
-        if test $OUTPUTFILE -ot $EXECUTABLE ; then
-	   ( eval $COMMAND ) > run.log 2>&1
-	   RETVAL=$?
+        if test ! -x $EXECUTABLE -a -x "../"$builddir"/"$EXECUTABLE ; then
+	    echo " link" $EXECUTABLE "from dir ../"$builddir > run.log_00
+	    ln -sf "../"$builddir"/"$EXECUTABLE .
+	fi
+        if test ! -x $EXECUTABLE ; then
+		rm -f run.log ; touch run.log
+		if test -f run.log_00 ; then cat run.log_00 >> run.log ; fi
+		echo " no executable:" $EXECUTABLE >> run.log
+		RETVAL=8
+		ENDVAL=-1
 	else
-           echo " $OUTPUTFILE is up to date " > run.log 2>&1
-	   RETVAL=0
+            if test $OUTPUTFILE -ot $EXECUTABLE ; then
+		rm -f run.log ; touch run.log
+		if test -f run.log_00 ; then cat run.log_00 >> run.log ; fi
+		( eval $COMMAND ) >> run.log 2>&1
+		RETVAL=$?
+	    else
+		RETVAL=0
+		if test -f run.log ; then
+		    if test -f run.log_00 ; then cat run.log_00 >> run.log ; fi
+     		    echo "---------->> $OUTPUTFILE is up to date " >> run.log 2>&1
+		else 
+		    touch run.log
+		    if test -f run.log_00 ; then cat run.log_00 >> run.log ; fi
+     		    echo "---------->> $OUTPUTFILE is up to date " >> run.log 2>&1
+     		    echo " no previous run.log: assume NORMAL END" >> run.log 2>&1
+		fi
+	    fi
+	    ENDVAL=`cat run.log | grep -v 'ABNORMAL END' | grep -c 'NORMAL END'`
 	fi
-	# echo "COMMAND='$COMMAND'"
-	# echo "pwd='"`pwd`"'"
-	if test "x$RETVAL" = x0 ; then
+	rm -f run.log_00
+	#if test "x$RETVAL" = x0 ; then
+	if [ $RETVAL -eq 0 -a $ENDVAL -gt 0 ] ; then
 	    tail run.log
 	    echo successful 1>&2
 	    # === Reduce the size of the testing emails!
-	    # if test "x$ADM" = x ; then
-	    #   cp output.txt $CDIR"/output.txt"
-	    # else
-	    #   cp output.txt_adm $CDIR"/output.txt_adm"
-	    # fi
+	    #cp $OUTPUTFILE $CDIR"/"$OUTPUTFILE
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 0
 	else
 	    tail run.log
-	    echo failed 1>&2
+	    echo failed '(run:' $RETVAL ' end:' $ENDVAL ')' 1>&2
 	    cp run.log $CDIR"/run.log"
             if test -s STDERR.0000 ; then cp STDERR.0000 $CDIR"/STDERR.0000" ; fi
 	    return 1
@@ -615,33 +666,14 @@
     
 }
 
-show_help()
-{
-    cat - << EOF
-$0 [-help] [-quick] [-verbose] dir1 [dir2] [...]
-
- -help|-h      Show this help message
- -quiet     Reduce the amount of output
- -verbose   Produce copious amounts of output
- -debug     Produce even more output which will mean nothing to most
- -force     Do "make CLEAN" before compiling. This forces a complete rebuild.
- -clean     Do "make CLEAN" after compiling and testing.
- -cleanup   Aggresively removes all model output, executables and object files
-            and then exits. Use with care.
-
-Normal usage:
- $0 *       Configure, compile, run and analyze in all experiment directories
-EOF
-}
-
 scandirs()
 {
-    if [ $# -eq 0 ]; then
-	for arg in * ; do
-	    test -d $arg/input && echo $arg
-	done
+    if [ $# -eq 1 ]; then
+ 	for arg in * ; do
+ 	    test -d $arg/$1 && echo $arg
+ 	done
     else
-	echo $*
+ 	echo $*
     fi
 }
 
@@ -673,6 +705,7 @@
 OPTFILE=NONE
 ADDRESSES=
 TESTDIRS=
+SKIPDIRS=
 MPACKDIR="../tools/mpack-1.6"
 HAVE_MPACK=
 MPACK="$MPACKDIR/mpack"
@@ -685,6 +718,7 @@
 fi
 JOBS=
 MPI=f
+MULTI_THREAD=f
 OUTDIR=
 DELDIR=
 
@@ -727,6 +761,11 @@
         -tdir=* | --tdir=*)
             TESTDIRS=$ac_optarg ;;
 
+	-skipdir | --skipdir | -skd | --skd)
+            ac_prev=SKIPDIRS ;;
+        -skipdir=* | --skipdir=*)
+            SKIPDIRS=$ac_optarg ;;
+
 	-bash | --bash | -b | --b)
             ac_prev=BASH ;;
         -bash=* | --bash=*)
@@ -772,6 +811,8 @@
 
 	-mpi) MPI=t ;;
 
+	-mth) MULTI_THREAD=t ;;
+
 	-adm | -ad) ADM=t ;;
 
 	-ieee) IEEE=true ;;
@@ -783,6 +824,12 @@
 
 	-deldir | -dd) DELDIR=t ;;
 
+	-ts) TS=t;;
+
+	-papis) PAPIS=t;;
+
+	-pcls) PCL=t;;
+
         -*)
             echo "Error: unrecognized option: "$ac_option
             usage
@@ -804,8 +851,49 @@
 fi
 
 if test "x$TESTDIRS" = x ; then
-    TESTDIRS=`scandirs`
+    if test "x$ADM" = xt ; then
+	LIST=`scandirs results_ad`
+    else
+	LIST=`scandirs results`
+    fi
+else
+    #- expand group of experiments:
+    LIST=" "
+    for xx in $TESTDIRS
+    do
+      case $xx in
+	'basic') LIST=${LIST}" aim.5l_cs hs94.128x64x5 ideal_2D_oce"
+		 LIST=${LIST}" lab_sea tutorial_baroclinic_gyre"
+		 LIST=${LIST}" tutorial_global_oce_latlon tutorial_plume_on_slope"
+		;;
+	'tutorials')
+		 LIST=${LIST}" "`ls | grep 'tutorial_'` ;;
+	*)	 LIST=${LIST}" "$xx ;;
+      esac
+    done 
 fi
+#echo 'LIST='${LIST}'<'
+#- skip dirs, remove duplicate and non-directory:
+TESTDIRS=" "
+count=0
+for xx in $LIST
+do
+    yy=`echo $SKIPDIRS | grep -c $xx`
+    if test $yy = 0 ; then
+	if test -d $xx ; then
+	    yy=`echo $TESTDIRS | grep -c $xx`
+	    if test $yy = 0 ; then TESTDIRS=${TESTDIRS}" "$xx ; fi
+	else count=1 ;
+	    echo ""; echo -n " -- skip \"$xx\" (not a directory !)"
+	fi
+    else
+        if test $count = 1 ; then echo -n ", \"$xx\""
+	else count=1 ; echo "" ;  echo -n " skip: \"$xx\""
+	fi
+    fi
+done 
+if test $count = 1 ; then echo "" ; echo -n " ... " ; fi
+#echo 'TESTDIRS='${TESTDIRS}'<'
 
 if test "x$OPTFILE" = xNONE -a "x$MITGCM_OF" != x ; then
     OPTFILE=$MITGCM_OF
@@ -813,19 +901,18 @@
 
 if test "x$ADM" = xt ; then
     EXECUTABLE="mitgcmuv_ad"
-    OUTPUTFILE="output.txt_adm"
+    OUTPUTFILE="output_adm.txt"
 else
     EXECUTABLE="mitgcmuv"
     OUTPUTFILE="output.txt"
 fi
 
-if test "x$ADM" = xt -a "x$COMMAND" = x ; then
-    COMMAND="./$EXECUTABLE > $OUTPUTFILE"
-fi
-
 if test "x$COMMAND" = x ; then
     COMMAND="./$EXECUTABLE > $OUTPUTFILE"
 fi
+if test "x$MPI" = xt ; then
+    OUTPUTFILE="STDOUT.0000"
+fi
 
 #echo "OK"
 echo "OK (COMMAND= $COMMAND )"
@@ -932,10 +1019,12 @@
     #  Cleanup only!
     if test "x$CLEANUP" = xt ; then
 	if test -r $dir/build/Makefile ; then
+            echo '  ------  clean dir:' $dir/build
 	    ( cd $dir/build ; make CLEAN )
 	fi
-	if test -r $dir/input/Makefile ; then
-	    ( cd $dir/input ; make CLEAN )
+	if test -d $dir/run/CVS ; then
+            echo '  ------  clean dir:' $dir/run
+	    run_clean $dir/run
 	fi
 	(
 	    cd $dir
@@ -950,7 +1039,7 @@
     if test "x$ADM" = x ; then
 	fout=$dir"/results/output.txt"
     else
-	fout=$dir"/results_ad/output.txt_adm"
+	fout=$dir"/results_ad/output_adm.txt"
     fi
     if test ! -r $fout ; then
 	echo "can't read \"$fout\" -- skipping $dir"
@@ -962,36 +1051,22 @@
 
     # Check for additional types of monitor output
 
-    builddir="input"
-    rundir="input"
-    use_seperate_build=0
-    if test -d $dir/build -a -r $dir/build ; then
-	builddir="build"
-	rundir="build"
-	use_seperate_build=1
-	linkdata $use_seperate_build $dir/$rundir
+    builddir="build"
+    if test ! -d $dir/$builddir ; then mkdir $dir/$builddir ; fi
+    rundir="run"
+   #rundir=$builddir
+    if test ! -d $dir/$rundir ; then
+	rundir=$builddir
     fi
     
-    #  Check whether there are "extra runs" for this testdir
-    extra_runs=
-    if test "x$ADM" = x -a "x$use_seperate_build" = x1 ; then
-	ex_run_dirs=`( cd $dir ; echo input.* )`
-	echo "ex_run_dirs='$ex_run_dirs'"
-	for exd in $ex_run_dirs ; do
-	    name=`echo $exd | sed -e 's/input.//g'`
-	    outf="$dir/results/output.txt.$name"
-	    if test -f $outf -a -r $outf ; then
-		extra_runs="$extra_runs $name"
-	    fi
-	done
-    fi
-
     if test "x$ADM" = x ; then
 	code_dir=code
 	CODE_DIR=$dir/code
+        input_dirs='input'
     else
 	code_dir=code_ad
 	CODE_DIR=$dir/code_ad
+        input_dirs='input_ad input'
     fi
     BUILD_DIR=$dir/$builddir
 
@@ -999,10 +1074,39 @@
 	echo "can't find \"$CODE_DIR/SIZE.h_mpi\" -- skipping $dir"
 	continue
     fi
+    if test ! -r $dir"/input/eedata.mth" -a "x$MULTI_THREAD" = "xt" ; then
+	echo "can't find \"$dir/input/eedata.mth\" -- skipping $dir"
+	continue
+    fi
+
+    #  Check whether there are "extra runs" for this testdir
+    extra_runs=
+    if test "x$ADM" = x ; then
+	ex_run_dirs=`( cd $dir ; echo input.* )`
+	#echo "ex_run_dirs='$ex_run_dirs'"
+	for exd in $ex_run_dirs ; do
+	    name=`echo $exd | sed -e 's/input.//g'`
+	    outf="$dir/results/output.$name.txt"
+            if test -f $outf -a -r $outf ; then
+		if test "x$MULTI_THREAD" = "xt" ; then 
+		    if test -r $dir"/"$exd"/eedata.mth" ; then
+			extra_runs="$extra_runs $name"
+		    #else echo $dir"/"$exd"/eedata.mth: not found"
+		    fi
+		else
+		    extra_runs="$extra_runs $name"
+		fi
+	    fi
+	done
+    fi
 
     echo "-------------------------------------------------------------------------------"
     echo
-    echo "Experiment:  $dir"
+    if test "x$extra_runs" = "x" ; then 
+       echo "Experiment:  $dir"
+    else
+       echo "Experiment:  $dir ; extra_runs=$extra_runs"
+    fi
     echo
     unset genmake makedepend make run
     results='-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --'
@@ -1013,16 +1117,19 @@
     CDIR=`pwd`"/$rel_CDIR"
     
     if test "x$CLEANUP" = xt ; then
-	makeclean $dir/$builddir
+	echo '====>>> this is to check that we never go through this part <<< ==='
+	makeclean $dir/$builddir \
+	    && run_clean $dir/$rundir
     else
 	genmakemodel $dir/$builddir && genmake=Y \
 	    && makeclean $dir/$builddir \
+	    && run_clean $dir/$rundir \
             && symlink_mpifiles $dir $code_dir $builddir \
 	    && makedependmodel $dir/$builddir && makedepend=Y \
 	    && makemodel $dir/$builddir && make=Y \
-	    && linkdata $use_seperate_build $dir/$rundir \
+	    && linkdata $dir/$rundir $input_dirs \
 	    && runmodel $dir/$rundir && run=Y \
-	    && results=`testoutput $dir $rundir`
+	    && results=`testoutput $dir $rundir "txt"`
     fi
     
     echo
@@ -1044,29 +1151,10 @@
 	    mkdir $rel_CDIR
 	    CDIR=`pwd`"/$rel_CDIR"
 	    test ! -e "$dir/tr_run.$ex" && mkdir "$dir/tr_run.$ex"
-	    for ldir in input.$ex input ; do
-		(
-		    cd "$dir/$ldir" > /dev/null 2>&1
-		    ls -1 2>/dev/null \
-			| sed -e 's|^CVS$||g' | sed -e 's|^output.txt$||g'
-		) > tr_exrun_links
-		(
-		    cd "$dir/tr_run.$ex"
-		    cat ../../tr_exrun_links | while read i ; do
-			if test ! "x$i" = x ; then
-			    test ! -r $i  &&  ln -s "../"$ldir"/"$i $i
-			fi
-		    done
-		)
-		test -e tr_exrun_links  &&  rm -f tr_exrun_links
-	    done
-	    ldir=build
-	    (
-		cd $dir/tr_run.$ex
-		test ! -e mitgcmuv  &&  ln -s "../"$ldir"/"mitgcmuv .
-	    )
+ 	    run_clean $dir/tr_run.$ex
+            linkdata $dir/tr_run.$ex input.$ex input
 	    runmodel $dir/tr_run.$ex && run=Y \
-		&& results=`testoutput $dir tr_run.$ex "."$ex`
+		&& results=`testoutput $dir tr_run.$ex ${ex}".txt"`
 	    fres=`printf '%s %s %s %s' ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N}`
 	    fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
 	    fres="$fres.$ex"
@@ -1077,6 +1165,9 @@
 	    echo "UNAMEA='$UNAMEA'" >> $CDIR"/summary.txt"
 	    echo "DATE='$DATE'" >> $CDIR"/summary.txt"
 	    echo "tdir='$dir.$ex'" >> $CDIR"/summary.txt"
+	    if test "x$POSTCLEAN" = xt ; then
+ 		run_clean $dir/tr_run.$ex
+	    fi
 	done
     else
 	fres=`printf '%s %s %s %s' ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N}`
@@ -1092,7 +1183,11 @@
 			   >> $CDIR"/summary.txt"
     fi
 
-    postclean $dir/$builddir
+    #postclean $dir/$builddir
+    if test "x$POSTCLEAN" = xt ; then
+ 	makeclean $dir/$builddir \
+ 	    && run_clean $dir/$rundir
+    fi
     
     echo "-------------------------------------------------------------------------------"