--- MITgcm/verification/testreport	2010/04/29 16:58:40	1.139
+++ MITgcm/verification/testreport	2010/11/05 16:45:02	1.148
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.139 2010/04/29 16:58:40 jmc Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.148 2010/11/05 16:45:02 jmc Exp $
 #  $Name:  $
 #
 
@@ -33,6 +33,7 @@
     echo "  (-adm|-ad)               perform an adjoint run"
     echo "  (-oad)                   perform an OpenAD adjoint run"
     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"
@@ -40,7 +41,7 @@
     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)"
@@ -317,6 +318,9 @@
 	(
 	    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
@@ -354,14 +358,14 @@
 	    fi
 	    fi
 	    printf 'genmake ... '
-	    eval $command > make.log 2>&1
+	    eval $command > genmake.tr_log 2>&1
 	    RETVAL=$?
 	    #  Reduce the size of the testing emails!
 	    head -100 Makefile > $CDIR/Makefile_head
 	    if test "x$RETVAL" != x0 ; then
-		tail make.log
+		tail genmake.tr_log
 		echo "genmakemodel: genmake failed"
-		cp genmake_* make.log $CDIR
+		cp genmake.log genmake_* genmake.tr_log $CDIR
 		return 1
 	    else
 		echo "successful"
@@ -373,6 +377,7 @@
 makeclean()
 {
     # makeclean directory
+    if test "x$NODEPEND" = xf ; then rm -f $1/make.tr_log ; fi
     if test "x$NOCLEAN" = xt ; then
 	echo "make Clean skipped!"
     else
@@ -381,12 +386,13 @@
 	    #if test -e $OUTPUTFILE ; then rm -f $OUTPUTFILE ; fi
 	    if test -r Makefile ; then
 		printf 'clean build-dir: make Clean ... '
-		$MAKE Clean >> make.log 2>&1
+		rm -f Makefile.old
+		$MAKE Clean >> make.tr_log 2>&1
 		RETVAL=$?
 		if test "x$RETVAL" != x0 ; then
-		    tail make.log
+		    tail make.tr_log
 		    echo "makeclean: \"make Clean\" failed"
-		    cp make.log $CDIR"/make.log"
+		    cp make.tr_log genmake.log genmake.tr_log $CDIR
 		    return 1
 		fi
 		echo successful
@@ -412,7 +418,7 @@
 	    find . -name "*.data" -exec rm {} \;
 	    find . -name "fort.*" -exec rm {} \;
 	    find . -type l -exec rm {} \;
-	    rm -f $EXECUTABLE *.txt STD* *diagnostics.log datetime
+	    rm -f $EXECUTABLE $RUNLOG *.txt STD* *diagnostics.log datetime
 	    rm -rf mnc_test_*
  	    rm -f *_MIT_CE_000.opt0000 costfunction*0000
 	    echo successful
@@ -430,12 +436,12 @@
 	(
 	    cd $1;
 	    printf 'make depend ... '
-	    $MAKE depend >> make.log 2>&1
+	    $MAKE depend >> make.tr_log 2>&1
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
-		tail make.log
+		tail make.tr_log
 		echo "makedependmodel: make depend failed"
-		cp make.log $CDIR"/make.log"
+		cp make.tr_log genmake.log genmake.tr_log $CDIR
 		return 1
 	    else
 		echo successful
@@ -461,21 +467,21 @@
 	if test -r Makefile ; then
 	    printf 'make ... '
 	    if test "x$ADM" = xt ; then
-		$MAKE adall >> make.log 2>&1
+		$MAKE adall >> make.tr_log 2>&1
 	    elif test "x$OADM" = xt ; then
-		$MAKE adAll >> make.log 2>&1
+		$MAKE adAll >> make.tr_log 2>&1
             else
 		if test "x$JOBS" = x ; then
-		    $MAKE >> make.log 2>&1
+		    $MAKE >> make.tr_log 2>&1
 		else
-		    $MAKE -j $JOBS >> make.log 2>&1
+		    $MAKE -j $JOBS >> make.tr_log 2>&1
 		fi
 	    fi
 	    RETVAL=$?
 	    if test "x$RETVAL" != x0 ; then
-		tail make.log
+		tail make.tr_log
 		echo failed
-		cp make.log $CDIR"/make.log"
+		cp make.tr_log genmake.log genmake.tr_log $CDIR
 		rm -f $EXECUTABLE
 		return 1
 	    else
@@ -829,6 +835,7 @@
 HAVE_MPACK=
 MPACK=
 COMMAND=
+MKDEPEND=
 if test "x$MAKE" = x ; then
     MAKE=make
 fi
@@ -848,7 +855,7 @@
 # list of pTracers to check for monitor output
 PTRACERS_NUM="1 2 3 4 5"
 
-MATCH_CRIT=13
+MATCH_CRIT=10
 
 printf "parsing options...  "
 
@@ -903,6 +910,11 @@
 	-command=* | --command=* | -c=* | --c=*)
 	    COMMAND=$ac_optarg ;;
 
+	-makedepend | --makedepend | -md | --md)
+	    ac_prev=MKDEPEND ;;
+	-makedepend=* | --makedepend=* | -md=* | --md=*)
+	    MKDEPEND=$ac_optarg ;;
+
 	-make | --make | -m | --m)
 	    ac_prev=MAKE ;;
 	-make=* | --make=* | -m=* | --m=*)
@@ -1005,8 +1017,12 @@
     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=" "
@@ -1050,7 +1066,7 @@
     OPTFILE=$MITGCM_OF
 fi
 
-RUNLOG="run.log"
+RUNLOG="run.tr_log"
 OUTPUTFILE=$ref_outp
 if test "x$COMMAND" = x ; then
     COMMAND="./$EXECUTABLE > $OUTPUTFILE"
@@ -1199,6 +1215,7 @@
     builddir="build"
     if test ! -d $dir/$builddir ; then mkdir $dir/$builddir ; fi
     rundir="run"
+    pfxdir="tr_$rundir"
     if test ! -d $dir/$rundir ; then
 	rundir=$builddir
     fi
@@ -1209,12 +1226,16 @@
     if test "x$CLEANUP" = xt ; then
 	echo -n '  --- dir:' $BUILD_DIR ': '
 	makeclean $BUILD_DIR
-        rm -f $BUILD_DIR/$EXECUTABLE
+	(   cd $BUILD_DIR
+	    rm -f $EXECUTABLE *.bak
+	    rm -f genmake_state genmake_*optfile genmake.log
+	    rm -f genmake.tr_log make.tr_log
+	)
 	if test -d $dir/$rundir/CVS ; then
             echo -n '  --- dir:' $dir/$rundir ': '
 	    run_clean $dir/$rundir
 	fi
-	trdir=`( cd $dir ; find . -type d -name "tr_run.*" -print | sed 's/^.\///')`
+	trdir=`( cd $dir ; find . -type d -name "$pfxdir.*" -print | sed 's/^.\///')`
 	ttd=`echo $trdir | wc -w`
 	if test $ttd != 0 ; then
 	    echo '  --- rm dir:' $trdir
@@ -1309,7 +1330,7 @@
 	    && makedependmodel $dir/$builddir && makedepend=Y \
 	    && makemodel $dir/$builddir && make=Y \
 	    && run_clean $dir/$rundir \
-	    && linkdata $dir/$rundir $inputdir input \
+	    && linkdata $dir/$rundir $inputdir \
 	    && runmodel $dir/$rundir && run=Y \
 	    && results=`testoutput_run $dir $rundir $ref_outp`
     fi
@@ -1339,11 +1360,11 @@
 	    locDIR=$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
-	    runmodel $dir/tr_run.$ex && run=Y \
-	    && results=`testoutput_run $dir tr_run.$ex $refExOut`
+	    test ! -e "$dir/$pfxdir.$ex" && mkdir "$dir/$pfxdir.$ex"
+	    run_clean $dir/$pfxdir.$ex
+	    linkdata $dir/$pfxdir.$ex $inputdir.$ex $inputdir
+	    runmodel $dir/$pfxdir.$ex && run=Y \
+	    && results=`testoutput_run $dir $pfxdir.$ex $refExOut`
 	    fres=`formatresults $dir ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N} $results`
 	    fres="$fres.$ex"
 	    echo 1>&2
@@ -1356,11 +1377,11 @@
 	    echo "tdir='$dir.$ex'" >> $locDIR"/summary.txt"
             if test "x$ADM" = xt ; then
 	        head -1 $dir/$builddir/taf_ad.log >> $locDIR"/summary.txt"
-	        grep -A3 'Seconds in section "ALL' $dir/tr_run.$ex/$OUTPUTFILE \
+	        grep -A3 'Seconds in section "ALL' $dir/$pfxdir.$ex/$OUTPUTFILE \
 			           >> $locDIR"/summary.txt"
             fi
 	    if test "x$POSTCLEAN" = xt ; then
-		run_clean $dir/tr_run.$ex
+		run_clean $dir/$pfxdir.$ex
 	    fi
 	done