--- MITgcm/verification/testreport	2004/12/01 16:59:42	1.52
+++ MITgcm/verification/testreport	2005/02/04 16:41:42	1.66
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.52 2004/12/01 16:59:42 edhill Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/verification/testreport,v 1.66 2005/02/04 16:41:42 edhill Exp $
 #  $Name:  $
 #
 
@@ -294,6 +294,9 @@
 	    if test "x$IEEE" != x ; then
 		command="$command -ieee"
 	    fi
+	    if test "x$MPI" = xt ; then
+		command="$command -mpi"
+	    fi
 	    printf 'genmake ... ' 1>&2
 	    $command > make.log 2>&1
 	    RETVAL=$?
@@ -450,7 +453,7 @@
 	    if test "x$ADM" = x ; then
 		files=`( cd ../input ; ls -1 | grep -v CVS )`
 		for i in $files ; do
-		    if test ! -d "../input/"$i ; then
+		    if test ! -d "../input/"$i -a ! -f $i ; then
 			ln -sf "../input/"$i $i
 		    fi
 		done
@@ -520,7 +523,7 @@
 int main( int argc, char** argv )  {
   int linnum,best,lncnt;
   double a,b,abave,relerr;
-  best = -16;
+  best = -22;
   lncnt = 0;
   while( 1 & (lncnt+=1) < 999 )  {
     scanf("%d", &linnum);
@@ -529,13 +532,9 @@
     abave = 0.5*(fabs(a)+fabs(b));
     if (abave > 0.0) {
       relerr=fabs(a-b)/abave;
-      if (relerr > 0.0) {
-        linnum = (int)log10(relerr);
-        best = (best > linnum) ? best : linnum;
-      }
-    }
-    else {
-      if (best == -16 && abave != 0)  best = -22;
+      if (relerr > 0.0) { linnum = (int)rint(log10(relerr)); }
+      else { linnum = -16 ; }
+      best = (best > linnum) ? best : linnum;
     }
   }
   if (lncnt == 999) best=-29;
@@ -543,14 +542,15 @@
   return 0;
 }
 EOF
-    cc -o tmp_cmpnum tmp_cmpnum.c -lm
+    $CC -o tmp_cmpnum tmp_cmpnum.c -lm
 
     if [ -x ./tmp_cmpnum ]; then
 	echo "OK"
 	return 0
     else
 	echo
-	echo "ERROR: failed to compile comparison code" 
+	echo "ERROR: failed to compile comparison code -- please specify" 
+	echo "  a C compiler using the CC environment variable."
 	exit 1
     fi
 }
@@ -639,7 +639,12 @@
 HAVE_MPACK=
 MPACK="$MPACKDIR/mpack"
 COMMAND=
-MAKE=make
+if test "x$MAKE" = x ; then
+    MAKE=make
+fi
+if test "x$CC" = x ; then
+    CC=cc
+fi
 JOBS=
 MPI=f
 DELDIR=
@@ -873,6 +878,10 @@
 	if test -r $dir/input/Makefile ; then
 	    ( cd $dir/input ; make CLEAN )
 	fi
+	(
+	    cd $dir
+	    rm -rf tr_run.*
+	)
 	continue
     fi
 
@@ -881,7 +890,6 @@
     fout=
     if test "x$ADM" = x ; then
 	fout=$dir"/results/output.txt"
-	check_for_add_mon_output  $fout
     else
 	fout=$dir"/results_ad/output.txt_adm"
     fi
@@ -889,6 +897,9 @@
 	echo "can't read \"$fout\" -- skipping $dir"
 	continue
     fi
+    if test "x$ADM" = x ; then
+	check_for_add_mon_output  $fout
+    fi
 
     # Check for additional types of monitor output
 
@@ -966,27 +977,39 @@
 	echo "DATE='$DATE'" >> $CDIR"/summary.txt"
 	echo "tdir='$dir'" >> $CDIR"/summary.txt"
 
-	OLD_COMMAND=$COMMAND
-	COMMAND="./mitgcmuv > output.txt"
 	for ex in $extra_runs ; do
-	    test -e "$dir/tr_run.$ex" && rm -rf "$dir/tr_run.$ex"
-	    mkdir "$dir/tr_run.$ex"
-	    links=`( cd "$dir/input" > /dev/null 2>&1 ; ls -1 | grep -v CVS )`
+	    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/$ldir" > /dev/null 2>&1
+		ls -1 Makefile *.[fFhco] mitgcmuv  2>/dev/null \
+		    | sed -e 's|^CVS$||g' | sed -e 's|^output.txt$||g'
+	    ) > tr_exrun_links
 	    (
 		cd "$dir/tr_run.$ex"
-		for i in $links; do
-		    ln -s ../input/$i $i
-		done
-	    )
-	    links=`( cd "$dir/input.$ex" > /dev/null 2>&1 ; ls -1 | grep -v CVS )`
-	    ( 
-		cd "$dir/tr_run.$ex"
-		for i in $links; do
-		    test -e $i  &&  rm -f $i
-		    ln -s ../input.$ex/$i $i
-		done
-		ln -s ../$builddir/mitgcmuv mitgcmuv
+		    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
 	    runmodel $dir/tr_run.$ex && run=Y \
 		&& results=`testoutput $dir tr_run.$ex "."$ex`
 	    fres=`printf '%s %s %s %s' ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N}`
@@ -1000,7 +1023,6 @@
 	    echo "DATE='$DATE'" >> $CDIR"/summary.txt"
 	    echo "tdir='$dir'" >> $CDIR"/summary.txt"
 	done
-	COMMAND=$OLD_COMMAND
     else
 	fres=`printf '%s %s %s %s' ${genmake:-N} ${makedepend:-N} ${make:-N} ${run:-N}`
 	fres=$fres"$results   $dir"
@@ -1053,11 +1075,11 @@
 rm -f tmp_cmpnum.c tmp_cmpnum
 
 if test "x$CLEANUP" != xt ; then
-    cat $SUMMARY
+    cat $SUMMARY | sed 's/ -- -- -- --//g'
     if test -e tr_out.txt ; then
         mv tr_out.txt tr_out.txt.old
     fi
-    cat $SUMMARY > tr_out.txt
+    cat $SUMMARY | sed 's/ -- -- -- --//g' > tr_out.txt
 fi
 
 if test "x$DELDIR" = xt ; then