diff --git a/regtests/bin/matrix.comp b/regtests/bin/matrix.comp
index 65a4050250..6a4acc294b 100755
--- a/regtests/bin/matrix.comp
+++ b/regtests/bin/matrix.comp
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 # --------------------------------------------------------------------------- #
 # matrix.comp Compare output of matrix for two model versions.                #
 #                                                                             #
@@ -111,13 +111,7 @@
 # 3.  Looping over work directories                                           #
 # --------------------------------------------------------------------------- #
 
-        cases=$(find . -maxdepth 1 -type d -name "work*" | grep -v work_oasis)
-        # skip to next tst if no work directory
-        echo 'run : ' $cases
-        if [ -z "$cases" ] ; then 
-          echo "skip"
-          continue
-        fi
+        cases=$(find . -maxdepth 1 -type d -name "work*" )
 
         for run in $cases
         do
@@ -153,20 +147,58 @@
 
               cd $return_base ; cd $run
               rm -f diff_tempfile
-              files_1=`find -type f | sed "s#^./##"`
-              
+              files_0=`ls`
+              files_1=""
+              for file in $files_0 
+              do 
+                if [[ -d $file ]]; then
+                  if [[ $file == build* ]] || [[ $file == exe* ]] || 
+                     [[ $file == *oasis3-mct* ]] || [[ $file == toy* ]]; then 
+                    echo "do not compare build or exe directories $file" 
+                  else 
+                    #add files: 
+                    files_dir=`ls $file`
+                    for file1 in $files_dir 
+                    do 
+                      files_1="$files_1 $file1"
+                    done 
+                  fi 
+                else
+                  files_1="$files_1 $file"
+                fi
+              done 
+
               #Generate list of binary files in the directory
               binaryfiles=`grep . -r * | grep 'Binary file' | sed -e "s/^Binary file //" -e "s/ matches$//"`
 
               #Generate list of files to skip
-              skipfiles="ww3_shel.out ww3_multi.out prf.*.mww3 finished ww3_systrk.out gmon.out time_count.txt oasis_make.out oasis_clean.out toy_make.out toy_clean.out toy_model"
+              skipfiles="ww3_shel.out ww3_multi.out prf.*.mww3 finished ww3_systrk.out gmon.out time_count.txt oasis_make.out oasis_clean.out toy_model toy_make.out toy_clean.out build.log"
 
               nf_1=`echo $files_1 | wc -w | awk '{print $1}'`
               echo "  found $nf_1 files in base directory" >> $home_dir/fulldiff.tmp
 
               cd $return_comp ; cd $run
               rm -f diff_tempfile
-              files_2=`find -type f | sed "s#^./##"`
+              files_0=`ls`
+              files_2=""
+              for file in $files_0
+              do
+                if [[ -d $file ]]; then
+                  if [[ $file == build* ]] || [[ $file == exe* ]] ||
+                     [[ $file == *oasis3-mct* ]] || [[ $file == toy* ]]; then
+                    echo "do not compare build or exe directories $file" 
+                  else
+                    #add files: 
+                    files_dir=`ls $file`
+                    for file1 in $files_dir
+                    do
+                      files_2="$files_1 $file1"
+                    done
+                  fi
+                else
+                  files_2="$files_2 $file"
+                fi
+              done
 
               nf_2=`echo $files_2 | wc -w | awk '{print $1}'`
               echo "  found $nf_2 files in compare directory" >> $home_dir/fulldiff.tmp
@@ -402,19 +434,6 @@
   rm -f $home_dir/summary.tmp
   rm -f $home_dir/fulldiff.tmp
 
-
-#  echo ' '
-#  cat $home_dir/fulldiff.tmp
-#  echo '**********************************************************************'
-#  
-#  echo ' '
-#  cat $home_dir/isIdenticalList.tmp
-#  echo '**********************************************************************'
-#
-#  echo ' '
-#  cat $home_dir/notIdenticalList.tmp
-#  echo '**********************************************************************'
-
   echo ' '
   echo " Saved summary to $home_dir/matrixCompSummary.txt"
   echo " Saved full output to $home_dir/matrixCompFull.txt"
diff --git a/regtests/bin/run_test b/regtests/bin/run_test
index 5773904549..c509b574c3 100755
--- a/regtests/bin/run_test
+++ b/regtests/bin/run_test
@@ -2090,6 +2090,7 @@ do
           then
             \rm -f $prog.inp
             \rm -f $prog.nml
+            \rm -f ounfmeta.inp
             if [ $multi -eq 2 ]
             then
               \rm -f mod_def.ww3