HDFFV-10120 verify nozlib checks and synchronize scripts with develop

14 files changed, 115 insertions, 99 deletions

diff --git a/tools/h5copy/CMakeTests.cmake b/tools/h5copy/CMakeTests.cmake
index a2131d1..c429377 100644
--- a/tools/h5copy/CMakeTests.cmake
+++ b/tools/h5copy/CMakeTests.cmake
@@ -108,6 +108,15 @@
     endif ()
   ENDMACRO ()
 
+  MACRO (ADD_SKIP_H5_TEST testname skipresultfile)
+    if (NOT HDF5_ENABLE_USING_MEMCHECKER)
+      add_test (
+          NAME H5COPY-${testname}-${skipresultfile}-SKIPPED
+          COMMAND ${CMAKE_COMMAND} -E echo "SKIP ${testname}-${skipresultfile} ${ARGN}"
+      )
+    endif ()
+  ENDMACRO ()
+
   MACRO (ADD_H5_TEST2 testname resultcode infile  psparam pdparam vparam sparam srcname dparam dstname)
     if (NOT HDF5_ENABLE_USING_MEMCHECKER)
       # Remove any output file left over from previous test run
@@ -168,7 +177,7 @@
       if (NOT "${last_test}" STREQUAL "")
         set_tests_properties (H5COPY_SAME-${testname}-prefill PROPERTIES DEPENDS ${last_test})
       endif ()
-    else ()
+    else (HDF5_ENABLE_USING_MEMCHECKER)
       set_tests_properties (H5COPY_SAME-${testname}-prefill PROPERTIES DEPENDS H5COPY_SAME-${testname}-clear-objects)
     endif ()
 
@@ -211,8 +220,6 @@
           COMMAND    ${CMAKE_COMMAND}
               -E remove
               ./testfiles/${testname}.out.h5
-              ./testfiles/${testname}.out.out
-              ./testfiles/${testname}.out.out.err
       )
       add_test (
           NAME H5COPY-CMP-${testname}
@@ -292,12 +299,31 @@
     set (last_test "H5COPY-clearall-objects")
   endif ()
 
+# See which filters are usable (and skip tests for filters we
+# don't have).  Do this by searching H5pubconf.h to see which
+# filters are defined.
+
+# detect whether the encoder is present.
+  if (H5_HAVE_FILTER_DEFLATE)
+    set (USE_FILTER_DEFLATE "true")
+  endif ()
+
+  if (H5_HAVE_FILTER_SZIP)
+    set (USE_FILTER_SZIP "true")
+  endif ()
+
   # "Test copying various forms of datasets"
   ADD_H5_TEST (simple 0 ${HDF_FILE1}.h5 -v -s simple -d simple)
   ADD_H5_TEST (chunk 0 ${HDF_FILE1}.h5 -v -s chunk -d chunk)
   ADD_H5_TEST (compact 0 ${HDF_FILE1}.h5 -v -s compact -d compact)
   ADD_H5_TEST (compound 0 ${HDF_FILE1}.h5 -v -s compound -d compound)
-  ADD_H5_TEST (compressed 0 ${HDF_FILE1}.h5 -v -s compressed -d compressed)
+
+  if (USE_FILTER_DEFLATE)
+    ADD_H5_TEST (compressed 0 ${HDF_FILE1}.h5 -v -s compressed -d compressed)
+  else ()
+    ADD_H5_TEST (compressed 2 ${HDF_FILE1}.h5 -v -s compressed -d compressed)
+  endif ()
+
   ADD_H5_TEST (named_vl 0 ${HDF_FILE1}.h5 -v -s named_vl -d named_vl)
   ADD_H5_TEST (nested_vl 0 ${HDF_FILE1}.h5 -v -s nested_vl -d nested_vl)
   ADD_H5_TEST (dset_attr 0 ${HDF_FILE1}.h5 -v -s dset_attr -d dset_attr)
@@ -310,25 +336,41 @@
 
   # "Test copying empty, 'full' & 'nested' groups"
   ADD_H5_TEST (grp_empty 0 ${HDF_FILE1}.h5 -v -s grp_empty -d grp_empty)
-  ADD_H5_TEST (grp_dsets 0 ${HDF_FILE1}.h5 -v -s grp_dsets -d grp_dsets)
-  ADD_H5_TEST (grp_nested 0 ${HDF_FILE1}.h5 -v -s grp_nested -d grp_nested)
+  if (USE_FILTER_DEFLATE)
+    ADD_H5_TEST (grp_dsets 0 ${HDF_FILE1}.h5 -v -s grp_dsets -d grp_dsets)
+    ADD_H5_TEST (grp_nested 0 ${HDF_FILE1}.h5 -v -s grp_nested -d grp_nested)
+  else ()
+    ADD_H5_TEST (grp_dsets 2 ${HDF_FILE1}.h5 -v -s grp_dsets -d grp_dsets)
+    ADD_H5_TEST (grp_nested 2 ${HDF_FILE1}.h5 -v -s grp_nested -d grp_nested)
+  endif ()
   ADD_H5_TEST (grp_attr 0 ${HDF_FILE1}.h5 -v -s grp_attr -d grp_attr)
 
   # "Test copying dataset within group in source file to group in destination"
   ADD_H5_TEST2 (simple_group 0 ${HDF_FILE1}.h5 grp_dsets grp_dsets -v -s /grp_dsets/simple -d /grp_dsets/simple_group)
 
-  # "Test copying & renaming group"
-  ADD_H5_TEST (grp_rename 0 ${HDF_FILE1}.h5 -v -s grp_dsets -d grp_rename)
-
-  # "Test copying 'full' group hierarchy into group in destination file"
-  ADD_H5_TEST2 (grp_dsets_rename 0 ${HDF_FILE1}.h5 grp_dsets grp_rename -v -s grp_dsets -d /grp_rename/grp_dsets)
+  if (USE_FILTER_DEFLATE)
+    # "Test copying & renaming group"
+    ADD_H5_TEST (grp_rename 0 ${HDF_FILE1}.h5 -v -s grp_dsets -d grp_rename)
+    # "Test copying 'full' group hierarchy into group in destination file"
+    ADD_H5_TEST2 (grp_dsets_rename 0 ${HDF_FILE1}.h5 grp_dsets grp_rename -v -s grp_dsets -d /grp_rename/grp_dsets)
+  else ()
+    # "Test copying & renaming group"
+    ADD_H5_TEST (grp_rename 2 ${HDF_FILE1}.h5 -v -s grp_dsets -d grp_rename)
+    # "Test copying 'full' group hierarchy into group in destination file"
+    ADD_H5_TEST2 (grp_dsets_rename 2 ${HDF_FILE1}.h5 grp_dsets grp_rename -v -s grp_dsets -d /grp_rename/grp_dsets)
+  endif ()
 
   # "Test copying objects into group hier. that doesn't exist yet in destination file"
   ADD_H5_TEST (A_B1_simple 0 ${HDF_FILE1}.h5 -vp -s simple -d /A/B1/simple)
   ADD_H5_TEST (A_B2_simple2 0 ${HDF_FILE1}.h5 -vp -s simple -d /A/B2/simple2)
   ADD_H5_TEST (C_D_simple 0 ${HDF_FILE1}.h5 -vp -s /grp_dsets/simple -d /C/D/simple)
-  ADD_H5_TEST (E_F_grp_dsets 0 ${HDF_FILE1}.h5 -vp -s /grp_dsets -d /E/F/grp_dsets)
-  ADD_H5_TEST (G_H_grp_nested 0 ${HDF_FILE1}.h5 -vp -s /grp_nested -d /G/H/grp_nested)
+  if (USE_FILTER_DEFLATE)
+    ADD_H5_TEST (E_F_grp_dsets 0 ${HDF_FILE1}.h5 -vp -s /grp_dsets -d /E/F/grp_dsets)
+    ADD_H5_TEST (G_H_grp_nested 0 ${HDF_FILE1}.h5 -vp -s /grp_nested -d /G/H/grp_nested)
+  else ()
+    ADD_H5_TEST (E_F_grp_dsets 2 ${HDF_FILE1}.h5 -vp -s /grp_dsets -d /E/F/grp_dsets)
+    ADD_H5_TEST (G_H_grp_nested 2 ${HDF_FILE1}.h5 -vp -s /grp_nested -d /G/H/grp_nested)
+  endif ()
 
 ############# COPY REFERENCES ##############
 
@@ -374,4 +416,8 @@
   # - dataset
   ADD_H5_TEST_SAME (samefile1 0 ${HDF_FILE1}.h5 /simple /simple -v -s /simple -d /simple_cp)
   # - group with some datasets
-  ADD_H5_TEST_SAME (samefile2 0 ${HDF_FILE1}.h5 /grp_dsets /grp_dsets -v -s /grp_dsets -d /grp_dsets_cp)
+  if (USE_FILTER_DEFLATE)
+    ADD_H5_TEST_SAME (samefile2 0 ${HDF_FILE1}.h5 /grp_dsets /grp_dsets -v -s /grp_dsets -d /grp_dsets_cp)
+  else ()
+    ADD_H5_TEST_SAME (samefile2 2 ${HDF_FILE1}.h5 /grp_dsets /grp_dsets -v -s /grp_dsets -d /grp_dsets_cp)
+  endif ()
diff --git a/tools/h5copy/testh5copy.sh.in b/tools/h5copy/testh5copy.sh.in
index d8abfd9..449ae1a 100644
--- a/tools/h5copy/testh5copy.sh.in
+++ b/tools/h5copy/testh5copy.sh.in
@@ -21,6 +21,10 @@
 
 srcdir=@srcdir@
 
+# Determine which filters are available
+USE_FILTER_SZIP="@USE_FILTER_SZIP@"
+USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@"
+
 # source dirs
 SRC_TOOLS="$srcdir/.."
 SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
@@ -128,7 +132,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $tstfile`
+    SDIR=$SRC_H5COPY_TESTFILES
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
@@ -487,7 +491,9 @@ COPY_OBJECTS()
     TOOLTEST -i $TESTFILE -o $TESTDIR/chunk.out.h5 -v -s chunk      -d chunk
     TOOLTEST -i $TESTFILE -o $TESTDIR/compact.out.h5 -v -s compact    -d compact
     TOOLTEST -i $TESTFILE -o $TESTDIR/compound.out.h5 -v -s compound   -d compound
+if test $USE_FILTER_DEFLATE = "yes" ; then
     TOOLTEST -i $TESTFILE -o $TESTDIR/compressed.out.h5 -v -s compressed -d compressed
+fi
     TOOLTEST -i $TESTFILE -o $TESTDIR/named_vl.out.h5 -v -s named_vl   -d named_vl
     TOOLTEST -i $TESTFILE -o $TESTDIR/nested_vl.out.h5 -v -s nested_vl  -d nested_vl
     TOOLTEST -i $TESTFILE -o $TESTDIR/dset_attr.out.h5 -v -s /dset_attr  -d /dset_attr
@@ -499,16 +505,19 @@ COPY_OBJECTS()
     TOOLTEST -i $TESTFILE -o $TESTDIR/dsrename.out.h5 -v -s compound   -d rename
 
     echo "Test copying empty, 'full' & 'nested' groups"
+if test $USE_FILTER_DEFLATE = "yes" ; then
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_empty.out.h5 -v -s grp_empty  -d grp_empty
+fi
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_dsets.out.h5 -v -s grp_dsets  -d grp_dsets
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_nested.out.h5 -v -s grp_nested -d grp_nested
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_attr.out.h5 -v -s grp_attr -d grp_attr
 
+if test $USE_FILTER_DEFLATE = "yes" ; then
     echo "Test copying dataset within group in source file to group in destination"
     TOOLTEST_PREFILL -i $TESTFILE -o $TESTDIR/simple_group.out.h5 grp_dsets grp_dsets /grp_dsets/simple /grp_dsets/simple_group
-
     echo "Test copying & renaming group"
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_rename.out.h5 -v -s grp_dsets  -d grp_rename
+fi
 
     echo "Test copying 'full' group hierarchy into group in destination file"
     TOOLTEST_PREFILL -i $TESTFILE -o $TESTDIR/grp_dsets_rename.out.h5 grp_dsets grp_rename grp_dsets /grp_rename/grp_dsets
@@ -517,8 +526,10 @@ COPY_OBJECTS()
     TOOLTEST -i $TESTFILE -o $TESTDIR/A_B1_simple.out.h5 -vp -s simple    -d /A/B1/simple
     TOOLTEST -i $TESTFILE -o $TESTDIR/A_B2_simple2.out.h5 -vp -s simple    -d /A/B2/simple2
     TOOLTEST -i $TESTFILE -o $TESTDIR/C_D_simple.out.h5 -vp -s /grp_dsets/simple    -d /C/D/simple
+if test $USE_FILTER_DEFLATE = "yes" ; then
     TOOLTEST -i $TESTFILE -o $TESTDIR/E_F_grp_dsets.out.h5 -vp -s /grp_dsets -d /E/F/grp_dsets
     TOOLTEST -i $TESTFILE -o $TESTDIR/G_H_grp_nested.out.h5 -vp -s /grp_nested -d /G/H/grp_nested
+fi
 }
 
 # Copy references in various way.
@@ -579,8 +590,10 @@ TEST_MISC()
     TOOLTEST_FAIL h5copy_misc1.out -i $TESTFILE -o $TESTDIR/h5copy_misc1.out.h5 -v -s /simple  -d /g1/g2/simple
 
     echo "Test copying objects to the same file "
-    TOOLTEST_SAME -i $TESTFILE -o $TESTDIR/samefile1.out.h5 /simple /simple_cp 
+    TOOLTEST_SAME -i $TESTFILE -o $TESTDIR/samefile1.out.h5 /simple /simple_cp
+if test $USE_FILTER_DEFLATE = "yes" ; then
     TOOLTEST_SAME -i $TESTFILE -o $TESTDIR/samefile2.out.h5 /grp_dsets /grp_dsets_cp
+fi
 }
 
 ##############################################################################
diff --git a/tools/h5diff/CMakeTests.cmake b/tools/h5diff/CMakeTests.cmake
index 91e0cab..a9ec683 100644
--- a/tools/h5diff/CMakeTests.cmake
+++ b/tools/h5diff/CMakeTests.cmake
@@ -335,13 +335,18 @@
               -D "TEST_ARGS:STRING=${ARGN}"
               -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/PAR/testfiles"
               -D "TEST_OUTPUT=${resultfile}.out"
-              -D "TEST_EXPECT=${resultcode}"
+              -D "TEST_EXPECT=0"
               -D "TEST_REFERENCE=${resultfile}.txt"
-#              -D "TEST_APPEND=EXIT CODE: [0-9]"
-#              -D "TEST_REF_FILTER=EXIT CODE: 0"
-              -D "TEST_SKIP_COMPARE=TRUE"
+              -D "TEST_APPEND=EXIT CODE:"
+              -D "TEST_REF_APPEND=EXIT CODE: [0-9]"
+              -D "TEST_REF_FILTER=EXIT CODE: 0"
+              -D "TEST_SORT_COMPARE=TRUE"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
+      if (NOT "${last_test}" STREQUAL "")
+        set_tests_properties (PH5DIFF-${resultfile} PROPERTIES DEPENDS ${last_test})
+      endif ()
+      set (last_test "PH5DIFF-${resultfile}")
     endif ()
   ENDMACRO ()
 
diff --git a/tools/h5import/CMakeTests.cmake b/tools/h5import/CMakeTests.cmake
index d1f1681..4e6e171 100644
--- a/tools/h5import/CMakeTests.cmake
+++ b/tools/h5import/CMakeTests.cmake
@@ -93,10 +93,6 @@
           COMMAND    ${CMAKE_COMMAND}
               -E remove
               ${testfile}
-              ${testfile}.new
-              ${testfile}.new.err
-              ${testfile}.out
-              ${testfile}.out.err
       )
       set_tests_properties (H5IMPORT-${testname}-clear-objects PROPERTIES DEPENDS H5IMPORT-h5importtest)
 
@@ -141,12 +137,6 @@
               -E remove
               d${testfile}
               d${testfile}.bin
-              d${testfile}.imp
-              d${testfile}.imp.err
-              d${testfile}.dmp
-              d${testfile}.dmp.err
-              d${testfile}.dff
-              d${testfile}.dff.err
       )
       set_tests_properties (H5IMPORT-DUMP-${testname}-clear-objects PROPERTIES DEPENDS H5IMPORT-h5importtest)
 
@@ -434,17 +424,17 @@
   ADD_H5_TEST (BINARY_F64 binfp64.bin testfiles/binfp64.conf binfp64.h5)
   if (NOT USE_FILTER_DEFLATE)
     ADD_H5_SKIP_DUMPTEST (BINARY_F64 "/fp/bin/64-bit" binfp64.h5 BINARY)
-  else (NOT USE_FILTER_DEFLATE)
+  else ()
     ADD_H5_DUMPTEST (BINARY_F64 "/fp/bin/64-bit" binfp64.h5 BINARY)
-  endif (NOT USE_FILTER_DEFLATE)
+  endif ()
 
   # ----- TESTING "BINARY I8 - rank 3 - Output I16LE + Chunked+Extended+Compressed "
   ADD_H5_TEST (BINARY_I8 binin8.bin testfiles/binin8.conf binin8.h5)
   if (NOT USE_FILTER_DEFLATE)
     ADD_H5_SKIP_DUMPTEST (BINARY_I8 "/int/bin/8-bit" binin8.h5 BINARY)
-  else (NOT USE_FILTER_DEFLATE)
+  else ()
     ADD_H5_DUMPTEST (BINARY_I8 "/int/bin/8-bit" binin8.h5 BINARY)
-  endif (NOT USE_FILTER_DEFLATE)
+  endif ()
 
   # ----- TESTING "BINARY I16 - rank 3 - Output order LE + CHUNKED + extended "
   ADD_H5_TEST (BINARY_I16 binin16.bin testfiles/binin16.conf binin16.h5)
diff --git a/tools/h5import/h5importtestutil.sh.in b/tools/h5import/h5importtestutil.sh.in
index e50ddac..6e747e7 100644
--- a/tools/h5import/h5importtestutil.sh.in
+++ b/tools/h5import/h5importtestutil.sh.in
@@ -153,7 +153,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $tstfile`
+    SDIR=$SRC_H5IMPORT_TESTFILES
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
@@ -161,6 +161,9 @@ CLEAN_TESTFILES_AND_TESTDIR()
     fi
 }
 
+# Print a line-line message left justified in a field of 70 characters
+# beginning with the word "Testing".
+#
 TESTING() {
    SPACES="                                                               "
    echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012'
diff --git a/tools/h5jam/CMakeTests.cmake b/tools/h5jam/CMakeTests.cmake
index 3752e55..f82e0d6 100644
--- a/tools/h5jam/CMakeTests.cmake
+++ b/tools/h5jam/CMakeTests.cmake
@@ -49,13 +49,6 @@
       endif ()
     else ()
       add_test (
-          NAME H5JAM-${expectfile}-clear-objects
-          COMMAND    ${CMAKE_COMMAND}
-              -E remove
-              ${expectfile}.out
-              ${expectfile}.out.err
-      )
-      add_test (
           NAME H5JAM-${expectfile}
           COMMAND "${CMAKE_COMMAND}"
               -D "TEST_PROGRAM=$<TARGET_FILE:h5jam>"
@@ -66,7 +59,6 @@
               -D "TEST_REFERENCE=testfiles/${expectfile}.txt"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
-      set_tests_properties (H5JAM-${expectfile} PROPERTIES DEPENDS H5JAM-${expectfile}-clear-objects)
     endif ()
   ENDMACRO ()
 
@@ -83,13 +75,6 @@
       endif ()
     else ()
       add_test (
-          NAME H5JAM-UNJAM-${expectfile}-clear-objects
-          COMMAND    ${CMAKE_COMMAND}
-              -E remove
-              ${expectfile}.out
-              ${expectfile}.out.err
-      )
-      add_test (
           NAME H5JAM-UNJAM-${expectfile}
           COMMAND "${CMAKE_COMMAND}"
               -D "TEST_PROGRAM=$<TARGET_FILE:h5unjam>"
@@ -100,7 +85,6 @@
               -D "TEST_REFERENCE=testfiles/${expectfile}.txt"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
-      set_tests_properties (H5JAM-UNJAM-${expectfile} PROPERTIES DEPENDS H5JAM-UNJAM-${expectfile}-clear-objects)
     endif ()
   ENDMACRO ()
 
@@ -108,16 +92,6 @@
     # If using memchecker add tests without using scripts
     if (NOT HDF5_ENABLE_USING_MEMCHECKER)
       add_test (
-          NAME H5JAM-${testname}-CHECKFILE-clear-objects
-          COMMAND    ${CMAKE_COMMAND}
-              -E remove
-              ${actual}.new
-              ${actual}.new.err
-              ${actual}.out
-              ${actual}.out.err
-      )
-      set_tests_properties (H5JAM-${testname}-CHECKFILE-clear-objects PROPERTIES DEPENDS ${testdepends})
-      add_test (
           NAME H5JAM-${testname}-CHECKFILE-H5DMP
           COMMAND "${CMAKE_COMMAND}"
               -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
@@ -129,7 +103,7 @@
               -D "TEST_SKIP_COMPARE=TRUE"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
-      set_tests_properties (H5JAM-${testname}-CHECKFILE-H5DMP PROPERTIES DEPENDS H5JAM-${testname}-CHECKFILE-clear-objects)
+      set_tests_properties (H5JAM-${testname}-CHECKFILE-H5DMP PROPERTIES DEPENDS ${testdepends})
       add_test (
           NAME H5JAM-${testname}-CHECKFILE-H5DMP_CMP
           COMMAND "${CMAKE_COMMAND}"
@@ -174,11 +148,6 @@
       else ()
         if (NOT "${ARGN}" STREQUAL "--delete")
           add_test (
-              NAME H5JAM-${testname}-UNJAM_D-clear-objects
-              COMMAND ${CMAKE_COMMAND} -E remove ${outfile}.ufile.txt ${outfile}.ufile.txt.err
-          )
-          set_tests_properties (H5JAM-${testname}-UNJAM_D-clear-objects PROPERTIES DEPENDS H5JAM-${testname}-UNJAM-clear-objects)
-          add_test (
               NAME H5JAM-${testname}-UNJAM
               COMMAND "${CMAKE_COMMAND}"
                   -D "TEST_PROGRAM=$<TARGET_FILE:h5unjam>"
@@ -189,7 +158,7 @@
                   -D "TEST_SKIP_COMPARE=TRUE"
                   -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
           )
-          set_tests_properties (H5JAM-${testname}-UNJAM PROPERTIES DEPENDS H5JAM-${testname}-UNJAM_D-clear-objects)
+          set_tests_properties (H5JAM-${testname}-UNJAM PROPERTIES DEPENDS H5JAM-${testname}-UNJAM-clear-objects)
           set (compare_test "${outfile}.ufile.txt")
         else ()
           add_test (NAME H5JAM-${testname}-UNJAM COMMAND $<TARGET_FILE:h5unjam> -i ${infile} -o ${outfile})
diff --git a/tools/h5jam/testh5jam.sh.in b/tools/h5jam/testh5jam.sh.in
index 1664d6b..d8c9274 100644
--- a/tools/h5jam/testh5jam.sh.in
+++ b/tools/h5jam/testh5jam.sh.in
@@ -126,7 +126,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $tstfile`
+    SDIR=$SRC_H5JAM_TESTFILES
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
diff --git a/tools/h5ls/CMakeTests.cmake b/tools/h5ls/CMakeTests.cmake
index f995c74..ad54cc2 100644
--- a/tools/h5ls/CMakeTests.cmake
+++ b/tools/h5ls/CMakeTests.cmake
@@ -431,8 +431,14 @@
     ADD_H5_TEST (tdataregle 0 -v tdatareg.h5)
   endif ()
 
+# test for file with datasets that use Fixed Array chunk indices
+  if (USE_FILTER_DEFLATE)
+    # data read internal filters
+    ADD_H5_TEST (tdset_idx 0 -w80 -d tdset_idx.h5)
+  endif (USE_FILTER_DEFLATE)
+
+
 ##############################################################################
 ###    P L U G I N  T E S T S
 ##############################################################################
 ADD_H5_UD_TEST (h5ls_plugin_test 0 tudfilter -w80 -d tudfilter.h5)
-
diff --git a/tools/h5repack/CMakeTests.cmake b/tools/h5repack/CMakeTests.cmake
index ebc2055..fa454ce 100644
--- a/tools/h5repack/CMakeTests.cmake
+++ b/tools/h5repack/CMakeTests.cmake
@@ -120,12 +120,6 @@
       set (last_test "H5REPACK-${testname}")
     else ()
       add_test (
-          NAME H5REPACK-h5repack-${testname}-clear-objects
-          COMMAND    ${CMAKE_COMMAND}
-              -E remove h5repack-${testname}.out h5repack-${testname}.out.err
-      )
-      set_tests_properties (H5REPACK-h5repack-${testname}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
-      add_test (
           NAME H5REPACK-h5repack-${testname}
           COMMAND "${CMAKE_COMMAND}"
               -D "TEST_PROGRAM=$<TARGET_FILE:h5repack>"
@@ -136,7 +130,6 @@
               -D "TEST_REFERENCE=h5repack-${testname}.txt"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
-      set_tests_properties (H5REPACK-h5repack-${testname} PROPERTIES DEPENDS "H5REPACK-h5repack-${testname}-clear-objects")
     endif ()
   ENDMACRO ()
 
@@ -346,10 +339,6 @@
           COMMAND    ${CMAKE_COMMAND}
               -E remove
               testfiles/out-${testname}.${resultfile}
-              testfiles/${testname}.${resultfile}.out
-              testfiles/${testname}.${resultfile}.out.err
-              testfiles/${resultfile}-${testname}.out
-              testfiles/${resultfile}-${testname}.out.err
       )
       add_test (
           NAME H5REPACK_UD-${testname}
@@ -961,7 +950,10 @@
   ADD_H5_TEST (upgrade_layout "TEST" ${FILE14})
 
 # test for datum size > H5TOOLS_MALLOCSIZE
-  ADD_H5_TEST (gt_mallocsize "TEST" ${FILE1} -f GZIP=1)
+  if (NOT USE_FILTER_DEFLATE)
+    set (TESTTYPE "SKIP")
+  endif ()
+  ADD_H5_TEST (gt_mallocsize ${TESTTYPE} ${FILE1} -f GZIP=1)
 
 # Check repacking file with committed datatypes in odd configurations
   ADD_H5_TEST (committed_dt "TEST" ${FILE15})
@@ -997,12 +989,12 @@
   set (TESTRETVAL 255)
   if (WIN32)
     set (TESTRETVAL -1)
-  endif()
+  endif ()
   ADD_H5_CMP_TEST (plugin_zero "" "TEST" ${TESTRETVAL} h5repack_layout.h5 -v -f UD=250,0)
 
   if (HDF5_TEST_VFD)
     # Run test with different Virtual File Driver
     foreach (vfd ${VFD_LIST})
       ADD_VFD_TEST (${vfd} 0)
-    endforeach (vfd ${VFD_LIST})
+    endforeach ()
   endif ()
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index de55f20..966aedf 100644
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -39,6 +39,8 @@ H5DUMP=../h5dump/h5dump         # The h5dump tool name
 H5DUMP_BIN=`pwd`/$H5DUMP        # The path of the h5dump tool binary
 
 RM='rm -rf'
+CMP='cmp'
+DIFF='diff -c'
 GREP='grep'
 CP='cp'
 DIRNAME='dirname'
@@ -165,7 +167,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $tstfile`
+    SDIR=$SRC_H5REPACK_TESTFILES
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
diff --git a/tools/h5stat/CMakeTests.cmake b/tools/h5stat/CMakeTests.cmake
index 00ce250..a3db0fc 100644
--- a/tools/h5stat/CMakeTests.cmake
+++ b/tools/h5stat/CMakeTests.cmake
@@ -75,11 +75,6 @@
       endif ()
     else (HDF5_ENABLE_USING_MEMCHECKER)
       add_test (
-          NAME H5STAT-${resultfile}-clear-objects
-          COMMAND    ${CMAKE_COMMAND}
-              -E remove ${resultfile}.out ${resultfile}.out.err
-      )
-      add_test (
           NAME H5STAT-${resultfile}
           COMMAND "${CMAKE_COMMAND}"
               -D "TEST_PROGRAM=$<TARGET_FILE:h5stat>"
@@ -90,7 +85,6 @@
               -D "TEST_REFERENCE=${resultfile}.ddl"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
-      set_tests_properties (H5STAT-${resultfile} PROPERTIES DEPENDS "H5STAT-${resultfile}-clear-objects")
     endif ()
   ENDMACRO ()
 
@@ -194,7 +188,7 @@
   ADD_H5_TEST (h5stat_filters-UD 0 -D h5stat_filters.h5)
   ADD_H5_TEST (h5stat_filters-UT 0 -T h5stat_filters.h5)
 # h5stat_tsohm.h5 is a copy of ../../../test/tsohm.h5 generated by tsohm.c
-# as of release 1.8.0-alpha4
+# as of release 1.8.7-snap0 (on a 64-bit machine)
   ADD_H5_TEST (h5stat_tsohm 0 h5stat_tsohm.h5)
 # h5stat_newgrat.h5 is generated by h5stat_gentest.c
   ADD_H5_TEST (h5stat_newgrat 0 h5stat_newgrat.h5)
diff --git a/tools/h5stat/testh5stat.sh.in b/tools/h5stat/testh5stat.sh.in
index 4d698da..9ceb943 100644
--- a/tools/h5stat/testh5stat.sh.in
+++ b/tools/h5stat/testh5stat.sh.in
@@ -149,7 +149,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $tstfile`
+    SDIR=$SRC_H5STAT_TESTFILES
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
diff --git a/tools/misc/CMakeTests.cmake b/tools/misc/CMakeTests.cmake
index d065b63..ee60bf8 100644
--- a/tools/misc/CMakeTests.cmake
+++ b/tools/misc/CMakeTests.cmake
@@ -76,8 +76,6 @@
           COMMAND    ${CMAKE_COMMAND}
               -E remove
                   ${resultfile}.h5
-                  ${resultfile}.out
-                  ${resultfile}.out.err
       )
       set_tests_properties (H5MKGRP-${resultfile}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
     endif ()
@@ -118,8 +116,6 @@
           COMMAND    ${CMAKE_COMMAND}
               -E remove
                   ${resultfile}.h5
-                  ${resultfile}.out
-                  ${resultfile}.out.err
       )
       set_tests_properties (H5MKGRP_CMP-${resultfile}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
       add_test (
diff --git a/tools/misc/testh5mkgrp.sh.in b/tools/misc/testh5mkgrp.sh.in
index 190e824..a0413e1 100644
--- a/tools/misc/testh5mkgrp.sh.in
+++ b/tools/misc/testh5mkgrp.sh.in
@@ -117,7 +117,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $tstfile`
+    SDIR=$SRC_H5MKGRP_TESTFILES
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then