Merge pull request #840 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop

* commit '17b8f0bb936633f01bf6deba247e37bcadbc6b82':
  Fix valgrind issues
  HDFFV-9724 init var to null
  HDFFV-9724 add valgrind ENV
  Fix memory leak due to addition of FORMAT check loop
  HDFFV-9724 prefix of 0 length should be null value
  HDFFV-9724 Corrected files and verified tests
  Add library INTERFACE and MPI to tools

9 files changed, 210 insertions, 2 deletions

diff --git a/tools/lib/CMakeLists.txt b/tools/lib/CMakeLists.txt
index ade7671..0fc1981 100644
--- a/tools/lib/CMakeLists.txt
+++ b/tools/lib/CMakeLists.txt
@@ -39,7 +39,10 @@ set (H5_TOOLS_LIB_HDRS
 
 add_library (${HDF5_TOOLS_LIB_TARGET} STATIC ${H5_TOOLS_LIB_SOURCES} ${H5_TOOLS_LIB_HDRS})
 TARGET_C_PROPERTIES (${HDF5_TOOLS_LIB_TARGET} STATIC " " " ")
-target_link_libraries (${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+target_link_libraries (${HDF5_TOOLS_LIB_TARGET} PUBLIC ${HDF5_LIB_TARGET})
+if (HDF5_ENABLE_PARALLEL AND MPI_C_FOUND)
+  target_link_libraries (${HDF5_TOOLS_LIB_TARGET} PRIVATE ${MPI_C_LIBRARIES})
+endif ()
 set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_TOOLS_LIB_TARGET}")
 H5_SET_LIB_OPTIONS (${HDF5_TOOLS_LIB_TARGET} ${HDF5_TOOLS_LIB_NAME} STATIC)
 set_target_properties (${HDF5_TOOLS_LIB_TARGET} PROPERTIES
@@ -52,7 +55,10 @@ set (install_targets ${HDF5_TOOLS_LIB_TARGET})
 if (BUILD_SHARED_LIBS)
   add_library (${HDF5_TOOLS_LIBSH_TARGET} SHARED ${H5_TOOLS_LIB_SOURCES} ${H5_TOOLS_LIB_HDRS})
   TARGET_C_PROPERTIES (${HDF5_TOOLS_LIBSH_TARGET} SHARED " " " ")
-  target_link_libraries (${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
+  target_link_libraries (${HDF5_TOOLS_LIBSH_TARGET} PUBLIC ${HDF5_LIBSH_TARGET})
+  if (HDF5_ENABLE_PARALLEL AND MPI_C_FOUND)
+    target_link_libraries (${HDF5_TOOLS_LIBSH_TARGET} PRIVATE ${MPI_C_LIBRARIES})
+  endif ()
   set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_TOOLS_LIBSH_TARGET}")
   H5_SET_LIB_OPTIONS (${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_TOOLS_LIB_NAME} SHARED ${HDF5_TOOLS_PACKAGE_SOVERSION})
   set_target_properties (${HDF5_TOOLS_LIBSH_TARGET} PROPERTIES
diff --git a/tools/test/h5dump/CMakeTestsVDS.cmake b/tools/test/h5dump/CMakeTestsVDS.cmake
index 3addecf..922e79e 100644
--- a/tools/test/h5dump/CMakeTestsVDS.cmake
+++ b/tools/test/h5dump/CMakeTestsVDS.cmake
@@ -72,6 +72,14 @@
       f-3.h5
       vds-eiger.h5
   )
+  set (HDF5_REFERENCE_PREFIX_VDS
+      1_vds.h5
+      2_vds.h5
+      4_vds.h5
+      5_vds.h5
+      vds-percival-unlim-maxmin.h5
+      vds-eiger.h5
+  )
   set (HDF5_ERROR_REFERENCE_VDS
   )
 
@@ -80,12 +88,21 @@
     HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/vds/${vds_h5_file}" "${PROJECT_BINARY_DIR}/testfiles/vds/${fname}" "h5dump_vds_files")
   endforeach ()
 
+  foreach (vds_h5_file ${HDF5_REFERENCE_PREFIX_VDS})
+    get_filename_component(fname "${vds_h5_file}" NAME)
+    HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/vds/${vds_h5_file}" "${PROJECT_BINARY_DIR}/testfiles/vds/prefix/${fname}" "h5dump_vds_files")
+  endforeach ()
 
   foreach (ddl_vds ${HDF5_REFERENCE_VDS})
     get_filename_component(fname "${ddl_vds}" NAME)
     HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/vds/${ddl_vds}" "${PROJECT_BINARY_DIR}/testfiles/vds/${fname}" "h5dump_vds_files")
   endforeach ()
 
+  foreach (ddl_vds ${HDF5_REFERENCE_VDS})
+    get_filename_component(fname "${ddl_vds}" NAME)
+    HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/vds/${ddl_vds}" "${PROJECT_BINARY_DIR}/testfiles/vds/prefix/${fname}" "h5dump_vds_files")
+  endforeach ()
+
   foreach (ddl_vds ${HDF5_ERROR_REFERENCE_VDS})
     get_filename_component(fname "${ddl_vds}" NAME)
     HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/errfiles/${ddl_vds}" "${PROJECT_BINARY_DIR}/testfiles/vds/${fname}" "h5dump_vds_files")
@@ -134,6 +151,47 @@
     endif ()
   endmacro ()
 
+  macro (ADD_H5_VDS_PREFIX_TEST resultfile resultcode)
+    # If using memchecker add tests without using scripts
+    if (HDF5_ENABLE_USING_MEMCHECKER)
+      add_test (NAME H5DUMP_PREFIX-${resultfile} COMMAND $<TARGET_FILE:h5dump> ${ARGN})
+      set_tests_properties (H5DUMP_PREFIX-${resultfile} PROPERTIES
+          ENVIRONMENT "HDF5_VDS_PREFIX=${PROJECT_BINARY_DIR}/testfiles/vds/"
+          WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles/vds/prefix"
+      )
+      if (NOT "${resultcode}" STREQUAL "0")
+        set_tests_properties (H5DUMP_PREFIX-${resultfile} PROPERTIES WILL_FAIL "true")
+      endif ()
+      if (NOT "${last_vds_test}" STREQUAL "")
+        set_tests_properties (H5DUMP_PREFIX-${resultfile} PROPERTIES DEPENDS ${last_VDS_test})
+      endif ()
+    else ()
+      # Remove any output file left over from previous test run
+      add_test (
+          NAME H5DUMP_PREFIX-${resultfile}-clear-objects
+          COMMAND    ${CMAKE_COMMAND}
+              -E remove
+              ${resultfile}.out
+              ${resultfile}.out.err
+      )
+      set_tests_properties (H5DUMP_PREFIX-${resultfile}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles/vds/prefix")
+      add_test (
+          NAME H5DUMP_PREFIX-${resultfile}
+          COMMAND "${CMAKE_COMMAND}"
+              -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
+              -D "TEST_ARGS:STRING=${ARGN}"
+              -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles/vds/prefix"
+              -D "TEST_OUTPUT=${resultfile}.out"
+              -D "TEST_EXPECT=${resultcode}"
+              -D "TEST_REFERENCE=${resultfile}.ddl"
+              -D "TEST_ENV_VAR=HDF5_VDS_PREFIX"
+              -D "TEST_ENV_VALUE=${PROJECT_BINARY_DIR}/testfiles/vds/"
+              -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
+      )
+      set_tests_properties (H5DUMP_PREFIX-${resultfile} PROPERTIES DEPENDS H5DUMP_PREFIX-${resultfile}-clear-objects)
+    endif ()
+  endmacro ()
+
   macro (ADD_H5_VDS_LAYOUT resultfile resultcode)
     # If using memchecker add tests without using scripts
     if (HDF5_ENABLE_USING_MEMCHECKER)
@@ -261,3 +319,15 @@
     ADD_H5_VDS_LAYOUT (vds_layout-eiger 0 --enable-error-stack vds-eiger.h5)
     ADD_H5_VDS_LAYOUT (vds_layout-maxmin 0 --enable-error-stack vds-percival-unlim-maxmin.h5)
   endif ()
+
+  # Data read with prefix
+  if (USE_FILTER_DEFLATE)
+    ADD_H5_VDS_PREFIX_TEST (tvds-1 0 --enable-error-stack 1_vds.h5)
+    ADD_H5_VDS_PREFIX_TEST (tvds-2 0 --enable-error-stack 2_vds.h5)
+    ADD_H5_VDS_PREFIX_TEST (tvds-4 0 --enable-error-stack 4_vds.h5)
+    ADD_H5_VDS_PREFIX_TEST (tvds-5 0 --enable-error-stack 5_vds.h5)
+    ADD_H5_VDS_PREFIX_TEST (vds-first 0 --vds-view-first-missing --enable-error-stack vds-percival-unlim-maxmin.h5)
+    ADD_H5_VDS_PREFIX_TEST (vds-gap1 0 -d /VDS-Eiger --vds-gap-size=1 --enable-error-stack vds-eiger.h5)
+    ADD_H5_VDS_PREFIX_TEST (vds-gap2 0 --vds-gap-size=2 --enable-error-stack vds-eiger.h5)
+  endif ()
+
diff --git a/tools/test/h5ls/CMakeTestsVDS.cmake b/tools/test/h5ls/CMakeTestsVDS.cmake
index 5df61bb..2b6f61e 100644
--- a/tools/test/h5ls/CMakeTestsVDS.cmake
+++ b/tools/test/h5ls/CMakeTestsVDS.cmake
@@ -61,6 +61,17 @@
     get_filename_component(fname "${listfiles}" NAME)
     HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/vds/${listfiles}" "${PROJECT_BINARY_DIR}/testfiles/vds/${fname}" "h5ls_vds_files")
   endforeach ()
+
+  foreach (listfiles ${LIST_HDF5_TEST_FILES})
+    get_filename_component(fname "${listfiles}" NAME)
+    HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/vds/${listfiles}" "${PROJECT_BINARY_DIR}/testfiles/vds/prefix/${fname}" "h5ls_vds_files")
+  endforeach ()
+
+  foreach (listfiles ${LIST_OTHER_TEST_FILES})
+    get_filename_component(fname "${listfiles}" NAME)
+    HDFTEST_COPY_FILE("${HDF5_TOOLS_TEST_H5LS_SOURCE_DIR}/vds_prefix/${listfiles}" "${PROJECT_BINARY_DIR}/testfiles/vds/prefix/${fname}" "h5ls_vds_files")
+  endforeach ()
+
   add_custom_target(h5ls_vds_files ALL COMMENT "Copying files needed by h5ls_vds tests" DEPENDS ${h5ls_vds_files_list})
 
 ##############################################################################
@@ -104,6 +115,46 @@
     endif ()
   endmacro ()
 
+  macro (ADD_H5_VDS_PREFIX_TEST resultfile resultcode)
+    # If using memchecker add tests without using scripts
+    if (HDF5_ENABLE_USING_MEMCHECKER)
+      add_test (NAME H5LS_PREFIX-${resultfile} COMMAND $<TARGET_FILE:h5ls> ${ARGN})
+      set_tests_properties (H5LS_PREFIX-${resultfile} PROPERTIES
+          ENVIRONMENT "HDF5_VDS_PREFIX=\${ORIGIN}"
+          WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles"
+      )
+      if ("${resultcode}" STREQUAL "1")
+        set_tests_properties (H5LS_PREFIX-${resultfile} PROPERTIES WILL_FAIL "true")
+      endif ()
+      if (NOT "${last_test}" STREQUAL "")
+        set_tests_properties (H5LS_PREFIX-${resultfile} PROPERTIES DEPENDS ${last_test})
+      endif ()
+    else ()
+      add_test (
+          NAME H5LS_PREFIX-${resultfile}-clear-objects
+          COMMAND    ${CMAKE_COMMAND}
+              -E remove
+              ${resultfile}.out
+              ${resultfile}.out.err
+      )
+      set_tests_properties (H5LS_PREFIX-${resultfile}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles/vds/prefix")
+      add_test (
+          NAME H5LS_PREFIX-${resultfile}
+          COMMAND "${CMAKE_COMMAND}"
+              -D "TEST_PROGRAM=$<TARGET_FILE:h5ls>"
+              -D "TEST_ARGS=${ARGN}"
+              -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
+              -D "TEST_OUTPUT=vds/prefix/${resultfile}.out"
+              -D "TEST_EXPECT=${resultcode}"
+              -D "TEST_REFERENCE=vds/prefix/${resultfile}.ls"
+              -D "TEST_ENV_VAR=HDF5_VDS_PREFIX"
+              -D "TEST_ENV_VALUE=\${ORIGIN}"
+              -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
+      )
+      set_tests_properties (H5LS_PREFIX-${resultfile} PROPERTIES DEPENDS H5LS_PREFIX-${resultfile}-clear-objects)
+    endif ()
+  endmacro ()
+
 ##############################################################################
 ##############################################################################
 ###           T H E   T E S T S                                            ###
@@ -155,3 +206,10 @@
   ADD_H5_VDS_TEST (tvds-4 0 -w80 -v -S 4_vds.h5)
   ADD_H5_VDS_TEST (tvds-5 0 -w80 -v -S 5_vds.h5)
 
+  ADD_H5_VDS_PREFIX_TEST (tvds-1 0 -w80 -v -S vds/prefix/1_vds.h5)
+  ADD_H5_VDS_PREFIX_TEST (tvds-2 0 -w80 -v -S vds/prefix/2_vds.h5)
+  ADD_H5_VDS_PREFIX_TEST (tvds-3_1 0 -w80 -v -S vds/prefix/3_1_vds.h5)
+  ADD_H5_VDS_PREFIX_TEST (tvds-3_2 0 -w80 -v -S vds/prefix/3_2_vds.h5)
+  ADD_H5_VDS_PREFIX_TEST (tvds-4 0 -w80 -v -S vds/prefix/4_vds.h5)
+  ADD_H5_VDS_PREFIX_TEST (tvds-5 0 -w80 -v -S vds/prefix/5_vds.h5)
+
diff --git a/tools/test/h5ls/vds_prefix/tvds-1.ls b/tools/test/h5ls/vds_prefix/tvds-1.ls
new file mode 100644
index 0000000..2830d1a
--- /dev/null
+++ b/tools/test/h5ls/vds_prefix/tvds-1.ls
@@ -0,0 +1,14 @@
+Opened "vds/prefix/1_vds.h5" with sec2 driver.
+vds_dset                 Dataset {5/Inf, 18/18, 8/8}
+    Location:  1:800
+    Links:     1
+    Maps:      {6} Source {
+                      1_a.h5   /source_dset
+                      1_b.h5   /source_dset
+                      1_c.h5   /source_dset
+                      1_d.h5   /source_dset
+                      1_e.h5   /source_dset
+                      1_f.h5   /source_dset
+               }
+    Storage:   2880 logical bytes, 0 allocated bytes
+    Type:      32-bit little-endian integer
diff --git a/tools/test/h5ls/vds_prefix/tvds-2.ls b/tools/test/h5ls/vds_prefix/tvds-2.ls
new file mode 100644
index 0000000..5c6f9d3
--- /dev/null
+++ b/tools/test/h5ls/vds_prefix/tvds-2.ls
@@ -0,0 +1,13 @@
+Opened "vds/prefix/2_vds.h5" with sec2 driver.
+vds_dset                 Dataset {6/Inf, 8/8, 14/14}
+    Location:  1:800
+    Links:     1
+    Maps:      {5} Source {
+                      2_a.h5   /source_dset
+                      2_b.h5   /source_dset
+                      2_c.h5   /source_dset
+                      2_d.h5   /source_dset
+                      2_e.h5   /source_dset
+               }
+    Storage:   2688 logical bytes, 0 allocated bytes
+    Type:      32-bit little-endian integer
diff --git a/tools/test/h5ls/vds_prefix/tvds-3_1.ls b/tools/test/h5ls/vds_prefix/tvds-3_1.ls
new file mode 100644
index 0000000..f4c8e78
--- /dev/null
+++ b/tools/test/h5ls/vds_prefix/tvds-3_1.ls
@@ -0,0 +1,14 @@
+Opened "vds/prefix/3_1_vds.h5" with sec2 driver.
+vds_dset                 Dataset {5/Inf, 25/25, 8/8}
+    Location:  1:800
+    Links:     1
+    Maps:      {6} Source {
+                      1_a.h5   /source_dset
+                      1_b.h5   /source_dset
+                      1_c.h5   /source_dset
+                      1_d.h5   /source_dset
+                      1_e.h5   /source_dset
+                      1_f.h5   /source_dset
+               }
+    Storage:   4000 logical bytes, 0 allocated bytes
+    Type:      32-bit little-endian integer
diff --git a/tools/test/h5ls/vds_prefix/tvds-3_2.ls b/tools/test/h5ls/vds_prefix/tvds-3_2.ls
new file mode 100644
index 0000000..5a7e2d8
--- /dev/null
+++ b/tools/test/h5ls/vds_prefix/tvds-3_2.ls
@@ -0,0 +1,13 @@
+Opened "vds/prefix/3_2_vds.h5" with sec2 driver.
+vds_dset                 Dataset {6/Inf, 13/13, 19/19}
+    Location:  1:800
+    Links:     1
+    Maps:      {5} Source {
+                      2_a.h5   /source_dset
+                      2_b.h5   /source_dset
+                      2_c.h5   /source_dset
+                      2_d.h5   /source_dset
+                      2_e.h5   /source_dset
+               }
+    Storage:   5928 logical bytes, 0 allocated bytes
+    Type:      32-bit little-endian integer
diff --git a/tools/test/h5ls/vds_prefix/tvds-4.ls b/tools/test/h5ls/vds_prefix/tvds-4.ls
new file mode 100644
index 0000000..c22d3a4
--- /dev/null
+++ b/tools/test/h5ls/vds_prefix/tvds-4.ls
@@ -0,0 +1,9 @@
+Opened "vds/prefix/4_vds.h5" with sec2 driver.
+vds_dset                 Dataset {9/Inf, 4/4, 4/4}
+    Location:  1:800
+    Links:     1
+    Maps:      {1} Source {
+                      4_%b.h5   /source_dset
+               }
+    Storage:   576 logical bytes, 0 allocated bytes
+    Type:      32-bit little-endian integer
diff --git a/tools/test/h5ls/vds_prefix/tvds-5.ls b/tools/test/h5ls/vds_prefix/tvds-5.ls
new file mode 100644
index 0000000..efba8dc
--- /dev/null
+++ b/tools/test/h5ls/vds_prefix/tvds-5.ls
@@ -0,0 +1,11 @@
+Opened "vds/prefix/5_vds.h5" with sec2 driver.
+vds_dset                 Dataset {9/Inf, 4/4, 4/4}
+    Location:  1:800
+    Links:     1
+    Maps:      {3} Source {
+                      5_a.h5   /source_dset
+                      5_b.h5   /source_dset
+                      5_c.h5   /source_dset
+               }
+    Storage:   576 logical bytes, 0 allocated bytes
+    Type:      32-bit little-endian integer