Merge remote-tracking branch 'canonical/develop' into HDoff_t_cleanup

.github/workflows/markdown-link-check.yml

@@ -6,9 +6,13 @@ on:
   pull_request:
     branches: [ develop ]
 
+# The config file handles things like http 500 errors from sites like GitLab
+# and http 200 responses
 jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
     - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        config-file: '.github/workflows/markdown_config.json'

.github/workflows/markdown_config.json

@@ -0,0 +1,3 @@
+{
+    "aliveStatusCodes": [200, 500]
+}

CMakeVOL.cmake

@@ -77,6 +77,7 @@ if (HDF5_VOL_ALLOW_EXTERNAL MATCHES "GIT" OR HDF5_VOL_ALLOW_EXTERNAL MATCHES "LO
   set (HDF5_LIBRARIES "${HDF5_LIBSH_TARGET};${LINK_LIBS};${LINK_COMP_LIBS};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>")
   set (HDF5_INCLUDE_DIRS "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   set (HDF5_IS_PARALLEL ${H5_HAVE_PARALLEL})
+  set (HDF5_VERSION ${HDF5_PACKAGE_VERSION})
 
   set (HDF5_C_LIBRARIES "${HDF5_LIBRARIES}")
 

release_docs/RELEASE.txt

@@ -750,7 +750,10 @@ New Features
 
     Tools:
     ------
-    -
+    - Allow h5repack to reserve space for a user block without a file
+
+      This is useful for users who want to reserve space
+      in the file for future use without requiring a file to copy.
 
 
     High-Level APIs:

src/H5CX.c

@@ -289,18 +289,18 @@ typedef struct H5CX_t {
                                                   (H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME) */
     bool mpio_coll_chunk_multi_ratio_ind_set;  /* Whether instrumented "collective chunk multi ratio ind"
                                                      value is set */
-    bool mpio_coll_rank0_bcast;                /* Instrumented "collective chunk multi ratio ind" value
-                                                     (H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME) */
-    bool mpio_coll_rank0_bcast_set; /* Whether instrumented "collective chunk multi ratio ind" value is set */
-#endif                              /* H5_HAVE_INSTRUMENTED_LIBRARY */
-#endif                              /* H5_HAVE_PARALLEL */
-    uint32_t no_selection_io_cause; /* Reason for not performing selection I/O
-                                          (H5D_XFER_NO_SELECTION_IO_CAUSE_NAME) */
-    bool no_selection_io_cause_set; /* Whether reason for not performing selection I/O is set */
+    bool mpio_coll_rank0_bcast;                /* Instrumented "collective rank 0 broadcast" value
+                                                     (H5D_XFER_COLL_RANK0_BCAST_NAME) */
+    bool mpio_coll_rank0_bcast_set;   /* Whether instrumented "collective rank 0 broadcast" value is set */
+#endif                                /* H5_HAVE_INSTRUMENTED_LIBRARY */
+#endif                                /* H5_HAVE_PARALLEL */
+    uint32_t no_selection_io_cause;   /* Reason for not performing selection I/O
+                                            (H5D_XFER_NO_SELECTION_IO_CAUSE_NAME) */
+    bool no_selection_io_cause_set;   /* Whether reason for not performing selection I/O is set */
     bool no_selection_io_cause_valid; /* Whether reason for not performing selection I/O is valid */
 
-    uint32_t
-         actual_selection_io_mode; /* Actual selection I/O mode used (H5D_ACTUAL_SELECTION_IO_MODE_NAME) */
+    uint32_t actual_selection_io_mode;   /* Actual selection I/O mode used
+                                            (H5D_XFER_ACTUAL_SELECTION_IO_MODE_NAME) */
     bool actual_selection_io_mode_set;   /* Whether actual selection I/O mode is set */
     bool actual_selection_io_mode_valid; /* Whether actual selection I/O mode is valid */
 

src/H5Ppublic.h

@@ -287,7 +287,7 @@ typedef herr_t (*H5P_cls_copy_func_t)(hid_t new_prop_id, hid_t old_prop_id, void
 /**
  * \brief Callback function for H5Pcreate_class()
  *
- * \param[in] prop_id    The identifier of the property list class being created
+ * \param[in] prop_id    The identifier of the property list class being closed
  * \param[in] close_data User pointer to any close data required
  * \return \herr_t
  *

test/tgenprop.c

@@ -413,9 +413,9 @@ test_genprop_cls_cpy_cb1(hid_t new_list_id, hid_t H5_ATTR_UNUSED old_list_id, vo
 }
 
 static herr_t
-test_genprop_cls_cls_cb1(hid_t list_id, void *create_data)
+test_genprop_cls_cls_cb1(hid_t list_id, void *close_data)
 {
-    count_data_t *cdata = (count_data_t *)create_data;
+    count_data_t *cdata = (count_data_t *)close_data;
 
     cdata->count++;
     cdata->id = list_id;
@@ -1006,9 +1006,9 @@ static prop_cb_info prop3_cb_info; /* Callback statistics for property #3 */
 **
 ****************************************************************/
 static herr_t
-test_genprop_cls_cpy_cb2(hid_t new_list_id, hid_t H5_ATTR_UNUSED old_list_id, void *create_data)
+test_genprop_cls_cpy_cb2(hid_t new_list_id, hid_t H5_ATTR_UNUSED old_list_id, void *copy_data)
 {
-    count_data_t *cdata = (count_data_t *)create_data;
+    count_data_t *cdata = (count_data_t *)copy_data;
 
     cdata->count++;
     cdata->id = new_list_id;

tools/src/h5repack/h5repack.c

@@ -746,8 +746,12 @@ check_options(pack_opt_t *options)
         }
     }
 
-    if (options->ublock_filename == NULL && options->ublock_size != 0)
-        H5TOOLS_GOTO_ERROR((-1), "file name missing for user block");
+    if (options->ublock_filename == NULL && options->ublock_size != 0) {
+        if (options->verbose > 0) {
+            printf("Warning: user block file name missing. Reserving a size of %ld...\n",
+                   options->ublock_size);
+        }
+    }
 
     /*------------------------------------------------------------------------
      * Verify alignment options; threshold is zero default but alignment not

tools/src/h5repack/h5repack_copy.c

@@ -368,7 +368,7 @@ copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options)
      *-------------------------------------------------------------------------
      */
 
-    if (options->ublock_size > 0) {
+    if (options->ublock_filename != NULL && options->ublock_size > 0) {
         if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0)
             H5TOOLS_GOTO_ERROR((-1), "Could not copy user block. Exiting...");
     }

tools/test/h5repack/CMakeTests.cmake

@@ -979,6 +979,51 @@
       )
   endmacro ()
 
+  macro (ADD_H5_VERIFY_USERBLOCK testname userblocksize testfile)
+    if (NOT HDF5_USING_ANALYSIS_TOOL)
+      add_test (
+          NAME H5REPACK_VERIFY_USERBLOCK-${testname}-clear-objects
+          COMMAND ${CMAKE_COMMAND} -E remove testfiles/out-${testname}.${testfile}
+      )
+      add_test (
+          NAME H5REPACK_VERIFY_USERBLOCK-${testname}
+          COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:h5repack> --enable-error-stack ${ARGN} ${PROJECT_BINARY_DIR}/testfiles/${testfile} ${PROJECT_BINARY_DIR}/testfiles/out-${testname}.${testfile}
+      )
+      set_tests_properties (H5REPACK_VERIFY_USERBLOCK-${testname} PROPERTIES
+          DEPENDS H5REPACK_VERIFY_USERBLOCK-${testname}-clear-objects
+      )
+      if ("H5REPACK_VERIFY_USERBLOCK-${testname}" MATCHES "${HDF5_DISABLE_TESTS_REGEX}")
+        set_tests_properties (H5REPACK_VERIFY_USERBLOCK-${testname} PROPERTIES DISABLED true)
+      endif ()
+      add_test (
+          NAME H5REPACK_VERIFY_USERBLOCK-${testname}_DMP
+          COMMAND "${CMAKE_COMMAND}"
+              -D "TEST_EMULATOR=${CMAKE_CROSSCOMPILING_EMULATOR}"
+              -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
+              -D "TEST_ARGS:STRING=-H;-B;out-${testname}.${testfile}"
+              -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
+              -D "TEST_OUTPUT=${testfile}-${testname}-v.out"
+              -D "TEST_EXPECT=${resultcode}"
+              -D "TEST_FILTER:STRING=USERBLOCK_SIZE ${userblocksize}"
+              -D "TEST_REFERENCE=USERBLOCK_SIZE ${userblocksize}"
+              -P "${HDF_RESOURCES_DIR}/grepTest.cmake"
+      )
+      set_tests_properties (H5REPACK_VERIFY_USERBLOCK-${testname}_DMP PROPERTIES
+          DEPENDS H5REPACK_VERIFY_USERBLOCK-${testname}
+      )
+      if ("H5REPACK_VERIFY_USERBLOCK-${testname}_DMP" MATCHES "${HDF5_DISABLE_TESTS_REGEX}")
+        set_tests_properties (H5REPACK_VERIFY_USERBLOCK-${testname}_DMP PROPERTIES DISABLED true)
+      endif ()
+      add_test (
+          NAME H5REPACK_VERIFY_USERBLOCK-${testname}-clean-objects
+          COMMAND ${CMAKE_COMMAND} -E remove testfiles/out-${testname}.${testfile}
+      )
+      set_tests_properties (H5REPACK_VERIFY_USERBLOCK-${testname}-clean-objects PROPERTIES
+          DEPENDS H5REPACK_VERIFY_USERBLOCK-${testname}_DMP
+      )
+    endif ()
+  endmacro ()
+
   macro (ADD_H5_TEST_META testname testfile)
       # Remove any output file left over from previous test run
       add_test (
@@ -1719,6 +1764,9 @@
   set (arg ${FILE1} -u ${PROJECT_BINARY_DIR}/testfiles/ublock.bin -b 2048)
   ADD_H5_TEST (add_userblock "TEST" ${arg})
 
+# add a userblock reserve to file
+  ADD_H5_VERIFY_USERBLOCK (reserve_userblock 2048 ${FILE1} -b 2048)
+
 # add alignment
   set (arg ${FILE1} -t 1 -a 1)
   ADD_H5_TEST (add_alignment "TEST" ${arg})

tools/test/h5repack/h5repack.sh.in

@@ -1805,6 +1805,10 @@ fi
 arg="h5repack_objs.h5 -u ublock.bin -b 2048"
 TOOLTEST add_userblock $arg
 
+# reserve a userblock to file
+arg="h5repack_objs.h5 -b 2048"
+TOOLTEST reserve_userblock $arg
+
 # add alignment
 arg="h5repack_objs.h5 -t 1 -a 1 "
 TOOLTEST add_alignment $arg