VFD SWMR: Sync with develop

.github/workflows/main.yml

@@ -36,7 +36,7 @@ jobs:
             os: ubuntu-latest
             build_type: "Release"
             cpp: ON
-            fortran: OFF
+            fortran: ON
             java: ON
             ts: OFF
             hl: ON

.github/workflows/pr-check.yml

@@ -31,7 +31,7 @@ jobs:
             os: ubuntu-latest
             build_type: "Release"
             cpp: ON
-            fortran: OFF
+            fortran: ON
             java: ON
             ts: OFF
             hl: ON

MANIFEST

@@ -915,6 +915,7 @@
 ./src/H5L.c
 ./src/H5Ldeprec.c
 ./src/H5Lexternal.c
+./src/H5Lint.c
 ./src/H5Lmodule.h
 ./src/H5Lpkg.h
 ./src/H5Lprivate.h
@@ -1402,8 +1403,10 @@
 ./test/vfd_swmr_addrem_writer.c
 ./test/vfd_swmr_attrdset_writer.c
 ./test/vfd_swmr_bigset_writer.c
+./test/vfd_swmr_check_compat.c
 ./test/vfd_swmr_common.c
 ./test/vfd_swmr_common.h
+./test/vfd_swmr_dsetops_writer.c
 ./test/vfd_swmr_generator.c
 ./test/vfd_swmr_group_writer.c
 ./test/vfd_swmr_reader.c

bin/trace

@@ -283,8 +283,8 @@ my $file_api = 0;
 my $file_args = 0;
 my $total_api = 0;
 my $total_args = 0;
-sub rewrite_func ($$$$$$$$) {
-  my ($file, $begin, $type, $aftertype, $name, $args, $close, $body) = @_;
+sub rewrite_func ($$$$$) {
+  my ($file, $type, $name, $args, $body) = @_;
   my ($arg, $trace, $argtrace);
   my (@arg_name, @arg_str, @arg_type);
   local $_;
@@ -459,7 +459,7 @@ sub rewrite_func ($$$$$$$$) {
   }
 
  error:
-  return "\n$begin$type$aftertype$name($orig_args)$close$body";
+  return "\n$type\n$name($orig_args)\n$body";
 }
 
 ##############################################################################
@@ -481,25 +481,12 @@ for $file (@ARGV) {
     # Make a copy of the original data
     my $original = $Source;
 
-    # Check which style of function declaration is used in this file
-    if ( $Source =~ /BEGIN_FUNC/ ) {
-        # Make modifications
-        $Source =~ s/\n(BEGIN_FUNC.*?\n)                      #begin
-                        ([A-Za-z]\w*(\s+[A-Za-z]\w*)*\s*\**)  #type
-                        (.*?\n)                               #aftertype
-                         (H5[A-Z]{0,2}_?[a-zA-Z0-9_]\w*)      #name
-                         \s*\((.*?)\)\s*                      #args
-                         (\))                                 #close
-                         (\n.*?\nEND_FUNC\([^\n]*)            #body
-                         /rewrite_func($file,$1,$2,$4,$5,$6,$7,$8)/segx;
-    } else {
-        # Make modifications
-        $Source =~ s/\n([A-Za-z]\w*(\s+[A-Za-z]\w*)*\s*\**)\n #type
-                         (H5[A-Z]{0,2}_?[a-zA-Z0-9_]\w*)      #name
-                         \s*\((.*?)\)\s*                      #args
-                         (\{.*?\n\}[^\n]*)                    #body
-                         /rewrite_func($file,"",$1,"\n",$3,$4,"\n",$5)/segx;
-    }
+    # Make modifications
+    $Source =~ s/\n([A-Za-z]\w*(\s+[A-Za-z]\w*)*\s*\**)\n #type
+                     (H5[A-Z]{0,2}_?[a-zA-Z0-9_]\w*)      #name
+                     \s*\((.*?)\)\s*                      #args
+                     (\{.*?\n\}[^\n]*)                    #body
+                     /rewrite_func($file,$1,$3,$4,$5)/segx;
 
 # If the source changed then print out the new version
     if ($original ne $Source) {

configure.ac

@@ -1365,16 +1365,15 @@ CFLAGS="$H5_CFLAGS $AM_CFLAGS $CFLAGS"
 ## Checkpoint the cache
 AC_CACHE_SAVE
 
-## Posix.1g types (C9x)
+## Write the confdefs.h header for checking sizes
 cat >>confdefs.h <<\EOF
-#include <sys/types.h>
-EOF
-
-if test "X$C9x" = "Xyes"; then
-  cat >>confdefs.h <<\EOF
+#include <stdbool.h>
 #include <stdint.h>
+#ifdef HAVE_UNISTD_H
+#include <sys/types.h>
+#endif
+#include <time.h>
 EOF
-fi
 
 AC_CHECK_SIZEOF(        [int8_t])
 AC_CHECK_SIZEOF(       [uint8_t])
@@ -1404,30 +1403,12 @@ AC_CHECK_SIZEOF([uint_least64_t])
 AC_CHECK_SIZEOF(  [int_fast64_t])
 AC_CHECK_SIZEOF( [uint_fast64_t])
 
+AC_CHECK_SIZEOF([bool])
+AC_CHECK_SIZEOF([off_t])
+AC_CHECK_SIZEOF([ptrdiff_t])
 AC_CHECK_SIZEOF([size_t])
 AC_CHECK_SIZEOF([ssize_t])
-AC_CHECK_SIZEOF([ptrdiff_t])
-
-cat >>confdefs.h <<\EOF
-#include <sys/types.h> /*for off_t definition*/
-EOF
-AC_CHECK_SIZEOF([off_t])
-
-if test "X$C9x" = "Xyes"; then
-  cat >>confdefs.h <<\EOF
-#include <stdbool.h>
-EOF
-AC_CHECK_SIZEOF([bool])
-fi
-
-AC_CHECK_SIZEOF(time_t, [], [
-#ifdef HAVE_SYS_TYPES_H
-#include <sys/types.h>
-#endif
-#ifdef HAVE_TIME_H
-#include <time.h>
-#endif
-])
+AC_CHECK_SIZEOF([time_t])
 
 ## Checkpoint the cache
 AC_CACHE_SAVE

fortran/src/CMakeLists.txt

@@ -74,15 +74,15 @@ add_executable (H5match_types
 target_include_directories (H5match_types PRIVATE "${HDF5_SRC_BINARY_DIR};${HDF5_SRC_DIR};${HDF5_F90_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
 
 add_custom_command (TARGET H5match_types POST_BUILD
-    BYPRODUCTS H5f90i_gen.h H5fortran_types.F90
+    BYPRODUCTS ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/H5fortran_types.F90
     COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5match_types>
     WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}
     DEPENDS H5match_types
 )
 
 if (NOT ONLY_SHARED_LIBS)
   add_custom_command (TARGET H5match_types POST_BUILD
-      BYPRODUCTS H5f90i_gen.h H5fortran_types.F90
+      BYPRODUCTS ${HDF5_F90_BINARY_DIR}/static/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/static/H5fortran_types.F90
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/static/H5f90i_gen.h
       COMMAND    ${CMAKE_COMMAND}
@@ -95,7 +95,7 @@ if (NOT ONLY_SHARED_LIBS)
 endif ()
 if (BUILD_SHARED_LIBS)
   add_custom_command (TARGET H5match_types POST_BUILD
-      BYPRODUCTS H5f90i_gen.h H5fortran_types.F90
+      BYPRODUCTS ${HDF5_F90_BINARY_DIR}/shared/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/shared/H5fortran_types.F90
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/shared/H5f90i_gen.h
       COMMAND    ${CMAKE_COMMAND}
@@ -235,7 +235,7 @@ add_custom_command (TARGET H5_buildiface POST_BUILD
 )
 if (NOT ONLY_SHARED_LIBS)
   add_custom_command (TARGET H5_buildiface POST_BUILD
-      BYPRODUCTS H5_gen.F90
+      BYPRODUCTS ${HDF5_F90_BINARY_DIR}/static/H5_gen.F90
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different ${HDF5_F90_BINARY_DIR}/H5_gen.F90 ${HDF5_F90_BINARY_DIR}/static/H5_gen.F90
       WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}/static
@@ -250,7 +250,7 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_custom_command (TARGET H5_buildiface POST_BUILD
-      BYPRODUCTS H5_gen.F90
+      BYPRODUCTS ${HDF5_F90_BINARY_DIR}/shared/H5_gen.F90
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different ${HDF5_F90_BINARY_DIR}/H5_gen.F90 ${HDF5_F90_BINARY_DIR}/shared/H5_gen.F90
       WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}/shared

fortran/test/CMakeLists.txt

@@ -92,7 +92,7 @@ endif ()
 
 if (NOT BUILD_SHARED_LIBS)
   add_custom_command (TARGET H5_test_buildiface POST_BUILD
-      BYPRODUCTS tf_gen.F90
+      BYPRODUCTS ${HDF5_FORTRAN_TESTS_BINARY_DIR}/static/tf_gen.F90
       COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5_test_buildiface>
       WORKING_DIRECTORY ${HDF5_FORTRAN_TESTS_BINARY_DIR}/static
       DEPENDS H5_test_buildiface
@@ -104,7 +104,7 @@ if (NOT BUILD_SHARED_LIBS)
   set_source_files_properties (${HDF5_FORTRAN_TESTS_BINARY_DIR}/static/tf_gen.F90 PROPERTIES GENERATED TRUE)
 else ()
   add_custom_command (TARGET H5_test_buildiface POST_BUILD
-      BYPRODUCTS tf_gen.F90
+      BYPRODUCTS ${HDF5_FORTRAN_TESTS_BINARY_DIR}/shared/tf_gen.F90
       COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5_test_buildiface>
       WORKING_DIRECTORY ${HDF5_FORTRAN_TESTS_BINARY_DIR}/shared
       DEPENDS H5_test_buildiface

hl/fortran/src/CMakeLists.txt

@@ -115,7 +115,7 @@ set (HDF5_HL_F90_F_BASE_SOURCES
 
 if (NOT ONLY_SHARED_LIBS)
   add_custom_command (TARGET H5HL_buildiface POST_BUILD
-      BYPRODUCTS $H5LTff_gen.F90 H5TBff_gen.F90
+      BYPRODUCTS ${HDF5_HL_F90_BINARY_DIR}/static/H5LTff_gen.F90 ${HDF5_HL_F90_BINARY_DIR}/static/H5TBff_gen.F90
       COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5HL_buildiface>
       WORKING_DIRECTORY ${HDF5_HL_F90_BINARY_DIR}/static
       DEPENDS ${HDF5_HL_F90_F_BASE_SOURCES}
@@ -132,7 +132,7 @@ if (NOT ONLY_SHARED_LIBS)
 endif ()
 if (BUILD_SHARED_LIBS)
   add_custom_command (TARGET H5HL_buildiface POST_BUILD
-      BYPRODUCTS H5LTff_gen.F90 H5TBff_gen.F90
+      BYPRODUCTS ${HDF5_HL_F90_BINARY_DIR}/shared/H5LTff_gen.F90 ${HDF5_HL_F90_BINARY_DIR}/shared/H5TBff_gen.F90
       COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5HL_buildiface>
       WORKING_DIRECTORY ${HDF5_HL_F90_BINARY_DIR}/shared
       DEPENDS ${HDF5_HL_F90_F_BASE_SOURCES}

java/src/hdf/hdf5lib/H5.java

@@ -10726,7 +10726,18 @@ public synchronized static native byte[] H5Rcopy(byte[] src_ref_ptr)
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+    public static long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_object(ref_ptr, rapl_id, oapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_object add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
@@ -10754,7 +10765,18 @@ public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+    public static long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_region(ref_ptr, rapl_id, oapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_region add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
@@ -10782,7 +10804,18 @@ public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+    public static long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_attr(ref_ptr, rapl_id, aapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_attr add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     // Get type //

java/src/jni/h5rImp.c

@@ -336,7 +336,7 @@ Java_hdf_hdf5lib_H5_H5Rcopy(JNIEnv *env, jclass clss, jbyteArray src_ref)
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;
@@ -371,7 +371,7 @@ Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jl
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;
@@ -406,7 +406,7 @@ Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jl
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;

java/src/jni/h5rImp.h

@@ -78,21 +78,21 @@ JNIEXPORT jbyteArray JNICALL Java_hdf_hdf5lib_H5_H5Rcopy(JNIEnv *, jclass, jbyte
  * Method:    H5Ropen_object
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Ropen_region
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Ropen_attr
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1attr(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5