Merge branch 'HDFGroup:develop' into develop

.github/workflows/release.yml

@@ -40,12 +40,19 @@ jobs:
       file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
       snap_name: hdf5-${{ needs.call-workflow-tarball.outputs.source_base }}
       use_environ: release
+    secrets:
+        AZURE_TENANT_ID: ${{ secrets.AZURE_TENANT_ID }}
+        AZURE_CLIENT_ID: ${{ secrets.AZURE_CLIENT_ID }}
+        AZURE_CLIENT_SECRET: ${{ secrets.AZURE_CLIENT_SECRET }}
+        AZURE_ENDPOINT: ${{ secrets.AZURE_ENDPOINT }}
+        AZURE_CODE_SIGNING_NAME: ${{ secrets.AZURE_CODE_SIGNING_NAME }}
+        AZURE_CERT_PROFILE_NAME: ${{ secrets.AZURE_CERT_PROFILE_NAME }}
 
   call-workflow-abi:
     needs: [log-the-inputs, call-workflow-tarball, call-workflow-ctest]
     uses: ./.github/workflows/abi-report.yml
     with:
-      file_ref: '1_14_3'
+      file_ref: '1.14.4.3'
       file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
       use_tag: ${{ needs.log-the-inputs.outputs.rel_tag }}
       use_environ: release

CMakePresets.json

@@ -53,6 +53,8 @@
         "BLOSC_ZLIB_PACKAGE_NAME": {"type": "STRING", "value": "zlib"},
         "BLOSC2_TGZ_NAME": {"type": "STRING", "value": "c-blosc2-2.14.4.tar.gz"},
         "BLOSC2_PACKAGE_NAME": {"type": "STRING", "value": "blosc2"},
+        "BLOSC2_ZLIB_TGZ_NAME": {"type": "STRING", "value": "zlib-1.3.tar.gz"},
+        "BLOSC2_ZLIB_PACKAGE_NAME": {"type": "STRING", "value": "zlib"},
         "BZ2_TGZ_NAME": {"type": "STRING", "value": "bzip2-bzip2-1.0.8.tar.gz"},
         "BZ2_PACKAGE_NAME": {"type": "STRING", "value": "bz2"},
         "FPZIP_TGZ_NAME": {"type": "STRING", "value": "fpzip-1.3.0.tar.gz"},

config/cmake/cacheinit.cmake

@@ -130,6 +130,14 @@ set (BLOSC2_TGZ_NAME "c-blosc2-2.14.4.tar.gz" CACHE STRING "Use BLOSC2 from comp
 
 set (BLOSC2_PACKAGE_NAME "blosc2" CACHE STRING "Name of BLOSC2 package" FORCE)
 
+set (BLOSC2_ZLIB_GIT_URL "https://github.com/madler/zlib.git" CACHE STRING "Use ZLIB from  GitHub repository" FORCE)
+set (BLOSC2_ZLIB_GIT_BRANCH "develop" CACHE STRING "" FORCE)
+
+set (BLOSC2_ZLIB_TGZ_ORIGPATH "https://github.com/madler/zlib/releases/download/v1.3" CACHE STRING "Use PLUGINS from original location" FORCE)
+set (BLOSC2_ZLIB_TGZ_NAME "zlib-1.3.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE)
+
+set (BLOSC2_ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of BLOSC2_ZLIB package" FORCE)
+
 ########
 # bzip2
 ########

release_docs/INSTALL_CMake.txt

@@ -144,6 +144,7 @@ To build HDF5 with the SZIP and ZLIB external libraries you will need to:
          ------bin
          ------include
          ------lib
+         --------plugins
          ------cmake
 
       On Linux, change to the install destination directory
@@ -162,6 +163,7 @@ To build HDF5 with the SZIP and ZLIB external libraries you will need to:
          ------bin
          ------include
          ------lib
+         --------plugins
          ------share
 
       On Mac you will find HDF5-1.15."X"-Darwin.dmg in the myhdfstuff folder. Click
@@ -173,6 +175,7 @@ To build HDF5 with the SZIP and ZLIB external libraries you will need to:
          ------bin
          ------include
          ------lib
+         --------plugins
          ------share
 
       By default the installation will create the bin, include, lib and cmake
@@ -239,6 +242,7 @@ Notes: This short set of instructions is written for users who want to
             ------bin
             ------include
             ------lib
+            --------plugins
             ------cmake
 
          On Linux, change to the install destination directory
@@ -257,6 +261,7 @@ Notes: This short set of instructions is written for users who want to
             ------bin
             ------include
             ------lib
+            --------plugins
             ------share
 
          On Mac you will find HDF5-1.15."X"-Darwin.dmg in the build folder. Click
@@ -268,6 +273,7 @@ Notes: This short set of instructions is written for users who want to
             ------bin
             ------include
             ------lib
+            --------plugins
             ------share
 
 
@@ -411,10 +417,8 @@ IV. Further considerations
 Notes: CMake and HDF5
 
    1. Using CMake for building and using HDF5 is under active development.
-      While we have attempted to provide error-free files, please
-      understand that development with CMake has not been extensively
-      tested outside of HDF. The CMake specific files may change
-      before the next release.
+      We have attempted to provide error-free files. The CMake specific
+      files may change before the next release.
 
    2. CMake support for HDF5 development should be usable on any
       system where CMake is supported. Please send us any comments on
@@ -587,6 +591,11 @@ These five steps are described in detail below.
             set (BLOSC2_TGZ_ORIGPATH "https://github.com/Blosc/c-blosc2/archive/refs/tags" CACHE STRING "Use PLUGINS from original location" FORCE)
             set (BLOSC2_TGZ_NAME "c-blosc2-2.14.4.tar.gz" CACHE STRING "Use BLOSC2 from compressed file" FORCE)
             set (BLOSC2_PACKAGE_NAME "blosc2" CACHE STRING "Name of BLOSC2 package" FORCE)
+            set (BLOSC2_ZLIB_GIT_URL "https://github.com/madler/zlib.git" CACHE STRING "Use ZLIB from  GitHub repository" FORCE)
+            set (BLOSC2_ZLIB_GIT_BRANCH "develop" CACHE STRING "" FORCE)
+            set (BLOSC2_ZLIB_TGZ_ORIGPATH "https://github.com/madler/zlib/releases/download/v1.3" CACHE STRING "Use PLUGINS from original location" FORCE)
+            set (BLOSC2_ZLIB_TGZ_NAME "zlib-1.3.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE)
+            set (BLOSC2_ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of BLOSC2_ZLIB package" FORCE)
             ########
             # bzip2
             ########
@@ -663,7 +672,7 @@ These five steps are described in detail below.
 
       2.1  Visual CMake users, click the Configure button. If this is the first time you are
            running cmake-gui in this directory, you will be prompted for the
-           generator you wish to use (for example on Windows, Visual Studio 12).
+           generator you wish to use (for example on Windows, Visual Studio 14).
            CMake will read in the CMakeLists.txt files from the source directory and
            display options for the HDF5 project. After the first configure you
            can adjust the cache settings and/or specify the locations of other programs.
@@ -1124,7 +1133,6 @@ Using individual command presets (where <compiler-type> is  GNUC or MSVC or Clan
     ctest --preset ci-StdShar-<compiler-type>
     cpack --preset ci-StdShar-<compiler-type>
 
-
 Using the workflow preset to configure, build, test and package the standard configuration:
     change directory to the hdf5 source folder
     execute "cmake --workflow --preset ci-StdShar-<compiler-type> --fresh"

src/H5Rdeprec.c

@@ -267,12 +267,12 @@ H5Rget_obj_type1(hid_t id, H5R_type_t ref_type, const void *ref)
 
     /* Check if using native VOL connector */
     if (H5VL_object_is_native(vol_obj, &is_native_vol_obj) < 0)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, FAIL,
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, H5G_UNKNOWN,
                     "can't determine if VOL object is native connector object");
 
     /* Must use native VOL connector for this operation */
     if (!is_native_vol_obj)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_VOL, FAIL,
+        HGOTO_ERROR(H5E_REFERENCE, H5E_VOL, H5G_UNKNOWN,
                     "H5Rget_obj_type1 is only meant to be used with the native VOL connector");
 
     /* Get object type */
@@ -341,12 +341,12 @@ H5Rdereference1(hid_t obj_id, H5R_type_t ref_type, const void *ref)
 
     /* Check if using native VOL connector */
     if (H5VL_object_is_native(vol_obj, &is_native_vol_obj) < 0)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, FAIL,
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, H5I_INVALID_HID,
                     "can't determine if VOL object is native connector object");
 
     /* Must use native VOL connector for this operation */
     if (!is_native_vol_obj)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_VOL, FAIL,
+        HGOTO_ERROR(H5E_REFERENCE, H5E_VOL, H5I_INVALID_HID,
                     "H5Rdereference1 is only meant to be used with the native VOL connector");
 
     /* Get object type */
@@ -614,12 +614,12 @@ H5Rdereference2(hid_t obj_id, hid_t oapl_id, H5R_type_t ref_type, const void *re
 
     /* Check if using native VOL connector */
     if (H5VL_object_is_native(vol_obj, &is_native_vol_obj) < 0)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, FAIL,
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, H5I_INVALID_HID,
                     "can't determine if VOL object is native connector object");
 
     /* Must use native VOL connector for this operation */
     if (!is_native_vol_obj)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_VOL, FAIL,
+        HGOTO_ERROR(H5E_REFERENCE, H5E_VOL, H5I_INVALID_HID,
                     "H5Rdereference2 is only meant to be used with the native VOL connector");
 
     /* Get object type */
@@ -694,7 +694,7 @@ H5Rget_region(hid_t id, H5R_type_t ref_type, const void *ref)
                     "can't query if file uses native VOL connector");
 
     if (!is_native_vol_obj)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_VOL, FAIL,
+        HGOTO_ERROR(H5E_REFERENCE, H5E_VOL, H5I_INVALID_HID,
                     "H5Rget_region is only meant to be used with the native VOL connector");
 
     /* Get object type */

src/H5TSsemaphore.h

@@ -179,7 +179,7 @@ H5TS_semaphore_wait(H5TS_semaphore_t *sem)
  *
  * Purpose:  Increments (unlocks) the semaphore.  If the semaphore's value
  *           becomes greater than zero, then another thread blocked in a wait
- *           call will be woken up and proceed to lock the semaphore.
+ *           call will proceed to lock the semaphore.
  *
  * Return:   Non-negative on success / Negative on failure
  *

test/tfile.c

@@ -8100,6 +8100,49 @@ test_min_dset_ohdr(void)
     CHECK(ret, FAIL, "H5Fclose");
 } /* end test_min_dset_ohdr() */
 
+/****************************************************************
+**
+**  test_unseekable_file():
+**    Test that attempting to open an unseekable file fails gracefully
+**    without a segfault (see hdf5#1498)
+****************************************************************/
+static void
+test_unseekable_file(void)
+{
+    hid_t file_id = H5I_INVALID_HID; /* File ID */
+
+    /* Output message about test being performed */
+    MESSAGE(5, ("Testing creating/opening an unseekable file\n"));
+
+    /* Creation */
+#ifdef H5_HAVE_WIN32_API
+    file_id = H5Fcreate("NUL", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+#else
+    file_id = H5Fcreate("/dev/null", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+#endif
+
+    H5Fclose(file_id);
+
+    /* Open, truncate */
+#ifdef H5_HAVE_WIN32_API
+    file_id = H5Fopen("NUL", H5F_ACC_TRUNC, H5P_DEFAULT);
+#else
+    file_id = H5Fopen("/dev/null", H5F_ACC_TRUNC, H5P_DEFAULT);
+#endif
+
+    H5Fclose(file_id);
+
+    /* Open, RDWR */
+#ifdef H5_HAVE_WIN32_API
+    file_id = H5Fopen("NUL", H5F_ACC_RDWR, H5P_DEFAULT);
+#else
+    file_id = H5Fopen("/dev/null", H5F_ACC_RDWR, H5P_DEFAULT);
+#endif
+
+    H5Fclose(file_id);
+
+    exit(EXIT_SUCCESS);
+}
 /****************************************************************
 **
 **  test_deprec():
@@ -8419,10 +8462,11 @@ test_file(void)
 
     test_libver_bounds(); /* Test compatibility for file space management */
     test_libver_bounds_low_high(driver_name);
-    test_libver_macros();  /* Test the macros for library version comparison */
-    test_libver_macros2(); /* Test the macros for library version comparison */
-    test_incr_filesize();  /* Test H5Fincrement_filesize() and H5Fget_eoa() */
-    test_min_dset_ohdr();  /* Test dataset object header minimization */
+    test_libver_macros();   /* Test the macros for library version comparison */
+    test_libver_macros2();  /* Test the macros for library version comparison */
+    test_incr_filesize();   /* Test H5Fincrement_filesize() and H5Fget_eoa() */
+    test_min_dset_ohdr();   /* Test dataset object header minimization */
+    test_unseekable_file(); /* Test attempting to open/create an unseekable file */
 #ifndef H5_NO_DEPRECATED_SYMBOLS
     test_file_ishdf5(driver_name); /* Test detecting HDF5 files correctly */
     test_deprec(driver_name);      /* Test deprecated routines */

test/trefer.c

@@ -618,21 +618,22 @@ test_reference_obj(void)
 
     /* Check file name for reference */
     namelen = H5Rget_file_name(&rbuf[0], NULL, 0);
-    CHECK(namelen, FAIL, "H5Dget_file_name");
-    VERIFY(namelen, strlen(FILE_REF_OBJ), "H5Dget_file_name");
+    CHECK(namelen, FAIL, "H5Rget_file_name");
+    VERIFY(namelen, strlen(FILE_REF_OBJ), "H5Rget_file_name");
 
     /* Make sure size parameter is ignored */
     namelen = H5Rget_file_name(&rbuf[0], NULL, 200);
-    CHECK(namelen, FAIL, "H5Dget_file_name");
-    VERIFY(namelen, strlen(FILE_REF_OBJ), "H5Dget_file_name");
+    CHECK(namelen, FAIL, "H5Rget_file_name");
+    VERIFY(namelen, strlen(FILE_REF_OBJ), "H5Rget_file_name");
 
     /* Get the file name for the reference */
     namebuf = (char *)malloc((size_t)namelen + 1);
-    namelen = H5Rget_file_name(&rbuf[0], (char *)namebuf, (size_t)namelen + 1);
-    CHECK(namelen, FAIL, "H5Dget_file_name");
+    namelen = H5Rget_file_name(&rbuf[0], namebuf, (size_t)namelen + 1);
+    CHECK(namelen, FAIL, "H5Rget_file_name");
+    VERIFY(strcmp(namebuf, FILE_REF_OBJ), 0, "namebuf vs FILE_REF_OBJ");
+    VERIFY(namelen, strlen(FILE_REF_OBJ), "H5Rget_file_name");
 
-    ret = !((strcmp(namebuf, FILE_REF_OBJ) == 0) && (namelen == strlen(FILE_REF_OBJ)));
-    CHECK(ret, FAIL, "H5Literate");
+    free(namebuf);
 
     /* Testing Dataset1 */
 
@@ -644,7 +645,8 @@ test_reference_obj(void)
     namebuf = (char *)malloc((size_t)namelen + 1);
     namelen = H5Rget_obj_name(&rbuf[0], H5P_DEFAULT, namebuf, (size_t)namelen + 1);
     CHECK(namelen, FAIL, "H5Rget_obj_name");
-    VERIFY(strcmp(namebuf, DS1_REF_OBJ), 0, "strcmp namebuf vs DS1_REF_OBJ");
+    VERIFY(strcmp(namebuf, DS1_REF_OBJ), 0, "namebuf vs DS1_REF_OBJ");
+    VERIFY(namelen, strlen(DS1_REF_OBJ), "H5Rget_obj_name");
 
     /* Open dataset object */
     ref_ds1 = H5Ropen_object(&rbuf[0], H5P_DEFAULT, dapl_id);
@@ -697,13 +699,12 @@ test_reference_obj(void)
 
     /* Getting the name of the referenced object and verify it */
     namelen = H5Rget_obj_name(&rbuf[1], H5P_DEFAULT, NULL, 0);
-    CHECK(namelen, FAIL, "H5Rget_obj_name");
     VERIFY(namelen, strlen(DS2_REF_OBJ), "H5Rget_obj_name");
 
     namebuf = (char *)malloc((size_t)namelen + 1);
     namelen = H5Rget_obj_name(&rbuf[1], H5P_DEFAULT, namebuf, (size_t)namelen + 1);
-    CHECK(namelen, FAIL, "H5Rget_obj_name");
-    VERIFY(strcmp(namebuf, DS2_REF_OBJ), 0, "strcmp namebuf vs DS2_REF_OBJ");
+    VERIFY(namelen, strlen(DS2_REF_OBJ), "H5Rget_obj_name");
+    VERIFY(strcmp(namebuf, DS2_REF_OBJ), 0, "namebuf vs DS2_REF_OBJ");
 
     /* Open dataset object */
     ref_ds2 = H5Ropen_object(&rbuf[1], H5P_DEFAULT, dapl_id);

test/ttsafe.c

@@ -138,9 +138,7 @@ main(int argc, char *argv[])
     AddTest("rec_rwlock_4", tts_rec_rw_lock_smoke_check_4, NULL,
             "recursive R/W lock smoke check 4 -- mixed mob", NULL);
 #endif /* !H5_HAVE_WIN_THREADS */
-#ifdef H5_HAVE_STDATOMIC_H
     AddTest("semaphore", tts_semaphore, NULL, "lightweight system semaphores", NULL);
-#endif /* H5_HAVE_STDATOMIC_H */
 
 #ifdef H5_HAVE_THREADSAFE
     AddTest("thread_id", tts_thread_id, NULL, "thread IDs", NULL);

test/ttsafe.h

@@ -38,9 +38,7 @@ void tts_is_threadsafe(void);
 #ifdef H5_HAVE_THREADS
 void tts_thread_pool(void);
 void tts_atomics(void);
-#ifdef H5_HAVE_STDATOMIC_H
 void tts_semaphore(void);
-#endif /* H5_HAVE_STDATOMIC_H */
 void tts_rec_rw_lock_smoke_check_1(void);
 void tts_rec_rw_lock_smoke_check_2(void);
 void tts_rec_rw_lock_smoke_check_3(void);

test/ttsafe_semaphore.c

@@ -18,7 +18,7 @@
 
 #include "ttsafe.h"
 
-#if defined(H5_HAVE_THREADS) && defined(H5_HAVE_STDATOMIC_H)
+#if defined(H5_HAVE_THREADS)
 
 #define NUM_PINGPONG     (1000 * 1000)
 #define NUM_CLIENTSERVER (50 * 1000)
@@ -40,18 +40,19 @@ static H5TS_THREAD_RETURN_TYPE
 ping(void *_test_info)
 {
     pingpong_t       *test_info = (pingpong_t *)_test_info;
+    unsigned          count;
     herr_t            result;
     H5TS_thread_ret_t ret_value = 0;
 
     do {
         result = H5TS_semaphore_wait(&test_info->ping_sem);
         CHECK_I(result, "H5TS_semaphore_wait");
 
-        test_info->counter++;
+        count = ++test_info->counter;
 
         result = H5TS_semaphore_signal(&test_info->pong_sem);
         CHECK_I(result, "H5TS_semaphore_signal");
-    } while (test_info->counter < NUM_PINGPONG);
+    } while (count < NUM_PINGPONG);
 
     return ret_value;
 }
@@ -60,18 +61,19 @@ static H5TS_THREAD_RETURN_TYPE
 pong(void *_test_info)
 {
     pingpong_t       *test_info = (pingpong_t *)_test_info;
+    unsigned          count;
     herr_t            result;
     H5TS_thread_ret_t ret_value = 0;
 
     do {
         result = H5TS_semaphore_wait(&test_info->pong_sem);
         CHECK_I(result, "H5TS_semaphore_wait");
 
-        test_info->counter++;
+        count = ++test_info->counter;
 
         result = H5TS_semaphore_signal(&test_info->ping_sem);
         CHECK_I(result, "H5TS_semaphore_signal");
-    } while (test_info->counter < NUM_PINGPONG);
+    } while (count < NUM_PINGPONG);
 
     return ret_value;
 }
@@ -268,4 +270,4 @@ tts_semaphore(void)
     tts_semaphore_clientserver();
 } /* end tts_semaphore() */
 
-#endif /* defined(H5_HAVE_THREADS) && defined(H5_HAVE_STDATOMIC_H) */
+#endif /* defined(H5_HAVE_THREADS) */