Update the VOL for HDF5 2.0.0 changes. (#73)

* Removed the use of H5VLpeek_connector_id_by_name as it was removed in newer than 1.14 HDF5 versions. * Updated for HDF5 2.0 VOL API changes, * Renaming of H5VLstart_lib_state and H5VLfinish_lib_state, along with new context state * Updated tests to pull from the newest HDF5 source.
HDFGroup · Nov 14, 2024 · 89db3d4 · 89db3d4
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diff --git a/.github/workflows/ubuntu_mpich.yml b/.github/workflows/ubuntu_mpich.yml
@@ -33,7 +33,7 @@ jobs:
         - name: Set up dependencies
           run: |
             sudo apt-get update
-            sudo apt-get install automake autoconf libtool libtool-bin m4
+            sudo apt-get install automake autoconf libtool libtool-bin m4 uuid-dev
             # The MPICH installed on github actions is too slow
             # sudo apt-get install mpich
             # mpicc -v
@@ -74,6 +74,7 @@ jobs:
                         --disable-tests \
                         --disable-fortran \
                         --disable-cxx \
+                        --enable-shared --disable-static \
                         CC=${GITHUB_WORKSPACE}/MPICH/bin/mpicc
             make -s LIBTOOLFLAGS=--silent V=1 -j 4 install > qout 2>&1
             make -s -j 4 distclean >> qout 2>&1

diff --git a/.github/workflows/ubuntu_openmpi.yml b/.github/workflows/ubuntu_openmpi.yml
@@ -32,7 +32,7 @@ jobs:
         - name: Set up dependencies
           run: |
             sudo apt-get update
-            sudo apt-get install automake autoconf libtool libtool-bin m4
+            sudo apt-get install automake autoconf libtool libtool-bin m4 uuid-dev
             # zlib
             sudo apt-get install zlib1g-dev
             # mpi
@@ -59,6 +59,7 @@ jobs:
                         --disable-tests \
                         --disable-fortran \
                         --disable-cxx \
+                        --enable-shared --disable-static \
                         CC=mpicc
             make -s LIBTOOLFLAGS=--silent V=1 -j 4 install > qout 2>&1
             make -s -j 4 distclean >> qout 2>&1

diff --git a/README.md b/README.md
@@ -23,7 +23,7 @@ but require the Log VOL to read them back.
 
 ### HDF5 VOL Connector ID
 * This Log VOL connector has been registered with the HDF group with
-  [Connector Identifier 514](https://portal.hdfgroup.org/display/support/Registered+VOL+Connectors).
+  [Connector Identifier 514](https://support.hdfgroup.org/documentation/hdf5-docs/registered_vol_connectors.html).
 
 ### Documents
 * [doc/userguide.md](doc/userguide.md) contains the compile and run instructions.

diff --git a/examples/hdf5_examples/Makefile.am b/examples/hdf5_examples/Makefile.am
@@ -66,31 +66,31 @@ nodist_h5_subset_SOURCES = h5_subset.c
 nodist_ph5example_SOURCES = ph5example.c
 endif
 
-HDF5_VERSION = hdf5-1_13_0
+HDF5_VERSION = develop
 HDF5_URL = https://raw.githubusercontent.com/HDFGroup/hdf5/${HDF5_VERSION}
 
 .SECONDEXPANSION:
 
-$(SEQ_SRCS): %.c : $$(wildcard %.patch.$(HDF5_VERSION))
-	@DOWNLOAD_CMD@ $(HDF5_URL)/examples/$@
-	if [ -f ${srcdir}/$(basename $@).patch.$(HDF5_VERSION) ]; then patch -st $@ < ${srcdir}/$(basename $@).patch.$(HDF5_VERSION); fi
+$(SEQ_SRCS): %.c : $$(wildcard %.patch)
+	@DOWNLOAD_CMD@ $(HDF5_URL)/HDF5Examples/C/TUTR/$@
+	if [ -f ${srcdir}/$(basename $@).patch ]; then patch -st $@ < ${srcdir}/$(basename $@).patch; fi
 	$(SED_I) -e "s|main(.*|main(int argc, char **argv)|g" $@
-	$(SED_I) -e "s|H5Fcreate(FILE|H5Fcreate(argv[1]|g" $@
+	$(SED_I) -e "s|H5Fcreate(FILENAME|H5Fcreate(argv[1]|g" $@
 	$(SED_I) -e "s|H5Fcreate(H5FILE_NAME|H5Fcreate(argv[1]|g" $@
-	$(SED_I) -e "s|H5Fopen(FILE|H5Fopen(argv[1]|g" $@
+	$(SED_I) -e "s|H5Fopen(FILENAME|H5Fopen(argv[1]|g" $@
 	$(SED_I) -e "s|H5Fopen(H5FILE_NAME|H5Fopen(argv[1]|g" $@
 
-$(PAR_SRCS): %.c : $$(wildcard %.patch.$(HDF5_VERSION))
-	@DOWNLOAD_CMD@ $(HDF5_URL)/examples/$@
-	if [ -f ${srcdir}/$(basename $@).patch.$(HDF5_VERSION) ]; then patch -st $@ < ${srcdir}/$(basename $@).patch.$(HDF5_VERSION); fi
+$(PAR_SRCS): %.c : $$(wildcard %.patch)
+	@DOWNLOAD_CMD@ $(HDF5_URL)/HDF5Examples/C/H5PAR/$@
+	if [ -f ${srcdir}/$(basename $@).patch ]; then patch -st $@ < ${srcdir}/$(basename $@).patch; fi
 
 check_PROGRAMS = $(TESTPROGRAMS)
 
 EXTRA_DIST = seq_runs.sh \
              parallel_run.sh \
-             ph5example.patch.$(HDF5_VERSION) \
-             h5_attribute.patch.$(HDF5_VERSION) \
-             h5_interm_group.patch.$(HDF5_VERSION)
+	     ph5example.patch \
+	     h5_attribute.patch \
+	     h5_interm_group.patch
 
 # autimake 1.11.3 has not yet implemented AM_TESTS_ENVIRONMENT
 # For newer versions, we can use AM_TESTS_ENVIRONMENT instead

diff --git a/examples/hdf5_examples/h5_attribute.patch b/examples/hdf5_examples/h5_attribute.patch
@@ -0,0 +1,45 @@
+--- h5_attribute.c	2024-11-12 16:49:52.466955555 -0600
++++ h5_attribute_logvol.c	2024-11-12 16:47:13.644521620 -0600
+@@ -41,7 +41,7 @@
+ /* Operator function */
+
+ int
+-main(void)
++main(int argc, char **argv)
+ {
+
+     hid_t file, dataset; /* File and dataset identifiers */
+@@ -79,7 +79,7 @@
+     /*
+      * Create a file.
+      */
+-    file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
++    file = H5Fcreate(argv[1], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+     /*
+      * Create the dataspace for the dataset in the file.
+@@ -167,7 +167,7 @@
+     /*
+      * Reopen the file.
+      */
+-    file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
++    file = H5Fopen(argv[1], H5F_ACC_RDONLY, H5P_DEFAULT);
+
+     /*
+      * Open the dataset.
+@@ -185,6 +185,7 @@
+
+     //! [H5Oget_info3_snip]
+
++#if 0
+     /*
+      * Find string attribute by iterating through all attributes
+      */
+@@ -203,6 +204,7 @@
+         ret = H5Aclose(attr);
+         ret = H5Tclose(atype);
+     }
++#endif
+
+     //! [H5Oget_info3_snip]
+     /*
diff --git a/examples/hdf5_examples/h5_attribute.patch.hdf5-1_13_0 b/examples/hdf5_examples/h5_attribute.patch.hdf5-1_13_0
diff --git a/...xamples/h5_interm_group.patch.hdf5-1_13_0 → examples/hdf5_examples/h5_interm_group.patch b/...xamples/h5_interm_group.patch.hdf5-1_13_0 → examples/hdf5_examples/h5_interm_group.patch
@@ -1,16 +1,16 @@
---- h5_interm_group.c	2022-03-16 18:21:18.837044757 -0500
-+++ h5_interm_group_logvol.c	2022-03-16 18:21:46.457044898 -0500
-@@ -88,10 +88,13 @@
+--- h5_interm_group.c	2024-11-13 11:56:00.913059201 -0600
++++ h5_interm_group_logvol.c	2024-11-13 11:56:54.281932771 -0600
+@@ -84,11 +84,12 @@
+         g2_id  = H5Gopen2(file, "/G1/G2", H5P_DEFAULT);
          status = H5Gget_info(g2_id, &g2_info);
          printf("Group /G1/G2 has %d member(s)\n", (int)g2_info.nlinks);
- 
+-
 +#if 0
          for (i = 0; i < (int)g2_info.nlinks; i++) {
              H5Lget_name_by_idx(g2_id, ".", H5_INDEX_NAME, H5_ITER_NATIVE, (hsize_t)i, name, 3, H5P_DEFAULT);
              printf("Object's name is %s\n", name);
          }
 +#endif
-+
          H5Gclose(g2_id);
      }
      H5Fclose(file);
diff --git a/...df5_examples/ph5example.patch.hdf5-1_13_0 → examples/hdf5_examples/ph5example.patch b/...df5_examples/ph5example.patch.hdf5-1_13_0 → examples/hdf5_examples/ph5example.patch
@@ -1,14 +1,22 @@
---- ph5example.c	2022-12-24 17:10:24.423988722 -0600
-+++ ph5example_logvol.c	2022-12-24 17:14:47.240314745 -0600
-@@ -51,6 +51,7 @@
-         printf("%s\n", x);
+--- ph5example.c	2024-11-12 14:13:11.462119142 -0600
++++ ph5example_logvol.c	2024-11-12 14:15:08.212012234 -0600
+@@ -52,12 +52,14 @@
+     } while (0)
 
  #define MPI_BANNER(mesg)                                                                                     \
-+    if (0)                                                                                                   \
-     {                                                                                                        \
++    if (0) {                                                                                                 \
+     do {                                                                                                     \
          printf("--------------------------------\n");                                                        \
          printf("Proc %d: ", mpi_rank);                                                                       \
-@@ -96,7 +97,7 @@
+         printf("*** %s\n", mesg);                                                                            \
+         printf("--------------------------------\n");                                                        \
+-    } while (0)
++    } while (0);                                                                                             \
++    }
+
+ #define SYNC(comm)                                                                                           \
+     do {                                                                                                     \
+@@ -97,7 +99,7 @@
  int verbose   = 0; /* verbose, default as no. */
  int doread    = 1; /* read test */
  int dowrite   = 1; /* write test */
@@ -17,17 +25,18 @@
 
  /* Prototypes */
  void slab_set(hsize_t start[], hsize_t count[], hsize_t stride[], int mode);
-@@ -888,6 +889,9 @@
+@@ -907,6 +909,10 @@
          mrc = MPI_File_delete(filenames[color], info);
          assert(mrc == MPI_SUCCESS);
      }
-+    
++
 +    // Prevent odd-rank to start the next test
 +    MPI_Barrier(MPI_COMM_WORLD);
++
+     MPI_Comm_free(&comm);
  }
 
- /*
-@@ -972,7 +976,7 @@
+@@ -992,7 +998,7 @@
                      }
                      break;
                  case 'c':
@@ -36,7 +45,7 @@
                      break;
                  case 'r':
                      doread = 0;
-@@ -1026,7 +1030,8 @@
+@@ -1046,7 +1052,8 @@
      char mpi_name[MPI_MAX_PROCESSOR_NAME];
      int  i, n;
 

diff --git a/src/H5VL_log_att.cpp b/src/H5VL_log_att.cpp
@@ -388,7 +388,7 @@ herr_t H5VL_log_attr_specific (void *obj,
                                void **req) {
     H5VL_log_obj_t *op = (H5VL_log_obj_t *)obj;
     herr_t err         = 0;
-    H5VL_log_req_t *rp;
+    H5VL_log_req_t *rp = NULL;
     void **ureqp, *ureq;
     char *iname                   = NULL;  // Internal name of object
     const char *original_name     = NULL;  // Original value in loc_params before being remapped

diff --git a/src/H5VL_log_dataset.cpp b/src/H5VL_log_dataset.cpp
@@ -76,9 +76,10 @@ void *H5VL_log_dataset_create (void *obj,
     void **ureqp, *ureq;
     H5D_fill_value_t stat;
     void *lib_state = NULL;
+    void *lib_context = NULL;
     // char lname[1024];
     H5VL_logi_err_finally finally (
-        [&dcpl_id, &lib_state] () -> void { H5VL_logi_restore_lib_stat (lib_state); });
+        [&dcpl_id, &lib_state, &lib_context] () -> void { H5VL_logi_restore_lib_stat (lib_state, lib_context); });
 
     try {
         H5VL_LOGI_PROFILING_TIMER_START;
@@ -160,7 +161,7 @@ void *H5VL_log_dataset_create (void *obj,
         H5VL_logi_get_filters (dcpl_id, dip->filters);
 
         // Reset hdf5 context to allow attr operations within a dataset operation
-        H5VL_logi_reset_lib_stat (lib_state);
+        H5VL_logi_reset_lib_stat (lib_state, lib_context);
 
         // Record dataset metadata as attributes
         H5VL_logi_add_att (dp, H5VL_LOG_DATASETI_ATTR_DIMS, H5T_STD_I64LE, H5T_NATIVE_INT64,
@@ -282,7 +283,7 @@ static herr_t H5VL_log_dataset_read_elements (void *dset,
     herr_t err                = 0;
     H5VL_log_dset_t *dp       = (H5VL_log_dset_t *)dset;
     H5VL_log_dset_info_t *dip = NULL;  // Dataset info
-    hid_t dsid;                        // Dataset space id
+    hid_t dsid = H5I_INVALID_HID;      // Dataset space id
     H5VL_log_selections *dsel = NULL;  // Selection blocks
 
     try {
@@ -325,7 +326,7 @@ static herr_t H5VL_log_dataset_write_elements (void *dset,
     H5VL_log_dset_t *dp = (H5VL_log_dset_t *)dset;
 
     H5VL_log_dset_info_t *dip = NULL;  // Dataset info
-    hid_t dsid;                        // Dataset space id
+    hid_t dsid = H5I_INVALID_HID;      // Dataset space id
     H5VL_log_selections *dsel = NULL;  // Selection blocks
 
     try {

diff --git a/src/H5VL_log_dataseti.cpp b/src/H5VL_log_dataseti.cpp
@@ -695,14 +695,15 @@ void *H5VL_log_dataseti_open (void *obj, void *uo, hid_t dxpl_id) {
     std::unique_ptr<H5VL_log_dset_info_t> dip;  // Dataset info
     H5D_fill_value_t stat;
     void *lib_state = NULL;
-    H5VL_logi_err_finally finally ([&dcpl_id, &lib_state] () -> void {
+    void *lib_context = NULL;
+    H5VL_logi_err_finally finally ([&dcpl_id, &lib_state, &lib_context] () -> void {
         if (dcpl_id >= 0) { H5Pclose (dcpl_id); }
-        H5VL_logi_restore_lib_stat (lib_state);
+        H5VL_logi_restore_lib_stat (lib_state, lib_context);
     });
     H5VL_LOGI_PROFILING_TIMER_START;
 
     // Reset hdf5 context to allow file operations within a dataset operation
-    H5VL_logi_reset_lib_stat (lib_state);
+    H5VL_logi_reset_lib_stat (lib_state, lib_context);
 
     dp = std::make_unique<H5VL_log_dset_t> (op, H5I_DATASET, uo);
 
@@ -806,9 +807,10 @@ void H5VL_log_dataseti_write (H5VL_log_dset_t *dp,
     int clen, inlen;  // Compressed size; Size of data to be compressed
 #endif
     void *lib_state = NULL;
-    H5VL_logi_err_finally finally ([&ptype, &lib_state] () -> void {
+    void *lib_context = NULL;
+    H5VL_logi_err_finally finally ([&ptype, &lib_state, &lib_context] () -> void {
         H5VL_log_type_free (ptype);
-        H5VL_logi_restore_lib_stat (lib_state);
+        H5VL_logi_restore_lib_stat (lib_state, lib_context);
     });
     H5VL_LOGI_PROFILING_TIMER_START;
 
@@ -830,7 +832,7 @@ void H5VL_log_dataseti_write (H5VL_log_dset_t *dp,
     H5VL_LOGI_PROFILING_TIMER_STOP (dp->fp, TIMER_H5VL_LOG_DATASET_WRITE_INIT);
 
     // Reset hdf5 context to allow file operations within a dataset operation
-    H5VL_logi_reset_lib_stat (lib_state);
+    H5VL_logi_reset_lib_stat (lib_state, lib_context);
 
     if (dp->fp->config ^ H5VL_FILEI_CONFIG_METADATA_MERGE) {
         H5VL_LOGI_PROFILING_TIMER_START;
@@ -1047,9 +1049,10 @@ void H5VL_log_dataseti_read (H5VL_log_dset_t *dp,
     hbool_t rtype;        // Non-blocking?
     size_t num_pending_writes = 0;
     void *lib_state = NULL;
+    void *lib_context = NULL;
     H5FD_mpio_xfer_t xfer_mode;
     H5VL_logi_err_finally finally (
-        [&lib_state] () -> void { H5VL_logi_restore_lib_stat (lib_state); });
+        [&lib_state, &lib_context] () -> void { H5VL_logi_restore_lib_stat (lib_state, lib_context); });
     H5VL_LOGI_PROFILING_TIMER_START;
 
     H5VL_LOGI_PROFILING_TIMER_START;
@@ -1059,7 +1062,7 @@ void H5VL_log_dataseti_read (H5VL_log_dset_t *dp,
     H5VL_LOGI_PROFILING_TIMER_STOP (dp->fp, TIMER_H5VL_LOG_DATASET_READ_INIT);
 
     // Reset hdf5 context to allow file operations within a dataset operation
-    H5VL_logi_reset_lib_stat (lib_state);
+    H5VL_logi_reset_lib_stat (lib_state, lib_context);
 
     // Check mem space selection
     if (mem_space_id == H5S_ALL)