Updated H5VOL for HDF5 v1.13

docs/user_guide/source/setting_up/source/cmake.rst

@@ -128,9 +128,9 @@ Notes:
 .. code-block:: bash
 
     # Several dependencies are installed under /opt/foo/bar and then a
-    # single dependency (HDF5 in this case) is installed in /opt/hdf5/1.12.0
+    # single dependency (HDF5 in this case) is installed in /opt/hdf5/1.13.0
     $ export CMAKE_PREFIX_PATH=/opt/foo/bar
-    $ cmake -DHDF5_ROOT=/opt/hdf5/1.12.0 ../ADIOS2
+    $ cmake -DHDF5_ROOT=/opt/hdf5/1.13.0 ../ADIOS2
 
 Example: the following configuration will build, test and install under /opt/adios2/2.7.1 an optimized (Release) version of ADIOS2.
 

scripts/ci/images/power8-el7-leaf-smpi/Dockerfile

@@ -12,15 +12,15 @@ ENV MPI_ROOT=/opt/ibm/spectrum_mpi \
     PATH=/opt/ibm/spectrum_mpi/bin:${PATH} \
     LD_LIBRARY_PATH=/opt/ibm/spectrum_mpi/lib:${PATH}
 
-# Install HDF5 1.12.0
+# Install HDF5 1.13.0
 WORKDIR /opt/hdf5
 ARG HDF5_ARGS
-RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.bz2 | \
+RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.0/src/hdf5-1.13.0.tar.bz2 | \
         tar -xvj && \
     mkdir build && \
     cd build && \
     cmake ${HDF5_ARGS} \
-        -DCMAKE_INSTALL_PREFIX=/opt/hdf5/1.12.0 \
+        -DCMAKE_INSTALL_PREFIX=/opt/hdf5/1.13.0 \
         -DBUILD_SHARED_LIBS=ON \
         -DBUILD_STATIC_LIBS=OFF \
         -DCMAKE_BUILD_TYPE=Release \
@@ -29,13 +29,13 @@ RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0
         -DBUILD_TESTING=OFF \
         -DHDF5_BUILD_TOOLS=ON \
         -DHDF5_ENABLE_PARALLEL=ON \
-        ../hdf5-1.12.0 && \
+        ../hdf5-1.13.0 && \
     make -j$(grep -c '^processor' /proc/cpuinfo) install && \
     cd .. && \
-    rm -rf hdf5-1.12.0 build
-ENV PATH=/opt/hdf5/1.12.0/bin:${PATH} \
-    LD_LIBRARY_PATH=/opt/hdf5/1.12.0/lib:${LD_LIBRARY_PATH} \
-    CMAKE_PREFIX_PATH=/opt/hdf5/1.12.0:${CMAKE_PREFIX_PATH}
+    rm -rf hdf5-1.13.0 build
+ENV PATH=/opt/hdf5/1.13.0/bin:${PATH} \
+    LD_LIBRARY_PATH=/opt/hdf5/1.13.0/lib:${LD_LIBRARY_PATH} \
+    CMAKE_PREFIX_PATH=/opt/hdf5/1.13.0:${CMAKE_PREFIX_PATH}
 
 # Misc cleanup of unneeded files
 RUN rm -rf /tmp/* && \

scripts/ci/images/power8-el7-leaf/Dockerfile

@@ -1,14 +1,14 @@
 ARG COMPILER
 FROM ornladios/adios2:ci-x86_64-power8-el7-${COMPILER}-base
 
-# Install HDF5 1.12.0
+# Install HDF5 1.13.0
 WORKDIR /opt/hdf5
-RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.bz2 | \
+RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.0/src/hdf5-1.13.0.tar.bz2 | \
         tar -xvj && \
     mkdir build && \
     cd build && \
     cmake \
-        -DCMAKE_INSTALL_PREFIX=/opt/hdf5/1.12.0 \
+        -DCMAKE_INSTALL_PREFIX=/opt/hdf5/1.13.0 \
         -DBUILD_SHARED_LIBS=ON \
         -DBUILD_STATIC_LIBS=OFF \
         -DCMAKE_BUILD_TYPE=Release \
@@ -17,13 +17,13 @@ RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0
         -DHDF5_BUILD_EXAMPLES=OFF \ 
         -DBUILD_TESTING=OFF \
         -DHDF5_BUILD_TOOLS=OFF \
-        ../hdf5-1.12.0 && \
+        ../hdf5-1.13.0 && \
     make -j$(grep -c '^processor' /proc/cpuinfo) install && \
     cd .. && \
-    rm -rf hdf5-1.12.0 build
-ENV PATH=/opt/hdf5/1.12.0/bin:${PATH} \
-    LD_LIBRARY_PATH=/opt/hdf5/1.12.0/lib:${LD_LIBRARY_PATH} \
-    CMAKE_PREFIX_PATH=/opt/hdf5/1.12.0:${CMAKE_PREFIX_PATH}
+    rm -rf hdf5-1.13.0 build
+ENV PATH=/opt/hdf5/1.13.0/bin:${PATH} \
+    LD_LIBRARY_PATH=/opt/hdf5/1.13.0/lib:${LD_LIBRARY_PATH} \
+    CMAKE_PREFIX_PATH=/opt/hdf5/1.13.0:${CMAKE_PREFIX_PATH}
 
 # Misc cleanup of unneeded files
 RUN rm -rf /tmp/* && \

scripts/ci/images/suse-nvhpcsdk-openmpi/Dockerfile

@@ -1,15 +1,15 @@
 FROM ornladios/adios2:ci-suse-nvhpcsdk-base
 
-# Install HDF5 1.12.0
+# Install HDF5 1.13.0
 WORKDIR /opt/hdf5
-RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.bz2 | \
+RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.0/src/hdf5-1.13.0.tar.bz2 | \
         tar -xvj && \
     mkdir build && \
     cd build && \
     source /etc/profile && \
     module load nvhpc && \
     /opt/cmake/bin/cmake \
-        -DCMAKE_INSTALL_PREFIX=/opt/hdf5/1.12.0 \
+        -DCMAKE_INSTALL_PREFIX=/opt/hdf5/1.13.0 \
         -DBUILD_SHARED_LIBS=ON \
         -DBUILD_STATIC_LIBS=OFF \
         -DCMAKE_BUILD_TYPE=Release \
@@ -18,13 +18,13 @@ RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0
         -DHDF5_BUILD_EXAMPLES=OFF \ 
         -DBUILD_TESTING=OFF \
         -DHDF5_BUILD_TOOLS=OFF \
-        ../hdf5-1.12.0 && \
+        ../hdf5-1.13.0 && \
     make -j$(grep -c '^processor' /proc/cpuinfo) install && \
     cd .. && \
-    rm -rf hdf5-1.12.0 build
-ENV PATH=/opt/hdf5/1.12.0/bin:${PATH} \
-    LD_LIBRARY_PATH=/opt/hdf5/1.12.0/lib:${LD_LIBRARY_PATH} \
-    CMAKE_PREFIX_PATH=/opt/hdf5/1.12.0:${CMAKE_PREFIX_PATH}
+    rm -rf hdf5-1.13.0 build
+ENV PATH=/opt/hdf5/1.13.0/bin:${PATH} \
+    LD_LIBRARY_PATH=/opt/hdf5/1.13.0/lib:${LD_LIBRARY_PATH} \
+    CMAKE_PREFIX_PATH=/opt/hdf5/1.13.0:${CMAKE_PREFIX_PATH}
 
 # Misc cleanup of unneeded files
 RUN rm -rf /tmp/* && \

scripts/ci/images/suse-nvhpcsdk/Dockerfile

@@ -2,14 +2,14 @@ FROM ornladios/adios2:ci-suse-nvhpcsdk-base
 
 # Install HDF5
 WORKDIR /opt/hdf5
-RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.bz2 | \
+RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.0/src/hdf5-1.13.0.tar.bz2 | \
         tar -xvj && \
     mkdir build && \
     cd build && \
     source /etc/profile && \
     module load nvhpc-nompi && \
     /opt/cmake/bin/cmake \
-        -DCMAKE_INSTALL_PREFIX=/opt/hdf5/1.12.0 \
+        -DCMAKE_INSTALL_PREFIX=/opt/hdf5/1.13.0 \
         -DBUILD_SHARED_LIBS=ON \
         -DBUILD_STATIC_LIBS=OFF \
         -DCMAKE_BUILD_TYPE=Release \
@@ -18,13 +18,13 @@ RUN curl -L https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0
         -DHDF5_BUILD_EXAMPLES=OFF \ 
         -DBUILD_TESTING=OFF \
         -DHDF5_BUILD_TOOLS=OFF \
-        ../hdf5-1.12.0 && \
+        ../hdf5-1.13.0 && \
     make -j$(grep -c '^processor' /proc/cpuinfo) install && \
     cd .. && \
-    rm -rf hdf5-1.12.0 build
-ENV PATH=/opt/hdf5/1.12.0/bin:${PATH} \
-    LD_LIBRARY_PATH=/opt/hdf5/1.12.0/lib:${LD_LIBRARY_PATH} \
-    CMAKE_PREFIX_PATH=/opt/hdf5/1.12.0:${CMAKE_PREFIX_PATH}
+    rm -rf hdf5-1.13.0 build
+ENV PATH=/opt/hdf5/1.13.0/bin:${PATH} \
+    LD_LIBRARY_PATH=/opt/hdf5/1.13.0/lib:${LD_LIBRARY_PATH} \
+    CMAKE_PREFIX_PATH=/opt/hdf5/1.13.0:${CMAKE_PREFIX_PATH}
 
 # Misc cleanup of unneeded files
 RUN rm -rf /tmp/* && \

source/h5vol/CMakeLists.txt

@@ -18,6 +18,16 @@ target_include_directories(adios2_h5vol PRIVATE ${HDF5_C_INCLUDE_DIRS})
 target_link_libraries(adios2_h5vol PRIVATE
   ${HDF5_C_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}
 )
+
+message(STATUS "HDF5_VERSION=${HDF5_VERSION}")
+if (HDF5_VERSION)
+  if (HDF5_VERSION VERSION_LESS "1.13")
+    message(FATAL_ERROR "HDF5 version 1.13+ is required")
+  endif()
+else()
+  message(WARNING "Version of HDF5 is unknown, but version 1.13+ is required.")
+endif()
+
 if(NOT HDF5_IS_PARALLEL)
   target_link_libraries(adios2_h5vol PRIVATE adios2::c)
 elseif(HDF5_IS_PARALLEL AND ADIOS2_HAVE_MPI)

source/h5vol/H5VolReadWrite.c

@@ -626,7 +626,7 @@ H5VL_GroupDef_t *gCreateGroupDef(const char *name)
     return grp;
 }
 
-ssize_t gGetBranchNameLength(H5VL_ObjDef_t *vol, size_t namelen)
+size_t gGetBranchNameLength(H5VL_ObjDef_t *vol, size_t namelen)
 {
     if (vol->m_Path != NULL)
         if ('/' == (vol->m_Path)[strlen(vol->m_Path) - 1])
@@ -654,7 +654,7 @@ void gGetBranchName(H5VL_ObjDef_t *vol, const char *fullPath, char *name)
 //
 //  returns length of name
 //
-ssize_t gGetNameOfNthAttr(H5VL_ObjDef_t *vol, uint32_t idx, char *name)
+size_t gGetNameOfNthAttr(H5VL_ObjDef_t *vol, uint32_t idx, char *name)
 {
     gLoadContent(vol);
     if (0 == vol->m_NumAttrs)
@@ -689,7 +689,7 @@ ssize_t gGetNameOfNthAttr(H5VL_ObjDef_t *vol, uint32_t idx, char *name)
 //  called from: H5Gget_info, then H5Gget_objname_by_idx
 //  (which calls H5Lget_name.. )
 //
-ssize_t gGetNameOfNthItem(H5VL_ObjDef_t *vol, uint32_t idx, char *name)
+size_t gGetNameOfNthItem(H5VL_ObjDef_t *vol, uint32_t idx, char *name)
 {
     gLoadContent(vol);
 

source/h5vol/H5VolReadWrite.h

@@ -34,7 +34,8 @@ extern herr_t H5VL_adios2_beginstep(const char *engine_name,
 extern herr_t H5VL_adios2_endstep(const char *engine_nane);
 
 static herr_t H5VL_adios2_introspect_opt_query(void *obj, H5VL_subclass_t cls,
-                                               int opt_type, hbool_t *supported)
+                                               int opt_type,
+                                               uint64_t *supported)
 {
     *supported = 0;
     return 0;
@@ -52,10 +53,11 @@ static herr_t H5VL_adios2_datatype_close(void *dt, hid_t H5_ATTR_UNUSED dxpl_id,
 static const H5VL_class_t H5VL_adios2_def = {
     H5VL_ADIOS2_VERSION,
     (H5VL_class_value_t)H5VL_ADIOS2_VALUE,
-    H5VL_ADIOS2_NAME, /* name */
-    0,
-    H5VL_adios2_init, /* initialize */
-    H5VL_adios2_term, /* terminate */
+    H5VL_ADIOS2_NAME,   /* name */
+    0,                  /* Version # of connector */
+    H5VL_CAP_FLAG_NONE, /* Capability flags for connector */
+    H5VL_adios2_init,   /* initialize */
+    H5VL_adios2_term,   /* terminate */
     {
         /* info_cls */
         (size_t)0, /* info size    */
@@ -118,6 +120,7 @@ static const H5VL_class_t H5VL_adios2_def = {
     {
         /* introspect_cls */
         NULL, // H5VL_pass_through_introspect_get_conn_cls,  /* get_conn_cls */
+        NULL, /* get_cap_flags */
         H5VL_adios2_introspect_opt_query, /* opt_query */
     },
     {

source/h5vol/H5Vol_attr.c

@@ -154,29 +154,39 @@ void GetFromAttribute(void *attrObj, hid_t *ret_id, H5VL_attr_get_t get_type)
     }
 }
 
-herr_t H5VL_adios2_attr_get(void *obj, H5VL_attr_get_t get_type, hid_t dxpl_id,
-                            void **req, va_list arguments)
+herr_t H5VL_adios2_attr_get(void *obj, H5VL_attr_get_args_t *args,
+                            hid_t dxpl_id, void **req)
 {
     REQUIRE_NOT_NULL_ERR(obj, -1);
     H5VL_ObjDef_t *vol = (H5VL_ObjDef_t *)obj;
 
-    if ((get_type == H5VL_ATTR_GET_SPACE) || (get_type == H5VL_ATTR_GET_TYPE))
+    switch (args->op_type)
     {
-        hid_t *ret_id = va_arg(arguments, hid_t *);
-        GetFromAttribute((vol->m_ObjPtr), ret_id, get_type);
+    case H5VL_ATTR_GET_SPACE:
+    {
+        hid_t *ret_id = (hid_t *)args->args.get_space.space_id;
+        GetFromAttribute((vol->m_ObjPtr), ret_id, args->op_type);
         return 0;
     }
+    case H5VL_ATTR_GET_TYPE:
+    {
+        hid_t *ret_id = (hid_t *)args->args.get_type.type_id;
+        GetFromAttribute((vol->m_ObjPtr), ret_id, args->op_type);
+        return 0;
+    }
+    default:
+        break;
+    }
 
-    const H5VL_loc_params_t *loc_params =
-        va_arg(arguments, const H5VL_loc_params_t *);
-    REQUIRE_NOT_NULL_ERR(loc_params, -1);
-
-    switch (get_type)
+    switch (args->op_type)
     {
     case H5VL_ATTR_GET_NAME:
     {
-        char *buf = va_arg(arguments, char *);
-        ssize_t *ret_val = va_arg(arguments, ssize_t *);
+        char *buf = args->args.get_name.buf;
+        size_t *ret_val = (size_t *)args->args.get_name.attr_name_len;
+
+        const H5VL_loc_params_t *loc_params = &args->args.get_name.loc_params;
+        REQUIRE_NOT_NULL_ERR(loc_params, -1);
 
         if (H5VL_OBJECT_BY_SELF == loc_params->type)
         {
@@ -222,19 +232,22 @@ herr_t H5VL_adios2_attr_close(void *attr, hid_t dxpl_id, void **req)
 }
 
 herr_t H5VL_adios2_attr_specific(void *obj, const H5VL_loc_params_t *loc_params,
-                                 H5VL_attr_specific_t specific_type,
-                                 hid_t dxpl_id, void **req, va_list arguments)
+                                 H5VL_attr_specific_args_t *args, hid_t dxpl_id,
+                                 void **req)
 {
     REQUIRE_NOT_NULL_ERR(obj, -1);
     H5VL_ObjDef_t *vol = (H5VL_ObjDef_t *)obj;
-    const char *attr_name = va_arg(arguments, const char *);
 
-    adios2_attribute *attr = gLocateAttrFrom(vol, attr_name);
+    const char *attr_name;
+    adios2_attribute *attr;
 
-    switch (specific_type)
+    switch (args->op_type)
     {
     case H5VL_ATTR_DELETE:
     {
+        attr_name = (const char *)args->args.del.name;
+        attr = gLocateAttrFrom(vol, attr_name);
+
         if (NULL != attr)
         {
             if (NULL == vol->m_Path)
@@ -250,7 +263,11 @@ herr_t H5VL_adios2_attr_specific(void *obj, const H5VL_loc_params_t *loc_params,
     }
     case H5VL_ATTR_EXISTS:
     {
-        htri_t *ret = va_arg(arguments, htri_t *);
+        hbool_t *ret = args->args.exists.exists;
+
+        attr_name = (const char *)args->args.exists.name;
+        attr = gLocateAttrFrom(vol, attr_name);
+
         if (NULL == attr)
         {
             *ret = 0;

source/h5vol/H5Vol_dataset.c

@@ -100,26 +100,26 @@ herr_t H5VL_adios2_dataset_read(void *dset, hid_t mem_type_id,
     return gADIOS2ReadVar(var);
 }
 
-herr_t H5VL_adios2_dataset_get(void *dset, H5VL_dataset_get_t get_type,
-                               hid_t dxpl_id, void **req, va_list arguments)
+herr_t H5VL_adios2_dataset_get(void *dset, H5VL_dataset_get_args_t *args,
+                               hid_t dxpl_id, void **req)
 {
     REQUIRE_NOT_NULL_ERR(dset, -1);
     H5VL_ObjDef_t *vol = (H5VL_ObjDef_t *)dset;
     H5VL_VarDef_t *varDef = (H5VL_VarDef_t *)(vol->m_ObjPtr);
 
-    switch (get_type)
+    switch (args->op_type)
     {
     case H5VL_DATASET_GET_SPACE:
     {
-        hid_t *ret_id = va_arg(arguments, hid_t *);
+        hid_t *ret_id = (hid_t *)args->args.get_space.space_id;
         *ret_id = H5Scopy(varDef->m_ShapeID);
         REQUIRE_SUCC_MSG((*ret_id >= 0), -1,
                          "H5VOL-ADIOS2: Unable to get space id.");
         break;
     }
     case H5VL_DATASET_GET_TYPE:
     {
-        hid_t *ret_id = va_arg(arguments, hid_t *);
+        hid_t *ret_id = (hid_t *)args->args.get_type.type_id;
         *ret_id = H5Tcopy(varDef->m_TypeID);
         break;
     }