Feature/subfiling

.github/workflows/codespell.yml

@@ -12,4 +12,4 @@ jobs:
       - uses: codespell-project/actions-codespell@master
         with:
           skip: ./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c
-          ignore_words_list: isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,minnum
+          ignore_words_list: isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,minnum,ake,gord,numer

CMakeLists.txt

@@ -738,6 +738,16 @@ if (H5_HAVE_PARALLEL)
   endif ()
 endif ()
 
+# see other find_package examples in /usr/share/cmake/Modules                                                                                                                                                                                 
+option (HDF5_BUILD_SUBFILING  "Build Parallel HDF5 Subfiling" OFF)
+if (HDF5_BUILD_SUBFILING AND HDF5_ENABLE_PARALLEL)
+  message (STATUS "Setting up to use Mercury components")
+  include_directories(${HDF5_SRC_DIR}/mercury/include)
+  set (WITH_SUBFILING 1)
+  set (H5_HAVE_MERCURY_H 1)
+  set (CMAKE_REQUIRED_INCLUDES "${HDF5_SRC_DIR}/mercury/include")
+endif()
+
 #option (DEFAULT_API_VERSION "Enable v1.14 API (v16, v18, v110, v112, v114)" "v114")
 set (DEFAULT_API_VERSION "v114" CACHE STRING "Enable v1.14 API (v16, v18, v110, v112, v114)")
 set_property (CACHE DEFAULT_API_VERSION PROPERTY STRINGS v16 v18 v110 v112 v114)

MANIFEST

@@ -810,6 +810,9 @@
 ./src/H5FDhdfs.c
 ./src/H5FDhdfs.h
 ./src/H5FDint.c
+./src/H5FDioc.c
+./src/H5FDioc.h
+./src/H5FDioc_threads.c
 ./src/H5FDlog.c
 ./src/H5FDlog.h
 ./src/H5FDmirror.c
@@ -836,6 +839,11 @@
 ./src/H5FDsplitter.c
 ./src/H5FDsplitter.h
 ./src/H5FDstdio.c
+./src/H5FDsubfile_int.c
+./src/H5FDsubfile_mpi.c
+./src/H5FDsubfiling.c
+./src/H5FDsubfiling.h
+./src/H5FDsubfiling_priv.h
 ./src/H5FDstdio.h
 ./src/H5FDtest.c
 ./src/H5FDwindows.c
@@ -1540,6 +1548,7 @@
 ./testpar/t_pshutdown.c
 ./testpar/t_prestart.c
 ./testpar/t_span_tree.c
+./testpar/t_subfiling_vfd.c
 ./testpar/t_vfd.c
 ./testpar/t_init_term.c
 ./testpar/t_2Gio.c
@@ -3008,6 +3017,9 @@
 ./utils/mirror_vfd/mirror_server_stop.c
 ./utils/mirror_vfd/mirror_writer.c
 
+# Subfiling VFD utilities
+./utils/subfiling_vfd/h5fuse.sh
+
 # test utilities
 ./utils/test/Makefile.am
 ./utils/test/swmr_check_compat_vfd.c

bin/trace

@@ -88,6 +88,7 @@ $Source = "";
                "H5_index_t"                 => "Ii",
                "H5I_iterate_func_t"         => "II",
                "H5_iter_order_t"            => "Io",
+               "ioc_selection_t"            => "IO",
                "H5I_future_realize_func_t"  => "IR",
                "int"                        => "Is",
                "int32_t"                    => "Is",
@@ -188,6 +189,7 @@ $Source = "";
                "H5Z_filter_t"               => "Zf",
                "H5Z_filter_func_t"          => "ZF",
                "ssize_t"                    => "Zs",
+
 # Types below must be defined here, as they appear in function arguments,
 # but they are not yet supported in the H5_trace_args() routine yet.  If
 # they are used as an actual parameter type (and not just as a pointer to

c++/src/H5FaccProp.cpp

@@ -156,7 +156,7 @@ FileAccPropList::getDriver() const
 // Function:    FileAccPropList::setDriver
 ///\brief       Set file driver for this property list.
 ///\param       new_driver_id   - IN: File driver
-///\param       new_driver_info - IN: Struct containing the driver-specific properites
+///\param       new_driver_info - IN: Struct containing the driver-specific properties
 ///\exception   H5::PropListIException
 ///\par Description
 ///             For information, please refer to the H5Pset_driver API in

config/sanitizer/LICENSE

@@ -124,7 +124,7 @@
       may provide additional or different license terms and conditions
       for use, reproduction, or distribution of Your modifications, or
       for any such Derivative Works as a whole, provided Your use,
-      reproduction, and distribution of the Work otherwise complies with
+      reproduction, and distribution of the Work otherwise compiles with
       the conditions stated in this License.
 
    5. Submission of Contributions. Unless You explicitly state otherwise,

configure.ac

@@ -1584,6 +1584,68 @@ case "X-$withval" in
 esac
 
 
+## ----------------------------------------------------------------------
+## Is mercury(an external RPC Framework library) requested? It has a 
+## header file `mercury.h' and a library `-lmercury_util' and their 
+## install locations might be specified with the `--with-mercury'
+## command-line switch. The value is an include path and/or a library path.
+## If the library path is specified then it must be preceded by a comma.
+##
+AC_SUBST([HAVE_MERCURY])
+
+## Default is not present
+HAVE_MERCURY=no
+
+AC_ARG_WITH([mercury],
+            [AS_HELP_STRING([--with-mercury=DIR],
+                            [Use the mercury library [default=no]])],,
+            [withval=no])
+
+case "X-$withval" in
+  X-yes)
+    HAVE_MERCURY="yes"
+    if test -z "$HAVE_MERCURY" -a -n "$HDF5_CONFIG_ABORT"; then
+      AC_MSG_ERROR([couldn't find mercury library])
+    fi
+    echo "HAVE_MERCURY flag = $HAVE_MERCURY"
+    ;;
+  X-|X-no|X-none)
+    HAVE_MERCURY="no"
+    AC_MSG_CHECKING([for mercury library])
+    AC_MSG_RESULT([suppressed])
+    ;;
+  *)
+    HAVE_MERCURY="yes"
+    case "$withval" in
+      *,*)
+        mercury_inc="`echo $withval |cut -f1 -d,`"
+        mercury_lib="`echo $withval |cut -f2 -d, -s`"
+        ;;
+      *)
+        if test -n "$withval"; then
+          mercury_inc="$withval/include"
+          mercury_lib="$withval/lib"
+        fi
+        ;;
+    esac
+
+    echo "checking include path: $mercury_inc"
+    saved_CPPFLAGS="$CPPFLAGS"
+    saved_AM_CPPFLAGS="$AM_CPPFLAGS"
+    saved_LDFLAGS="$LDFLAGS"
+    saved_AM_LDFLAGS="$AM_LDFLAGS"
+
+    if test -n "$mercury_inc"; then
+      CPPFLAGS="$CPPFLAGS -I$mercury_inc"
+      AM_CPPFLAGS="$AM_CPPFLAGS -I$mercury_inc"
+    fi
+
+    AC_CHECK_HEADERS([mercury.h],,[CPPFLAGS="$saved_CPPFLAGS"; AM_CPPFLAGS="$saved_AM_CPPFLAGS"] [unset HAVE_MERCURY])
+    ;;
+esac
+
+AM_CONDITIONAL([HAVE_MERCURY_CONDITIONAL], [test "X$HAVE_MERCURY" = "Xyes"])
+
 ## ----------------------------------------------------------------------
 ## Make the external filters list available to *.in files
 ## At this point it's unset (no external filters by default) but it
@@ -3043,6 +3105,7 @@ if test -n "$PARALLEL"; then
 fi
 
 ## ----------------------------------------------------------------------
+
 ## Build parallel tools if parallel tools, parallel, and build tools options
 ## are all enabled.
 ##
@@ -3200,6 +3263,34 @@ else
     AC_MSG_RESULT([no])
 fi
 
+## ----------------------------------------------------------------------
+## Check if Subfiling I/O driver is enabled by --enable-subfiling-vfd
+##
+AC_SUBST([SUBFILING_VFD])
+
+## Default is no direct VFD
+SUBFILING_VFD=no
+
+AC_MSG_CHECKING([if the subfiling I/O virtual file driver (VFD) is enabled])
+
+AC_ARG_ENABLE([subfiling-vfd],
+              [AS_HELP_STRING([--enable-subfiling-vfd],
+                              [Build the subfiling I/O virtual file driver (VFD).
+                               [default=no]])],
+              [SUBFILING_VFD=$enableval], [SUBFILING_VFD=no])
+
+if test "X$SUBFILING_VFD" = "Xyes"; then
+        AC_MSG_RESULT([yes])
+        AC_DEFINE([HAVE_SUBFILING], [1],
+                [Define if the subfiling I/O virtual file driver (VFD) should be compiled])
+else
+    AC_MSG_RESULT([no])
+fi
+
+## Subfiling VFD files are not built if not required.
+AM_CONDITIONAL([SUBFILING_VFD_CONDITIONAL], [test "X$SUBFILING_VFD" = "Xyes"])
+
+
 ## ----------------------------------------------------------------------
 ## Check if Direct I/O driver is enabled by --enable-direct-vfd
 ##

fortran/test/tH5P.F90

@@ -541,7 +541,7 @@ SUBROUTINE test_chunk_cache(cleanup, total_error)
   CALL H5Dclose_f(dsid, error)
   CALL H5Oopen_f(fid, "dset", dsid, error, dapl1)
 
-  ! Retrieve dapl from dataset, verfiy cache values are the same as on dapl1
+  ! Retrieve dapl from dataset, verify cache values are the same as on dapl1
   !
   ! Note we rely on the knowledge that H5Pget_chunk_cache retrieves these
   ! values directly from the dataset structure, and not from a copy of the
@@ -563,7 +563,7 @@ SUBROUTINE test_chunk_cache(cleanup, total_error)
   CALL H5Oopen_f(fid, "dset", dsid, error)
   CALL check("H5Oopen_f", error, total_error)
 
-  ! Retrieve dapl from dataset, verfiy cache values are the same as on fapl_local
+  ! Retrieve dapl from dataset, verify cache values are the same as on fapl_local
 
   CALL H5Dget_access_plist_f(dsid, dapl2, error)
   CALL check("H5Dget_access_plist_f", error, total_error)

release_docs/HISTORY-1_0-1_8_0_rc3.txt

@@ -1245,7 +1245,7 @@ Known Problems
   causes failures in several HDF5 library tests.
 * For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
   shared libraries (tested for 1.8.0-beta2)
-* For SNL, Red Storm: only paralle HDF5 is supported.  The serial tests pass
+* For SNL, Red Storm: only parallel HDF5 is supported.  The serial tests pass
   and the parallel tests also pass with lots of non-fatal error messages.
 * For LLNL, uP: both serial and parallel pass.  Zeus: serial passes but
   parallel fails with a known proglem in MPI.  ubgl: serial passes but

release_docs/HISTORY-1_8_0-1_10_0.txt

@@ -1581,7 +1581,7 @@ Known Problems
   causes failures in several HDF5 library tests.
 * For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
   shared libraries (tested for 1.8.0-beta2)
-* For SNL, Red Storm: only paralle HDF5 is supported.  The serial tests pass
+* For SNL, Red Storm: only parallel HDF5 is supported.  The serial tests pass
   and the parallel tests also pass with lots of non-fatal error messages.
 * on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test
 * configuring with --enable-debug=all produces compiler errors on most

src/CMakeLists.txt

@@ -227,6 +227,39 @@ set (H5FA_HDRS
 )
 IDE_GENERATED_PROPERTIES ("H5FA" "${H5FA_HDRS}" "${H5FA_SOURCES}" )
 
+set (MERCURY_UTIL_SOURCES
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_atomic_queue.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_dlog.c
+	 ${HDF5_SRC_DIR}/mercury/src/util/mercury_event.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_hash_table.c
+	 ${HDF5_SRC_DIR}/mercury/src/util/mercury_log.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_mem.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_mem_pool.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_poll.c
+     ${HDF5_SRC_DIR}/ mercury/src/util/mercury_request.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_thread.c
+     ${HDF5_SRC_DIR}/ mercury/src/util/mercury_thread_condition.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_thread_pool.c
+     ${HDF5_SRC_DIR}/ mercury/src/util/mercury_thread_mutex.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_thread_rwlock.c
+     ${HDF5_SRC_DIR}/ mercury/src/util/mercury_thread_spin.c
+     ${HDF5_SRC_DIR}/mercury/src/util/mercury_util.c
+)
+
+set (H5FD_SUBFILING_SOURCES
+    ${HDF5_SRC_DIR}/H5FDioc.c
+    ${HDF5_SRC_DIR}/H5FDioc_threads.c
+    ${HDF5_SRC_DIR}/H5FDsubfiling.c
+    ${HDF5_SRC_DIR}/H5FDsubfile_int.c
+    ${HDF5_SRC_DIR}/H5FDsubfile_mpi.c
+    ${MERCURY_UTIL_SOURCES}
+)
+
+set (H5FD_SUBFILING_HDRS
+    ${HDF5_SRC_DIR}/H5FDioc.h
+    ${HDF5_SRC_DIR}/H5FDsubfiling.h
+    ${HDF5_SRC_DIR}/H5FDsubfile_int.h
+)
 
 set (H5FD_SOURCES
     ${HDF5_SRC_DIR}/H5FD.c
@@ -764,6 +797,12 @@ set (H5_MODULE_HEADERS
     ${HDF5_SRC_DIR}/H5Zmodule.h
 )
 
+set (subfile_SOURCES )
+if (WITH_SUBFILING)
+  message (STATUS "Appending to common_SRCS ${H5FD_SUBFILING_SOURCES}")
+  list(APPEND subfile_SOURCES ${H5FD_SUBFILING_SOURCES})
+endif(WITH_SUBFILING)
+
 set (common_SRCS
     ${H5_SOURCES}
     ${H5A_SOURCES}
@@ -810,8 +849,11 @@ set (common_SRCS
     ${H5VM_SOURCES}
     ${H5WB_SOURCES}
     ${H5Z_SOURCES}
+    ${subfile_SOURCES}
 )
 
+
+
 set (H5_PUBLIC_HEADERS
     ${H5_HDRS}
     ${H5A_HDRS}
@@ -848,6 +890,7 @@ set (H5_PUBLIC_HEADERS
     ${H5TS_HDRS}
     ${H5VL_HDRS}
     ${H5Z_HDRS}
+    ${subfile_HDRS}
 )
 
 set (H5_PRIVATE_HEADERS

src/H5B2internal.c

@@ -17,7 +17,7 @@
  *			Dec 01 2016
  *			Quincey Koziol
  *
- * Purpose:		Routines for managing v2 B-tree internal ndoes.
+ * Purpose:		Routines for managing v2 B-tree internal nodes.
  *
  *-------------------------------------------------------------------------
  */

src/H5B2leaf.c

@@ -17,7 +17,7 @@
  *			Dec 01 2016
  *			Quincey Koziol
  *
- * Purpose:		Routines for managing v2 B-tree leaf ndoes.
+ * Purpose:		Routines for managing v2 B-tree leaf nodes.
  *
  *-------------------------------------------------------------------------
  */

src/H5ES.c

@@ -269,7 +269,7 @@ H5ESget_requests(hid_t es_id, H5_iter_order_t order, hid_t *connector_ids, void
     herr_t  ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "iIo*i**xx", es_id, order, connector_ids, requests, count);
+    H5TRACE6("e", "iIo*i**xzx", es_id, order, connector_ids, requests, array_len, count);
 
     /* Check arguments */
     if (NULL == (es = H5I_object_verify(es_id, H5I_EVENTSET)))