Subfiling VFD source cleanup (#3241)

* Subfiling VFD source cleanup

Modularize Subfiling CMake code into separate CMakeLists.txt file

Update Mercury util code to latest version and update Copyright

Generate mercury_util_config.h header file instead of using
pre-generated file

Remove unnecessary Mercury functionality

Fix minor warning in Subfiling VFD code

* Remove Mercury headers from Autotools publicly-distributed header list

CMakeLists.txt

@@ -760,8 +760,22 @@ if (HDF5_ENABLE_SUBFILING_VFD)
       ${HDF5_SRC_INCLUDE_DIRS}
       ${H5FD_SUBFILING_MERCURY_DIR}
   )
-  set (H5_HAVE_MERCURY_H 1)
   set (CMAKE_REQUIRED_INCLUDES "${H5FD_SUBFILING_MERCURY_DIR}")
+
+  # Run some configure checks for the Mercury util files
+  set (CMAKE_EXTRA_INCLUDE_FILES pthread.h)
+  set (CMAKE_REQUIRED_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+
+  check_type_size(PTHREAD_MUTEX_ADAPTIVE_NP PTHREAD_MUTEX_ADAPTIVE_NP_SIZE)
+  if (HAVE_PTHREAD_MUTEX_ADAPTIVE_NP_SIZE)
+    set (${HDF_PREFIX}_HAVE_PTHREAD_MUTEX_ADAPTIVE_NP 1)
+  endif ()
+
+  check_symbol_exists(pthread_condattr_setclock pthread.h
+    ${HDF_PREFIX}_HAVE_PTHREAD_CONDATTR_SETCLOCK)
+
+  unset (CMAKE_EXTRA_INCLUDE_FILES)
+  unset (CMAKE_REQUIRED_LIBRARIES)
 endif()
 
 #option (DEFAULT_API_VERSION "Enable v1.14 API (v16, v18, v110, v112, v114)" "v114")

config/cmake/ConfigureChecks.cmake

@@ -665,6 +665,15 @@ if (MINGW OR NOT WINDOWS)
     list (APPEND LINK_LIBS posix4)
   endif ()
 endif ()
+
+# Check for clock_gettime() CLOCK_MONOTONIC_COARSE
+set (CMAKE_EXTRA_INCLUDE_FILES time.h)
+check_type_size(CLOCK_MONOTONIC_COARSE CLOCK_MONOTONIC_COARSE_SIZE)
+if (HAVE_CLOCK_MONOTONIC_COARSE_SIZE)
+  set (${HDF_PREFIX}_HAVE_CLOCK_MONOTONIC_COARSE 1)
+endif ()
+unset (CMAKE_EXTRA_INCLUDE_FILES)
+
 #-----------------------------------------------------------------------------
 
 #-----------------------------------------------------------------------------

config/cmake/H5pubconf.h.in

@@ -101,6 +101,9 @@
 /* Define to 1 if you have the `clock_gettime' function. */
 #cmakedefine H5_HAVE_CLOCK_GETTIME @H5_HAVE_CLOCK_GETTIME@
 
+/* Define to 1 if CLOCK_MONOTONIC_COARSE is available */
+#cmakedefine H5_HAVE_CLOCK_MONOTONIC_COARSE @H5_HAVE_CLOCK_MONOTONIC_COARSE@
+
 /* Define if the function stack tracing code is to be compiled in */
 #cmakedefine H5_HAVE_CODESTACK @H5_HAVE_CODESTACK@
 
@@ -249,6 +252,12 @@
 /* Define to 1 if you have the <pthread.h> header file. */
 #cmakedefine H5_HAVE_PTHREAD_H @H5_HAVE_PTHREAD_H@
 
+/* Define to 1 if 'pthread_condattr_setclock()' is available */
+#cmakedefine H5_HAVE_PTHREAD_CONDATTR_SETCLOCK @H5_HAVE_PTHREAD_CONDATTR_SETCLOCK@
+
+/* Define to 1 if PTHREAD_MUTEX_ADAPTIVE_NP is available */
+#cmakedefine H5_HAVE_PTHREAD_MUTEX_ADAPTIVE_NP @H5_HAVE_PTHREAD_MUTEX_ADAPTIVE_NP@
+
 /* Define to 1 if you have the <pwd.h> header file. */
 #cmakedefine H5_HAVE_PWD_H @H5_HAVE_PWD_H@
 

configure.ac

@@ -3088,6 +3088,23 @@ if test "X$SUBFILING_VFD" = "Xyes"; then
     AC_SEARCH_LIBS([shm_open], [rt])
     AC_CHECK_LIB([pthread], [pthread_self],[], [echo "Error: Required library pthread not found." && exit 1])
 
+    # Perform various checks for Mercury util code
+    AC_CHECK_DECL([PTHREAD_MUTEX_ADAPTIVE_NP],
+                  [AC_DEFINE([HAVE_PTHREAD_MUTEX_ADAPTIVE_NP], [1],
+                      [Define if has PTHREAD_MUTEX_ADAPTIVE_NP])],
+                  [],
+                  [[#include <pthread.h>]])
+    AC_CHECK_DECL([pthread_condattr_setclock],
+                  [AC_DEFINE([HAVE_PTHREAD_CONDATTR_SETCLOCK], [1],
+                      [Define if has pthread_condattr_setclock()])],
+                  [],
+                  [[#include <pthread.h>]])
+    AC_CHECK_DECL([CLOCK_MONOTONIC_COARSE],
+                  [AC_DEFINE([HAVE_CLOCK_MONOTONIC_COARSE], [1],
+                      [Define if has CLOCK_MONOTONIC_COARSE])],
+                  [],
+                  [[#include <time.h>]])
+
 else
     AC_MSG_RESULT([no])
 fi

release_docs/RELEASE.txt

@@ -484,6 +484,13 @@ Bug Fixes since HDF5-1.14.0 release
 
     Configuration
     -------------
+    - Fixed a configuration issue that prevented building of the Subfiling VFD on macOS
+
+      Checks were added to the CMake and Autotools code to verify that CLOCK_MONOTONIC_COARSE,
+      PTHREAD_MUTEX_ADAPTIVE_NP and pthread_condattr_setclock() are available before attempting
+      to use them in Subfiling VFD-related utility code. Without these checks, attempting
+      to build the Subfiling VFD on macOS would fail. 
+
     - The accum test now passes on macOS 12+ (Monterey) w/ CMake
 
       Due to changes in the way macOS handles LD_LIBRARY_PATH, the accum test

src/CMakeLists.txt

@@ -278,33 +278,11 @@ set (H5FD_HDRS
     ${HDF5_SRC_DIR}/H5FDsplitter.h
     ${HDF5_SRC_DIR}/H5FDstdio.h
     ${HDF5_SRC_DIR}/H5FDwindows.h
-    ${H5FD_SUBFILING_DIR}/H5FDsubfiling.h
-    ${H5FD_SUBFILING_DIR}/H5FDioc.h
 )
 
 # Append Subfiling VFD and Mercury sources to H5FD interface if Subfiling VFD is built
 if (HDF5_ENABLE_SUBFILING_VFD)
-  set (MERCURY_UTIL_SOURCES
-      ${H5FD_SUBFILING_DIR}/mercury/src/util/mercury_dlog.c
-      ${H5FD_SUBFILING_DIR}/mercury/src/util/mercury_log.c
-      ${H5FD_SUBFILING_DIR}/mercury/src/util/mercury_thread.c
-      ${H5FD_SUBFILING_DIR}/mercury/src/util/mercury_thread_condition.c
-      ${H5FD_SUBFILING_DIR}/mercury/src/util/mercury_thread_pool.c
-      ${H5FD_SUBFILING_DIR}/mercury/src/util/mercury_thread_mutex.c
-      ${H5FD_SUBFILING_DIR}/mercury/src/util/mercury_util.c
-  )
-
-  set (H5FD_SUBFILING_SOURCES
-      ${H5FD_SUBFILING_DIR}/H5FDioc.c
-      ${H5FD_SUBFILING_DIR}/H5FDioc_int.c
-      ${H5FD_SUBFILING_DIR}/H5FDioc_threads.c
-      ${H5FD_SUBFILING_DIR}/H5FDsubfiling.c
-      ${H5FD_SUBFILING_DIR}/H5FDsubfile_int.c
-      ${H5FD_SUBFILING_DIR}/H5subfiling_common.c
-      ${MERCURY_UTIL_SOURCES}
-  )
-
-  list (APPEND H5FD_SOURCES ${H5FD_SUBFILING_SOURCES})
+  add_subdirectory (${H5FD_SUBFILING_DIR})
 endif()
 
 IDE_GENERATED_PROPERTIES ("H5FD" "${H5FD_HDRS}" "${H5FD_SOURCES}" )
@@ -864,7 +842,6 @@ set (H5_PUBLIC_HEADERS
     ${H5TS_HDRS}
     ${H5VL_HDRS}
     ${H5Z_HDRS}
-    ${subfile_HDRS}
 )
 
 set (H5_PRIVATE_HEADERS

src/H5FDsubfiling/CMakeLists.txt

@@ -0,0 +1,53 @@
+cmake_minimum_required (VERSION 3.18)
+project (HDF5_H5FD_SUBFILING C)
+
+# Sanity checking
+if (NOT H5FD_SOURCES)
+  message (FATAL_ERROR "internal configure error - H5FD_SOURCES not set")
+endif ()
+if (NOT H5FD_HDRS)
+  message (FATAL_ERROR "internal configure error - H5FD_HDRS not set")
+endif ()
+if (NOT H5FD_SUBFILING_DIR)
+  message (FATAL_ERROR "internal configure error - H5FD_SUBFILING_DIR not set")
+endif ()
+if (NOT H5FD_SUBFILING_MERCURY_DIR)
+  message (FATAL_ERROR "internal configure error - H5FD_SUBFILING_MERCURY_DIR not set")
+endif ()
+
+# Add mercury util sources to Subfiling VFD sources
+set (MERCURY_UTIL_SOURCES
+  ${H5FD_SUBFILING_MERCURY_DIR}/mercury_thread.c
+  ${H5FD_SUBFILING_MERCURY_DIR}/mercury_thread_condition.c
+  ${H5FD_SUBFILING_MERCURY_DIR}/mercury_thread_pool.c
+  ${H5FD_SUBFILING_MERCURY_DIR}/mercury_thread_mutex.c
+)
+
+set (HDF5_H5FD_SUBFILING_SOURCES
+  ${H5FD_SUBFILING_DIR}/H5FDioc.c
+  ${H5FD_SUBFILING_DIR}/H5FDioc_int.c
+  ${H5FD_SUBFILING_DIR}/H5FDioc_threads.c
+  ${H5FD_SUBFILING_DIR}/H5FDsubfiling.c
+  ${H5FD_SUBFILING_DIR}/H5FDsubfile_int.c
+  ${H5FD_SUBFILING_DIR}/H5subfiling_common.c
+  ${MERCURY_UTIL_SOURCES}
+)
+
+set (HDF5_H5FD_SUBFILING_HEADERS
+  ${H5FD_SUBFILING_DIR}/H5FDsubfiling.h
+  ${H5FD_SUBFILING_DIR}/H5FDioc.h
+)
+
+# Add Subfiling VFD sources to HDF5 library's H5FD sources
+set (H5FD_SOURCES
+  ${H5FD_SOURCES}
+  ${HDF5_H5FD_SUBFILING_SOURCES}
+  PARENT_SCOPE
+)
+
+# Add Subfiling VFD public headers to HDF5 library's public H5FD headers
+set (H5FD_HDRS
+  ${H5FD_HDRS}
+  ${HDF5_H5FD_SUBFILING_HEADERS}
+  PARENT_SCOPE
+)

src/H5FDsubfiling/H5subfiling_common.c

@@ -1077,6 +1077,7 @@ init_app_topology(H5FD_subfiling_params_t *subfiling_config, MPI_Comm comm, MPI_
         }
 
         case SELECT_IOC_WITH_CONFIG:
+        case ioc_selection_options:
         default:
             H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_BADVALUE, FAIL, "invalid IOC selection strategy");
             break;
@@ -1705,6 +1706,7 @@ identify_ioc_ranks(sf_topology_t *app_topology, int rank_stride)
         }
 
         case SELECT_IOC_WITH_CONFIG:
+        case ioc_selection_options:
         default:
             H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_BADVALUE, FAIL, "invalid IOC selection strategy");
             break;

src/H5FDsubfiling/mercury/LICENSE.txt

@@ -1,4 +1,5 @@
-Copyright (c) 2013-2021, UChicago Argonne, LLC and The HDF Group.
+Copyright (c) 2013-2022, UChicago Argonne, LLC and The HDF Group.
+Copyright (c) 2022-2023, Intel Corporation.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -24,4 +25,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.