Support SWMR in HDF5 (updated)

CMakeLists.txt

@@ -574,6 +574,8 @@ IF(ENABLE_HDF4)
   ENDIF()
 ENDIF()
 
+OPTION(ENABLE_HDF5_SWMR "Support SWMR in HDF5. This requires HDF version 1.10 or later" OFF)
+
 # Option to Build DLL
 IF(WIN32)
   OPTION(ENABLE_DLL "Build a Windows DLL." ${BUILD_SHARED_LIBS})
@@ -653,7 +655,10 @@ IF(USE_HDF5)
   # Assert HDF5 version meets minimum required version.
   ##
   SET(HDF5_VERSION_REQUIRED 1.8.10)
-
+  IF(ENABLE_HDF5_SWMR)
+      SET(HDF5_VERSION_REQUIRED 1.10)
+      MESSAGE(STATUS "HDF5 SWMR is enabled. This implies that HDF5 version at least ${HDF5_VERSION_REQUIRED} is required.")
+  ENDIF()
 
   ##
   # Accommodate developers who have hdf5 libraries and
@@ -774,8 +779,6 @@ IF(USE_HDF5)
       MESSAGE(FATAL_ERROR "netCDF requires at least HDF5 ${HDF5_VERSION_REQUIRED}. Found ${HDF5_VERSION}.")
     ENDIF()
 
-
-
     ##
     # Include the HDF5 include directory.
     ##
@@ -840,6 +843,11 @@ IF(USE_HDF5)
 
   ENDIF(HDF5_C_LIBRARY AND HDF5_HL_LIBRARY AND HDF5_INCLUDE_DIR)
 
+  # Requesting SWMR support sets the minimum version to 1.10, so if
+  # we've got this far, we've got SWMR support
+  set(HDF5_HAS_SWMR ${ENABLE_HDF5_SWMR})
+  message(STATUS "HDF5 SWMR support: ${HDF5_HAS_SWMR}")
+
   FIND_PACKAGE(Threads)
 
   # There is a missing case in the above code so default it
@@ -2575,6 +2583,7 @@ is_enabled(ENABLE_V2_API HAS_NC2)
 is_enabled(ENABLE_NETCDF_4 HAS_NC4)
 is_enabled(ENABLE_HDF4 HAS_HDF4)
 is_enabled(USE_HDF5 HAS_HDF5)
+is_enabled(HDF5_HAS_SWMR HAS_HDF5_SWMR)
 is_enabled(OFF HAS_BENCHMARKS)
 is_enabled(STATUS_PNETCDF HAS_PNETCDF)
 is_enabled(STATUS_PARALLEL HAS_PARALLEL)

config.h.cmake.in

@@ -462,6 +462,9 @@ with zip */
 /* if true, HDF5 is at least version 1.10.5 and supports UTF8 paths */
 #cmakedefine HDF5_UTF8_PATHS 1
 
+/* if true, HDF5 is at least version 1.10 and supports single-writer multiple-reader IO */
+#cmakedefine HDF5_HAS_SWMR 1
+
 /* if true, include JNA bug fix */
 #cmakedefine JNA 1
 

configure.ac

@@ -156,6 +156,14 @@ if test "x$enable_netcdf4" = xno ; then enable_hdf5=no ; fi
 # disable-netcdf4 is synonym for disable-hdf5
 AC_MSG_RESULT([$enable_hdf5])
 
+AC_MSG_CHECKING([whether we should build with HDF5 SWMR support])
+AC_ARG_ENABLE([hdf5_swmr], [AS_HELP_STRING([--enable-hdf5-swmr],
+              [build with HDF5 SWMR support (requires HDF5 version 1.10 or later)])])
+test "x$enable_hdf5_swmr" = xyes || enable_hdf5_swmr=no
+if test "x$enable_hdf5" = xno ; then enable_hdf5_swmr=no ; fi
+# Don't enable HDF5 SWMR if we're not using HDF5
+AC_MSG_RESULT([$enable_hdf5_swmr])
+
 # Check whether we want to enable CDF5 support.
 AC_MSG_CHECKING([whether CDF5 support should be disabled])
 AC_ARG_ENABLE([cdf5],
@@ -1593,6 +1601,7 @@ fi
 hdf5_parallel=no
 hdf5_supports_par_filters=no
 enable_hdf5_szip=no
+hdf5_swmr=no
 has_hdf5_ros3=no
 
 if test "x$enable_hdf5" = xyes; then
@@ -1619,7 +1628,7 @@ if test "x$enable_hdf5" = xyes; then
    # H5Pset_fapl_mpiposix and H5Pget_fapl_mpiposix have been removed since HDF5 1.8.12.
    # Use H5Pset_fapl_mpio and H5Pget_fapl_mpio, instead.
 
-   AC_CHECK_FUNCS([H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5Pset_all_coll_metadata_ops H5Literate])
+   AC_CHECK_FUNCS([H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5Pset_all_coll_metadata_ops H5Literate H5Fstart_swmr_write])
 
    # Check to see if HDF5 library has collective metadata APIs, (HDF5 >= 1.10.0)
    if test "x$ac_cv_func_H5Pset_all_coll_metadata_ops" = xyes; then
@@ -1681,6 +1690,13 @@ if test "x$enable_hdf5" = xyes; then
       AC_DEFINE([HDF5_UTF8_PATHS], [1], [if true, HDF5 paths can be utf-8])
    fi
 
+   if test "x$enable_hdf5_swmr" = xyes && test "x$ac_cv_func_H5Fstart_swmr_write" = xyes; then
+      hdf5_swmr=yes
+      AC_DEFINE([HDF5_HAS_SWMR], [1], [if true, HDF5 supports single-writer multiple-reader])
+   fi
+   AC_MSG_CHECKING([whether HDF5 supports SWMR])
+   AC_MSG_RESULT([$hdf5_swmr])
+
 fi
 
 AM_CONDITIONAL(ENABLE_NCDUMPCHUNKS, [test "x$has_readchunks" = xyes ])
@@ -2029,6 +2045,7 @@ AC_SUBST(HAS_CDF5,[$enable_cdf5])
 AC_SUBST(HAS_HDF4,[$enable_hdf4])
 AC_SUBST(HAS_BENCHMARKS,[$enable_benchmarks])
 AC_SUBST(HAS_HDF5,[$enable_hdf5])
+AC_SUBST(HAS_HDF5_SWMR,[$hdf5_swmr])
 AC_SUBST(HAS_PNETCDF,[$enable_pnetcdf])
 AC_SUBST(HAS_LOGGING, [$enable_logging])
 AC_SUBST(HAS_PARALLEL,[$enable_parallel])
@@ -2194,6 +2211,7 @@ AX_SET_META([NC_HAS_NC4],[$enable_netcdf_4],[yes])
 AX_SET_META([NC_HAS_HDF4],[$enable_hdf4],[yes])
 AX_SET_META([NC_HAS_BENCHMARKS],[$enable_benchmarks],[yes])
 AX_SET_META([NC_HAS_HDF5],[$enable_hdf5],[yes])
+AX_SET_META([NC_HAS_HDF5_SWMR],[$enable_hdf5_swmr],[yes])
 AX_SET_META([NC_HAS_DAP2],[$enable_dap],[yes])
 AX_SET_META([NC_HAS_DAP4],[$enable_dap4],[yes])
 AX_SET_META([NC_HAS_DISKLESS],[yes],[yes])

include/netcdf.h

@@ -161,6 +161,7 @@ Use this in mode flags for both nc_create() and nc_open(). */
 
 #define NC_PERSIST       0x4000  /**< Save diskless contents to disk. Mode flag for nc_open() or nc_create() */
 #define NC_INMEMORY      0x8000  /**< Read from memory. Mode flag for nc_open() or nc_create() */
+#define NC_HDF5_SWMR     0x2000 /** Reuse deprecated MPIIO flag for SWMR **/
 
 /* Upper 16 bits */
 #define NC_NOATTCREORD  0x20000 /**< Disable the netcdf-4 (hdf5) attribute creation order tracking */

include/netcdf_meta.h.in

@@ -43,6 +43,7 @@
 #define NC_HAS_NC4       @NC_HAS_NC4@ /*!< API version 4 support. */
 #define NC_HAS_HDF4      @NC_HAS_HDF4@ /*!< HDF4 support. */
 #define NC_HAS_HDF5      @NC_HAS_HDF5@ /*!< HDF5 support. */
+#define NC_HAS_HDF5_SWMR @NC_HAS_HDF5_SWMR@ /*!< HDF5 single-writer multiple reader support. */
 #define NC_HAS_SZIP      @NC_HAS_SZIP@ /*!< szip support */
 #define NC_HAS_SZIP_WRITE @NC_HAS_SZIP@ /*!< szip write support */
 #define NC_HAS_DAP2      @NC_HAS_DAP2@ /*!< DAP2 support. */

libhdf5/hdf5create.c

@@ -48,6 +48,7 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
     NC_FILE_INFO_T *nc4_info;
     NC_HDF5_FILE_INFO_T *hdf5_info;
     NC_HDF5_GRP_INFO_T *hdf5_grp;
+    H5F_libver_t low, high;
 
 #ifdef USE_PARALLEL4
     NC_MPI_INFO *mpiinfo = NULL;
@@ -103,6 +104,11 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
     else
         flags = H5F_ACC_TRUNC;
 
+#ifdef HDF5_HAS_SWMR
+    if (cmode & NC_HDF5_SWMR)
+        flags |= H5F_ACC_SWMR_WRITE;
+#endif
+
     /* If this file already exists, and NC_NOCLOBBER is specified,
        return an error (unless diskless|inmemory) */
     if (!nc4_info->mem.diskless && !nc4_info->mem.inmemory) {
@@ -161,6 +167,22 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
 	     gs->chunkcache.preemption));
     }
 
+#if H5_VERSION_GE(1,10,2)
+    low = H5F_LIBVER_EARLIEST;
+    high = H5F_LIBVER_V18;
+#ifdef HDF5_HAS_SWMR
+    if ((cmode & NC_HDF5_SWMR)) {
+      low = H5F_LIBVER_LATEST;
+      high = H5F_LIBVER_LATEST;
+    }
+#endif /* HDF5_HAS_SWMR */
+#else
+    low = H5F_LIBVER_EARLIEST;
+    high = H5F_LIBVER_LATEST;
+#endif
+    if (H5Pset_libver_bounds(fapl_id, low, high) < 0)
+        BAIL(NC_EHDFERR);
+
     {
 	NCglobalstate* gs = NC_getglobalstate();
         if(gs->alignment.defined) {

libhdf5/hdf5open.c

@@ -9,6 +9,7 @@
  * @author Ed Hartnett
  */
 
+#include "H5version.h"
 #include "config.h"
 #include "hdf5internal.h"
 #include "hdf5err.h"
@@ -724,7 +725,21 @@ nc4_open_file(const char *path, int mode, void* parameters, int ncid)
     assert(nc);
 
     /* Determine the HDF5 open flag to use. */
-    flags = (mode & NC_WRITE) ? H5F_ACC_RDWR : H5F_ACC_RDONLY;
+    if((mode & NC_WRITE)) {
+      flags = H5F_ACC_RDWR;
+#ifdef HDF5_HAS_SWMR
+      if((mode & NC_HDF5_SWMR)) {
+        flags |= H5F_ACC_SWMR_WRITE;
+      }
+#endif
+    } else {
+      flags = H5F_ACC_RDONLY;
+#ifdef HDF5_HAS_SWMR
+      if((mode & NC_HDF5_SWMR)) {
+        flags |= H5F_ACC_SWMR_READ;
+      }
+#endif
+    }
 
     /* Add necessary structs to hold netcdf-4 file data. */
     if ((retval = nc4_nc4f_list_add(nc, path, mode)))
@@ -841,6 +856,25 @@ nc4_open_file(const char *path, int mode, void* parameters, int ncid)
 	}
     }
 
+    {
+      H5F_libver_t low, high;
+#if H5_VERSION_GE(1,10,2)
+      low = H5F_LIBVER_EARLIEST;
+      high = H5F_LIBVER_V18;
+#ifdef HDF5_HAS_SWMR
+      if ((mode & NC_HDF5_SWMR)) {
+        low = H5F_LIBVER_LATEST;
+        high = H5F_LIBVER_LATEST;
+      }
+#endif /* HDF5_HAS_SWMR */
+#else
+      low = H5F_LIBVER_EARLIEST;
+      high = H5F_LIBVER_LATEST;
+#endif
+      if (H5Pset_libver_bounds(fapl_id, low, high) < 0)
+        BAIL(NC_EHDFERR);
+    }
+
     /* Set HDF5 format compatibility in the FILE ACCESS property list.
      * Compatibility is transient and must be reselected every time
      * a file is opened for writing. */

libhdf5/hdf5var.c

@@ -1796,6 +1796,15 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
                  mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
         BAIL(NC_EHDFERR);
 
+#ifdef HDF5_HAS_SWMR
+    /* Flush data for SWMR */
+    if (h5->cmode & NC_HDF5_SWMR)
+    {
+      if (H5Dflush(hdf5_var->hdf_datasetid) < 0)
+        BAIL(NC_EHDFERR);
+    }
+#endif
+
     /* Remember that we have written to this var so that Fill Value
      * can't be set for it. */
     if (!var->written_to)
@@ -1824,6 +1833,7 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
         return retval;
     if (range_error)
         return NC_ERANGE;
+
     return NC_NOERR;
 }
 
@@ -1898,6 +1908,15 @@ NC4_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
     LOG((3, "%s: var->hdr.name %s mem_nc_type %d", __func__,
          var->hdr.name, mem_nc_type));
 
+#ifdef HDF5_HAS_SWMR
+    /* Refresh dataset metadata, required if opened in SWMR mode */
+    if (h5->cmode & NC_HDF5_SWMR)
+    {
+      if (H5Drefresh(hdf5_var->hdf_datasetid) < 0)
+        BAIL(NC_EHDFERR);
+    }
+#endif
+
     /* Check some stuff about the type and the file. Also end define
      * mode, if needed. */
     if ((retval = check_for_vara(&mem_nc_type, var, h5)))

nc-config.cmake.in

@@ -74,6 +74,13 @@ else
     has_hdf5="yes"
 fi
 
+has_hdf5_swmr="@HDF5_HAS_SWMR@"
+if [ -z "$has_hdf5_swmr" -o "$has_hdf5_swmr" = "OFF" ]; then
+    has_hdf5_swmr="no"
+else
+    has_hdf5_swmr="yes"
+fi
+
 has_szlib="@USE_SZIP@"
 if [ -z "$has_szlib" -o "$has_szlib" = "OFF" ]; then
     has_szlib="no"
@@ -152,6 +159,7 @@ Available values for OPTION include:
   --has-nc2          whether NetCDF-2 API is enabled
   --has-nc4          whether NetCDF-4/HDF-5 is enabled in this build
   --has-hdf5         whether HDF5 is used in build (always the same as --has-nc4)
+  --has-hdf5-swmr    whether HDF5 single-writer multiple-reader mode is supported
   --has-hdf4         whether HDF4 was used in build
   --has-logging      whether logging is enabled with --enable-logging.
   --has-pnetcdf      whether PnetCDF was used in build
@@ -197,6 +205,7 @@ all()
         echo "  --has-nc2          -> $has_nc2"
         echo "  --has-nc4          -> $has_nc4"
         echo "  --has-hdf5         -> $has_hdf5"
+        echo "  --has-hdf5-swmr    -> $has_hdf5_swmr"
         echo "  --has-hdf4         -> $has_hdf4"
         echo "  --has-logging      -> $has_logging"
         echo "  --has-pnetcdf      -> $has_pnetcdf"
@@ -288,6 +297,10 @@ while test $# -gt 0; do
         echo $has_hdf5
         ;;
 
+    --has-hdf5-swmr)
+        echo $has_hdf5_swmr
+        ;;
+
     --has-hdf4)
         echo $has_hdf4
         ;;

nc-config.in

@@ -27,6 +27,7 @@ has_nc4="@HAS_NC4@"
 has_hdf4="@HAS_HDF4@"
 has_pnetcdf="@HAS_PNETCDF@"
 has_hdf5="@HAS_HDF5@"
+has_hdf5_swmr="@HAS_HDF5_SWMR@"
 has_logging="@HAS_LOGGING@"
 has_cdf5="@HAS_CDF5@"
 has_szlib="@HAS_SZLIB@"
@@ -59,6 +60,7 @@ Available values for OPTION include:
   --has-nc2          whether NetCDF-2 API is enabled
   --has-nc4          whether NetCDF-4/HDF-5 is enabled in this build
   --has-hdf5         whether HDF5 is used in build (always the same as --has-nc4)
+  --has-hdf5-swmr    whether HDF5 single-writer multiple-reader mode is supported
   --has-hdf4         whether HDF4 was used in build
   --has-logging      whether logging is enabled with --enable-logging.
   --has-pnetcdf      whether PnetCDF was used in build
@@ -101,6 +103,7 @@ all()
         echo "  --has-nc2          -> $has_nc2"
         echo "  --has-nc4          -> $has_nc4"
         echo "  --has-hdf5         -> $has_hdf5"
+        echo "  --has-hdf5-swmr    -> $has_hdf5_swmr"
         echo "  --has-hdf4         -> $has_hdf4"
         echo "  --has-logging      -> $has_logging"
         echo "  --has-pnetcdf      -> $has_pnetcdf"
@@ -193,6 +196,10 @@ while test $# -gt 0; do
         echo $has_hdf5
         ;;
 
+    --has-hdf5-swmr)
+        echo $has_hdf5_swmr
+        ;;
+
     --has-hdf4)
         echo $has_hdf4
         ;;