Rebase netcdf-c PR #1448

CMakeLists.txt

@@ -531,6 +531,8 @@ 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})
@@ -693,6 +695,15 @@ IF(USE_HDF5)
     ##
 
     # Some versions of HDF5 set HDF5_VERSION_STRING instead of HDF5_VERSION
+    ##
+    # Assert HDF5 version meets minimum required version.
+    ##
+    SET(HDF5_VERSION_REQUIRED 1.8.10)
+    IF(ENABLE_HDF5_SWMR_SUPPORT)
+        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()
+
     IF(HDF5_VERSION_STRING AND NOT HDF5_VERSION)
       SET(HDF5_VERSION ${HDF5_VERSION_STRING})
     ENDIF()
@@ -711,6 +722,9 @@ IF(USE_HDF5)
         unset(_hdf5_version)
         unset(_hdf5_version_lines)
         MESSAGE(STATUS "Found HDF5 libraries version ${HDF5_VERSION}")
+        IF(ENABLE_HDF5_SWMR_SUPPORT)
+            ADD_DEFINITIONS(-DHDF5_HAS_SWMR)
+        ENDIF()
       ENDIF()
     ELSE()
       SET(HDF5_VERSION ${HDF5_VERSION} CACHE STRING "")

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 */

libhdf5/hdf5create.c

@@ -49,6 +49,10 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
     NC_HDF5_FILE_INFO_T *hdf5_info;
     NC_HDF5_GRP_INFO_T *hdf5_grp;
 
+#ifdef HAVE_H5PSET_LIBVER_BOUNDS
+    H5F_libver_t low, high;
+#endif
+
 #ifdef USE_PARALLEL4
     NC_MPI_INFO *mpiinfo = NULL;
     MPI_Comm comm;
@@ -103,6 +107,13 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
     else
         flags = H5F_ACC_TRUNC;
 
+#ifdef HDF5_HAS_SWMR
+#ifndef HAVE_H5PSET_LIBVER_BOUNDS
+    if (cmode & NC_HDF5_SWMR)
+        flags |= H5F_ACC_SWMR_WRITE;
+#endif
+#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) {
@@ -160,6 +171,23 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
 	     __func__, gs->chunkcache.size, gs->chunkcache.nelems,
 	     gs->chunkcache.preemption));
     }
+#ifdef HAVE_H5PSET_LIBVER_BOUNDS
+#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);
+#endif
 
     {
 	NCglobalstate* gs = NC_getglobalstate();
@@ -253,6 +281,14 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
     if ((retval = NC4_new_provenance(nc4_info)))
         BAIL(retval);
 
+#ifdef HDF5_HAS_SWMR
+    if ((cmode & NC_HDF5_SWMR)) {
+      /* Prepare for single writer multiple readers */
+      if ((retval = H5Fstart_swmr_write(hdf5_info->hdfid)))
+        BAIL(retval);
+    }
+#endif
+
     return NC_NOERR;
 
 exit: /*failure exit*/

libhdf5/hdf5open.c

@@ -709,7 +709,16 @@ 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;
+    } 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)))
@@ -975,6 +984,15 @@ nc4_open_file(const char *path, int mode, void* parameters, int ncid)
     if (H5Pclose(fapl_id) < 0)
         BAIL(NC_EHDFERR);
 
+#ifdef HDF5_HAS_SWMR
+    /* Prepare for single writer multiple reader. */
+    if (mode & NC_WRITE && mode & NC_HDF5_SWMR) {
+      if ((retval = H5Fstart_swmr_write(h5->hdfid))) {
+        BAIL(retval);
+      }
+    }
+#endif
+
     return NC_NOERR;
 
 exit:

libhdf5/hdf5var.c

@@ -1766,6 +1766,12 @@ 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 (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)
@@ -1794,6 +1800,7 @@ 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;
 }
 

nc_test4/tst_files.c

@@ -292,6 +292,79 @@ main(int argc, char **argv)
       if (nc_close(ncid)) ERR;
    }
    SUMMARIZE_ERR;
+#ifdef HDF5_HAS_SWMR
+   printf("*** testing HDF5 SWMR...");
+   {
+#define DATA_LEN 3
+
+      int ncid, ncid2, varid, dimids[2];
+      size_t time_len, beam_len;
+      int i;
+      int values[DATA_LEN];
+      size_t start[2] = {0,0}, count[2] = {1, DATA_LEN};
+
+      /* Initialize some phony data. */
+      for (i = 0; i < DATA_LEN; i++)
+         values[i] = DATA_LEN*2 - i;
+
+      /* Create a file in SWMR mode for writing, create structure and close. */
+      if (nc_create(FILE_NAME, NC_NETCDF4|NC_HDF5_SWMR, &ncid)) ERR;
+      if (nc_def_dim(ncid, "time", NC_UNLIMITED, &dimids[0])) ERR;
+      if (nc_def_dim(ncid, "beam", NC_UNLIMITED, &dimids[1])) ERR;
+      if (nc_def_var(ncid, "depth", NC_INT, 2, dimids, &varid)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      /* Open the file for SWMR reading and close. */
+      if (nc_open(FILE_NAME, NC_HDF5_SWMR, &ncid)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      /* Open the file for SWMR writing, append data, and close. */
+      if (nc_open(FILE_NAME, NC_WRITE|NC_HDF5_SWMR, &ncid)) ERR;
+      if (nc_inq_varid(ncid, "depth", &varid)) ERR;
+      if (nc_put_vara_int(ncid, varid, start, count, values)) ERR;
+      if (nc_inq_dimlen(ncid, dimids[0], &time_len)) ERR;
+      if (time_len != 1) ERR;
+      if (nc_inq_dimlen(ncid, dimids[1], &beam_len)) ERR;
+      if (beam_len != DATA_LEN) ERR;
+      if (nc_close(ncid)) ERR;
+
+      /* Open the file for SWMR reading, verify data, and close. */
+      if (nc_open(FILE_NAME, NC_HDF5_SWMR, &ncid)) ERR;
+      if (nc_inq_varid(ncid, "depth", &varid)) ERR;
+      if (nc_put_vara_int(ncid, varid, start, count, values) == 0) ERR; // Writing should fail
+      if (nc_inq_dimlen(ncid, dimids[0], &time_len)) ERR;
+      if (time_len != 1) ERR;
+      if (nc_inq_dimlen(ncid, dimids[1], &beam_len)) ERR;
+      if (beam_len != DATA_LEN) ERR;
+      if (nc_close(ncid)) ERR;
+
+      /* Append data to the file from one writer (ncid1) and verify from a reader (ncid2) */
+      if (nc_open(FILE_NAME, NC_WRITE|NC_HDF5_SWMR, &ncid)) ERR;
+      if (nc_open(FILE_NAME, NC_HDF5_SWMR, &ncid2)) ERR;
+
+      // Verify length of time dimension == 1 in both reader and writer
+      if (nc_inq_dimlen(ncid, dimids[0], &time_len)) ERR;
+      if (time_len != 1) ERR;
+      if (nc_inq_dimlen(ncid2, dimids[0], &time_len)) ERR;
+      if (time_len != 1) ERR;
+
+      // Append data
+      start[0] = 1; start[1] = 0;
+      if (nc_inq_varid(ncid, "depth", &varid)) ERR;
+      if (nc_put_vara_int(ncid, varid, start, count, values)) ERR;
+
+      // Verify length of time dimension == 2 in both reader and writer
+      if (nc_inq_dimlen(ncid, dimids[0], &time_len)) ERR;
+      if (time_len != 2) ERR;
+      if (nc_inq_dimlen(ncid2, dimids[0], &time_len)) ERR;
+      if (time_len != 2) ERR;
+
+      if (nc_close(ncid)) ERR;
+      if (nc_close(ncid2)) ERR;
+
+   }
+   SUMMARIZE_ERR;
+#endif /* HDF_HAS_SWMR */
    printf("*** testing CLASSIC_MODEL flag with classic formats...");
    {
       int ncid;