count argument in H5Sselect_hyperslab

Argument 'count' in NetCDF is not exactly the same as the 'count' in
H5Sselect_hyperslabs(space_id, op, start, stride, count, block).
When the argument 'stride' is NULL, NetCDF's 'count' should be used in
argument 'block', for example,
   H5Sselect_hyperslabs(space_id, op, start, NULL, ones, count);
where 'one' is an array of all 1s. Although using NULL 'block' below
   H5Sselect_hyperslabs(space_id, op, start, NULL, count, NULL);
has the same effect, HDF5 internally stores the space of a subarray as a
list of single elements, instead of a "block", which can affect the
performance.

h5_test/tst_h_dimscales2.c

@@ -633,6 +633,7 @@ main()
 	 hsize_t h5dimlen[DIMS2], h5dimlenmax[DIMS2], xtend_size[DIMS2] = {1, NUM_VALS};
 	 hsize_t start[DIMS2] = {0, 0};
 	 hsize_t count[DIMS2] = {1, NUM_VALS};
+	 hsize_t ones[DIMS2] = {1, 1};
 	 double value[NUM_VALS];
 	 int dataset_ndims;
 	 int i;
@@ -661,7 +662,7 @@ main()
 
 	 /* Set up the file and memory spaces. */
 	 if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
-				 start, NULL, count, NULL) < 0) ERR;
+				 start, NULL, ones, count) < 0) ERR;
 	 if ((mem_spaceid = H5Screate_simple(DIMS2, count, NULL)) < 0) ERR;
 
 	 /* Write a slice of data. */
@@ -683,7 +684,7 @@ main()
 	 /* Set up the file and memory spaces for a second slice. */
 	 start[0]++;
 	 if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
-				 start, NULL, count, NULL) < 0) ERR;
+				 start, NULL, ones, count) < 0) ERR;
 	 if ((mem_spaceid = H5Screate_simple(DIMS2, count, NULL)) < 0) ERR;
 
 	 /* Write a second slice of data. */

h5_test/tst_h_enums.c

@@ -154,7 +154,7 @@ main()
       char lang[NUM_LANG][STR_LEN + 1] = {"C", "Fortran", "C++", "MISSING"};
       enum langs {CLANG=0, Fortran=1, CPP=2, MISSING=255};
       short the_value, fill_value = MISSING, data_point = CLANG;
-      hsize_t start[1] = {1}, count[1] = {1};
+      hsize_t start[1] = {1}, count[1] = {1}, one[1] = {1};
       int num_members;
       size_t size;
       hid_t base_hdf_typeid;
@@ -197,7 +197,7 @@ main()
       if ((mem_spaceid = H5Screate(H5S_SCALAR)) < 0) ERR;
       if ((file_spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
       if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
-			      start, NULL, count, NULL) < 0) ERR;
+			      start, NULL, one, count) < 0) ERR;
       if (H5Dwrite(datasetid, typeid, mem_spaceid, file_spaceid,
 		   H5P_DEFAULT, &data_point) < 0) ERR;
 

h5_test/tst_h_files.c

@@ -174,7 +174,7 @@ main()
 #define MILLION 1000000
 
         hid_t fileid, write_spaceid, datasetid, mem_spaceid;
-        hsize_t start[NDIMS], count[NDIMS];
+        hsize_t start[NDIMS], count[NDIMS], ones[NDIMS];
         hsize_t dims[1];
         int *data;
         int num_steps;
@@ -210,8 +210,9 @@ main()
         {
             /* Select hyperslab for write of one slice. */
             start[0] = s * SC;
+            ones[0] = 1;
             if (H5Sselect_hyperslab(write_spaceid, H5S_SELECT_SET,
-                                    start, NULL, count, NULL) < 0) ERR;
+                                    start, NULL, ones, count) < 0) ERR;
 
             if (H5Dwrite(datasetid, H5T_NATIVE_INT, mem_spaceid, write_spaceid,
                          H5P_DEFAULT, data) < 0) ERR;
@@ -242,7 +243,7 @@ main()
         hid_t mem_spaceid, xfer_plistid, native_typeid;
         hsize_t *chunksize, dims[1], maxdims[1], *dimsize, *maxdimsize;
         hsize_t fdims[MAX_DIMS], fmaxdims[MAX_DIMS];
-        hsize_t start[MAX_DIMS],  count[MAX_DIMS];
+        hsize_t start[MAX_DIMS], count[MAX_DIMS], ones[MAX_DIMS];
         char file_name[STR_LEN + 1];
         char dimscale_wo_var[STR_LEN];
         void *bufr;
@@ -342,7 +343,8 @@ main()
         start[1] = 0;
         count[0] = 1;
         count[1] = 2097153;
-        if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, NULL, count, NULL) < 0) ERR;
+        ones[0] = ones[1] = 1;
+        if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, NULL, ones, count) < 0) ERR;
         if ((mem_spaceid = H5Screate_simple(NDIMS2, count, NULL)) < 0) ERR;
         if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0) ERR;
         if ((native_typeid = H5Tget_native_type(H5T_NATIVE_SCHAR, H5T_DIR_DEFAULT)) < 0) ERR;

h5_test/tst_h_par.c

@@ -66,7 +66,7 @@ main(int argc, char **argv)
         printf("*** Creating file for parallel I/O read, and rereading it...");
     {
         hid_t fapl_id, fileid, whole_spaceid, dsid, slice_spaceid, whole_spaceid1, xferid;
-        hsize_t start[NDIMS], count[NDIMS];
+        hsize_t start[NDIMS], count[NDIMS], ones[NDIMS];
         hsize_t dims[1];
         int data[SC1], data_in[SC1];
         int num_steps;
@@ -126,8 +126,9 @@ main(int argc, char **argv)
             /* Select hyperslab for write of one slice. */
             start[0] = s * SC1 * p + my_rank * SC1;
             count[0] = SC1;
+            ones[0] = 1;
             if (H5Sselect_hyperslab(whole_spaceid, H5S_SELECT_SET,
-                                    start, NULL, count, NULL) < 0) ERR;
+                                    start, NULL, ones, count) < 0) ERR;
 
             if (H5Dwrite(dsid, H5T_NATIVE_INT, slice_spaceid, whole_spaceid,
                          xferid, data) < 0) ERR;
@@ -185,8 +186,9 @@ main(int argc, char **argv)
             /* Select hyperslab for read of one slice. */
             start[0] = s * SC1 * p + my_rank * SC1;
             count[0] = SC1;
+            ones[0] = 1;
             if (H5Sselect_hyperslab(whole_spaceid1, H5S_SELECT_SET,
-                                    start, NULL, count, NULL) < 0)
+                                    start, NULL, ones, count) < 0)
             {
                 ERR;
                 return 2;

h5_test/tst_h_par_compress.c

@@ -51,7 +51,7 @@ main(int argc, char **argv)
 	{
 	    hid_t fapl_id, fileid, whole_spaceid, dsid, slice_spaceid, whole_spaceid1, xferid;
 	    hid_t plistid;
-	    hsize_t start[NDIMS], count[NDIMS];
+	    hsize_t start[NDIMS], count[NDIMS], ones[NDIMS];
 	    hsize_t dims[1], chunksize = SC1;
 	    int data[SC1], data_in[SC1];
 	    int num_steps;
@@ -120,8 +120,9 @@ main(int argc, char **argv)
 		/* Select hyperslab for write of one slice. */
 		start[0] = s * SC1 * p + my_rank * SC1;
 		count[0] = SC1;
+		ones[0] = 1;
 		if (H5Sselect_hyperslab(whole_spaceid, H5S_SELECT_SET,
-					start, NULL, count, NULL) < 0) ERR;
+					start, NULL, ones, count) < 0) ERR;
 
 		if (H5Dwrite(dsid, H5T_NATIVE_INT, slice_spaceid, whole_spaceid,
 			     xferid, data) < 0) ERR;
@@ -160,8 +161,9 @@ main(int argc, char **argv)
 		/* Select hyperslab for read of one slice. */
 		start[0] = s * SC1 * p + my_rank * SC1;
 		count[0] = SC1;
+		ones[0] = 1;
 		if (H5Sselect_hyperslab(whole_spaceid1, H5S_SELECT_SET,
-					start, NULL, count, NULL) < 0)
+					start, NULL, ones, count) < 0)
 		{
 		    ERR;
 		    return 2;

h5_test/tst_h_strings2.c

@@ -30,6 +30,7 @@ main()
       hid_t file_spaceid, mem_spaceid;
       hsize_t dims[1] = {0}, max_dims[1] = {H5S_UNLIMITED}, chunk_dims[1] = {1};
       hsize_t xtend_size[NDIMS] = {2}, start[NDIMS] = {1}, count[NDIMS] = {1};
+      hsize_t ones[NDIMS] = {1};
 /*      void *fillp;*/
       char *data = "A man who carries a cat by the tail learns "
 	 "something he can learn in no other way.";
@@ -91,7 +92,7 @@ main()
       /* Select space in file to write a record. */
       if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
       if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
-			      start, NULL, count, NULL) < 0) ERR;
+			      start, NULL, ones, count) < 0) ERR;
 
       /* Select space in memory to read from. */
       if ((mem_spaceid = H5Screate_simple(NDIMS, count, NULL)) < 0) ERR;
@@ -126,7 +127,7 @@ main()
       hid_t typeid, datasetid, plistid;
       hid_t file_spaceid, mem_spaceid;
       hsize_t dims[1] = {2}, chunk_dims[1] = {1}; 
-      hsize_t start[NDIMS] = {1}, count[NDIMS] = {1};
+      hsize_t start[NDIMS] = {1}, count[NDIMS] = {1}, ones[NDIMS] = {1};
 /*      void *fillp;*/
       char *data = "A man who carries a cat by the tail learns "
 	 "something he can learn in no other way.";
@@ -179,7 +180,7 @@ To be good is noble; but to show others how to be good is nobler and no trouble.
       /* Select space in file to write a record. */
       if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
       if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, 
-			      start, NULL, count, NULL) < 0) ERR;
+			      start, NULL, ones, count) < 0) ERR;
 
       /* Select space in memory to read from. */
       if ((mem_spaceid = H5Screate_simple(NDIMS, count, NULL)) < 0) 

h5_test/tst_h_vars.c

@@ -69,7 +69,7 @@ main()
         float float_data_out[LAT_LEN][LON_LEN];
         hsize_t dims[NDIMS], max_dims[NDIMS];
         hsize_t dims_in[NDIMS], max_dims_in[NDIMS];
-        hsize_t start[MAX_DIMS], count[MAX_DIMS];
+        hsize_t start[MAX_DIMS], count[MAX_DIMS], ones[MAX_DIMS];
         int lat, lon;
 
         /* Set up some phoney data, 1 record's worth. In C, first
@@ -153,8 +153,9 @@ main()
         start[0] = 1;
         start[1] = 0;
         start[2] = 0;
+        ones[0] = ones[1] = ones[2] = 1;
         if (H5Sselect_hyperslab(write_spaceid, H5S_SELECT_SET,
-                                start, NULL, count, NULL) < 0) ERR;
+                                start, NULL, ones, count) < 0) ERR;
 
         /* Write second record of data to each dataset. */
         if (H5Dwrite(pres_dsid, H5T_IEEE_F32LE, mem_spaceid, write_spaceid,

libhdf5/hdf5var.c

@@ -1541,11 +1541,12 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
     NC_VAR_INFO_T *var;
     NC_DIM_INFO_T *dim;
     NC_HDF5_VAR_INFO_T *hdf5_var;
+    herr_t herr;
     hid_t file_spaceid = 0, mem_spaceid = 0, xfer_plistid = 0;
     long long unsigned xtend_size[NC_MAX_VAR_DIMS];
     hsize_t fdims[NC_MAX_VAR_DIMS], fmaxdims[NC_MAX_VAR_DIMS];
     hsize_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
-    hsize_t stride[NC_MAX_VAR_DIMS];
+    hsize_t stride[NC_MAX_VAR_DIMS], ones[NC_MAX_VAR_DIMS];
     int need_to_extend = 0;
 #ifdef USE_PARALLEL4
     int extend_possible = 0;
@@ -1596,6 +1597,7 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
         start[i] = startp[i];
         count[i] = countp ? countp[i] : var->dim[i]->len;
         stride[i] = stridep ? stridep[i] : 1;
+        ones[i] = 1;
 	LOG((4, "start[%d] %ld count[%d] %ld stride[%d] %ld", i, start[i], i, count[i], i, stride[i]));
 
         /* Check to see if any counts are zero. */
@@ -1646,8 +1648,13 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
     }
     else
     {
-        if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, stride,
-                                count, NULL) < 0)
+        if (stridep == NULL)
+            herr = H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start,
+                                       NULL, ones, count);
+        else
+            herr = H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start,
+                                       stride, count, NULL);
+        if (herr < 0)
             BAIL(NC_EHDFERR);
 
         /* Create a space for the memory, just big enough to hold the slab
@@ -1777,8 +1784,14 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
                 BAIL2(NC_EHDFERR);
             if ((file_spaceid = H5Dget_space(hdf5_var->hdf_datasetid)) < 0)
                 BAIL(NC_EHDFERR);
-            if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
-                                    start, stride, count, NULL) < 0)
+
+            if (stridep == NULL)
+                herr = H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
+                                           start, NULL, ones, count);
+            else
+                herr = H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
+                                           start, stride, count, NULL);
+            if (herr < 0)
                 BAIL(NC_EHDFERR);
         }
     }
@@ -1877,7 +1890,7 @@ NC4_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
     hsize_t count[NC_MAX_VAR_DIMS];
     hsize_t fdims[NC_MAX_VAR_DIMS], fmaxdims[NC_MAX_VAR_DIMS];
     hsize_t start[NC_MAX_VAR_DIMS];
-    hsize_t stride[NC_MAX_VAR_DIMS];
+    hsize_t stride[NC_MAX_VAR_DIMS], ones[NC_MAX_VAR_DIMS];
     void *fillvalue = NULL;
     int no_read = 0, provide_fill = 0;
     hssize_t fill_value_size[NC_MAX_VAR_DIMS];
@@ -1925,6 +1938,7 @@ NC4_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
         start[i] = startp[i];
         count[i] = countp[i];
         stride[i] = stridep ? stridep[i] : 1;
+        ones[i] = 1;
 
         /* if any of the count values are zero don't actually read. */
         if (count[i] == 0)
@@ -2054,9 +2068,16 @@ NC4_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
         }
         else
         {
-            if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
-                                    start, stride, count, NULL) < 0)
+            herr_t herr;
+            if (stridep == NULL)
+                herr = H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
+                                           start, NULL, ones, count);
+            else
+                herr = H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
+                                           start, stride, count, NULL);
+            if (herr < 0)
                 BAIL(NC_EHDFERR);
+
             /* Create a space for the memory, just big enough to hold the slab
                we want. */
             if ((mem_spaceid = H5Screate_simple(var->ndims, count, NULL)) < 0)

libnczarr/zvar.c

@@ -1542,7 +1542,7 @@ NCZ_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
 #endif
     size64_t fdims[NC_MAX_VAR_DIMS];
     size64_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
-    size64_t stride[NC_MAX_VAR_DIMS];
+    size64_t stride[NC_MAX_VAR_DIMS], ones[NC_MAX_VAR_DIMS];
     int retval, range_error = 0, i, d2;
     void *bufr = NULL;
     int bufrd = 0; /* 1 => we allocated bufr */
@@ -1584,6 +1584,7 @@ NCZ_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
 	start[0] = 0;
 	count[0] = 1;
 	stride[0] = 1;
+	ones[0] = 1;
     } else {
         for (i = 0; i < var->ndims; i++)
         {
@@ -1594,6 +1595,7 @@ NCZ_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
 	    start[i] = startp[i];
 	    count[i] = countp ? countp[i] : var->dim[i]->len;
 	    stride[i] = stridep ? stridep[i] : 1;
+	    ones[i] = 1;
 
   	    /* Check to see if any counts are zero. */
 	    if (!count[i])
@@ -1649,7 +1651,7 @@ NCZ_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
     else
     {
 	if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, stride,
-				count, NULL) < 0)
+				ones, count) < 0)
 	    BAIL(NC_EHDFERR);
 
 	/* Create a space for the memory, just big enough to hold the slab
@@ -1757,7 +1759,7 @@ NCZ_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
 	    if ((file_spaceid = H5Dget_space(ncz_var->hdf_datasetid)) < 0)
 		BAIL(NC_EHDFERR);
 	    if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
-				    start, stride, count, NULL) < 0)
+				    start, stride, ones, count) < 0)
 		BAIL(NC_EHDFERR);
 	}
 #endif
@@ -1864,6 +1866,7 @@ NCZ_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
     size64_t fmaxdims[NC_MAX_VAR_DIMS];
     size64_t start[NC_MAX_VAR_DIMS];
     size64_t stride[NC_MAX_VAR_DIMS];
+    size64_t ones[NC_MAX_VAR_DIMS];
     int no_read = 0, provide_fill = 0;
     int fill_value_size[NC_MAX_VAR_DIMS];
     int retval, range_error = 0, i, d2;
@@ -1898,6 +1901,7 @@ NCZ_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
 	start[0] = 0;
 	count[0] = 1;
 	stride[0] = 1;
+	ones[0] = 1;
     } else {
         for (i = 0; i < var->ndims; i++)
         {
@@ -1907,6 +1911,7 @@ NCZ_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
 	    start[i] = startp[i];
 	    count[i] = countp[i];
 	    stride[i] = stridep ? stridep[i] : 1;
+	    ones[i] = 1;
 	    /* if any of the count values are zero don't actually read. */
 	    if (count[i] == 0)
 	        no_read++;
@@ -2040,7 +2045,7 @@ NCZ_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
 	else
 	{
 	    if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
-				    start, stride, count, NULL) < 0)
+				    start, stride, ones, count) < 0)
 		BAIL(NC_EHDFERR);
 	    /* Create a space for the memory, just big enough to hold the slab
 	       we want. */

nc_perf/tst_files3.c

@@ -100,6 +100,7 @@ int dump_hdf_file(const float *data, int docompression)
    hsize_t dims[NDIMS] = {X_LEN, Y_LEN, Z_LEN};
    hsize_t start[NDIMS] = {0, 0, 0};
    hsize_t count[NDIMS] = {1, 1, Z_LEN};
+   hsize_t ones[NDIMS] = {1, 1, 1};
 
    /* create file */
    file_id = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC,
@@ -138,7 +139,7 @@ int dump_hdf_file(const float *data, int docompression)
       for (start[1] = 0; start[1] < Y_LEN; start[1]++)
       {
 	 if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, NULL,
-				 count, NULL) < 0) ERR_RET;
+				 ones, count) < 0) ERR_RET;
 	 if (H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, mem_spaceid, file_spaceid,
 		      xfer_plistid, data) < 0) ERR_RET;
       }