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count argument in H5Sselect_hyperslab #2296

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merged 4 commits into from
Dec 13, 2023
Merged

count argument in H5Sselect_hyperslab #2296

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64d3f2b
count argument in H5Sselect_hyperslab
wkliao Apr 20, 2022
52198b3
count argument in H5Sselect_hyperslab
wkliao Apr 20, 2022
6a628b9
Rebased PR by hand against main.
WardF Dec 12, 2023
2ffd1c0
Merge branch 'H5Sselect_hyperslab' of github.com:wkliao/netcdf-c into…
WardF Dec 12, 2023
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5 changes: 3 additions & 2 deletions h5_test/tst_h_dimscales2.c
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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. */
Expand All @@ -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. */
Expand Down
4 changes: 2 additions & 2 deletions h5_test/tst_h_enums.c
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;

Expand Down
10 changes: 6 additions & 4 deletions h5_test/tst_h_files.c
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down
8 changes: 5 additions & 3 deletions h5_test/tst_h_par.c
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down
8 changes: 5 additions & 3 deletions h5_test/tst_h_par_compress.c
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down
7 changes: 4 additions & 3 deletions h5_test/tst_h_strings2.c
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Expand Up @@ -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.";
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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.";
Expand Down Expand Up @@ -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)
Expand Down
5 changes: 3 additions & 2 deletions h5_test/tst_h_vars.c
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Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down
37 changes: 29 additions & 8 deletions libhdf5/hdf5var.c
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Expand Up @@ -1542,11 +1542,12 @@ 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;
Expand Down Expand Up @@ -1597,6 +1598,7 @@ 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. */
Expand Down Expand Up @@ -1647,8 +1649,13 @@ 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
Expand Down Expand Up @@ -1773,8 +1780,14 @@ 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);
}
}
Expand Down Expand Up @@ -1873,7 +1886,7 @@ 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];
Expand Down Expand Up @@ -1924,6 +1937,7 @@ 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)
Expand Down Expand Up @@ -2053,9 +2067,16 @@ 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)
Expand Down
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