Hi Ed,
> How does this code look? This is what I'm timing to get the baseline
> answer: how fast can HDF5 write a file of longs?
I added a couple of comments about the datatypes you use below, but
otherwise
the code below looks good.
Quincey
> Thanks!
>
> Ed
>
> #define NDIMS 3
> #define XLEN 2000
> #define YLEN 300
> #define ZLEN 500
> #define HDF5_FILE "/tmp/a1.h5"
> #define VAR_NAME "V"
>
> hid_t hdfid, mem_spaceid, file_spaceid, datasetid, plistid;
> hsize_t h5dim[] = {XLEN, YLEN, ZLEN}, h5count[] = {1, YLEN, ZLEN};
> hssize_t h5start[] = {0, 0, 0};
> hsize_t h5dimmax[] = {H5S_UNLIMITED, YLEN, ZLEN}, chunksize[NDIMS];
> int *data;
>
> /* Allocate memory for data and fill it with a phoney value. */
> {
> size_t len = YLEN*ZLEN*sizeof(int);
> if (!(data = (int *)malloc(len)))
> BAIL(-2);
> for (i=0; i<YLEN*ZLEN; i++)
> data[i] = i;
> }
>
> /* Create a HDF5 file, with an unlimited dimension, and write
> the data that way. */
> {
> /* Create the file and dataset. */
> if ((hdfid = H5Fcreate(HDF5_REC_FILE, H5F_ACC_TRUNC,
> H5P_DEFAULT, H5P_DEFAULT)) < 0)
> BAIL(-1);
> h5dim[0] = 0;
> h5dim[1] = YLEN;
> h5dim[2] = ZLEN;
> if ((file_spaceid = H5Screate_simple(NDIMS, h5dim, h5dimmax)) < 0)
> BAIL(-3);
> if ((plistid = H5Pcreate (H5P_DATASET_CREATE)) < 0)
> BAIL(-10);
> chunksize[0] = 1;
> chunksize[1] = YLEN;
> chunksize[2] = ZLEN;
> if (H5Pset_chunk(plistid, NDIMS, chunksize) < 0)
> BAIL(-11);
> if ((datasetid = H5Dcreate(hdfid, VAR_NAME, H5T_STD_I32BE,
> file_spaceid, plistid)) < 0)
Although using 'H5T_STD_I32BE' is a very "apples-to-apples" comparison with
nc3, it does mitigate one of the advantages of HDF5 - writing in the machine's
native datatype without [potentially] forcing a conversion to big-endian data
on disk. It would be more "HDF5-like" to use H5T_NATIVE_INT here.
> BAIL(-4);
> H5Sclose(file_spaceid);
> H5Pclose(plistid);
>
> /* Now write the data. Use the same mem space for all
> writes. This memspace is only big enough to hold one
> record. */
> h5dim[0] = 1;
> h5dim[1] = YLEN;
> h5dim[2] = ZLEN;
> if ((mem_spaceid = H5Screate_simple(NDIMS, h5dim, NULL)) < 0)
> BAIL(-3);
> for (h5start[0] = 0; h5start[0]<XLEN; h5start[0]++)
> {
> h5dim[0] = h5start[0] + 1;
> if (H5Dextend(datasetid, h5dim) < 0)
> BAIL(-3);
> if ((file_spaceid = H5Dget_space(datasetid)) < 0)
> BAIL(-3);
> if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, h5start,
> NULL, h5count, NULL) < 0)
> BAIL(-3);
> if (H5Dwrite(datasetid, H5T_STD_I32BE, mem_spaceid,
> file_spaceid, H5P_DEFAULT, data))
Also, the 'H5T_STD_I32BE' here is technically not a good idea because you
are "lying" to the HDF5 library about the datatype in memory, using
H5T_NATIVE_INT here is definitely correct.
> BAIL(-5);
> H5Sclose(file_spaceid);
> }
>
> /* Clean up. */
> H5Sclose(mem_spaceid);
> H5Dclose(datasetid);
> H5Fclose(hdfid);
> }
>
