/* Return size of chunk in bytes for a variable varid in a group igrp, or 0 if
* layout is contiguous */
static int
inq_var_chunksize(int igrp, int varid, size_t* chunksizep) {
int stat = NC_NOERR;
int ndims;
size_t *chunksizes;
int dim;
int contig = 1;
nc_type vartype;
size_t value_size;
size_t prod;
NC_CHECK(nc_inq_vartype(igrp, varid, &vartype));
/* from type, get size in memory needed for each value */
NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
prod = value_size;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
chunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
if(ndims > 0) {
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, NULL));
}
if(contig == 1) {
*chunksizep = 0;
} else {
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, chunksizes));
for(dim = 0; dim < ndims; dim++) {
prod *= chunksizes[dim];
}
*chunksizep = prod;
}
free(chunksizes);
return stat;
}
/* Initialize iteration for a variable. Just a wrapper for
* nc_blkio_init() that makes the netCDF calls needed to initialize
* lower-level iterator. */
int
nc_get_iter(int ncid,
int varid,
size_t bufsize, /* size in bytes of memory buffer */
nciter_t **iterpp /* returned opaque iteration state */)
{
int stat = NC_NOERR;
nciter_t *iterp;
nc_type vartype;
size_t value_size = 0; /* size in bytes of each variable element */
int ndims; /* number of dimensions for variable */
int *dimids;
long long nvalues = 1;
int dim;
int chunked = 0;
/* Caller should free this by calling nc_free_iter(iterp) */
iterp = (nciter_t *) emalloc(sizeof(nciter_t));
memset((void*)iterp,0,sizeof(nciter_t)); /* make sure it is initialized */
NC_CHECK(nc_inq_varndims(ncid, varid, &ndims));
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
iterp->dimsizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
iterp->chunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
NC_CHECK(nc_inq_vardimid (ncid, varid, dimids));
for(dim = 0; dim < ndims; dim++) {
size_t len;
NC_CHECK(nc_inq_dimlen(ncid, dimids[dim], &len));
nvalues *= len;
iterp->dimsizes[dim] = len;
}
NC_CHECK(nc_inq_vartype(ncid, varid, &vartype));
NC_CHECK(inq_value_size(ncid, vartype, &value_size));
#ifdef USE_NETCDF4
{
int contig = 1;
if(ndims > 0) {
NC_CHECK(nc_inq_var_chunking(ncid, varid, &contig, NULL));
}
if(contig == 0) { /* chunked */
NC_CHECK(nc_inq_var_chunking(ncid, varid, &contig, iterp->chunksizes));
chunked = 1;
}
}
#endif /* USE_NETCDF4 */
NC_CHECK(nc_blkio_init(bufsize, value_size, ndims, chunked, iterp));
iterp->to_get = 0;
free(dimids);
*iterpp = iterp;
return stat;
}
/* Initialize iteration for a variable. Just a wrapper for
* nc_blkio_init() that makes the netCDF calls needed to initialize
* lower-level iterator. */
int
nc_get_iter(Symbol* vsym,
size_t bufsize, /* size in bytes of memory buffer */
nciter_t *iterp /* returned opaque iteration state */)
{
int stat = NC_NOERR;
Symbol* vartype;
size_t value_size; /* size in bytes of each variable element */
int ndims; /* number of dimensions for variable */
size_t dimsizes[NC_MAX_VAR_DIMS]; /* variable dimension sizes */
size_t chunksizes[NC_MAX_VAR_DIMS]; /* corresponding chunk sizes */
long long nvalues = 1;
int dim;
int chunked = 0;
memset((void*)iterp,0,sizeof(nciter_t)); /* make sure it is initialized */
stat = nciter_ndims(vsym, &ndims);
CHECK(stat, nciter_ndims);
stat = nciter_dimlens(vsym,dimsizes);
/* compute total # elements */
nvalues=1;
for(dim = 0; dim < ndims; dim++) {
nvalues *= dimsizes[dim];
}
stat = nciter_vartype(vsym, &vartype);
CHECK(stat, nciter_vartype);
stat = nciter_valuesize(vartype,&value_size);
CHECK(stat, nciter_valuesize);
#ifdef USE_NETCDF4
#ifdef DOCHUNK
{
int contig = 1;
if(ndims > 0) {
stat = nc_inq_var_chunking(ncid, varid, &contig, NULL);
CHECK(stat, nc_inq_var_chunking);
}
if(contig == 0) { /* chunked */
stat = nc_inq_var_chunking(ncid, varid, &contig, chunksizes);
CHECK(stat, nc_inq_var_chunking);
chunked = 1;
}
}
#else
chunked = 0;
#endif
#endif /* USE_NETCDF4 */
stat = nc_blkio_init(bufsize, value_size, ndims, dimsizes,
chunked, chunksizes, iterp);
CHECK(stat, nc_blkio_init);
iterp->to_get = 0;
return stat;
}
/* Inputs:
root_id: netcdfID of the root group
varid: var ID to set the deflate params for
ndims: number of dims in the variable
Outputs:
storage: either 1 for NC_CONTIGUOUS or 2 for NC_CHUNKED
chunksizesp: pointer to array indicating chunk sizes along each dimension. NOTE:
THIS MUST BE ALLOCATED BEFORE CALLING THIS ROUTINE!!
Returned values are in C order (which is opposite R order)
ierr: 0 on success, otherwise an error was encountered
*/
void R_nc4_inq_var_chunking( int *root_id, int *varid, int *ndims, int *storage, int *chunksizesp, int *ierr )
{
int stor_param, i;
size_t sizet_chunkparam[MAX_NC_DIMS];
*ierr = nc_inq_var_chunking( *root_id, *varid, &stor_param, sizet_chunkparam );
if( *ierr != NC_NOERR ) {
Rprintf( "Error in R_nc4_inq_var_chunking: %s\n", nc_strerror(*ierr) );
return;
}
if( stor_param == NC_CONTIGUOUS )
*storage = 1;
else if( stor_param == NC_CHUNKED )
*storage = 2;
else
{
Rprintf( "Error in R_nc4_inq_var_chunking: obtained value of storage is neither NC_CONTIGUOUS nor NC_CHUNKED! Value=%d\n",
stor_param );
*ierr = -1;
return;
}
for( i=0; i<(*ndims); i++ )
chunksizesp[i] = (int)(sizet_chunkparam[i]);
}
static int
verifychunks(void)
{
int i;
int store = -1;
size_t localchunks[MAXDIMS];
memset(localchunks,0,sizeof(localchunks));
CHECK(nc_inq_var_chunking(ncid, varid, &store, localchunks));
if(store != NC_CHUNKED) {
fprintf(stderr,"bad chunk store\n");
return 0;
}
for(i=0;i<ndims;i++) {
if(chunksize[i] != localchunks[i]) {
fprintf(stderr,"bad chunk size: %d\n",i);
return 0;
}
}
return 1;
}
static int
verifychunks(void)
{
int i;
int store = -1;
size_t chunksizes[NDIMS];
memset(chunksizes,0,sizeof(chunksizes));
CHECK(nc_inq_var_chunking(ncid, varid, &store, chunksizes));
/* Storate must be chunked, not contiguous */
if(store != NC_CHUNKED) {
fprintf(stderr,"bad chunk store\n");
return NC_ESTORAGE;
}
/* Chunk sizes must match our predefined set */
for(i=0;i<actualdims;i++) {
if(chunksizes[i] != chunks[i]) {
fprintf(stderr,"bad chunk size: %d\n",i);
return NC_EBADCHUNK;
}
}
return 1;
}
int
main(int argc, char **argv)
{
extern int optind;
extern int opterr;
extern char *optarg;
int c, header = 0, verbose = 0, timeseries = 0;
int ncid, varid, storage;
char name_in[NC_MAX_NAME + 1];
size_t len;
size_t cs[NDIMS3] = {0, 0, 0};
int cache = MEGABYTE;
int ndims, dimid[NDIMS3];
float hor_data[LAT_LEN * LON_LEN];
int read_1_us, avg_read_us;
float ts_data[TIME_LEN];
size_t start[NDIMS3], count[NDIMS3];
int deflate, shuffle, deflate_level;
struct timeval start_time, end_time, diff_time;
while ((c = getopt(argc, argv, "vhtc:")) != EOF)
switch(c)
{
case 'v':
verbose++;
break;
case 'h':
header++;
break;
case 't':
timeseries++;
break;
case 'c':
sscanf(optarg, "%d", &cache);
break;
case '?':
usage();
return 1;
}
argc -= optind;
argv += optind;
/* If no file arguments left, report and exit */
if (argc < 1)
{
printf("no file specified\n");
return 0;
}
/* Print the header if desired. */
if (header)
{
printf("cs[0]\tcs[1]\tcs[2]\tcache(MB)\tdeflate\tshuffle");
if (timeseries)
printf("\t1st_read_ser(us)\tavg_read_ser(us)\n");
else
printf("\t1st_read_hor(us)\tavg_read_hor(us)\n");
}
#define PREEMPTION .75
/* Also tried NELEMS of 2500009*/
#define NELEMS 7919
if (nc_set_chunk_cache(cache, NELEMS, PREEMPTION)) ERR;
if (nc_open(argv[0], 0, &ncid)) ERR;
/* Check to make sure that all the dimension information is
* correct. */
if (nc_inq_varid(ncid, DATA_VAR_NAME, &varid)) ERR;
if (nc_inq_dim(ncid, LON_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "lon") || len != LON_LEN) ERR;
if (nc_inq_dim(ncid, LAT_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "lat") || len != LAT_LEN) ERR;
if (nc_inq_dim(ncid, BNDS_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "bnds") || len != BNDS_LEN) ERR;
if (nc_inq_dim(ncid, TIME_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "time") || len != TIME_LEN) ERR;
if (nc_inq_var(ncid, varid, NULL, NULL, &ndims, dimid, NULL)) ERR;
if (ndims != NDIMS3 || dimid[0] != TIME_DIMID ||
dimid[1] != LAT_DIMID || dimid[2] != LON_DIMID) ERR;
/* Get info about the main data var. */
if (nc_inq_var_chunking(ncid, varid, &storage, cs)) ERR;
if (nc_inq_var_deflate(ncid, varid, &shuffle, &deflate,
&deflate_level)) ERR;
if (timeseries)
{
/* Read the var as a time series. */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = TIME_LEN;
count[1] = 1;
count[2] = 1;
/* Read the first timeseries. */
if (gettimeofday(&start_time, NULL)) ERR;
if (nc_get_vara_float(ncid, varid, start, count, ts_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
read_1_us = (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
/* Read all the rest. */
if (gettimeofday(&start_time, NULL)) ERR;
for (start[1] = 0; start[1] < LAT_LEN; start[1]++)
for (start[2] = 1; start[2] < LON_LEN; start[2]++)
if (nc_get_vara_float(ncid, varid, start, count, ts_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
avg_read_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec + read_1_us) /
(LAT_LEN * LON_LEN);
}
else
{
/* Read the data variable in horizontal slices. */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = LAT_LEN;
count[2] = LON_LEN;
/* Read (and time) the first one. */
if (gettimeofday(&start_time, NULL)) ERR;
if (nc_get_vara_float(ncid, varid, start, count, hor_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
read_1_us = (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
/* Read (and time) all the rest. */
if (gettimeofday(&start_time, NULL)) ERR;
for (start[0] = 1; start[0] < TIME_LEN; start[0]++)
if (nc_get_vara_float(ncid, varid, start, count, hor_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
avg_read_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec +
read_1_us) / TIME_LEN;
}
/* Close file. */
if (nc_close(ncid)) ERR;
/* Print results. */
printf("%d\t%d\t%d\t%.1f\t\t%d\t%d\t\t",
(int)cs[0], (int)cs[1], (int)cs[2],
(storage == NC_CHUNKED) ? (cache/(float)MEGABYTE) : 0,
deflate, shuffle);
if (timeseries)
printf("%d\t\t%d\n", (int)read_1_us, (int)avg_read_us);
else
printf("%d\t\t%d\n", (int)read_1_us, (int)avg_read_us);
return 0;
}
int
main(int argc, char **argv)
{
printf("\n*** Testing netcdf-4 variable chunking.\n");
printf("**** testing that fixed vars with filter end up being chunked, with good sizes...");
{
int ncid;
int nvars, ndims, ngatts, unlimdimid;
int contig;
int ndims_in, natts_in, dimids_in;
int small_dimid, medium_dimid, large_dimid;
int small_varid, medium_varid, large_varid;
char var_name_in[NC_MAX_NAME + 1];
size_t chunksize_in[NDIMS1];
nc_type xtype_in;
/* Create a netcdf-4 file with three dimensions. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, D_SMALL, D_SMALL_LEN, &small_dimid)) ERR;
if (nc_def_dim(ncid, D_MEDIUM, D_MEDIUM_LEN, &medium_dimid)) ERR;
if (nc_def_dim(ncid, D_LARGE, D_LARGE_LEN, &large_dimid)) ERR;
/* Add three vars, with filters to force chunking. */
if (nc_def_var(ncid, V_SMALL, NC_INT64, NDIMS1, &small_dimid, &small_varid)) ERR;
if (nc_def_var_deflate(ncid, small_varid, 0, 1, 4)) ERR;
if (nc_def_var(ncid, V_MEDIUM, NC_INT64, NDIMS1, &medium_dimid, &medium_varid)) ERR;
if (nc_def_var_deflate(ncid, medium_varid, 1, 0, 0)) ERR;
if (nc_def_var(ncid, V_LARGE, NC_INT64, NDIMS1, &large_dimid, &large_varid)) ERR;
if (nc_def_var_fletcher32(ncid, large_varid, 1)) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid)) ERR;
if (nvars != 3 || ndims != 3 || ngatts != 0 || unlimdimid != -1) ERR;
if (nc_inq_var(ncid, 0, var_name_in, &xtype_in, &ndims_in, &dimids_in, &natts_in)) ERR;
if (strcmp(var_name_in, V_SMALL) || xtype_in != NC_INT64 || ndims_in != 1 ||
natts_in != 0) ERR;
/* Make sure chunking sizes are what we expect. */
if (nc_inq_var_chunking(ncid, small_varid, &contig, chunksize_in)) ERR;
if (contig || chunksize_in[0] != D_SMALL_LEN) ERR;
if (nc_inq_var_chunking(ncid, medium_varid, &contig, chunksize_in)) ERR;
if (contig || chunksize_in[0] * sizeof(long long) > DEFAULT_CHUNK_SIZE) ERR;
if (nc_inq_var_chunking(ncid, large_varid, &contig, chunksize_in)) ERR;
if (contig || chunksize_in[0] * sizeof(long long) > DEFAULT_CHUNK_SIZE) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes...");
{
int nvars, ndims, ngatts, unlimdimid;
int contig;
#define NUM_DIM 4
#define NUM_TYPE 2
int ncid;
int dim_len[NUM_DIM] = {NC_UNLIMITED, 100, 1000, 2000};
size_t chunksize_in[NUM_DIM];
int type_id[NUM_TYPE] = {NC_BYTE, NC_INT};
int dimid[NUM_DIM], varid[NUM_TYPE];
char dim_name[NC_MAX_NAME + 1], var_name[NC_MAX_NAME + 1];
int d, t;
/* Create a netcdf-4 file with NUM_DIM dimensions. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
for (d = 0; d < NUM_DIM; d++)
{
sprintf(dim_name, "dim_%d", dim_len[d]);
#ifdef PRINT_DEFAULT_CHUNKSIZE_TABLE
printf("creating dim %s\n", dim_name);
#endif
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimid[d])) ERR;
}
for (t = 0; t < NUM_TYPE; t++)
{
sprintf(var_name, "var_%d", type_id[t]);
if (nc_def_var(ncid, var_name, type_id[t], NUM_DIM, dimid, &varid[t])) ERR;
if (nc_inq_var_chunking(ncid, varid[t], &contig, chunksize_in)) ERR;
#ifdef PRINT_DEFAULT_CHUNKSIZE_TABLE
printf("chunksizes for %d x %d x %d x %d var: %d x %d x %d x %d (=%d)\n",
dim_len[0], dim_len[1], dim_len[2], dim_len[3],
(int)chunksize_in[0], (int)chunksize_in[1], (int)chunksize_in[2],
(int)chunksize_in[3],
(int)(chunksize_in[0] * chunksize_in[1] * chunksize_in[2] * chunksize_in[3]));
#endif
}
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid)) ERR;
if (nvars != NUM_TYPE || ndims != NUM_DIM || ngatts != 0 || unlimdimid != 0) ERR;
for (t = 0; t < NUM_TYPE; t++)
{
sprintf(var_name, "var_%d", type_id[t]);
if (nc_inq_var_chunking(ncid, varid[t], &contig, chunksize_in)) ERR;
if (contig) ERR;
#ifdef PRINT_DEFAULT_CHUNKSIZE_TABLE
printf("chunksizes for %d x %d x %d x %d var: %d x %d x %d x %d (=%d)\n",
dim_len[0], dim_len[1], dim_len[2], dim_len[3],
(int)chunksize_in[0], (int)chunksize_in[1], (int)chunksize_in[2],
(int)chunksize_in[3],
(int)(chunksize_in[0] * chunksize_in[1] * chunksize_in[2] * chunksize_in[3]));
#endif
}
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing that chunking works on classic mode files...");
{
#define D_SMALL_LEN2 66
int ncid;
int nvars, ndims, ngatts, unlimdimid;
int contig;
int ndims_in, natts_in, dimids_in;
int small_dimid, medium_dimid, large_dimid;
int small_varid, medium_varid, large_varid;
char var_name_in[NC_MAX_NAME + 1];
size_t chunks[1], chunksize_in;
nc_type xtype_in;
/* Create a netcdf-4 file with three dimensions. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, D_SMALL, D_SMALL_LEN2, &small_dimid)) ERR;
if (nc_def_dim(ncid, D_MEDIUM, D_MEDIUM_LEN, &medium_dimid)) ERR;
if (nc_def_dim(ncid, D_LARGE, D_LARGE_LEN, &large_dimid)) ERR;
/* Add three vars. */
if (nc_def_var(ncid, V_SMALL, NC_INT64, NDIMS1, &small_dimid, &small_varid)) ERR;
if (nc_def_var_chunking(ncid, small_varid, 1, NULL)) ERR;
if (nc_def_var(ncid, V_MEDIUM, NC_INT64, NDIMS1, &medium_dimid, &medium_varid)) ERR;
chunks[0] = D_MEDIUM_LEN / 100;
if (nc_def_var_chunking(ncid, medium_varid, 0, chunks)) ERR;
if (nc_def_var_deflate(ncid, medium_varid, 1, 0, 0)) ERR;
if (nc_def_var(ncid, V_LARGE, NC_INT64, NDIMS1, &large_dimid, &large_varid)) ERR;
chunks[0] = D_LARGE_LEN / 1000;
if (nc_def_var_chunking(ncid, large_varid, 0, chunks)) ERR;
if (nc_def_var_fletcher32(ncid, large_varid, 1)) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid)) ERR;
if (nvars != 3 || ndims != 3 || ngatts != 0 || unlimdimid != -1) ERR;
if (nc_inq_var(ncid, 0, var_name_in, &xtype_in, &ndims_in, &dimids_in, &natts_in)) ERR;
if (strcmp(var_name_in, V_SMALL) || xtype_in != NC_INT64 || ndims_in != 1 ||
natts_in != 0) ERR;
/* Make sure chunking settings are what we expect. */
if (nc_inq_var_chunking(ncid, small_varid, &contig, &chunksize_in)) ERR;
if (!contig) ERR;
if (nc_inq_var_chunking(ncid, medium_varid, &contig, &chunksize_in)) ERR;
if (contig || chunksize_in != D_MEDIUM_LEN / 100) ERR;
if (nc_inq_var_chunking(ncid, large_varid, &contig, &chunksize_in)) ERR;
if (contig || chunksize_in != D_LARGE_LEN / 1000) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing many chunking and contiguous variables...");
{
#define NDIMS_3 3
#define NUM_PLANS 30
#define D_SNEAKINESS "sneakiness"
#define D_SNEAKINESS_LEN 5
#define D_CLEVERNESS "clevernesss"
#define D_CLEVERNESS_LEN 3
#define D_EFFECTIVENESS "effectiveness"
#define D_EFFECTIVENESS_LEN 2
int ncid, dimids[NDIMS_3], varid[NUM_PLANS];
size_t chunksize[NDIMS_3] = {D_SNEAKINESS_LEN, D_CLEVERNESS_LEN,
D_EFFECTIVENESS_LEN};
char plan_name[NC_MAX_NAME + 1];
int contig;
size_t chunksize_in[NDIMS_3];
int i, j;
/* Create a netcdf-4 file with three dimensions. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, D_SNEAKINESS, D_SNEAKINESS_LEN, &dimids[0])) ERR;
if (nc_def_dim(ncid, D_CLEVERNESS, D_CLEVERNESS_LEN, &dimids[1])) ERR;
if (nc_def_dim(ncid, D_EFFECTIVENESS, D_EFFECTIVENESS_LEN, &dimids[2])) ERR;
/* Oh that tricky Cardinal Richelieu, he had many plans! */
for (i = 0; i < NUM_PLANS; i++)
{
sprintf(plan_name, "Richelieu_sneaky_plan_%d", i);
if (nc_def_var(ncid, plan_name, i % (NC_STRING - 1) + 1, NDIMS_3,
dimids, &varid[i])) ERR;
if (i % 2 && nc_def_var_chunking(ncid, varid[i], 0, chunksize)) ERR;
}
/* Check the chunking. */
for (i = 0; i < NUM_PLANS; i++)
{
if (nc_inq_var_chunking(ncid, varid[i], &contig, chunksize_in)) ERR;
if (i % 2)
{
for (j = 0; j < NDIMS_3; j++)
if (chunksize_in[j] != chunksize[j]) ERR;
}
else
if (!contig) ERR;
}
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
/* Check the chunking. */
for (i = 0; i < NUM_PLANS; i++)
{
if (nc_inq_var_chunking(ncid, varid[i], &contig, chunksize_in)) ERR;
if (i % 2)
{
for (j = 0; j < NDIMS_3; j++)
if (chunksize_in[j] != chunksize[j]) ERR;
}
else
if (!contig) ERR;
}
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing that too large chunksizes fail...");
{
#define D_SMALL_LEN2 66
int stat = NC_NOERR;
int ncid;
int nvars, ndims, ngatts, unlimdimid;
int contig;
int ndims_in, natts_in, dimids_in;
int small_dimid, medium_dimid, large_dimid;
int small_varid;
char var_name_in[NC_MAX_NAME + 1];
size_t chunks[1], chunksize_in;
nc_type xtype_in;
/* Create a netcdf-4 file with three dimensions. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, D_SMALL, D_SMALL_LEN2, &small_dimid)) ERR;
/* Add one var. */
if (nc_def_var(ncid, V_SMALL, NC_INT64, NDIMS1, &small_dimid, &small_varid)) ERR;
/* Attempt to set too large chunksizes */
chunks[0] = D_SMALL_LEN2 + 1;
stat = nc_def_var_chunking(ncid, small_varid, NC_CHUNKED, chunks);
if(stat != NC_EBADCHUNK) {
printf("Return code is '%s', expected NC_BADCHUNK",nc_strerror(stat));
ERR;
}
/* try agains with proper chunksize */
chunks[0] = D_SMALL_LEN2;
stat = nc_def_var_chunking(ncid, small_varid, NC_CHUNKED, chunks);
if(stat != NC_NOERR) {
printf("Return code is '%s', expected NC_NOERR",nc_strerror(stat));
ERR;
}
if (nc_abort(ncid)) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
int
main(int argc, char **argv)
{
int ncid;
int varid;
int rank;
int d;
int storage;
size_t chunksizes[NC_MAX_VAR_DIMS];
const char* srcdir = ".";
printf("\n*** Testing HDF4/NetCDF-4 chunking API: chunked...\n");
{
/* Open with netCDF */
if (nc_open(CHUNKEDFILE, NC_NOWRITE, &ncid)) ERR;
/* Get a variable id */
if(nc_inq_varid(ncid,CHUNKEDVAR,&varid)) ERR;
/* get rank */
if(nc_inq_varndims(ncid,varid,&rank)) ERR;
/* get chunk info */
memset(chunksizes,0,sizeof(chunksizes));
if(nc_inq_var_chunking(ncid,varid,&storage,chunksizes)) ERR;
if(storage == NC_CONTIGUOUS) {
fprintf(stderr,"nc_inq_var_chunking did not return CHUNKED\n");
ERR;
}
for(d=0;d<rank;d++) {
if(EXPECTED_CHUNKSIZES[d] != chunksizes[d]) {
fprintf(stderr,"chunk size mismatch: [%d] %ld :: %ld\n",d,chunksizes[d],EXPECTED_CHUNKSIZES[d]);
ERR;
}
}
if (nc_close(ncid)) ERR;
}
printf("\n*** Testing HDF4/NetCDF-4 chunking API: contiguous...\n");
{
/* Open with netCDF */
if (nc_open(CONTIGFILE, NC_NOWRITE, &ncid)) ERR;
/* Get a variable id */
if(nc_inq_varid(ncid,CONTIGVAR,&varid)) ERR;
/* get rank */
if(nc_inq_varndims(ncid,varid,&rank)) ERR;
/* get chunk info */
memset(chunksizes,0,sizeof(chunksizes));
if(nc_inq_var_chunking(ncid,varid,&storage,chunksizes)) ERR;
if(storage != NC_CONTIGUOUS) {
fprintf(stderr,"nc_inq_var_chunking did not return CONTIGUOUS\n");
ERR;
}
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
/***********************************************************************
*
* HANDLE_NC_INQ_VAR_CHUNKING:
*
* code for handling the nc_inq_var_chunking routine.
*
* [storage,chunksize,status] = mexnc('inq_var_chunking',ncid,varid);
*
**********************************************************************/
void handle_nc_inq_var_chunking ( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[], op *nc_op ) {
int ncid;
int varid;
int storage;
size_t chunksize[NC_MAX_DIMS];
/*
* Pointer shortcut to matrix data.
* */
double *pr;
mwSize mxsize[2]; /* Size of chunking matrix. */
int status, j;
/*
* Number of dimensions (inferred from length of chunk argument)
* */
int ndims;
/*
* File format.
* */
int format;
/*
* Make sure that the inputs are the right type.
* */
check_numeric_argument_type ( prhs, nc_op->opname, 1 );
check_numeric_argument_type ( prhs, nc_op->opname, 2 );
pr = mxGetData ( prhs[1] );
ncid = (int)(pr[0]);
pr = mxGetData ( prhs[2] );
varid = (int)(pr[0]);
status = nc_inq_format(ncid,&format);
if ( status != NC_NOERR ) {
sprintf ( error_message,
"Internal call to nc_inq_format failed, operation \"%s\", line %d file \"%s\"\n",
nc_op->opname, __LINE__, __FILE__ );
mexErrMsgTxt ( error_message );
return;
}
switch(format){
case NC_FORMAT_CLASSIC:
case NC_FORMAT_64BIT:
plhs[0] = mxCreateString ( "contiguous" );
plhs[1] = mxCreateNumericArray(0,0, mxDOUBLE_CLASS, mxREAL );
plhs[2] = mxCreateNumericArray(0,0, mxDOUBLE_CLASS, mxREAL );
return;
}
status = nc_inq_varndims(ncid,varid,&ndims);
if ( status != NC_NOERR ) {
sprintf ( error_message,
"Internal call to nc_inq_varndims failed, operation \"%s\", line %d file \"%s\"\n",
nc_op->opname, __LINE__, __FILE__ );
mexErrMsgTxt ( error_message );
return;
}
status = nc_inq_var_chunking ( ncid, varid, &storage, chunksize );
plhs[2] = mexncCreateDoubleScalar ( status );
if ( storage == NC_CONTIGUOUS ) {
plhs[0] = mxCreateString ( "contiguous" );
/*
* Return [] for the chunksize
* */
mxsize[0] = 0;
mxsize[1] = 0;
plhs[1] = mxCreateNumericArray ( 2, mxsize, mxDOUBLE_CLASS, mxREAL );
return;
}
plhs[0] = mxCreateString ( "chunked" );
mxsize[0] = 1;
mxsize[1] = ndims;
plhs[1] = mxCreateNumericArray ( 2, mxsize, mxDOUBLE_CLASS, mxREAL );
pr = mxGetData ( plhs[1] );
for ( j = 0; j < ndims; ++j ) {
pr[j] = chunksize[j];
}
return;
}
int
main(int argc, char **argv)
{
int ncid, dimids[NUM_DIMS];
int varid;
int nvars_in, varids_in[NUM_DIMS];
signed char fill_value = 42, fill_value_in;
nc_type xtype_in;
size_t len_in;
char name_in[NC_MAX_NAME + 1];
int attnum_in;
int cnum;
#ifdef USE_PARALLEL
MPI_Init(&argc, &argv);
#endif
printf("\n*** Testing netcdf-4 variable functions, even more.\n");
for (cnum = 0; cnum < MAX_CNUM; cnum++)
{
int cmode;
switch(cnum)
{
case 0:
printf("*** Testing with classic format:\n");
cmode = 0;
break;
case 1:
printf("*** Testing with 64-bit offset format:\n");
cmode = NC_64BIT_OFFSET;
break;
case 2:
printf("*** Testing with HDF5:\n");
cmode = NC_NETCDF4|NC_CLOBBER;
break;
case 3:
printf("*** Testing with HDF5, netCDF Classic Model:\n");
cmode = NC_CLASSIC_MODEL | NC_NETCDF4;
}
printf("**** testing simple fill value attribute creation...");
{
/* Create a netcdf-4 file with one scalar var. Add fill
* value. */
if (nc_create(FILE_NAME, cmode, &ncid)) ERR;
if (nc_def_var(ncid, VAR_NAME, NC_BYTE, 0, NULL, &varid)) ERR;
if (nc_enddef(ncid)) ERR;
if (nc_redef(ncid)) ERR;
if (nc_put_att_schar(ncid, varid, _FillValue, NC_BYTE, 1, &fill_value)) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq_varids(ncid, &nvars_in, varids_in)) ERR;
if (nvars_in != 1 || varids_in[0] != 0) ERR;
if (nc_inq_varname(ncid, 0, name_in)) ERR;
if (strcmp(name_in, VAR_NAME)) ERR;
if (nc_inq_att(ncid, varid, _FillValue, &xtype_in, &len_in)) ERR;
if (xtype_in != NC_BYTE || len_in != 1) ERR;
if (nc_get_att(ncid, varid, _FillValue, &fill_value_in)) ERR;
if (fill_value_in != fill_value) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing simple fill value with data read...");
{
size_t start[NUM_DIMS], count[NUM_DIMS];
signed char data = 99, data_in;
/* Create a netcdf-4 file with one unlimited dim and one
* var. Add fill value. */
if (nc_create(FILE_NAME, cmode, &ncid)) ERR;
if (nc_def_dim(ncid, DIM1_NAME, DIM1_LEN, &dimids[0])) ERR;
if (nc_def_var(ncid, VAR_NAME, NC_BYTE, NUM_DIMS, dimids, &varid)) ERR;
if (nc_enddef(ncid)) ERR;
if (nc_redef(ncid)) ERR;
if (nc_put_att_schar(ncid, varid, _FillValue, NC_BYTE, 1, &fill_value)) ERR;
if (nc_enddef(ncid)) ERR;
/* Write the second record. */
start[0] = 1;
count[0] = 1;
if (nc_put_vara_schar(ncid, varid, start, count, &data)) ERR;
/* Read the first record, it should be the fill value. */
start[0] = 0;
if (nc_get_vara_schar(ncid, varid, start, count, &data_in)) ERR;
if (data_in != fill_value) ERR;
/* Read the second record, it should be the value we just wrote
* there. */
start[0] = 1;
if (nc_get_vara_schar(ncid, varid, start, count, &data_in)) ERR;
if (data_in != data) ERR;
/* Close up. */
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
/* Check metadata. */
if (nc_inq_varids(ncid, &nvars_in, varids_in)) ERR;
if (nvars_in != 1 || varids_in[0] != 0) ERR;
if (nc_inq_varname(ncid, 0, name_in)) ERR;
if (strcmp(name_in, VAR_NAME)) ERR;
/* Check fill value att. */
if (nc_inq_att(ncid, varid, _FillValue, &xtype_in, &len_in)) ERR;
if (xtype_in != NC_BYTE || len_in != 1) ERR;
if (nc_get_att(ncid, varid, _FillValue, &fill_value_in)) ERR;
if (fill_value_in != fill_value) ERR;
/* Read the first record, it should be the fill value. */
start[0] = 0;
if (nc_get_vara_schar(ncid, varid, start, count, &data_in)) ERR;
if (data_in != fill_value) ERR;
/* Read the second record, it should be the value we just wrote
* there. */
start[0] = 1;
if (nc_get_vara_schar(ncid, varid, start, count, &data_in)) ERR;
if (data_in != data) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing fill value with one other attribute...");
{
int losses_value = 192, losses_value_in;
/* Create a netcdf-4 file with one dim and one var. Add another
* attribute, then fill value. */
if (nc_create(FILE_NAME, cmode, &ncid)) ERR;
if (nc_def_dim(ncid, DIM1_NAME, DIM1_LEN, &dimids[0])) ERR;
if (nc_def_var(ncid, VAR_NAME, NC_BYTE, NUM_DIMS, dimids, &varid)) ERR;
if (nc_put_att_int(ncid, varid, LOSSES_NAME, NC_INT, 1, &losses_value)) ERR;
if (nc_put_att_schar(ncid, varid, _FillValue, NC_BYTE, 1, &fill_value)) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq_att(ncid, 0, LOSSES_NAME, &xtype_in, &len_in)) ERR;
if (xtype_in != NC_INT || len_in != 1) ERR;
if (nc_get_att(ncid, 0, LOSSES_NAME, &losses_value_in)) ERR;
if (losses_value_in != losses_value) ERR;
if (nc_inq_att(ncid, 0, _FillValue, &xtype_in, &len_in)) ERR;
if (xtype_in != NC_BYTE || len_in != 1) ERR;
if (nc_get_att(ncid, 0, _FillValue, &fill_value_in)) ERR;
if (fill_value_in != fill_value) ERR;
if (nc_inq_attid(ncid, 0, LOSSES_NAME, &attnum_in)) ERR;
if (attnum_in != 0) ERR;
if (nc_inq_attid(ncid, 0, _FillValue, &attnum_in)) ERR;
if (attnum_in != 1) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing fill value with three other attributes...");
{
#define NUM_LEADERS 3
char leader[NUM_LEADERS][NC_MAX_NAME + 1] = {"hair_length_of_strategoi",
"hair_length_of_Miltiades",
"hair_length_of_Darius_I"};
short hair_length[NUM_LEADERS] = {3, 11, 4};
short short_in;
int a;
/* Create a netcdf file with one dim and one var. Add 3
* attributes, then fill value. */
if (nc_create(FILE_NAME, cmode, &ncid)) ERR;
if (nc_def_dim(ncid, DIM1_NAME, DIM1_LEN, &dimids[0])) ERR;
if (nc_def_var(ncid, VAR_NAME, NC_BYTE, NUM_DIMS, dimids, &varid)) ERR;
for (a = 0; a < NUM_LEADERS; a++)
if (nc_put_att_short(ncid, varid, leader[a], NC_SHORT, 1, &hair_length[a])) ERR;
if (nc_put_att_schar(ncid, varid, _FillValue, NC_BYTE, 1, &fill_value)) ERR;
if (nc_close(ncid)) ERR;
/* Open the file. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
/* Check our three hair-related attributes. */
for (a = 0; a < NUM_LEADERS; a++)
{
if (nc_inq_att(ncid, 0, leader[a], &xtype_in, &len_in)) ERR;
if (xtype_in != NC_SHORT || len_in != 1) ERR;
if (nc_get_att(ncid, 0, leader[a], &short_in)) ERR;
if (short_in != hair_length[a]) ERR;
if (nc_inq_attid(ncid, 0, leader[a], &attnum_in)) ERR;
if (attnum_in != a) ERR;
}
/* Check our fill value attribute. */
if (nc_inq_att(ncid, 0, _FillValue, &xtype_in, &len_in)) ERR;
if (xtype_in != NC_BYTE || len_in != 1) ERR;
if (nc_get_att(ncid, 0, _FillValue, &fill_value_in)) ERR;
if (fill_value_in != fill_value) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing fill value with simple example...");
{
/* Dims stuff. */
#define NDIMS 3
#define VAR_DIMS 3
#define DIM_A "dim1"
#define DIM_A_LEN 4
#define DIM_B "dim2"
#define DIM_B_LEN 3
#define DIM_C "dim3"
#define DIM_C_LEN NC_UNLIMITED
/* Var stuff. */
#define CXX_VAR_NAME "P"
/* Att stuff. */
#define NUM_ATTS 4
#define LONG_NAME "long_name"
#define PRES_MAX_WIND "pressure at maximum wind"
#define UNITS "units"
#define HECTOPASCALS "hectopascals"
int dimid[NDIMS], var_dimids[VAR_DIMS] = {2, 1, 0};
float fill_value = -9999.0f;
char long_name[] = PRES_MAX_WIND;
if (nc_create(FILE_NAME, cmode, &ncid)) ERR;
/* Create dims. */
if (nc_def_dim(ncid, DIM_A, DIM_A_LEN, &dimid[0])) ERR;
if (nc_def_dim (ncid, DIM_B, DIM_B_LEN, &dimid[1])) ERR;
if (nc_def_dim(ncid, DIM_C, DIM_C_LEN, &dimid[2])) ERR;
/* Create var. */
if (nc_def_var(ncid, CXX_VAR_NAME, NC_FLOAT, VAR_DIMS,
var_dimids, &varid)) ERR;
if (varid) ERR;
if (nc_put_att(ncid, varid, LONG_NAME, NC_CHAR, strlen(long_name) + 1,
long_name)) ERR;
if (nc_put_att(ncid, varid, UNITS, NC_CHAR, strlen(UNITS) + 1,
UNITS)) ERR;
/* Check to ensure the atts have their expected attnums. */
if (nc_inq_attid(ncid, 0, LONG_NAME, &attnum_in)) ERR;
if (attnum_in != 0) ERR;
if (nc_inq_attid(ncid, 0, UNITS, &attnum_in)) ERR;
if (attnum_in != 1) ERR;
/* Now add a fill value. This will acutually cause HDF5 to
* destroy the dataset and recreate it, recreating also the
* three attributes that are attached to it. */
if (nc_put_att(ncid, varid, _FillValue, NC_FLOAT,
1, &fill_value)) ERR;
/* Check to ensure the atts have their expected attnums. */
if (nc_inq_attid(ncid, 0, LONG_NAME, &attnum_in)) ERR;
if (attnum_in != 0) ERR;
if (nc_inq_attid(ncid, 0, UNITS, &attnum_in)) ERR;
if (attnum_in != 1) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, 0, &ncid)) ERR;
if (nc_inq_attid(ncid, 0, LONG_NAME, &attnum_in)) ERR;
if (attnum_in != 0) ERR;
if (nc_inq_attid(ncid, 0, UNITS, &attnum_in)) ERR;
if (attnum_in != 1) ERR;
if (nc_inq_attid(ncid, 0, _FillValue, &attnum_in)) ERR;
if (attnum_in != 2) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
#ifndef NO_NETCDF_2
/* The following test is an attempt to recreate a problem occuring
in the cxx tests. The file is created in c++ in nctsts.cpp. */
printf("**** testing fill value with example from cxx tests in v2 api...");
{
/* Dims stuff. */
#define NDIMS_1 4
#define VAR_DIMS 3
#define LAT "lat"
#define LAT_LEN 4
#define LON "lon"
#define LON_LEN 3
#define FRTIMED "frtimed"
#define FRTIMED_LEN NC_UNLIMITED
#define TIMELEN "timelen"
#define TIMELEN_LEN 20
/* Var stuff. */
#define CXX_VAR_NAME "P"
/* Att stuff. */
#define NUM_ATTS 4
#define LONG_NAME "long_name"
#define UNITS "units"
int dimid[NDIMS_1], var_dimids[VAR_DIMS] = {2, 0, 1};
float fill_value = -9999.0f;
char long_name[] = PRES_MAX_WIND;
int i, attid[NUM_ATTS];
ncid = nccreate(FILE_NAME, NC_NETCDF4);
/* Create dims. */
dimid[0] = ncdimdef(ncid, LAT, LAT_LEN);
dimid[1] = ncdimdef(ncid, LON, LON_LEN);
dimid[2] = ncdimdef(ncid, FRTIMED, FRTIMED_LEN);
dimid[3] = ncdimdef(ncid, TIMELEN, TIMELEN_LEN);
/* Just check our dimids to see that they are correct. */
for (i = 0; i < NDIMS_1; i++)
if (dimid[i] != i) ERR;
/* Create var. */
varid = ncvardef(ncid, CXX_VAR_NAME, NC_FLOAT, VAR_DIMS, var_dimids);
if (varid) ERR;
/* Add three atts to the var, long_name, units, and
* valid_range. */
if (nc_put_att(ncid, varid, LONG_NAME, NC_CHAR, strlen(long_name) + 1,
long_name)) ERR;
if (nc_put_att(ncid, varid, UNITS, NC_CHAR, strlen(UNITS) + 1,
UNITS)) ERR;
/* Check to ensure the atts have their expected attnums. */
if (nc_inq_attid(ncid, 0, LONG_NAME, &attnum_in)) ERR;
if (attnum_in != 0) ERR;
if (nc_inq_attid(ncid, 0, UNITS, &attnum_in)) ERR;
if (attnum_in != 1) ERR;
/* Now add a fill value. This will acutually cause HDF5 to
* destroy the dataset and recreate it, recreating also the
* three attributes that are attached to it. */
attid[3] = ncattput(ncid, varid, _FillValue, NC_FLOAT,
1, &fill_value);
/* Check to ensure the atts have their expected attnums. */
if (nc_inq_attid(ncid, 0, LONG_NAME, &attnum_in)) ERR;
if (attnum_in != 0) ERR;
if (nc_inq_attid(ncid, 0, UNITS, &attnum_in)) ERR;
if (attnum_in != 1) ERR;
ncclose(ncid);
/* Open the file and check. */
ncid = ncopen(FILE_NAME, 0);
if (nc_inq_attid(ncid, 0, LONG_NAME, &attnum_in)) ERR;
if (attnum_in != 0) ERR;
if (nc_inq_attid(ncid, 0, UNITS, &attnum_in)) ERR;
if (attnum_in != 1) ERR;
if (nc_inq_attid(ncid, 0, _FillValue, &attnum_in)) ERR;
if (attnum_in != 2) ERR;
ncclose(ncid);
}
SUMMARIZE_ERR;
#endif /* NO_NETCDF_2 */
}
printf("**** testing create order varids...");
#define UNITS "units"
#define DIMNAME "x"
#define VARNAME "data"
{
/* This test contributed by Jeff Whitaker of NOAA - Thanks Jeff! */
int ncid, dimid, varid, xvarid;
char units[] = "zlotys";
if (nc_create(FILE_NAME, NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
if (nc_def_dim(ncid, DIMNAME, 1, &dimid)) ERR;
if (nc_enddef(ncid)) ERR;
if (nc_redef(ncid)) ERR;
if (nc_def_var(ncid, DIMNAME, NC_INT, 1, &dimid, &xvarid)) ERR;
if (nc_put_att_text(ncid, xvarid, UNITS, strlen(units), units)) ERR;
if (nc_def_var(ncid, VARNAME, NC_INT, 1, &dimid, &varid)) ERR;
if (nc_close(ncid)) ERR;
if (nc_open(FILE_NAME, 0, &ncid)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
#define RANK_wind 1
printf("**** testing simple variable renaming...");
{
/* This test contributed by Jeff Whitaker of NOAA - Thanks Jeff! */
int ncid, lat_dim, time_dim, lon_dim, wind_id;
size_t lat_len = 73, time_len = 10, lon_len = 145;
int cdf_goober[1];
/* if (nc_set_default_format(NC_FORMAT_NETCDF4, NULL)) ERR;*/
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
/* define dimensions */
if (nc_def_dim(ncid, "a", lon_len, &lon_dim)) ERR;
if (nc_def_dim(ncid, "b", lat_len, &lat_dim)) ERR;
if (nc_def_dim(ncid, "c", time_len, &time_dim)) ERR;
if (nc_put_att_text(ncid, NC_GLOBAL, "a", 3, "bar")) ERR;
cdf_goober[0] = 2;
if (nc_put_att_int(ncid, NC_GLOBAL, "b", NC_INT, 1, cdf_goober)) ERR;
/* define variables */
if (nc_def_var(ncid, "aa", NC_FLOAT, RANK_wind, &lon_dim, &wind_id)) ERR;
if (nc_close(ncid)) ERR;
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_rename_var(ncid, 0, "az")) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing dimension and variable renaming...");
{
/* This test contributed by Jeff Whitaker of NOAA - Thanks Jeff! */
int ncid, lat_dim, time_dim, lon_dim, wind_id;
size_t lat_len = 73, time_len = 10, lon_len = 145;
int wind_dims[RANK_wind], wind_slobber[1], cdf_goober[1];
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
/* define dimensions */
if (nc_def_dim(ncid, "lon", lon_len, &lon_dim)) ERR;
if (nc_def_dim(ncid, "lat", lat_len, &lat_dim)) ERR;
if (nc_def_dim(ncid, "time", time_len, &time_dim)) ERR;
if (nc_put_att_text(ncid, NC_GLOBAL, "foo", 3, "bar")) ERR;
cdf_goober[0] = 2;
if (nc_put_att_int(ncid, NC_GLOBAL, "goober", NC_INT, 1, cdf_goober)) ERR;
/* define variables */
wind_dims[0] = lon_dim;
if (nc_def_var(ncid, "temp", NC_FLOAT, RANK_wind, wind_dims, &wind_id)) ERR;
if (nc_put_att_text(ncid, wind_id, "bar", 3, "foo")) ERR;
wind_slobber[0] = 3;
if (nc_put_att_int(ncid, wind_id, "slobber", NC_INT, 1, wind_slobber)) ERR;
if (nc_close(ncid)) ERR;
/* re-open dataset*/
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq_dimid(ncid, "lon", &lon_dim)) ERR;
/* rename dimension */
if (nc_rename_dim(ncid, lon_dim, "longitude")) ERR;
if (nc_inq_varid(ncid, "temp", &wind_id)) ERR;
/* rename variable */
if (nc_rename_var(ncid, wind_id, "wind")) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
/* printf("*** testing 2D array of NC_CHAR..."); */
/* { */
/* int dimid[NDIMS_1], var_dimids[VAR_DIMS] = {2, 0, 1}; */
/* float fill_value = -9999.0f; */
/* char long_name[] = PRES_MAX_WIND; */
/* int i, attid[NUM_ATTS]; */
/* ncid = nccreate(FILE_NAME, NC_NETCDF4); */
/* /\* Create dims. *\/ */
/* dimid[0] = ncdimdef(ncid, LAT, LAT_LEN); */
/* dimid[1] = ncdimdef(ncid, LON, LON_LEN); */
/* /\* Create var. *\/ */
/* varid = ncvardef(ncid, CXX_VAR_NAME, NC_FLOAT, VAR_DIMS, var_dimids); */
/* if (varid) ERR; */
/* ncclose(ncid); */
/* /\* Open the file and check. *\/ */
/* ncid = ncopen(FILE_NAME, 0); */
/* ncclose(ncid); */
/* } */
/* SUMMARIZE_ERR; */
#define NDIMS 3
#define NNAMES 4
#define NLINES 13
/* printf("**** testing funny names for netCDF-4..."); */
/* { */
/* int ncid, wind_id; */
/* size_t len[NDIMS] = {7, 3, 1}; */
/* int dimids[NDIMS], dimids_in[NDIMS], ndims_in; */
/* char funny_name[NNAMES][NC_MAX_NAME] = {"\a\t", "\f\n", "\r\v", "\b"}; */
/* char name_in[NC_MAX_NAME + 1]; */
/* char *speech[NLINES] = {"who would fardels bear, ", */
/* "To grunt and sweat under a weary life, ", */
/* "But that the dread of something after death, ", */
/* "The undiscover'd country from whose bourn ", */
/* "No traveller returns, puzzles the will ", */
/* "And makes us rather bear those ills we have ", */
/* "Than fly to others that we know not of? ", */
/* "Thus conscience does make cowards of us all; ", */
/* "And thus the native hue of resolution ", */
/* "Is sicklied o'er with the pale cast of thought, ", */
/* "And enterprises of great pith and moment ", */
/* "With this regard their currents turn awry, ", */
/* "And lose the name of action."}; */
/* char *speech_in[NLINES]; */
/* int i; */
/* unsigned short nlines = NLINES; */
/* unsigned int nlines_in; */
/* if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR; */
/* /\* Define dimensions. *\/ */
/* for (i = 0; i < NDIMS; i++) */
/* if (nc_def_dim(ncid, funny_name[i], len[i], &dimids[i])) ERR; */
/* /\* Write some global atts. *\/ */
/* if (nc_put_att_string(ncid, NC_GLOBAL, funny_name[0], NLINES, */
/* (const char **)speech)) ERR; */
/* if (nc_put_att_ushort(ncid, NC_GLOBAL, funny_name[1], NC_UINT, 1, &nlines)) ERR; */
/* /\* Define variables. *\/ */
/* if (nc_def_var(ncid, funny_name[3], NC_INT64, NDIMS, dimids, &wind_id)) ERR; */
/* if (nc_close(ncid)) ERR; */
/* /\* Open the file and check. *\/ */
/* if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR; */
/* if (nc_inq_dimids(ncid, &ndims_in, dimids_in, 0)) ERR; */
/* if (ndims_in != NDIMS) ERR; */
/* for (i = 0; i < NDIMS; i++) */
/* { */
/* if (dimids_in[i] != i) ERR; */
/* if (nc_inq_dimname(ncid, i, name_in)) ERR; */
/* if (strcmp(name_in, funny_name[i])) ERR; */
/* } */
/* if (nc_get_att_string(ncid, NC_GLOBAL, funny_name[0], (char **)speech_in)) ERR; */
/* for (i = 0; i < NLINES; i++) */
/* if (strcmp(speech_in[i], speech[i])) ERR; */
/* if (nc_get_att_uint(ncid, NC_GLOBAL, funny_name[1], &nlines_in)) ERR; */
/* if (nlines_in != NLINES) ERR; */
/* if (nc_free_string(NLINES, (char **)speech_in)) ERR; */
/* if (nc_inq_varname(ncid, 0, name_in)) ERR; */
/* if (strcmp(name_in, funny_name[3])) ERR; */
/* if (nc_close(ncid)) ERR; */
/* } */
/* SUMMARIZE_ERR; */
printf("**** testing endianness...");
#define NDIMS4 1
#define DIM4_NAME "Joe"
#define VAR_NAME4 "Ed"
#define DIM4_LEN 10
{
int dimids[NDIMS4], dimids_in[NDIMS4];
int varid;
int ndims, nvars, natts, unlimdimid;
nc_type xtype_in;
char name_in[NC_MAX_NAME + 1];
int data[DIM4_LEN], data_in[DIM4_LEN];
int endian_in;
int i;
for (i = 0; i < DIM4_LEN; i++)
data[i] = i;
/* Create a netcdf-4 file with one dim and one var. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, DIM4_NAME, DIM4_LEN, &dimids[0])) ERR;
if (dimids[0] != 0) ERR;
if (nc_def_var(ncid, VAR_NAME4, NC_INT, NDIMS4, dimids, &varid)) ERR;
if (nc_def_var_endian(ncid, varid, NC_ENDIAN_BIG)) ERR;
if (varid != 0) ERR;
if (nc_put_var_int(ncid, varid, data)) ERR;
/* Check stuff. */
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != NDIMS4 || nvars != 1 || natts != 0 ||
unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1) ERR;
if (varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims,
dimids_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME4) || xtype_in != NC_INT ||
ndims != 1 || natts != 0 || dimids_in[0] != 0) ERR;
if (nc_inq_var_endian(ncid, 0, &endian_in)) ERR;
if (endian_in != NC_ENDIAN_BIG) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check the same stuff. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != NDIMS4 || nvars != 1 || natts != 0 ||
unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1) ERR;
if (varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims,
dimids_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME4) || xtype_in != NC_INT ||
ndims != 1 || natts != 0 || dimids_in[0] != 0) ERR;
if (nc_inq_var_endian(ncid, 0, &endian_in)) ERR;
if (endian_in != NC_ENDIAN_BIG) ERR;
if (nc_get_var_int(ncid, varid, data_in)) ERR;
for (i = 0; i < DIM4_LEN; i++)
if (data[i] != data_in[i]) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing chunking...");
{
#define NDIMS5 1
#define DIM5_NAME "D5"
#define VAR_NAME5 "V5"
#define DIM5_LEN 1000
int dimids[NDIMS5], dimids_in[NDIMS5];
int varid;
int ndims, nvars, natts, unlimdimid;
nc_type xtype_in;
char name_in[NC_MAX_NAME + 1];
int data[DIM5_LEN], data_in[DIM5_LEN];
int chunksize[NDIMS5] = {5};
int chunksize_in[NDIMS5];
int contiguous_in;
int i, d;
for (i = 0; i < DIM5_LEN; i++)
data[i] = i;
/* Create a netcdf-4 file with one dim and one var. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, DIM5_NAME, DIM5_LEN, &dimids[0])) ERR;
if (dimids[0] != 0) ERR;
if (nc_def_var(ncid, VAR_NAME5, NC_INT, NDIMS5, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, 0, chunksize)) ERR;
if (nc_put_var_int(ncid, varid, data)) ERR;
/* Check stuff. */
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != NDIMS5 || nvars != 1 || natts != 0 ||
unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1) ERR;
if (varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims, dimids_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME5) || xtype_in != NC_INT || ndims != 1 || natts != 0 ||
dimids_in[0] != 0) ERR;
if (nc_inq_var_chunking(ncid, 0, &contiguous_in, chunksize_in)) ERR;
for (d = 0; d < NDIMS5; d++)
if (chunksize[d] != chunksize_in[d]) ERR;
if (contiguous_in != 0) ERR;
if (nc_get_var_int(ncid, varid, data_in)) ERR;
for (i = 0; i < DIM5_LEN; i++)
if (data[i] != data_in[i])
ERR_RET;
if (nc_close(ncid)) ERR;
/* Open the file and check the same stuff. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
/* Check stuff. */
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != NDIMS5 || nvars != 1 || natts != 0 ||
unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1) ERR;
if (varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims, dimids_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME5) || xtype_in != NC_INT || ndims != 1 || natts != 0 ||
dimids_in[0] != 0) ERR;
if (nc_inq_var_chunking(ncid, 0, &contiguous_in, chunksize_in)) ERR;
for (d = 0; d < NDIMS5; d++)
if (chunksize[d] != chunksize_in[d]) ERR;
if (contiguous_in != 0) ERR;
if (nc_get_var_int(ncid, varid, data_in)) ERR;
for (i = 0; i < DIM5_LEN; i++)
if (data[i] != data_in[i])
ERR_RET;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing contiguous storage...");
{
#define NDIMS6 1
#define DIM6_NAME "D5"
#define VAR_NAME6 "V5"
#define DIM6_LEN 100
int dimids[NDIMS6], dimids_in[NDIMS6];
int varid;
int ndims, nvars, natts, unlimdimid;
nc_type xtype_in;
char name_in[NC_MAX_NAME + 1];
int data[DIM6_LEN], data_in[DIM6_LEN];
int chunksize_in[NDIMS6];
int contiguous_in;
int i, d;
for (i = 0; i < DIM6_LEN; i++)
data[i] = i;
/* Create a netcdf-4 file with one dim and one var. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, DIM6_NAME, DIM6_LEN, &dimids[0])) ERR;
if (dimids[0] != 0) ERR;
if (nc_def_var(ncid, VAR_NAME6, NC_INT, NDIMS6, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, 1, NULL)) ERR;
if (nc_put_var_int(ncid, varid, data)) ERR;
/* Check stuff. */
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != NDIMS6 || nvars != 1 || natts != 0 ||
unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1) ERR;
if (varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims, dimids_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME6) || xtype_in != NC_INT || ndims != 1 || natts != 0 ||
dimids_in[0] != 0) ERR;
if (nc_inq_var_chunking(ncid, 0, &contiguous_in, chunksize_in)) ERR;
for (d = 0; d < NDIMS6; d++)
if (chunksize_in[d] != 0) ERR;
if (!contiguous_in) ERR;
if (nc_get_var_int(ncid, varid, data_in)) ERR;
for (i = 0; i < DIM6_LEN; i++)
if (data_in[i] != data[i])
ERR_RET;
if (nc_close(ncid)) ERR;
/* Open the file and check the same stuff. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
/* Check stuff. */
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != NDIMS6 || nvars != 1 || natts != 0 ||
unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1) ERR;
if (varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims, dimids_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME6) || xtype_in != NC_INT || ndims != 1 || natts != 0 ||
dimids_in[0] != 0) ERR;
if (nc_inq_var_chunking(ncid, 0, &contiguous_in, chunksize_in)) ERR;
for (d = 0; d < NDIMS6; d++)
if (chunksize_in[d] != 0) ERR;
if (!contiguous_in) ERR;
if (nc_get_var_int(ncid, varid, data_in)) ERR;
for (i = 0; i < DIM6_LEN; i++)
if (data[i] != data_in[i])
ERR_RET;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing extreme numbers dude...");
{
#define VAR_NAME7 "V5"
#define DIM6_LEN 100
int varid;
int ndims, nvars, natts, unlimdimid;
nc_type xtype_in;
char name_in[NC_MAX_NAME + 1];
/* unsigned long long data = 9223372036854775807ull, data_in;*/
unsigned long long data = 9223372036854775817ull, data_in;
/* Create a netcdf-4 file with scalar var. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_var(ncid, VAR_NAME7, NC_UINT64, 0, NULL, &varid)) ERR;
if (nc_put_var_ulonglong(ncid, varid, &data)) ERR;
/* Check stuff. */
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != 0 || nvars != 1 || natts != 0 || unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1 || varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims, NULL, &natts)) ERR;
if (strcmp(name_in, VAR_NAME7) || xtype_in != NC_UINT64 || ndims != 0 || natts != 0) ERR;
if (nc_get_var_ulonglong(ncid, varid, &data_in)) ERR;
if (data_in != data) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check the same stuff. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != 0 || nvars != 1 || natts != 0 || unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1 || varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims, NULL, &natts)) ERR;
if (strcmp(name_in, VAR_NAME7) || xtype_in != NC_UINT64 || ndims != 0 || natts != 0) ERR;
if (nc_get_var_ulonglong(ncid, varid, &data_in)) ERR;
if (data_in != data) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing error codes for name clashes...");
{
#define GENERIC_NAME "bob"
int ncid, varid, numgrps, ntypes;
/* Create a netcdf-4 file with one var. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_var(ncid, GENERIC_NAME, NC_BYTE, 0, NULL, &varid)) ERR;
/* These don'e work, becuase the name is already in use. Make
* sure the correct error is returned. */
if (nc_def_grp(ncid, GENERIC_NAME, NULL) != NC_ENAMEINUSE) ERR;
if (nc_def_opaque(ncid, 1, GENERIC_NAME, NULL) != NC_ENAMEINUSE) ERR;
/* Close it. */
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq_varids(ncid, &nvars_in, varids_in)) ERR;
if (nvars_in != 1 || varids_in[0] != 0) ERR;
if (nc_inq_varname(ncid, 0, name_in)) ERR;
if (strcmp(name_in, GENERIC_NAME)) ERR;
if (nc_inq_grps(ncid, &numgrps, NULL)) ERR;
if (numgrps) ERR;
if (nc_inq_typeids(ncid, &ntypes, NULL)) ERR;
if (ntypes) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing error codes for name clashes some more...");
{
#define GENERIC_NAME "bob"
int ncid, varid, numgrps, ntypes;
/* Create a netcdf-4 file with one type. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_opaque(ncid, 1, GENERIC_NAME, NULL)) ERR;
/* These don'e work, becuase the name is already in use. Make
* sure the correct error is returned. */
if (nc_def_grp(ncid, GENERIC_NAME, NULL) != NC_ENAMEINUSE) ERR;
if (nc_def_var(ncid, GENERIC_NAME, NC_BYTE, 0, NULL, &varid) != NC_ENAMEINUSE) ERR;
/* Close it. */
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq_varids(ncid, &nvars_in, varids_in)) ERR;
if (nvars_in) ERR;
if (nc_inq_grps(ncid, &numgrps, NULL)) ERR;
if (numgrps) ERR;
if (nc_inq_typeids(ncid, &ntypes, NULL)) ERR;
if (ntypes != 1) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing error codes for name clashes even more...");
{
#define GENERIC_NAME "bob"
int ncid, varid, numgrps, ntypes;
/* Create a netcdf-4 file with one group. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_grp(ncid, GENERIC_NAME, NULL)) ERR;
/* These don'e work, becuase the name is already in use. Make
* sure the correct error is returned. */
if (nc_def_opaque(ncid, 1, GENERIC_NAME, NULL) != NC_ENAMEINUSE) ERR;
if (nc_def_var(ncid, GENERIC_NAME, NC_BYTE, 0, NULL, &varid) != NC_ENAMEINUSE) ERR;
/* Close it. */
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq_varids(ncid, &nvars_in, varids_in)) ERR;
if (nvars_in) ERR;
if (nc_inq_grps(ncid, &numgrps, NULL)) ERR;
if (numgrps != 1) ERR;
if (nc_inq_typeids(ncid, &ntypes, NULL)) ERR;
if (ntypes) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing error code for too-large chunks...");
{
#define NDIMS17 2
#define DIM17_NAME "personality"
#define DIM17_NAME_2 "good_looks"
#define VAR_NAME17 "ed"
#define DIM17_LEN 2147483644 /* max dimension size - 2GB - 4. */
#define DIM17_2_LEN 1000
int dimids[NDIMS17], dimids_in[NDIMS17];
int varid;
int ndims, nvars, natts, unlimdimid;
nc_type xtype_in;
char name_in[NC_MAX_NAME + 1];
int chunksize[NDIMS17] = {5, 5};
int bad_chunksize[NDIMS17] = {5, DIM17_LEN};
int chunksize_in[NDIMS17];
int contiguous_in;
int d;
/* Create a netcdf-4 file with two dims and one var. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, DIM17_NAME, DIM17_LEN, &dimids[0])) ERR;
if (nc_def_dim(ncid, DIM17_NAME_2, DIM17_2_LEN, &dimids[1])) ERR;
if (dimids[0] != 0 || dimids[1] != 1) ERR;
if (nc_def_var(ncid, VAR_NAME17, NC_UINT64, NDIMS17, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, 0, bad_chunksize) != NC_EBADCHUNK) ERR;
if (nc_def_var_chunking(ncid, varid, 0, chunksize)) ERR;
/* Check stuff. */
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != NDIMS17 || nvars != 1 || natts != 0 ||
unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1) ERR;
if (varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims, dimids_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME17) || xtype_in != NC_UINT64 || ndims != 2 || natts != 0 ||
dimids_in[0] != 0 || dimids_in[1] != 1) ERR;
if (nc_inq_var_chunking(ncid, 0, &contiguous_in, chunksize_in)) ERR;
for (d = 0; d < NDIMS17; d++)
if (chunksize[d] != chunksize_in[d]) ERR;
if (contiguous_in != 0) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check the same stuff. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
/* Check stuff. */
if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
if (ndims != NDIMS17 || nvars != 1 || natts != 0 ||
unlimdimid != -1) ERR;
if (nc_inq_varids(ncid, &nvars, varids_in)) ERR;
if (nvars != 1) ERR;
if (varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, name_in, &xtype_in, &ndims, dimids_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME17) || xtype_in != NC_UINT64 || ndims != 2 || natts != 0 ||
dimids_in[0] != 0 || dimids_in[1] != 1) ERR;
if (nc_inq_var_chunking(ncid, 0, &contiguous_in, chunksize_in)) ERR;
for (d = 0; d < NDIMS17; d++)
if (chunksize[d] != chunksize_in[d]) ERR;
if (contiguous_in != 0) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
#ifdef USE_PARALLEL
MPI_Finalize();
#endif
}
/**
* @ingroup PIO_inq_var
* Inquire about chunksizes for a variable.
*
* This function only applies to netCDF-4 files. When used with netCDF
* classic files, the error PIO_ENOTNC4 will be returned.
*
* See the <a
* href="http://www.unidata.ucar.edu/software/netcdf/docs/group__variables.html">netCDF
* variable documentation</a> for details about the operation of this
* function.
*
* @param ncid the ncid of the open file.
* @param varid the ID of the variable to set chunksizes for.
* @param storagep pointer to int which will be set to either
* NC_CONTIGUOUS or NC_CHUNKED.
* @param chunksizep pointer to memory where chunksizes will be
* set. There are the same number of chunksizes as there are
* dimensions.
*
* @return PIO_NOERR for success, otherwise an error code.
*/
int PIOc_inq_var_chunking(int ncid, int varid, int *storagep, PIO_Offset *chunksizesp)
{
int ierr;
int msg;
int mpierr;
iosystem_desc_t *ios;
file_desc_t *file;
char *errstr;
int ndims;
errstr = NULL;
ierr = PIO_NOERR;
if (!(file = pio_get_file_from_id(ncid)))
return PIO_EBADID;
ios = file->iosystem;
msg = PIO_MSG_INQ_VAR_CHUNKING;
if (ios->async_interface && ! ios->ioproc)
{
if (ios->compmaster)
mpierr = MPI_Send(&msg, 1,MPI_INT, ios->ioroot, 1, ios->union_comm);
mpierr = MPI_Bcast(&(file->fh),1, MPI_INT, 0, ios->intercomm);
}
if (ios->ioproc)
{
switch (file->iotype)
{
#ifdef _NETCDF
#ifdef _NETCDF4
case PIO_IOTYPE_NETCDF4P:
ierr = nc_inq_var_chunking(file->fh, varid, storagep, chunksizesp);
break;
case PIO_IOTYPE_NETCDF4C:
if (ios->io_rank == 0)
{
if ((ierr = nc_inq_var_chunking(file->fh, varid, storagep, chunksizesp)))
return ierr;
if ((ierr = nc_inq_varndims(file->fh, varid, &ndims)))
return ierr;
}
break;
#endif
case PIO_IOTYPE_NETCDF:
return PIO_ENOTNC4;
break;
#endif
#ifdef _PNETCDF
case PIO_IOTYPE_PNETCDF:
return PIO_ENOTNC4;
break;
#endif
default:
ierr = iotype_error(file->iotype,__FILE__,__LINE__);
}
}
/* If there is an error, allocate space for the error string. */
if (ierr != PIO_NOERR)
{
errstr = (char *) malloc((strlen(__FILE__) + 20)* sizeof(char));
sprintf(errstr,"in file %s",__FILE__);
}
/* Check the netCDF return code, and broadcast it to all tasks. */
ierr = check_netcdf(file, ierr, errstr,__LINE__);
/* Free the error stringif it was allocated. */
if (errstr != NULL)
free(errstr);
/* Broadcast results to all tasks. */
ierr = MPI_Bcast(&ndims, 1, MPI_INT, ios->ioroot, ios->my_comm);
if (storagep)
ierr = MPI_Bcast(storagep, 1, MPI_INT, ios->ioroot, ios->my_comm);
if (chunksizesp)
ierr = MPI_Bcast(chunksizesp, ndims, MPI_OFFSET, ios->ioroot, ios->my_comm);
return ierr;
}
int
main(int argc, char **argv)
{
printf("\n*** Testing netcdf-4 file functions, some more.\n");
last_sbrk = sbrk(0);
printf("*** testing lots of open files...\n");
{
#define NUM_TRIES 6
int *ncid_in;
int mem_used, mem_used2;
/* int mem_per_file; */
int num_files[NUM_TRIES] = {1, 5, 10, 20, 35, 50};
char file_name[NUM_TRIES][NC_MAX_NAME + 1];
int num_vars[NUM_TRIES];
size_t cache_size[NUM_TRIES];
int mode[NUM_TRIES];
char mode_name[NUM_TRIES][8];
int ndims[NUM_TRIES];
int dim_len[NUM_TRIES][MAX_DIMS];
int dim_4d[MAX_DIMS] = {NC_UNLIMITED, 10, 100, 100};
char dimstr[30];
char chunkstr[30];
int num_recs[NUM_TRIES] = {1, 1, 1, 1, 1, 1};
struct timeval start_time, end_time, diff_time;
struct timeval close_start_time, close_end_time, close_diff_time;
int open_us, close_us, create_us;
size_t chunksize[MAX_DIMS];
int storage;
int d, f, t;
printf("dims\t\tchunks\t\tformat\tnum_files\tcache(kb)\tnum_vars\tmem(kb)\t"
"open_time(us/file)\tclose_time(us/file)\tcreate_time(us/file)\n");
for (t = 0; t < NUM_TRIES; t++)
{
strcpy(mode_name[t], "netcdf4");
mode[t] = NC_NETCDF4;
cache_size[t] = 16000000;
num_vars[t] = 10;
ndims[t] = 4;
for (d = 0; d < ndims[t]; d++)
dim_len[t][d] = dim_4d[d];
/* Create sample files. */
if (gettimeofday(&start_time, NULL)) ERR;
for (f = 0; f < num_files[t]; f++)
{
/* Set up filename. */
sprintf(file_name[t], "tst_files2_%d_%d.nc", t, f);
if (create_sample_file(file_name[t], ndims[t], dim_len[t], num_vars[t],
mode[t], num_recs[t])) ERR;
/* How long did it take? */
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
create_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec) / num_files[t];
}
/* /\* Change the cache settings. *\/ */
/* if (nc_set_chunk_cache(cache_size[t], 20000, .75)) ERR; */
/* We need storage for an array of ncids. */
if (!(ncid_in = malloc(num_files[t] * sizeof(int)))) ERR;
/* How much memory is in use now? */
if (get_mem_used1(&mem_used)) ERR;
/* Open the first file to get chunksizes. */
if (gettimeofday(&start_time, NULL)) ERR;
if (nc_open(file_name[t], 0, &ncid_in[0])) ERR;
if (nc_inq_var_chunking(ncid_in[0], 0, &storage, chunksize)) ERR;
/* Now reopen this file a large number of times. */
for (f = 1; f < num_files[t]; f++)
if (nc_open(file_name[t], 0, &ncid_in[f])) ERR_RET;
/* How long did it take per file? */
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
open_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec) / num_files[t];
/* How much memory is in use by this process now? */
if (get_mem_used1(&mem_used2)) ERR;
/* Close all netcdf files. */
if (gettimeofday(&close_start_time, NULL)) ERR;
for (f = 0; f < num_files[t]; f++)
if (nc_close(ncid_in[f])) ERR_RET;
/* How long did it take to close all files? */
if (gettimeofday(&close_end_time, NULL)) ERR;
if (nc4_timeval_subtract(&close_diff_time, &close_end_time, &close_start_time)) ERR;
close_us = ((int)close_diff_time.tv_sec * MILLION +
(int)close_diff_time.tv_usec) / num_files[t];
/* We're done with this. */
free(ncid_in);
/* How much memory was used for each open file? */
/* mem_per_file = mem_used2/num_files[t]; */
/* Prepare the dimensions string. */
if (ndims[t] == MAX_DIMS)
sprintf(dimstr, "%dx%dx%dx%d", dim_len[t][0], dim_len[t][1],
dim_len[t][2], dim_len[t][3]);
else
sprintf(dimstr, "%dx%dx%d", dim_len[t][0], dim_len[t][1],
dim_len[t][2]);
/* Prepare the chunksize string. */
if (storage == NC_CHUNKED)
{
if (ndims[t] == MAX_DIMS)
sprintf(chunkstr, "%dx%dx%dx%d", (int)chunksize[0], (int)chunksize[1],
(int)chunksize[2], (int)chunksize[3]);
else
sprintf(chunkstr, "%dx%dx%d", (int)chunksize[0], (int)chunksize[1],
(int)chunksize[2]);
}
else
strcpy(chunkstr, "contig ");
/* Output results. */
printf("%s\t%s\t%s\t%d\t\t%d\t\t%d\t\t%d\t\t%d\t\t%d\t\t%d\n",
dimstr, chunkstr, mode_name[t], num_files[t], (int)(cache_size[t]/1024),
num_vars[t], mem_used2, open_us, close_us, create_us);
}
}
SUMMARIZE_ERR;
printf("Test for memory consumption...\n");
{
#define NUM_TRIES_100 100
int ncid, i;
int mem_used, mem_used1, mem_used2;
get_mem_used2(&mem_used);
mem_used1 = mem_used;
mem_used2 = mem_used;
printf("start: memuse= %d\t%d\t%d \n",mem_used, mem_used1,
mem_used2);
printf("bef_open\taft_open\taft_close\tused_open\tused_closed\n");
for (i=0; i < NUM_TRIES_100; i++)
{
/* Open the file. NC_NOWRITE tells netCDF we want read-only access
* to the file.*/
get_mem_used2(&mem_used);
nc_set_chunk_cache(10,10,.5);
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
get_mem_used2(&mem_used1);
/* Close the file, freeing all resources. ???? */
if (nc_close(ncid)) ERR;
get_mem_used2(&mem_used2);
if (mem_used2 - mem_used)
printf("try %d - %d\t\t%d\t\t%d\t\t%d\t\t%d \n", i,
mem_used, mem_used1, mem_used2, mem_used1 - mem_used,
mem_used2 - mem_used);
}
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
