1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357
|
/*********************************************************************
* Copyright 2009, University Corporation for Atmospheric Research
* See netcdf/README file for copying and redistribution conditions.
* "$Id $"
*********************************************************************/
#include "includes.h"
#include "nciter.h"
#undef DOCHUNK
#define CHECK(stat,f) if(stat != NC_NOERR) {check(stat,#f,__FILE__,__LINE__);} else {}
/* forward declarations */
static int nc_blkio_init(size_t bufsize, size_t value_size, int rank,
const size_t *dims, int chunked, size_t *chunksizes,
nciter_t *iter);
static int up_start(int ndims, const size_t *dims, int incdim, size_t inc,
size_t* odom);
#ifdef DOCHUNK
static int up_start_by_chunks(int ndims, const size_t *dims,
const size_t *chunks, size_t* odom);
#endif
static int nciter_ndims(Symbol*,int*);
static int nciter_dimlens(Symbol*,size_t*);
static int nciter_vartype(Symbol*,Symbol**);
static int nciter_valuesize(Symbol*,size_t*);
#ifdef DOCHUNK
static int nciter_contiguous(Symbol*,int*); /* always returns contiguous */
static int nciter_chunking(Symbol*,int,size_t*); /* no-op */
#endif
static void
check(int err, const char* fcn, const char* file, const int line)
{
fprintf(stderr,"%s\n",nc_strerror(err));
fprintf(stderr,"Location: function %s; file %s; line %d\n",
fcn,file,line);
fflush(stderr); fflush(stdout);
exit(1);
}
/* 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;
}
/* Iterate on blocks for variables, by updating start and count vector
* for next vara call. Assumes nc_get_iter called first. Returns
* number of variable values to get, 0 if done, negative number if
* error, so use like this:
size_t to_get;
while((to_get = nc_next_iter(&iter, start, count)) > 0) {
... iteration ...
}
if(to_get < 0) { ... handle error ... }
*/
size_t
nc_next_iter(nciter_t *iter, /* returned opaque iteration state */
size_t *start, /* returned start vector for next vara call */
size_t *count /* returned count vector for next vara call */
) {
int i;
/* Note: special case for chunked variables is just an
* optimization, the contiguous code below is OK even
* for chunked variables, but in general will do more I/O ... */
if(iter->first) {
if(!iter->chunked) { /* contiguous storage */
for(i = 0; i < iter->right_dim; i++) {
start[i] = 0;
count[i] = 1;
}
start[iter->right_dim] = 0;
count[iter->right_dim] = iter->rows;
for(i = iter->right_dim + 1; i < iter->rank; i++) {
start[i] = 0;
count[i] = iter->dimsizes[i];
}
} else { /* chunked storage */
#ifdef DOCHUNK
for(i = 0; i < iter->rank; i++) {
start[i] = 0;
count[i] = iter->chunksizes[i];
}
#endif
}
iter->first = 0;
} else {
if(!iter->chunked) { /* contiguous storage */
iter->more = up_start(iter->rank, iter->dimsizes, iter->right_dim,
iter->inc, start);
/* iterate on pieces of variable */
if(iter->cur < iter->numrows) {
iter->inc = iter->rows;
count[iter->right_dim] = iter->rows;
iter->cur++;
} else {
if(iter->leftover > 0) {
count[iter->right_dim] = iter->leftover;
iter->inc = iter->leftover;
iter->cur = 0;
}
}
} else { /* chunked storage */
#ifdef DOCHUNK
iter->more = up_start_by_chunks(iter->rank, iter->dimsizes,
iter->chunksizes, start);
/* adjust count to stay in range of dimsizes */
for(i = 0; i < iter->rank; i++) {
int leftover = iter->dimsizes[i] - start[i];
count[i] = iter->chunksizes[i];
if(leftover < count[i])
count[i] = leftover;
}
#endif
}
}
iter->to_get = 1;
for(i = 0; i < iter->rank; i++) {
iter->to_get *= count[i];
}
return iter->more == 0 ? 0 : iter->to_get ;
}
/* Initialize block iteration for variables, including those that
* won't fit in the copy buffer all at once. Returns error if
* variable is chunked but size of chunks is too big to fit in bufsize
* bytes. */
static int
nc_blkio_init(size_t bufsize, /* size in bytes of in-memory copy buffer */
size_t value_size, /* size in bytes of each variable element */
int rank, /* number of dimensions for variable */
const size_t *dims, /* variable dimension sizes */
int chunked, /* 1 if variable is chunked, 0 otherwise */
size_t *chunksizes, /* if chunked, variable chunk sizes */
nciter_t *iter /* returned iteration state, don't mess with it */
) {
int stat = NC_NOERR;
int i;
long long prod;
iter->rank = rank;
iter->first = 1;
iter->more = 1;
iter->chunked = chunked;
for(i = 0; i < rank; i++)
iter->dimsizes[i] = dims[i];
prod = value_size;
if(iter->chunked == 0) { /* contiguous */
iter->right_dim = rank - 1;
for(i = rank; i > 0; i--) {
if(prod*dims[i-1] <= bufsize) {
prod *= dims[i-1];
iter->right_dim--;
} else {
break;
}
}
if (i > 0) { /* variable won't fit in bufsize bytes */
iter->rows = bufsize/prod;
iter->numrows = dims[iter->right_dim] / iter->rows;
iter->leftover = dims[iter->right_dim] - iter->numrows * iter->rows;
iter->cur = 1;
iter->inc = iter->rows;
return stat;
}
/* else, variable will fit in bufsize bytes of memory. */
iter->right_dim = 0;
iter->rows = dims[0];
iter->inc = 0;
return stat;
}
#ifdef DOCHUNK
/* else, handle chunked case */
for(i = 0; i < rank; i++) {
iter->chunksizes[i] = chunksizes[i];
prod *= chunksizes[i];
}
if(prod > bufsize) {
stat = NC_ENOMEM;
fprintf(stderr, "chunksize (= %ld) > copy_buffer size (= %ld)\n", prod, bufsize);
}
#endif
return stat;
}
/*
* Updates a vector of size_t, odometer style. Returns 0 if odometer
* overflowed, else 1.
*/
static int
up_start(
int ndims, /* Number of dimensions */
const size_t *dims, /* The "odometer" limits for each dimension */
int incdim, /* the odmometer increment dimension */
size_t inc, /* the odometer increment for that dimension */
size_t* odom /* The "odometer" vector to be updated */
)
{
int id;
int ret = 1;
if(inc == 0) {
return 0;
}
odom[incdim] += inc;
for (id = incdim; id > 0; id--) {
if(odom[id] >= dims[id]) {
odom[id-1]++;
odom[id] -= dims[id];
}
}
if (odom[0] >= dims[0])
ret = 0;
return ret;
}
#ifdef DOCHUNK
/*
* Updates a vector of size_t, odometer style, for chunk access.
* Returns 0 if odometer overflowed, else 1.
*/
static int
up_start_by_chunks(
int ndims, /* Number of dimensions */
const size_t *dims, /* The "odometer" limits for each dimension */
const size_t *chunks, /* the odometer increments for each dimension */
size_t* odom /* The "odometer" vector to be updated */
)
{
int incdim = ndims - 1;
int id;
int ret = 1;
odom[incdim] += chunks[incdim];
for (id = incdim; id > 0; id--) {
if(odom[id] >= dims[id]) {
odom[id-1] += chunks[id-1];
/* odom[id] -= dims[id]; */
odom[id] = 0;
}
}
if (odom[0] >= dims[0])
ret = 0;
return ret;
}
#endif
static int
nciter_ndims(Symbol* sym, int* ndimsp)
{
if(ndimsp) *ndimsp = sym->typ.dimset.ndims;
return NC_NOERR;
}
static int
nciter_dimlens(Symbol* sym, size_t* dimlens)
{
int i;
int ndims = sym->typ.dimset.ndims;
for(i=0;i<ndims;i++) {
Symbol* dim = sym->typ.dimset.dimsyms[i];
dimlens[i] = MAX(dim->dim.declsize,dim->dim.unlimitedsize);
}
return NC_NOERR;
}
static int
nciter_vartype(Symbol* sym, Symbol** tsymp)
{
if(tsymp)
*tsymp = sym->typ.basetype;
return NC_NOERR;
}
/* For ncgen, we want the iterator to return
dimension indices, not offsets, so force size
to be one.
*/
static int
nciter_valuesize(Symbol* tsym, size_t* valuesizep)
{
if(valuesizep)
*valuesizep = 1;
return NC_NOERR;
}
#ifdef DOCHUNK
static int
nciter_contiguous(Symbol* sym, int* iscontiguous)
{
if(iscontiguous != NULL)
*iscontiguous = 1; /* always returns contiguous */
return NC_NOERR;
}
static int
nciter_chunking(Symbol* sym, int contig, size_t* sizep)
{
return NC_NOERR; /* no-op */
}
#endif
|