[528] | 1 | #include <fstream> |
---|
| 2 | |
---|
[219] | 3 | #include "onetcdf4.hpp" |
---|
[352] | 4 | #include "group_template.hpp" |
---|
[382] | 5 | #include "mpi.hpp" |
---|
[379] | 6 | #include "netcdf.hpp" |
---|
[498] | 7 | #include "netCdfInterface.hpp" |
---|
| 8 | #include "netCdfException.hpp" |
---|
[1158] | 9 | #include "timer.hpp" |
---|
[219] | 10 | |
---|
[335] | 11 | namespace xios |
---|
[219] | 12 | { |
---|
| 13 | /// ////////////////////// Définitions ////////////////////// /// |
---|
| 14 | |
---|
[686] | 15 | CONetCDF4::CONetCDF4(const StdString& filename, bool append, bool useClassicFormat, |
---|
[878] | 16 | bool useCFConvention, |
---|
[1639] | 17 | const MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
---|
[686] | 18 | : path() |
---|
| 19 | , wmpi(false) |
---|
| 20 | , useClassicFormat(useClassicFormat) |
---|
[878] | 21 | , useCFConvention(useCFConvention) |
---|
[219] | 22 | { |
---|
[878] | 23 | this->initialize(filename, append, useClassicFormat, useCFConvention, comm, multifile, timeCounterName); |
---|
[219] | 24 | } |
---|
[498] | 25 | |
---|
[219] | 26 | //--------------------------------------------------------------- |
---|
[286] | 27 | |
---|
[219] | 28 | CONetCDF4::~CONetCDF4(void) |
---|
| 29 | { |
---|
| 30 | } |
---|
| 31 | |
---|
| 32 | ///-------------------------------------------------------------- |
---|
| 33 | |
---|
[878] | 34 | void CONetCDF4::initialize(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, |
---|
[1639] | 35 | const MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
---|
[219] | 36 | { |
---|
[517] | 37 | this->useClassicFormat = useClassicFormat; |
---|
[878] | 38 | this->useCFConvention = useCFConvention; |
---|
[517] | 39 | |
---|
| 40 | int mode = useClassicFormat ? 0 : NC_NETCDF4; |
---|
[605] | 41 | |
---|
| 42 | // Don't use parallel mode if there is only one process |
---|
| 43 | if (comm) |
---|
| 44 | { |
---|
| 45 | int commSize = 0; |
---|
[1639] | 46 | MPI_Comm_size(*comm, &commSize); |
---|
[605] | 47 | if (commSize <= 1) |
---|
| 48 | comm = NULL; |
---|
| 49 | } |
---|
| 50 | wmpi = comm && !multifile; |
---|
| 51 | |
---|
| 52 | if (wmpi) |
---|
[517] | 53 | mode |= useClassicFormat ? NC_PNETCDF : NC_MPIIO; |
---|
| 54 | |
---|
[528] | 55 | // If the file does not exist, we always create it |
---|
| 56 | if (!append || !std::ifstream(filename.c_str())) |
---|
[219] | 57 | { |
---|
[1158] | 58 | CTimer::get("Files : create").resume(); |
---|
[605] | 59 | if (wmpi) |
---|
[1639] | 60 | CNetCdfInterface::createPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
---|
[605] | 61 | else |
---|
| 62 | CNetCdfInterface::create(filename, mode, this->ncidp); |
---|
[1158] | 63 | CTimer::get("Files : create").suspend(); |
---|
| 64 | |
---|
[528] | 65 | this->appendMode = false; |
---|
[219] | 66 | } |
---|
| 67 | else |
---|
| 68 | { |
---|
[528] | 69 | mode |= NC_WRITE; |
---|
[1158] | 70 | CTimer::get("Files : open").resume(); |
---|
[605] | 71 | if (wmpi) |
---|
[1639] | 72 | CNetCdfInterface::openPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
---|
[605] | 73 | else |
---|
| 74 | CNetCdfInterface::open(filename, mode, this->ncidp); |
---|
[1158] | 75 | CTimer::get("Files : open").suspend(); |
---|
[528] | 76 | this->appendMode = true; |
---|
[219] | 77 | } |
---|
[517] | 78 | |
---|
| 79 | // If the classic NetCDF format is used, we enable the "no-fill mode" globally. |
---|
| 80 | // This is done per variable for the NetCDF4 format. |
---|
| 81 | if (useClassicFormat) |
---|
[606] | 82 | CNetCdfInterface::setFill(this->ncidp, false); |
---|
[802] | 83 | |
---|
| 84 | this->timeCounterName = timeCounterName; |
---|
[219] | 85 | } |
---|
[498] | 86 | |
---|
[286] | 87 | void CONetCDF4::close() |
---|
| 88 | { |
---|
[1158] | 89 | CTimer::get("Files : close").resume(); |
---|
[686] | 90 | CNetCdfInterface::close(this->ncidp); |
---|
[1158] | 91 | CTimer::get("Files : close").suspend(); |
---|
[286] | 92 | } |
---|
[498] | 93 | |
---|
[219] | 94 | //--------------------------------------------------------------- |
---|
[498] | 95 | |
---|
[219] | 96 | void CONetCDF4::definition_start(void) |
---|
[498] | 97 | { |
---|
[686] | 98 | CNetCdfInterface::reDef(this->ncidp); |
---|
[219] | 99 | } |
---|
[498] | 100 | |
---|
[219] | 101 | //--------------------------------------------------------------- |
---|
[498] | 102 | |
---|
[219] | 103 | void CONetCDF4::definition_end(void) |
---|
| 104 | { |
---|
[686] | 105 | CNetCdfInterface::endDef(this->ncidp); |
---|
[219] | 106 | } |
---|
| 107 | |
---|
| 108 | //--------------------------------------------------------------- |
---|
[498] | 109 | |
---|
[219] | 110 | int CONetCDF4::getCurrentGroup(void) |
---|
| 111 | { |
---|
[686] | 112 | return this->getGroup(this->getCurrentPath()); |
---|
[219] | 113 | } |
---|
[498] | 114 | |
---|
[219] | 115 | //--------------------------------------------------------------- |
---|
[498] | 116 | |
---|
[686] | 117 | int CONetCDF4::getGroup(const CONetCDF4Path& path) |
---|
[219] | 118 | { |
---|
| 119 | int retvalue = this->ncidp; |
---|
[498] | 120 | |
---|
[686] | 121 | CONetCDF4Path::const_iterator it = path.begin(), end = path.end(); |
---|
[219] | 122 | |
---|
[686] | 123 | for (; it != end; it++) |
---|
[219] | 124 | { |
---|
[686] | 125 | const StdString& groupid = *it; |
---|
| 126 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
---|
[219] | 127 | } |
---|
[686] | 128 | return retvalue; |
---|
[219] | 129 | } |
---|
[498] | 130 | |
---|
[219] | 131 | //--------------------------------------------------------------- |
---|
[498] | 132 | |
---|
[686] | 133 | int CONetCDF4::getVariable(const StdString& varname) |
---|
[219] | 134 | { |
---|
| 135 | int varid = 0; |
---|
| 136 | int grpid = this->getCurrentGroup(); |
---|
[686] | 137 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
---|
| 138 | return varid; |
---|
[219] | 139 | } |
---|
[498] | 140 | |
---|
[219] | 141 | //--------------------------------------------------------------- |
---|
[498] | 142 | |
---|
[686] | 143 | int CONetCDF4::getDimension(const StdString& dimname) |
---|
[219] | 144 | { |
---|
| 145 | int dimid = 0; |
---|
| 146 | int grpid = this->getCurrentGroup(); |
---|
[686] | 147 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
---|
| 148 | return dimid; |
---|
[219] | 149 | } |
---|
[498] | 150 | |
---|
[219] | 151 | //--------------------------------------------------------------- |
---|
[498] | 152 | |
---|
[219] | 153 | int CONetCDF4::getUnlimitedDimension(void) |
---|
| 154 | { |
---|
| 155 | int dimid = 0; |
---|
| 156 | int grpid = this->getCurrentGroup(); |
---|
[686] | 157 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
---|
| 158 | return dimid; |
---|
[219] | 159 | } |
---|
[498] | 160 | |
---|
[266] | 161 | StdString CONetCDF4::getUnlimitedDimensionName(void) |
---|
| 162 | { |
---|
| 163 | int grpid = this->getGroup(path); |
---|
| 164 | int dimid = this->getUnlimitedDimension(); |
---|
[498] | 165 | |
---|
| 166 | StdString dimname; |
---|
[686] | 167 | if (dimid != -1) |
---|
| 168 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
---|
| 169 | return dimname; |
---|
[266] | 170 | } |
---|
[498] | 171 | |
---|
[219] | 172 | //--------------------------------------------------------------- |
---|
[498] | 173 | |
---|
[686] | 174 | std::vector<StdSize> CONetCDF4::getDimensions(const StdString& varname) |
---|
[219] | 175 | { |
---|
| 176 | StdSize size = 0; |
---|
| 177 | std::vector<StdSize> retvalue; |
---|
| 178 | int grpid = this->getCurrentGroup(); |
---|
| 179 | int varid = this->getVariable(varname); |
---|
| 180 | int nbdim = 0, *dimid = NULL; |
---|
| 181 | |
---|
[686] | 182 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
---|
[219] | 183 | dimid = new int[nbdim](); |
---|
[686] | 184 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
---|
[219] | 185 | |
---|
| 186 | for (int i = 0; i < nbdim; i++) |
---|
| 187 | { |
---|
[686] | 188 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
---|
[219] | 189 | if (size == NC_UNLIMITED) |
---|
| 190 | size = UNLIMITED_DIM; |
---|
| 191 | retvalue.push_back(size); |
---|
| 192 | } |
---|
[401] | 193 | delete [] dimid; |
---|
[686] | 194 | return retvalue; |
---|
[219] | 195 | } |
---|
| 196 | |
---|
[686] | 197 | std::vector<std::string> CONetCDF4::getDimensionsIdList(const std::string* _varname) |
---|
[266] | 198 | { |
---|
[498] | 199 | int nDimNull = 0; |
---|
[266] | 200 | int nbdim = 0, *dimid = NULL; |
---|
| 201 | int grpid = this->getCurrentGroup(); |
---|
| 202 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
---|
| 203 | std::vector<std::string> retvalue; |
---|
[498] | 204 | |
---|
[266] | 205 | if (_varname != NULL) |
---|
| 206 | { |
---|
[686] | 207 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
---|
[266] | 208 | dimid = new int[nbdim](); |
---|
[686] | 209 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
---|
[266] | 210 | } |
---|
| 211 | else |
---|
| 212 | { |
---|
[686] | 213 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
---|
[266] | 214 | dimid = new int[nbdim](); |
---|
[686] | 215 | CNetCdfInterface::inqDimIds(grpid, nDimNull, dimid, 1); |
---|
[266] | 216 | } |
---|
[498] | 217 | |
---|
[266] | 218 | for (int i = 0; i < nbdim; i++) |
---|
| 219 | { |
---|
[498] | 220 | std::string dimname; |
---|
[686] | 221 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
---|
[266] | 222 | retvalue.push_back(dimname); |
---|
| 223 | } |
---|
| 224 | delete [] dimid; |
---|
[498] | 225 | |
---|
[686] | 226 | return retvalue; |
---|
[266] | 227 | } |
---|
| 228 | |
---|
[219] | 229 | //--------------------------------------------------------------- |
---|
| 230 | |
---|
[707] | 231 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective) |
---|
| 232 | { |
---|
| 233 | int grpid = this->getCurrentGroup(); |
---|
| 234 | int varid = this->getVariable(name); |
---|
| 235 | |
---|
| 236 | std::vector<StdSize> start(2), count(2); |
---|
| 237 | start[0] = 0; |
---|
| 238 | // Find out how many temporal records have been written already to the file we are opening |
---|
| 239 | int ncUnlimitedDimId; |
---|
| 240 | CNetCdfInterface::inqUnLimDim(this->ncidp, ncUnlimitedDimId); |
---|
| 241 | CNetCdfInterface::inqDimLen(this->ncidp, ncUnlimitedDimId, count[0]); |
---|
| 242 | start[1] = 0; |
---|
| 243 | count[1] = 2; |
---|
| 244 | |
---|
| 245 | timeAxisBounds.resize(count[1], count[0]); |
---|
| 246 | |
---|
| 247 | if (this->wmpi && collective) |
---|
| 248 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
| 249 | if (this->wmpi && !collective) |
---|
| 250 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
| 251 | |
---|
| 252 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
---|
| 253 | } |
---|
| 254 | |
---|
[1158] | 255 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective, size_t record) |
---|
| 256 | { |
---|
| 257 | int grpid = this->getCurrentGroup(); |
---|
| 258 | int varid = this->getVariable(name); |
---|
[707] | 259 | |
---|
[1158] | 260 | std::vector<StdSize> start(2), count(2); |
---|
| 261 | start[0] = record; |
---|
| 262 | count[0] = 1 ; |
---|
| 263 | start[1] = 0; |
---|
| 264 | count[1] = 2; |
---|
| 265 | |
---|
| 266 | timeAxisBounds.resize(2, 1); |
---|
| 267 | |
---|
| 268 | if (this->wmpi && collective) |
---|
| 269 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
| 270 | if (this->wmpi && !collective) |
---|
| 271 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
| 272 | |
---|
| 273 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
---|
| 274 | } |
---|
| 275 | |
---|
| 276 | |
---|
| 277 | |
---|
[686] | 278 | const CONetCDF4::CONetCDF4Path& CONetCDF4::getCurrentPath(void) const |
---|
| 279 | { return this->path; } |
---|
[219] | 280 | |
---|
[686] | 281 | void CONetCDF4::setCurrentPath(const CONetCDF4Path& path) |
---|
[219] | 282 | { this->path = path; } |
---|
| 283 | |
---|
| 284 | //--------------------------------------------------------------- |
---|
| 285 | |
---|
[686] | 286 | int CONetCDF4::addGroup(const StdString& name) |
---|
[219] | 287 | { |
---|
| 288 | int retvalue = 0; |
---|
| 289 | int grpid = this->getCurrentGroup(); |
---|
[686] | 290 | CNetCdfInterface::defGrp(grpid, name, retvalue); |
---|
| 291 | return retvalue; |
---|
[219] | 292 | } |
---|
[498] | 293 | |
---|
[219] | 294 | //--------------------------------------------------------------- |
---|
[498] | 295 | |
---|
[219] | 296 | int CONetCDF4::addDimension(const StdString& name, const StdSize size) |
---|
| 297 | { |
---|
| 298 | int retvalue = 0; |
---|
| 299 | int grpid = this->getCurrentGroup(); |
---|
| 300 | if (size != UNLIMITED_DIM) |
---|
[686] | 301 | CNetCdfInterface::defDim(grpid, name, size, retvalue); |
---|
[219] | 302 | else |
---|
[686] | 303 | CNetCdfInterface::defDim(grpid, name, NC_UNLIMITED, retvalue); |
---|
| 304 | return retvalue; |
---|
[219] | 305 | } |
---|
[498] | 306 | |
---|
[219] | 307 | //--------------------------------------------------------------- |
---|
[498] | 308 | |
---|
[686] | 309 | int CONetCDF4::addVariable(const StdString& name, nc_type type, |
---|
[1456] | 310 | const std::vector<StdString>& dim, int compressionLevel) |
---|
[219] | 311 | { |
---|
[350] | 312 | int varid = 0; |
---|
[219] | 313 | std::vector<int> dimids; |
---|
[606] | 314 | std::vector<StdSize> dimsizes; |
---|
[857] | 315 | int dimSize = dim.size(); |
---|
[2478] | 316 | |
---|
| 317 | int grpid = this->getCurrentGroup(); |
---|
| 318 | |
---|
| 319 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
---|
| 320 | |
---|
| 321 | for (int idx = 0; it != end; it++, ++idx) |
---|
| 322 | { |
---|
| 323 | const StdString& dimid = *it; |
---|
| 324 | dimids.push_back(this->getDimension(dimid)); |
---|
| 325 | } |
---|
| 326 | |
---|
| 327 | CNetCdfInterface::defVar(grpid, name, type, dimids.size(), &dimids[0], varid); |
---|
[878] | 328 | |
---|
[2478] | 329 | return varid; |
---|
| 330 | } |
---|
| 331 | |
---|
| 332 | //--------------------------------------------------------------- |
---|
| 333 | |
---|
| 334 | int CONetCDF4::addChunk(CField* field, nc_type type, |
---|
| 335 | const std::vector<StdString>& dim, int compressionLevel) |
---|
| 336 | { |
---|
| 337 | const StdString& name = field->getFieldOutputName(); |
---|
| 338 | int varid = 0; |
---|
| 339 | std::vector<StdSize> dimsizes; |
---|
| 340 | int dimSize = dim.size(); |
---|
| 341 | |
---|
[606] | 342 | StdSize size; |
---|
| 343 | StdSize totalSize; |
---|
[498] | 344 | |
---|
[2478] | 345 | // default chunk size |
---|
| 346 | StdSize maxSize = 1024 * 1024 * 20; // = 20 Mo (exp using large NEMO like grids) |
---|
| 347 | StdSize targetSize = maxSize; |
---|
| 348 | if (!field->chunking_blocksize_target.isEmpty()) |
---|
| 349 | { |
---|
| 350 | targetSize = field->chunking_blocksize_target.getValue()*1024*1024; |
---|
| 351 | } |
---|
| 352 | StdSize recordSize = 1; //sizeof(type); |
---|
| 353 | if (field->prec.isEmpty()) recordSize *= 4; |
---|
| 354 | else recordSize *= field->prec; |
---|
| 355 | |
---|
[219] | 356 | int grpid = this->getCurrentGroup(); |
---|
[498] | 357 | |
---|
[606] | 358 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
---|
[219] | 359 | |
---|
[878] | 360 | for (int idx = 0; it != end; it++, ++idx) |
---|
[219] | 361 | { |
---|
[686] | 362 | const StdString& dimid = *it; |
---|
[606] | 363 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
---|
| 364 | if (size == NC_UNLIMITED) size = 1; |
---|
[2478] | 365 | recordSize *= size; |
---|
[606] | 366 | dimsizes.push_back(size); |
---|
[219] | 367 | } |
---|
[2478] | 368 | double chunkingRatio = (double)recordSize / (double)targetSize; |
---|
[453] | 369 | |
---|
[2478] | 370 | varid = this->getVariable(name); |
---|
[498] | 371 | |
---|
[517] | 372 | // The classic NetCDF format does not support chunking nor fill parameters |
---|
| 373 | if (!useClassicFormat) |
---|
[453] | 374 | { |
---|
[2478] | 375 | // Browse field's elements (domain, axis) and NetCDF meta-data to retrieve corresponding chunking coefficients |
---|
| 376 | // in the file order ! |
---|
| 377 | CGrid* grid = field->getGrid(); |
---|
| 378 | std::vector<CDomain*> domains = grid->getDomains(); |
---|
| 379 | std::vector<CAxis*> axis = grid->getAxis(); |
---|
| 380 | |
---|
| 381 | std::vector<double> userChunkingWeights; // store chunking coefficients defined by users |
---|
| 382 | std::vector<StdString>::const_reverse_iterator itId = dim.rbegin(); // NetCDF is fed using dim, see this::addVariable() |
---|
| 383 | int elementIdx(0); |
---|
| 384 | int outerAxis(-1), outerDomJ(-1), outerDomI(-1); |
---|
| 385 | for (vector<StdSize>::reverse_iterator itDim = dimsizes.rbegin(); itDim != dimsizes.rend(); ++itDim, ++itId, ++elementIdx) |
---|
[517] | 386 | { |
---|
[2478] | 387 | bool isAxis(false); |
---|
| 388 | for ( auto ax : axis ) |
---|
| 389 | { |
---|
| 390 | StdString axisDim; |
---|
| 391 | // Rebuild axis name from axis before comparing |
---|
| 392 | if (ax->dim_name.isEmpty()) axisDim = ax->getAxisOutputName(); |
---|
| 393 | else axisDim=ax->dim_name.getValue(); |
---|
| 394 | if (axisDim == *itId) |
---|
| 395 | { |
---|
| 396 | if (!ax->chunking_weight.isEmpty()) userChunkingWeights.push_back( ax->chunking_weight.getValue() ); |
---|
| 397 | else userChunkingWeights.push_back( 0. ); |
---|
| 398 | isAxis = true; |
---|
| 399 | outerAxis = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 400 | break; |
---|
| 401 | } |
---|
| 402 | } // end scanning axis |
---|
| 403 | bool isDomain(false); |
---|
| 404 | for ( auto dom : domains ) |
---|
| 405 | { |
---|
| 406 | StdString axisDim; |
---|
| 407 | // Rebuild axis I name from domain before comparing |
---|
| 408 | if (!dom->dim_i_name.isEmpty()) axisDim = dom->dim_i_name.getValue(); |
---|
| 409 | else |
---|
| 410 | { |
---|
| 411 | if (dom->type==CDomain::type_attr::curvilinear) axisDim="x"; |
---|
| 412 | if (dom->type==CDomain::type_attr::unstructured) axisDim="cell"; |
---|
| 413 | if (dom->type==CDomain::type_attr::rectilinear) axisDim="lon"; |
---|
| 414 | } |
---|
| 415 | if (axisDim == *itId) |
---|
| 416 | { |
---|
| 417 | if (!dom->chunking_weight_i.isEmpty()) userChunkingWeights.push_back( dom->chunking_weight_i.getValue() ); |
---|
| 418 | else userChunkingWeights.push_back( 0. ); |
---|
| 419 | isDomain = true; |
---|
| 420 | outerDomI = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 421 | break; |
---|
| 422 | } |
---|
| 423 | // Rebuild axis J name from domain before comparing |
---|
| 424 | if (!dom->dim_j_name.isEmpty()) axisDim = dom->dim_j_name.getValue(); |
---|
| 425 | else { |
---|
| 426 | if (dom->type==CDomain::type_attr::curvilinear) axisDim="y"; |
---|
| 427 | if (dom->type==CDomain::type_attr::rectilinear) axisDim="lat"; |
---|
| 428 | } |
---|
| 429 | if (axisDim == *itId) |
---|
| 430 | { |
---|
| 431 | if (!dom->chunking_weight_j.isEmpty()) userChunkingWeights.push_back( dom->chunking_weight_j.getValue() ); |
---|
| 432 | else userChunkingWeights.push_back( 0. ); |
---|
| 433 | outerDomJ = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 434 | isDomain = true; |
---|
| 435 | break; |
---|
| 436 | } |
---|
| 437 | } // end scanning domain |
---|
| 438 | // No chunking applied on scalars or time |
---|
| 439 | if ((!isAxis)&&(!isDomain)) |
---|
| 440 | { |
---|
| 441 | userChunkingWeights.push_back( 0. ); |
---|
| 442 | } |
---|
[517] | 443 | } |
---|
[2478] | 444 | |
---|
| 445 | double sumChunkingWeights(0); |
---|
| 446 | for (int i=0;i<userChunkingWeights.size();i++) sumChunkingWeights += userChunkingWeights[i]; |
---|
| 447 | if ( (!sumChunkingWeights) && (chunkingRatio > 1) ) |
---|
| 448 | { |
---|
| 449 | if (outerAxis!=-1) userChunkingWeights[outerAxis] = 1; // chunk along outer axis |
---|
| 450 | else if (outerDomJ!=-1) userChunkingWeights[outerDomJ] = 1; // if no axis ? -> along j |
---|
| 451 | else if (outerDomI!=-1) userChunkingWeights[outerDomI] = 1; // if no j -> along i |
---|
| 452 | else {;} |
---|
| 453 | } |
---|
| 454 | |
---|
| 455 | int countChunkingDims(0); // number of dimensions on which chunking is operated : algo uses pow(value, 1/countChunkingDims) |
---|
| 456 | double normalizingWeight(0); // use to relativize chunking coefficients for all dimensions |
---|
| 457 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 458 | if (userChunkingWeights[i]>0.) |
---|
| 459 | { |
---|
| 460 | countChunkingDims++; |
---|
| 461 | normalizingWeight = userChunkingWeights[i]; |
---|
| 462 | } |
---|
| 463 | |
---|
| 464 | std::vector<double> chunkingRatioPerDims; // will store coefficients used to compute chunk size |
---|
| 465 | double productRatios = 1; // last_coeff = pow( shrink_ratio / (product of all ratios), 1/countChunkingDims ) |
---|
| 466 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 467 | { |
---|
| 468 | chunkingRatioPerDims.push_back( userChunkingWeights[i] / normalizingWeight ); |
---|
| 469 | if (chunkingRatioPerDims[i]) productRatios *= chunkingRatioPerDims[i]; |
---|
| 470 | } |
---|
| 471 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 472 | { |
---|
| 473 | chunkingRatioPerDims[i] *= pow( chunkingRatio / productRatios, 1./countChunkingDims ); |
---|
| 474 | } |
---|
| 475 | |
---|
| 476 | std::vector<double>::iterator itChunkingRatios = chunkingRatioPerDims.begin(); |
---|
| 477 | //itId = dim.rbegin(); |
---|
| 478 | double correctionFromPreviousDim = 1.; |
---|
| 479 | for (vector<StdSize>::reverse_iterator itDim = dimsizes.rbegin(); itDim != dimsizes.rend(); ++itDim, ++itChunkingRatios, ++itId) |
---|
| 480 | { |
---|
| 481 | *itChunkingRatios *= correctionFromPreviousDim; |
---|
| 482 | correctionFromPreviousDim = 1; |
---|
| 483 | if (*itChunkingRatios > 1) // else target larger than size ! |
---|
| 484 | { |
---|
| 485 | StdSize dimensionSize = *itDim; |
---|
| 486 | //info(0) << *itId << " " << *itDim << " " << *itChunkingRatios << " " << (*itDim)/(*itChunkingRatios) << endl; |
---|
| 487 | *itDim = ceil( *itDim / ceil(*itChunkingRatios) ); |
---|
| 488 | correctionFromPreviousDim = *itChunkingRatios/ ((double)dimensionSize/(*itDim)); |
---|
| 489 | } |
---|
| 490 | } |
---|
[857] | 491 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
---|
| 492 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
---|
[517] | 493 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
---|
[453] | 494 | } |
---|
| 495 | |
---|
[1456] | 496 | setCompressionLevel(name, compressionLevel) ; |
---|
| 497 | |
---|
[606] | 498 | return varid; |
---|
[219] | 499 | } |
---|
| 500 | |
---|
| 501 | //--------------------------------------------------------------- |
---|
| 502 | |
---|
[606] | 503 | void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel) |
---|
| 504 | { |
---|
[607] | 505 | if (compressionLevel < 0 || compressionLevel > 9) |
---|
| 506 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
---|
| 507 | "Invalid compression level for variable \"" << varname << "\", the value should range between 0 and 9."); |
---|
| 508 | if (compressionLevel && wmpi) |
---|
| 509 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
---|
| 510 | "Impossible to use compression for variable \"" << varname << "\" when using parallel mode."); |
---|
| 511 | |
---|
[606] | 512 | int grpid = this->getCurrentGroup(); |
---|
| 513 | int varid = this->getVariable(varname); |
---|
| 514 | CNetCdfInterface::defVarDeflate(grpid, varid, compressionLevel); |
---|
| 515 | } |
---|
| 516 | |
---|
| 517 | //--------------------------------------------------------------- |
---|
| 518 | |
---|
[219] | 519 | template <> |
---|
[686] | 520 | void CONetCDF4::addAttribute(const StdString& name, const StdString& value, const StdString* varname) |
---|
[219] | 521 | { |
---|
| 522 | int grpid = this->getCurrentGroup(); |
---|
| 523 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 524 | CNetCdfInterface::putAttType(grpid, varid, name, value.size(), value.c_str()); |
---|
[219] | 525 | } |
---|
[498] | 526 | |
---|
[219] | 527 | //--------------------------------------------------------------- |
---|
[498] | 528 | |
---|
[219] | 529 | template <> |
---|
[686] | 530 | void CONetCDF4::addAttribute(const StdString& name, const double& value, const StdString* varname) |
---|
[219] | 531 | { |
---|
| 532 | int grpid = this->getCurrentGroup(); |
---|
| 533 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 534 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 535 | } |
---|
[391] | 536 | |
---|
[686] | 537 | template <> |
---|
| 538 | void CONetCDF4::addAttribute(const StdString& name, const CArray<double,1>& value, const StdString* varname) |
---|
[391] | 539 | { |
---|
| 540 | int grpid = this->getCurrentGroup(); |
---|
| 541 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 542 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 543 | } |
---|
[219] | 544 | //--------------------------------------------------------------- |
---|
[498] | 545 | |
---|
[219] | 546 | template <> |
---|
[686] | 547 | void CONetCDF4::addAttribute(const StdString& name, const float& value, const StdString* varname) |
---|
[219] | 548 | { |
---|
| 549 | int grpid = this->getCurrentGroup(); |
---|
| 550 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 551 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 552 | } |
---|
[391] | 553 | |
---|
[686] | 554 | template <> |
---|
| 555 | void CONetCDF4::addAttribute(const StdString& name, const CArray<float,1>& value, const StdString* varname) |
---|
[391] | 556 | { |
---|
| 557 | int grpid = this->getCurrentGroup(); |
---|
| 558 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 559 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 560 | } |
---|
| 561 | |
---|
[219] | 562 | //--------------------------------------------------------------- |
---|
[498] | 563 | |
---|
[219] | 564 | template <> |
---|
[686] | 565 | void CONetCDF4::addAttribute(const StdString& name, const int& value, const StdString* varname) |
---|
[219] | 566 | { |
---|
| 567 | int grpid = this->getCurrentGroup(); |
---|
| 568 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 569 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 570 | } |
---|
| 571 | |
---|
[686] | 572 | template <> |
---|
| 573 | void CONetCDF4::addAttribute(const StdString& name, const CArray<int,1>& value, const StdString* varname) |
---|
[391] | 574 | { |
---|
| 575 | int grpid = this->getCurrentGroup(); |
---|
| 576 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 577 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 578 | } |
---|
| 579 | |
---|
[472] | 580 | template <> |
---|
[686] | 581 | void CONetCDF4::addAttribute(const StdString& name, const short int& value, const StdString* varname) |
---|
[472] | 582 | { |
---|
| 583 | int grpid = this->getCurrentGroup(); |
---|
| 584 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 585 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[472] | 586 | } |
---|
[219] | 587 | |
---|
[686] | 588 | template <> |
---|
| 589 | void CONetCDF4::addAttribute(const StdString& name, const CArray<short int,1>& value, const StdString* varname) |
---|
[472] | 590 | { |
---|
| 591 | int grpid = this->getCurrentGroup(); |
---|
| 592 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 593 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 594 | } |
---|
| 595 | |
---|
[472] | 596 | template <> |
---|
[686] | 597 | void CONetCDF4::addAttribute(const StdString& name, const long int& value, const StdString* varname) |
---|
[472] | 598 | { |
---|
| 599 | int grpid = this->getCurrentGroup(); |
---|
| 600 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 601 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[472] | 602 | } |
---|
| 603 | |
---|
[686] | 604 | template <> |
---|
| 605 | void CONetCDF4::addAttribute(const StdString& name, const CArray<long int,1>& value, const StdString* varname) |
---|
[472] | 606 | { |
---|
| 607 | int grpid = this->getCurrentGroup(); |
---|
| 608 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 609 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 610 | } |
---|
| 611 | |
---|
[686] | 612 | //--------------------------------------------------------------- |
---|
[498] | 613 | |
---|
[686] | 614 | void CONetCDF4::getWriteDataInfos(const StdString& name, StdSize record, StdSize& array_size, |
---|
| 615 | std::vector<StdSize>& sstart, |
---|
| 616 | std::vector<StdSize>& scount, |
---|
| 617 | const std::vector<StdSize>* start, |
---|
| 618 | const std::vector<StdSize>* count) |
---|
[498] | 619 | { |
---|
[266] | 620 | std::vector<std::size_t> sizes = this->getDimensions(name); |
---|
[857] | 621 | if (sizes.size()==0) |
---|
[266] | 622 | { |
---|
[2264] | 623 | |
---|
| 624 | if ((start != NULL) && (count != NULL) && start->size()==1 && count->size()==1) // pur scalar case |
---|
| 625 | array_size*=(*count)[0] ; |
---|
| 626 | else array_size=1 ; |
---|
[266] | 627 | } |
---|
[857] | 628 | else |
---|
| 629 | { |
---|
| 630 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
---|
| 631 | std::vector<std::size_t>::const_iterator |
---|
| 632 | it = sizes.begin(), end = sizes.end(); |
---|
| 633 | int i = 0; |
---|
[219] | 634 | |
---|
[857] | 635 | if (iddims.begin()->compare(timeCounterName) == 0) |
---|
| 636 | { |
---|
| 637 | sstart.push_back(record); |
---|
| 638 | scount.push_back(1); |
---|
[2264] | 639 | if ((start == NULL) && (count == NULL)) i++; |
---|
| 640 | it++; |
---|
| 641 | if (it==end) |
---|
| 642 | { |
---|
| 643 | if ((start != NULL) && (count != NULL) && start->size()==1 && count->size()==1) // pur scalar case |
---|
| 644 | { |
---|
| 645 | scount[0]=(*count)[0] ; |
---|
| 646 | array_size *= (*count)[0]; |
---|
| 647 | } |
---|
| 648 | } |
---|
[857] | 649 | } |
---|
[2264] | 650 | |
---|
[857] | 651 | for (;it != end; it++) |
---|
| 652 | { |
---|
| 653 | if ((start != NULL) && (count != NULL)) |
---|
| 654 | { |
---|
| 655 | sstart.push_back((*start)[i]); |
---|
| 656 | scount.push_back((*count)[i]); |
---|
| 657 | array_size *= (*count)[i]; |
---|
| 658 | i++; |
---|
| 659 | } |
---|
| 660 | else |
---|
| 661 | { |
---|
| 662 | sstart.push_back(0); |
---|
| 663 | scount.push_back(sizes[i]); |
---|
| 664 | array_size *= sizes[i]; |
---|
| 665 | i++; |
---|
| 666 | } |
---|
| 667 | } |
---|
| 668 | |
---|
[219] | 669 | } |
---|
| 670 | } |
---|
[498] | 671 | |
---|
[857] | 672 | |
---|
[219] | 673 | template <> |
---|
[686] | 674 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 675 | const std::vector<StdSize>& sstart, |
---|
| 676 | const std::vector<StdSize>& scount, const double* data) |
---|
[219] | 677 | { |
---|
[686] | 678 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 679 | } |
---|
[498] | 680 | |
---|
[219] | 681 | //--------------------------------------------------------------- |
---|
[498] | 682 | |
---|
[219] | 683 | template <> |
---|
[686] | 684 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 685 | const std::vector<StdSize>& sstart, |
---|
[1158] | 686 | const std::vector<StdSize>& scount, char* data) |
---|
| 687 | { |
---|
| 688 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 689 | } |
---|
| 690 | |
---|
| 691 | template <> |
---|
| 692 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 693 | const std::vector<StdSize>& sstart, |
---|
[686] | 694 | const std::vector<StdSize>& scount, const int* data) |
---|
[219] | 695 | { |
---|
[686] | 696 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 697 | } |
---|
| 698 | //--------------------------------------------------------------- |
---|
[498] | 699 | |
---|
[219] | 700 | template <> |
---|
[686] | 701 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 702 | const std::vector<StdSize>& sstart, |
---|
[1957] | 703 | const std::vector<StdSize>& scount, const size_t* data) |
---|
| 704 | { |
---|
| 705 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 706 | } |
---|
| 707 | //--------------------------------------------------------------- |
---|
| 708 | |
---|
| 709 | template <> |
---|
| 710 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 711 | const std::vector<StdSize>& sstart, |
---|
[686] | 712 | const std::vector<StdSize>& scount, const float* data) |
---|
[219] | 713 | { |
---|
[686] | 714 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 715 | } |
---|
| 716 | |
---|
| 717 | //--------------------------------------------------------------- |
---|
| 718 | |
---|
[686] | 719 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString& name) |
---|
[219] | 720 | { |
---|
| 721 | int grpid = this->getCurrentGroup(); |
---|
| 722 | int varid = this->getVariable(name); |
---|
[2264] | 723 | |
---|
[219] | 724 | StdSize array_size = 1; |
---|
| 725 | std::vector<StdSize> sstart, scount; |
---|
| 726 | |
---|
| 727 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
---|
[1158] | 728 | |
---|
[369] | 729 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
[1158] | 730 | |
---|
[219] | 731 | } |
---|
| 732 | |
---|
[686] | 733 | void CONetCDF4::writeTimeAxisData(const CArray<double, 1>& data, const StdString& name, |
---|
[413] | 734 | bool collective, StdSize record, bool isRoot) |
---|
| 735 | { |
---|
| 736 | int grpid = this->getCurrentGroup(); |
---|
| 737 | int varid = this->getVariable(name); |
---|
[498] | 738 | |
---|
[686] | 739 | map<int,size_t>::iterator it=timeAxis.find(varid); |
---|
| 740 | if (it == timeAxis.end()) timeAxis[varid] = record; |
---|
[498] | 741 | else |
---|
[413] | 742 | { |
---|
[686] | 743 | if (it->second >= record) return; |
---|
| 744 | else it->second =record; |
---|
[413] | 745 | } |
---|
[498] | 746 | |
---|
[413] | 747 | StdSize array_size = 1; |
---|
| 748 | std::vector<StdSize> sstart, scount; |
---|
[498] | 749 | |
---|
[413] | 750 | if (this->wmpi && collective) |
---|
[686] | 751 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
[413] | 752 | if (this->wmpi && !collective) |
---|
[686] | 753 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
[498] | 754 | |
---|
[413] | 755 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
---|
[1158] | 756 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
| 757 | } |
---|
| 758 | |
---|
| 759 | void CONetCDF4::writeTimeAxisDataBounds(const CArray<double, 1>& data, const StdString& name, |
---|
| 760 | bool collective, StdSize record, bool isRoot) |
---|
| 761 | { |
---|
| 762 | int grpid = this->getCurrentGroup(); |
---|
| 763 | int varid = this->getVariable(name); |
---|
| 764 | |
---|
| 765 | map<int,size_t>::iterator it=timeAxis.find(varid); |
---|
| 766 | if (it == timeAxis.end()) timeAxis[varid] = record; |
---|
| 767 | else |
---|
[686] | 768 | { |
---|
[1158] | 769 | if (it->second >= record) return; |
---|
| 770 | else it->second =record; |
---|
[686] | 771 | } |
---|
[1158] | 772 | |
---|
| 773 | StdSize array_size = 1; |
---|
| 774 | std::vector<StdSize> sstart, scount; |
---|
| 775 | |
---|
| 776 | if (this->wmpi && collective) |
---|
| 777 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
| 778 | if (this->wmpi && !collective) |
---|
| 779 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
| 780 | |
---|
| 781 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
---|
[413] | 782 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
| 783 | } |
---|
| 784 | |
---|
[1158] | 785 | |
---|
[219] | 786 | //--------------------------------------------------------------- |
---|
[498] | 787 | |
---|
[686] | 788 | bool CONetCDF4::varExist(const StdString& varname) |
---|
[219] | 789 | { |
---|
| 790 | int grpid = this->getCurrentGroup(); |
---|
[686] | 791 | return CNetCdfInterface::isVarExisted(grpid, varname); |
---|
[219] | 792 | } |
---|
| 793 | |
---|
[878] | 794 | bool CONetCDF4::dimExist(const StdString& dimname) |
---|
| 795 | { |
---|
| 796 | int grpid = this->getCurrentGroup(); |
---|
| 797 | return CNetCdfInterface::isDimExisted(grpid, dimname); |
---|
| 798 | } |
---|
| 799 | |
---|
[286] | 800 | void CONetCDF4::sync(void) |
---|
| 801 | { |
---|
[686] | 802 | CNetCdfInterface::sync(this->ncidp); |
---|
[498] | 803 | } |
---|
[219] | 804 | ///-------------------------------------------------------------- |
---|
[337] | 805 | } // namespace xios |
---|