 |
Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
|
|
Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
|
1 #include "ReadNC.hpp"
2 #include "NCHelper.hpp"
3
4 #include "moab/ReadUtilIface.hpp"
5 #include "MBTagConventions.hpp"
6 #include "moab/FileOptions.hpp"
7
8 namespace moab
9 {
10
11 ReaderIface* ReadNC::factory( Interface* iface )
12 {
13 return new ReadNC( iface );
14 }
15
16 ReadNC::ReadNC( Interface* impl )
17 : mbImpl( impl ), fileId( -1 ), mGlobalIdTag( 0 ), mpFileIdTag( NULL ), dbgOut( stderr ), isParallel( false ),
18 partMethod( ScdParData::ALLJORKORI ), scdi( NULL ),
19 #ifdef MOAB_HAVE_MPI
20 myPcomm( NULL ),
21 #endif
22 noMesh( false ), noVars( false ), spectralMesh( false ), noMixedElements( false ), noEdges( false ), culling(true),
23 repartition(false), gatherSetRank( -1 ), tStepBase( -1 ), trivialPartitionShift( 0 ), myHelper( NULL )
24 {
25 assert( impl != NULL );
26 impl->query_interface( readMeshIface );
27 }
28
29 ReadNC::~ReadNC()
30 {
31 mbImpl->release_interface( readMeshIface );
32 if( myHelper != NULL ) delete myHelper;
33 }
34
35 ErrorCode ReadNC::load_file( const char* file_name,
36 const EntityHandle* file_set,
37 const FileOptions& opts,
38 const ReaderIface::SubsetList* /*subset_list*/,
39 const Tag* file_id_tag )
40 {
41 // See if opts has variable(s) specified
42 std::vector< std::string > var_names;
43 std::vector< int > tstep_nums;
44 std::vector< double > tstep_vals;
45
46 // Get and cache predefined tag handles
47 mGlobalIdTag = mbImpl->globalId_tag();
48 // Store the pointer to the tag; if not null, set when global id tag
49 // is set too, with the same data, duplicated
50 mpFileIdTag = file_id_tag;
51
52 ErrorCode rval = parse_options( opts, var_names, tstep_nums, tstep_vals );MB_CHK_SET_ERR( rval, "Trouble parsing option string" );
53
54 // Open the file
55 dbgOut.tprintf( 1, "Opening file %s\n", file_name );
56 fileName = std::string( file_name );
57 int success;
58
59 #ifdef MOAB_HAVE_PNETCDF
60 if( isParallel )
61 success = NCFUNC( open )( myPcomm->proc_config().proc_comm(), file_name, 0, MPI_INFO_NULL, &fileId );
62 else
63 success = NCFUNC( open )( MPI_COMM_SELF, file_name, 0, MPI_INFO_NULL, &fileId );
64 #else
65 success = NCFUNC( open )( file_name, 0, &fileId );
66 #endif
67 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble opening file " << file_name );
68
69 // Read the header (num dimensions, dimensions, num variables, global attribs)
70 rval = read_header();MB_CHK_SET_ERR( rval, "Trouble reading file header" );
71
72 // Make sure there's a file set to put things in
73 EntityHandle tmp_set;
74 if( noMesh && !file_set )
75 {
76 MB_SET_ERR( MB_FAILURE, "NOMESH option requires non-NULL file set on input" );
77 }
78 else if( !file_set || ( file_set && *file_set == 0 ) )
79 {
80 rval = mbImpl->create_meshset( MESHSET_SET, tmp_set );MB_CHK_SET_ERR( rval, "Trouble creating file set" );
81 }
82 else
83 tmp_set = *file_set;
84
85 // Get the scd interface
86 scdi = NULL;
87 rval = mbImpl->query_interface( scdi );
88 if( NULL == scdi ) return MB_FAILURE;
89
90 if( NULL != myHelper ) delete myHelper;
91
92 // Get appropriate NC helper instance based on information read from the header
93 myHelper = NCHelper::get_nc_helper( this, fileId, opts, tmp_set );
94 if( NULL == myHelper )
95 {
96 MB_SET_ERR( MB_FAILURE, "Failed to get NCHelper class instance" );
97 }
98
99 // Initialize mesh values
100 rval = myHelper->init_mesh_vals();MB_CHK_SET_ERR( rval, "Trouble initializing mesh values" );
101
102 // Check existing mesh from last read
103 if( noMesh && !noVars )
104 {
105 rval = myHelper->check_existing_mesh();MB_CHK_SET_ERR( rval, "Trouble checking mesh from last read" );
106 }
107
108 // Create some conventional tags, e.g. __NUM_DIMS
109 // For multiple reads to a specified file set, we assume a single file, or a series of
110 // files with separated timesteps. Keep a flag on the file set to prevent conventional
111 // tags from being created again on a second read
112 Tag convTagsCreated = 0;
113 int def_val = 0;
114 rval = mbImpl->tag_get_handle( "__CONV_TAGS_CREATED", 1, MB_TYPE_INTEGER, convTagsCreated,
115 MB_TAG_SPARSE | MB_TAG_CREAT, &def_val );MB_CHK_SET_ERR( rval, "Trouble getting _CONV_TAGS_CREATED tag" );
116 int create_conv_tags_flag = 0;
117 rval = mbImpl->tag_get_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag );
118 // The first read to the file set
119 if( 0 == create_conv_tags_flag )
120 {
121 // Read dimensions (coordinate variables) by default to create tags like __<var_name>_DIMS
122 // This is done only once (assume that all files read to the file set have the same
123 // dimensions)
124 rval = myHelper->read_variables( dimNames, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading dimensions" );
125
126 rval = myHelper->create_conventional_tags( tstep_nums );MB_CHK_SET_ERR( rval, "Trouble creating NC conventional tags" );
127
128 create_conv_tags_flag = 1;
129 rval = mbImpl->tag_set_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag );MB_CHK_SET_ERR( rval, "Trouble setting data to _CONV_TAGS_CREATED tag" );
130 }
131 // Another read to the file set
132 else
133 {
134 if( tStepBase > -1 )
135 {
136 // If timesteps spread across files, merge time values read
137 // from current file to existing time tag
138 rval = myHelper->update_time_tag_vals();MB_CHK_SET_ERR( rval, "Trouble updating time tag values" );
139 }
140 }
141
142 // Create mesh vertex/edge/face sequences
143 Range faces;
144 if( !noMesh )
145 {
146 rval = myHelper->create_mesh( faces );MB_CHK_SET_ERR( rval, "Trouble creating mesh" );
147 }
148
149 // Read specified variables onto grid
150 if( !noVars )
151 {
152 if( var_names.empty() )
153 {
154 // If VARIABLE option is missing, read all variables
155 rval = myHelper->read_variables( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading all variables" );
156 }
157 else
158 {
159 // Exclude dimensions that are read to the file set by default
160 std::vector< std::string > non_dim_var_names;
161 for( unsigned int i = 0; i < var_names.size(); i++ )
162 {
163 if( std::find( dimNames.begin(), dimNames.end(), var_names[i] ) == dimNames.end() )
164 non_dim_var_names.push_back( var_names[i] );
165 }
166
167 if( !non_dim_var_names.empty() )
168 {
169 rval = myHelper->read_variables( non_dim_var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading specified variables" );
170 }
171 }
172 }
173
174 #ifdef MOAB_HAVE_MPI
175 // Create partition set, and populate with elements
176 if( isParallel )
177 {
178 // Write partition tag name on partition set
179 Tag part_tag = myPcomm->partition_tag();
180 int dum_rank = myPcomm->proc_config().proc_rank();
181 // the tmp_set is the file_set
182 rval = mbImpl->tag_set_data( part_tag, &tmp_set, 1, &dum_rank );MB_CHK_SET_ERR( rval, "Trouble writing partition tag name on partition set" );
183 }
184 #endif
185
186 mbImpl->release_interface( scdi );
187 scdi = NULL;
188
189 // Close the file
190 success = NCFUNC( close )( fileId );
191 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble closing file" );
192
193 return MB_SUCCESS;
194 }
195
196 ErrorCode ReadNC::parse_options( const FileOptions& opts,
197 std::vector< std::string >& var_names,
198 std::vector< int >& tstep_nums,
199 std::vector< double >& tstep_vals )
200 {
201 int tmpval;
202 if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) )
203 {
204 dbgOut.set_verbosity( tmpval );
205 dbgOut.set_prefix( "NC " );
206 }
207
208 ErrorCode rval = opts.get_strs_option( "VARIABLE", var_names );
209 if( MB_TYPE_OUT_OF_RANGE == rval )
210 noVars = true;
211 else
212 noVars = false;
213
214 opts.get_ints_option( "TIMESTEP", tstep_nums );
215 opts.get_reals_option( "TIMEVAL", tstep_vals );
216
217 rval = opts.get_null_option( "NOMESH" );
218 if( MB_SUCCESS == rval ) noMesh = true;
219
220 rval = opts.get_null_option( "SPECTRAL_MESH" );
221 if( MB_SUCCESS == rval ) spectralMesh = true;
222
223 rval = opts.get_null_option( "NO_MIXED_ELEMENTS" );
224 if( MB_SUCCESS == rval ) noMixedElements = true;
225
226 rval = opts.get_null_option( "NO_EDGES" );
227 if( MB_SUCCESS == rval ) noEdges = true;
228
229 rval = opts.get_null_option( "NO_CULLING" ); // used now only for domain nc convention
230 if( MB_SUCCESS == rval ) culling = false;
231
232 rval = opts.get_null_option( "REPARTITION" ); // used now only for domain nc, to repartition with zoltan
233 if( MB_SUCCESS == rval ) repartition = true;
234
235 if( 2 <= dbgOut.get_verbosity() )
236 {
237 if( !var_names.empty() )
238 {
239 std::cerr << "Variables requested: ";
240 for( unsigned int i = 0; i < var_names.size(); i++ )
241 std::cerr << var_names[i];
242 std::cerr << std::endl;
243 }
244
245 if( !tstep_nums.empty() )
246 {
247 std::cerr << "Timesteps requested: ";
248 for( unsigned int i = 0; i < tstep_nums.size(); i++ )
249 std::cerr << tstep_nums[i];
250 std::cerr << std::endl;
251 }
252
253 if( !tstep_vals.empty() )
254 {
255 std::cerr << "Time vals requested: ";
256 for( unsigned int i = 0; i < tstep_vals.size(); i++ )
257 std::cerr << tstep_vals[i];
258 std::cerr << std::endl;
259 }
260 }
261
262 rval = opts.get_int_option( "GATHER_SET", 0, gatherSetRank );
263 if( MB_TYPE_OUT_OF_RANGE == rval )
264 {
265 MB_SET_ERR( rval, "Invalid value for GATHER_SET option" );
266 }
267
268 rval = opts.get_int_option( "TIMESTEPBASE", 0, tStepBase );
269 if( MB_TYPE_OUT_OF_RANGE == rval )
270 {
271 MB_SET_ERR( rval, "Invalid value for TIMESTEPBASE option" );
272 }
273
274 rval = opts.get_int_option( "TRIVIAL_PARTITION_SHIFT", 1, trivialPartitionShift );
275 if( MB_TYPE_OUT_OF_RANGE == rval )
276 {
277 MB_SET_ERR( rval, "Invalid value for TRIVIAL_PARTITION_SHIFT option" );
278 }
279
280 #ifdef MOAB_HAVE_MPI
281 isParallel = ( opts.match_option( "PARALLEL", "READ_PART" ) != MB_ENTITY_NOT_FOUND );
282
283 if( !isParallel )
284 // Return success here, since rval still has _NOT_FOUND from not finding option
285 // in this case, myPcomm will be NULL, so it can never be used; always check for isParallel
286 // before any use for myPcomm
287 return MB_SUCCESS;
288
289 int pcomm_no = 0;
290 rval = opts.get_int_option( "PARALLEL_COMM", pcomm_no );
291 if( MB_TYPE_OUT_OF_RANGE == rval )
292 {
293 MB_SET_ERR( rval, "Invalid value for PARALLEL_COMM option" );
294 }
295 myPcomm = ParallelComm::get_pcomm( mbImpl, pcomm_no );
296 if( 0 == myPcomm )
297 {
298 myPcomm = new ParallelComm( mbImpl, MPI_COMM_WORLD );
299 }
300 const int rank = myPcomm->proc_config().proc_rank();
301 dbgOut.set_rank( rank );
302
303 int dum;
304 rval = opts.match_option( "PARTITION_METHOD", ScdParData::PartitionMethodNames, dum );
305 if( MB_FAILURE == rval )
306 {
307 MB_SET_ERR( rval, "Unknown partition method specified" );
308 }
309 else if( MB_ENTITY_NOT_FOUND == rval )
310 partMethod = ScdParData::ALLJORKORI;
311 else
312 partMethod = dum;
313 #endif
314
315 return MB_SUCCESS;
316 }
317
318 ErrorCode ReadNC::read_header()
319 {
320 dbgOut.tprint( 1, "Reading header...\n" );
321
322 // Get the global attributes
323 int numgatts;
324 int success;
325 success = NCFUNC( inq_natts )( fileId, &numgatts );
326 if( success ) MB_SET_ERR( MB_FAILURE, "Couldn't get number of global attributes" );
327
328 // Read attributes into globalAtts
329 ErrorCode result = get_attributes( NC_GLOBAL, numgatts, globalAtts );MB_CHK_SET_ERR( result, "Trouble getting global attributes" );
330 dbgOut.tprintf( 1, "Read %u attributes\n", (unsigned int)globalAtts.size() );
331
332 // Read in dimensions into dimNames and dimLens
333 result = get_dimensions( fileId, dimNames, dimLens );MB_CHK_SET_ERR( result, "Trouble getting dimensions" );
334 dbgOut.tprintf( 1, "Read %u dimensions\n", (unsigned int)dimNames.size() );
335
336 // Read in variables into varInfo
337 result = get_variables();MB_CHK_SET_ERR( result, "Trouble getting variables" );
338 dbgOut.tprintf( 1, "Read %u variables\n", (unsigned int)varInfo.size() );
339
340 return MB_SUCCESS;
341 }
342
343 ErrorCode ReadNC::get_attributes( int var_id, int num_atts, std::map< std::string, AttData >& atts, const char* prefix )
344 {
345 char dum_name[120];
346
347 for( int i = 0; i < num_atts; i++ )
348 {
349 // Get the name
350 int success = NCFUNC( inq_attname )( fileId, var_id, i, dum_name );
351 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting attribute name" );
352
353 AttData& data = atts[std::string( dum_name )];
354 data.attName = std::string( dum_name );
355 success = NCFUNC( inq_att )( fileId, var_id, dum_name, &data.attDataType, &data.attLen );
356 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting info for attribute " << data.attName );
357 data.attVarId = var_id;
358
359 dbgOut.tprintf( 2, "%sAttribute %s: length=%u, varId=%d, type=%d\n", ( prefix ? prefix : "" ),
360 data.attName.c_str(), (unsigned int)data.attLen, data.attVarId, data.attDataType );
361 }
362
363 return MB_SUCCESS;
364 }
365
366 ErrorCode ReadNC::get_dimensions( int file_id, std::vector< std::string >& dim_names, std::vector< int >& dim_lens )
367 {
368 // Get the number of dimensions
369 int num_dims;
370 int success = NCFUNC( inq_ndims )( file_id, &num_dims );
371 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dimensions" );
372
373 if( num_dims > NC_MAX_DIMS )
374 {
375 MB_SET_ERR( MB_FAILURE,
376 "ReadNC: File contains " << num_dims << " dims but NetCDF library supports only " << NC_MAX_DIMS );
377 }
378
379 char dim_name[NC_MAX_NAME + 1];
380 NCDF_SIZE dim_len;
381 dim_names.resize( num_dims );
382 dim_lens.resize( num_dims );
383
384 for( int i = 0; i < num_dims; i++ )
385 {
386 success = NCFUNC( inq_dim )( file_id, i, dim_name, &dim_len );
387 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimension info" );
388
389 dim_names[i] = std::string( dim_name );
390 dim_lens[i] = dim_len;
391
392 dbgOut.tprintf( 2, "Dimension %s, length=%u\n", dim_name, (unsigned int)dim_len );
393 }
394
395 return MB_SUCCESS;
396 }
397
398 ErrorCode ReadNC::get_variables()
399 {
400 // First cache the number of time steps
401 std::vector< std::string >::iterator vit = std::find( dimNames.begin(), dimNames.end(), "time" );
402 if( vit == dimNames.end() ) vit = std::find( dimNames.begin(), dimNames.end(), "t" );
403
404 int ntimes = 0;
405 if( vit != dimNames.end() ) ntimes = dimLens[vit - dimNames.begin()];
406 if( !ntimes ) ntimes = 1;
407
408 // Get the number of variables
409 int num_vars;
410 int success = NCFUNC( inq_nvars )( fileId, &num_vars );
411 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of variables" );
412
413 if( num_vars > NC_MAX_VARS )
414 {
415 MB_SET_ERR( MB_FAILURE,
416 "ReadNC: File contains " << num_vars << " vars but NetCDF library supports only " << NC_MAX_VARS );
417 }
418
419 char var_name[NC_MAX_NAME + 1];
420 int var_ndims;
421
422 for( int i = 0; i < num_vars; i++ )
423 {
424 // Get the name first, so we can allocate a map iterate for this var
425 success = NCFUNC( inq_varname )( fileId, i, var_name );
426 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting variable name" );
427 VarData& data = varInfo[std::string( var_name )];
428 data.varName = std::string( var_name );
429 data.varId = i;
430 data.varTags.resize( ntimes, 0 );
431
432 // Get the data type
433 success = NCFUNC( inq_vartype )( fileId, i, &data.varDataType );
434 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting data type for variable " << data.varName );
435
436 // Get the number of dimensions, then the dimensions
437 success = NCFUNC( inq_varndims )( fileId, i, &var_ndims );
438 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
439 data.varDims.resize( var_ndims );
440
441 success = NCFUNC( inq_vardimid )( fileId, i, &data.varDims[0] );
442 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimensions for variable " << data.varName );
443
444 // Finally, get the number of attributes, then the attributes
445 success = NCFUNC( inq_varnatts )( fileId, i, &data.numAtts );
446 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
447
448 // Print debug info here so attribute info comes afterwards
449 dbgOut.tprintf( 2, "Variable %s: Id=%d, numAtts=%d, datatype=%d, num_dims=%u\n", data.varName.c_str(),
450 data.varId, data.numAtts, data.varDataType, (unsigned int)data.varDims.size() );
451
452 ErrorCode rval = get_attributes( i, data.numAtts, data.varAtts, " " );MB_CHK_SET_ERR( rval, "Trouble getting attributes for variable " << data.varName );
453 }
454
455 return MB_SUCCESS;
456 }
457
458 ErrorCode ReadNC::read_tag_values( const char*,
459 const char*,
460 const FileOptions&,
461 std::vector< int >&,
462 const SubsetList* )
463 {
464 return MB_FAILURE;
465 }
466
467 } // namespace moab
1.9.1.