MOAB: Mesh Oriented datABase  (version 5.2.1)
NCWriteGCRM.cpp
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00001 /*
00002  * NCWriteGCRM.cpp
00003  *
00004  *  Created on: April 9, 2014
00005  */
00006 
00007 #include "NCWriteGCRM.hpp"
00008 #include "MBTagConventions.hpp"
00009 
00010 namespace moab
00011 {
00012 
00013 NCWriteGCRM::~NCWriteGCRM()
00014 {
00015     // TODO Auto-generated destructor stub
00016 }
00017 
00018 ErrorCode NCWriteGCRM::collect_mesh_info()
00019 {
00020     Interface*& mbImpl                   = _writeNC->mbImpl;
00021     std::vector< std::string >& dimNames = _writeNC->dimNames;
00022     std::vector< int >& dimLens          = _writeNC->dimLens;
00023     Tag& mGlobalIdTag                    = _writeNC->mGlobalIdTag;
00024 
00025     ErrorCode rval;
00026 
00027     // Look for time dimension
00028     std::vector< std::string >::iterator vecIt;
00029     if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "Time" ) ) != dimNames.end() )
00030         tDim = vecIt - dimNames.begin();
00031     else if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "time" ) ) != dimNames.end() )
00032         tDim = vecIt - dimNames.begin();
00033     else
00034     {
00035         MB_SET_ERR( MB_FAILURE, "Couldn't find 'Time' or 'time' dimension" );
00036     }
00037     nTimeSteps = dimLens[tDim];
00038 
00039     // Get number of levels
00040     if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "layers" ) ) != dimNames.end() )
00041         levDim = vecIt - dimNames.begin();
00042     else
00043     {
00044         MB_SET_ERR( MB_FAILURE, "Couldn't find 'layers' dimension" );
00045     }
00046     nLevels = dimLens[levDim];
00047 
00048     // Get local vertices
00049     rval = mbImpl->get_entities_by_dimension( _fileSet, 0, localVertsOwned );MB_CHK_SET_ERR( rval, "Trouble getting local vertices in current file set" );
00050     assert( !localVertsOwned.empty() );
00051 
00052     // Get local edges
00053     rval = mbImpl->get_entities_by_dimension( _fileSet, 1, localEdgesOwned );MB_CHK_SET_ERR( rval, "Trouble getting local edges in current file set" );
00054     // There are no edges if NO_EDGES read option is set
00055 
00056     // Get local cells
00057     rval = mbImpl->get_entities_by_dimension( _fileSet, 2, localCellsOwned );MB_CHK_SET_ERR( rval, "Trouble getting local cells in current file set" );
00058     assert( !localCellsOwned.empty() );
00059 
00060 #ifdef MOAB_HAVE_MPI
00061     bool& isParallel = _writeNC->isParallel;
00062     if( isParallel )
00063     {
00064         ParallelComm*& myPcomm = _writeNC->myPcomm;
00065         int rank               = myPcomm->proc_config().proc_rank();
00066         int procs              = myPcomm->proc_config().proc_size();
00067         if( procs > 1 )
00068         {
00069 #ifndef NDEBUG
00070             unsigned int num_local_verts = localVertsOwned.size();
00071 #endif
00072             rval = myPcomm->filter_pstatus( localVertsOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT );MB_CHK_SET_ERR( rval, "Trouble getting owned vertices in current file set" );
00073 
00074             // Assume that PARALLEL_RESOLVE_SHARED_ENTS option is set
00075             // Verify that not all local vertices are owned by the last processor
00076             if( procs - 1 == rank )
00077                 assert( "PARALLEL_RESOLVE_SHARED_ENTS option is set" && localVertsOwned.size() < num_local_verts );
00078 
00079             if( !localEdgesOwned.empty() )
00080             {
00081                 rval = myPcomm->filter_pstatus( localEdgesOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT );MB_CHK_SET_ERR( rval, "Trouble getting owned edges in current file set" );
00082             }
00083 
00084             rval = myPcomm->filter_pstatus( localCellsOwned, PSTATUS_NOT_OWNED, PSTATUS_NOT );MB_CHK_SET_ERR( rval, "Trouble getting owned cells in current file set" );
00085         }
00086     }
00087 #endif
00088 
00089     std::vector< int > gids( localVertsOwned.size() );
00090     rval = mbImpl->tag_get_data( mGlobalIdTag, localVertsOwned, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting global IDs on local vertices" );
00091 
00092     // Get localGidVertsOwned
00093     std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidVertsOwned ) );
00094 
00095     if( !localEdgesOwned.empty() )
00096     {
00097         gids.resize( localEdgesOwned.size() );
00098         rval = mbImpl->tag_get_data( mGlobalIdTag, localEdgesOwned, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting global IDs on local edges" );
00099 
00100         // Get localGidEdgesOwned
00101         std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidEdgesOwned ) );
00102     }
00103 
00104     gids.resize( localCellsOwned.size() );
00105     rval = mbImpl->tag_get_data( mGlobalIdTag, localCellsOwned, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting global IDs on local cells" );
00106 
00107     // Get localGidCellsOwned
00108     std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidCellsOwned ) );
00109 
00110     return MB_SUCCESS;
00111 }
00112 
00113 ErrorCode NCWriteGCRM::collect_variable_data( std::vector< std::string >& var_names, std::vector< int >& tstep_nums )
00114 {
00115     NCWriteHelper::collect_variable_data( var_names, tstep_nums );
00116 
00117     std::vector< std::string >& dimNames = _writeNC->dimNames;
00118     std::vector< int >& dimLens          = _writeNC->dimLens;
00119 
00120     // Dimension indices for other optional levels
00121     std::vector< unsigned int > opt_lev_dims;
00122 
00123     unsigned int lev_idx;
00124     std::vector< std::string >::iterator vecIt;
00125 
00126     // Get index of interface levels
00127     if( ( vecIt = std::find( dimNames.begin(), dimNames.end(), "interfaces" ) ) != dimNames.end() )
00128     {
00129         lev_idx = vecIt - dimNames.begin();
00130         opt_lev_dims.push_back( lev_idx );
00131     }
00132 
00133     std::map< std::string, WriteNC::VarData >& varInfo = _writeNC->varInfo;
00134 
00135     for( size_t i = 0; i < var_names.size(); i++ )
00136     {
00137         std::string varname                                     = var_names[i];
00138         std::map< std::string, WriteNC::VarData >::iterator vit = varInfo.find( varname );
00139         if( vit == varInfo.end() ) MB_SET_ERR( MB_FAILURE, "Can't find variable " << varname );
00140 
00141         WriteNC::VarData& currentVarData = vit->second;
00142         std::vector< int >& varDims      = currentVarData.varDims;
00143 
00144         // Skip edge variables, if there are no edges
00145         if( localEdgesOwned.empty() && currentVarData.entLoc == WriteNC::ENTLOCEDGE ) continue;
00146 
00147         // If layers dimension is not found, try other optional levels such as interfaces
00148         if( std::find( varDims.begin(), varDims.end(), levDim ) == varDims.end() )
00149         {
00150             for( unsigned int j = 0; j < opt_lev_dims.size(); j++ )
00151             {
00152                 if( std::find( varDims.begin(), varDims.end(), opt_lev_dims[j] ) != varDims.end() )
00153                 {
00154                     currentVarData.numLev = dimLens[opt_lev_dims[j]];
00155                     break;
00156                 }
00157             }
00158         }
00159 
00160         // Skip set variables, which were already processed in
00161         // NCWriteHelper::collect_variable_data()
00162         if( WriteNC::ENTLOCSET == currentVarData.entLoc ) continue;
00163 
00164         // Set up writeStarts and writeCounts (maximum number of dimensions is 3)
00165         currentVarData.writeStarts.resize( 3 );
00166         currentVarData.writeCounts.resize( 3 );
00167         unsigned int dim_idx = 0;
00168 
00169         // First: time
00170         if( currentVarData.has_tsteps )
00171         {
00172             // Non-set variables with timesteps
00173             // 3 dimensions like (time, cells, layers)
00174             // 2 dimensions like (time, cells)
00175             assert( 3 == varDims.size() || 2 == varDims.size() );
00176 
00177             // Time should be the first dimension
00178             assert( tDim == varDims[0] );
00179 
00180             currentVarData.writeStarts[dim_idx] = 0;  // This value is timestep dependent, will be set later
00181             currentVarData.writeCounts[dim_idx] = 1;
00182             dim_idx++;
00183         }
00184         else
00185         {
00186             // Non-set variables without timesteps
00187             // 2 dimensions like (cells, layers)
00188             // 1 dimension like (cells)
00189             assert( 2 == varDims.size() || 1 == varDims.size() );
00190         }
00191 
00192         // Next: corners / cells / edges
00193         switch( currentVarData.entLoc )
00194         {
00195             case WriteNC::ENTLOCVERT:
00196                 // Vertices
00197                 // Start from the first localGidVerts
00198                 // Actually, this will be reset later for writing
00199                 currentVarData.writeStarts[dim_idx] = localGidVertsOwned[0] - 1;
00200                 currentVarData.writeCounts[dim_idx] = localGidVertsOwned.size();
00201                 break;
00202             case WriteNC::ENTLOCFACE:
00203                 // Faces
00204                 // Start from the first localGidCells
00205                 // Actually, this will be reset later for writing
00206                 currentVarData.writeStarts[dim_idx] = localGidCellsOwned[0] - 1;
00207                 currentVarData.writeCounts[dim_idx] = localGidCellsOwned.size();
00208                 break;
00209             case WriteNC::ENTLOCEDGE:
00210                 // Edges
00211                 // Start from the first localGidEdges
00212                 // Actually, this will be reset later for writing
00213                 currentVarData.writeStarts[dim_idx] = localGidEdgesOwned[0] - 1;
00214                 currentVarData.writeCounts[dim_idx] = localGidEdgesOwned.size();
00215                 break;
00216             default:
00217                 MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << varname );
00218         }
00219         dim_idx++;
00220 
00221         // Finally: layers or other optional levels, it is possible that there is no
00222         // level dimension (numLev is 0) for this non-set variable
00223         if( currentVarData.numLev > 0 )
00224         {
00225             // Non-set variables with levels
00226             // 3 dimensions like (time, cells, layers)
00227             // 2 dimensions like (cells, layers)
00228             assert( 3 == varDims.size() || 2 == varDims.size() );
00229 
00230             currentVarData.writeStarts[dim_idx] = 0;
00231             currentVarData.writeCounts[dim_idx] = currentVarData.numLev;
00232             dim_idx++;
00233         }
00234         else
00235         {
00236             // Non-set variables without levels
00237             // 2 dimensions like (time, cells)
00238             // 1 dimension like (cells)
00239             assert( 2 == varDims.size() || 1 == varDims.size() );
00240         }
00241 
00242         // Get variable size
00243         currentVarData.sz = 1;
00244         for( std::size_t idx = 0; idx < dim_idx; idx++ )
00245             currentVarData.sz *= currentVarData.writeCounts[idx];
00246     }  // for (size_t i = 0; i < var_names.size(); i++)
00247 
00248     return MB_SUCCESS;
00249 }
00250 
00251 ErrorCode NCWriteGCRM::write_nonset_variables( std::vector< WriteNC::VarData >& vdatas, std::vector< int >& tstep_nums )
00252 {
00253     Interface*& mbImpl = _writeNC->mbImpl;
00254 
00255     int success;
00256 
00257     // For each indexed variable tag, write a time step data
00258     for( unsigned int i = 0; i < vdatas.size(); i++ )
00259     {
00260         WriteNC::VarData& variableData = vdatas[i];
00261 
00262         // Skip edge variables, if there are no edges
00263         if( localEdgesOwned.empty() && variableData.entLoc == WriteNC::ENTLOCEDGE ) continue;
00264 
00265         // Get local owned entities of this variable
00266         Range* pLocalEntsOwned    = NULL;
00267         Range* pLocalGidEntsOwned = NULL;
00268         switch( variableData.entLoc )
00269         {
00270             case WriteNC::ENTLOCVERT:
00271                 // Vertices
00272                 pLocalEntsOwned    = &localVertsOwned;
00273                 pLocalGidEntsOwned = &localGidVertsOwned;
00274                 break;
00275             case WriteNC::ENTLOCEDGE:
00276                 // Edges
00277                 pLocalEntsOwned    = &localEdgesOwned;
00278                 pLocalGidEntsOwned = &localGidEdgesOwned;
00279                 break;
00280             case WriteNC::ENTLOCFACE:
00281                 // Cells
00282                 pLocalEntsOwned    = &localCellsOwned;
00283                 pLocalGidEntsOwned = &localGidCellsOwned;
00284                 break;
00285             default:
00286                 MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << variableData.varName );
00287         }
00288 
00289         unsigned int num_timesteps;
00290         unsigned int ents_idx = 0;
00291         if( variableData.has_tsteps )
00292         {
00293             // Non-set variables with timesteps
00294             // 3 dimensions like (time, cells, layers)
00295             // 2 dimensions like (time, cells)
00296             num_timesteps = tstep_nums.size();
00297             ents_idx++;
00298         }
00299         else
00300         {
00301             // Non-set variables without timesteps
00302             // 2 dimensions like (cells, layers)
00303             // 1 dimension like (cells)
00304             num_timesteps = 1;
00305         }
00306 
00307         unsigned int num_lev;
00308         if( variableData.numLev > 0 )
00309         {
00310             // Non-set variables with levels
00311             // 3 dimensions like (time, cells, layers)
00312             // 2 dimensions like (cells, layers)
00313             num_lev = variableData.numLev;
00314         }
00315         else
00316         {
00317             // Non-set variables without levels
00318             // 2 dimensions like (time, cells)
00319             // 1 dimension like (cells)
00320             num_lev = 1;
00321         }
00322 
00323         for( unsigned int t = 0; t < num_timesteps; t++ )
00324         {
00325             // We will write one time step, and count will be one; start will be different
00326             // Use tag_get_data instead of tag_iterate to copy tag data, as localEntsOwned
00327             // might not be contiguous.
00328             if( tDim == variableData.varDims[0] ) variableData.writeStarts[0] = t;  // This is start for time
00329             std::vector< double > tag_data( pLocalEntsOwned->size() * num_lev );
00330             ErrorCode rval = mbImpl->tag_get_data( variableData.varTags[t], *pLocalEntsOwned, &tag_data[0] );MB_CHK_SET_ERR( rval, "Trouble getting tag data on owned entities" );
00331 
00332 #ifdef MOAB_HAVE_PNETCDF
00333             size_t nb_writes = pLocalGidEntsOwned->psize();
00334             std::vector< int > requests( nb_writes ), statuss( nb_writes );
00335             size_t idxReq = 0;
00336 #endif
00337 
00338             // Now write copied tag data
00339             // Use nonblocking put (request aggregation)
00340             switch( variableData.varDataType )
00341             {
00342                 case NC_DOUBLE: {
00343                     size_t indexInDoubleArray = 0;
00344                     size_t ic                 = 0;
00345                     for( Range::pair_iterator pair_iter = pLocalGidEntsOwned->pair_begin();
00346                          pair_iter != pLocalGidEntsOwned->pair_end(); ++pair_iter, ic++ )
00347                     {
00348                         EntityHandle starth                = pair_iter->first;
00349                         EntityHandle endh                  = pair_iter->second;
00350                         variableData.writeStarts[ents_idx] = ( NCDF_SIZE )( starth - 1 );
00351                         variableData.writeCounts[ents_idx] = ( NCDF_SIZE )( endh - starth + 1 );
00352 
00353                         // Do a partial write, in each subrange
00354 #ifdef MOAB_HAVE_PNETCDF
00355                         // Wait outside this loop
00356                         success =
00357                             NCFUNCREQP( _vara_double )( _fileId, variableData.varId, &( variableData.writeStarts[0] ),
00358                                                         &( variableData.writeCounts[0] ),
00359                                                         &( tag_data[indexInDoubleArray] ), &requests[idxReq++] );
00360 #else
00361                         success = NCFUNCAP(
00362                             _vara_double )( _fileId, variableData.varId, &( variableData.writeStarts[0] ),
00363                                             &( variableData.writeCounts[0] ), &( tag_data[indexInDoubleArray] ) );
00364 #endif
00365                         if( success )
00366                             MB_SET_ERR( MB_FAILURE,
00367                                         "Failed to write double data in a loop for variable " << variableData.varName );
00368                         // We need to increment the index in double array for the
00369                         // next subrange
00370                         indexInDoubleArray += ( endh - starth + 1 ) * num_lev;
00371                     }
00372                     assert( ic == pLocalGidEntsOwned->psize() );
00373 #ifdef MOAB_HAVE_PNETCDF
00374                     success = ncmpi_wait_all( _fileId, requests.size(), &requests[0], &statuss[0] );
00375                     if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
00376 #endif
00377                     break;
00378                 }
00379                 default:
00380                     MB_SET_ERR( MB_NOT_IMPLEMENTED, "Writing non-double data is not implemented yet" );
00381             }
00382         }
00383     }
00384 
00385     return MB_SUCCESS;
00386 }
00387 
00388 } /* namespace moab */
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