MOAB: Mesh Oriented datABase  (version 5.4.1)
WriteHDF5.cpp
Go to the documentation of this file.
00001 /**
00002  * MOAB, a Mesh-Oriented datABase, is a software component for creating,
00003  * storing and accessing finite element mesh data.
00004  *
00005  * Copyright 2004 Sandia Corporation.  Under the terms of Contract
00006  * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
00007  * retains certain rights in this software.
00008  *
00009  * This library is free software; you can redistribute it and/or
00010  * modify it under the terms of the GNU Lesser General Public
00011  * License as published by the Free Software Foundation; either
00012  * version 2.1 of the License, or (at your option) any later version.
00013  *
00014  */
00015 
00016 //-------------------------------------------------------------------------
00017 // Filename      : WriteHDF5.cpp
00018 //
00019 // Purpose       : TSTT HDF5 Writer
00020 //
00021 // Special Notes : WriteSLAC used as template for this
00022 //
00023 // Creator       : Jason Kraftcheck
00024 //
00025 // Creation Date : 04/01/04
00026 //-------------------------------------------------------------------------
00027 
00028 #include <cassert>
00029 #if defined( _MSC_VER )
00030 typedef int id_t;
00031 #elif defined( __MINGW32__ )
00032 #include <sys/time.h>
00033 #else
00034 #include <ctime>
00035 #endif
00036 
00037 #include <cstdlib>
00038 #include <cstring>
00039 #include <cstdarg>
00040 #include <limits>
00041 #include <cstdio>
00042 #include <iostream>
00043 #include "WriteHDF5.hpp"
00044 #include <H5Tpublic.h>
00045 #include <H5Ppublic.h>
00046 #include <H5Epublic.h>
00047 #include "moab/Interface.hpp"
00048 #include "Internals.hpp"
00049 #include "MBTagConventions.hpp"
00050 #include "moab/CN.hpp"
00051 #include "moab/FileOptions.hpp"
00052 #include "moab/CpuTimer.hpp"
00053 #include "IODebugTrack.hpp"
00054 #include "mhdf.h"
00055 
00056 #ifndef MOAB_HAVE_HDF5
00057 #error Attempt to compile WriteHDF5 with HDF5 support disabled
00058 #endif
00059 
00060 #undef BLOCKED_COORD_IO
00061 
00062 #ifdef MOAB_HAVE_VALGRIND
00063 #include <valgrind/memcheck.h>
00064 
00065 template < typename T >
00066 inline void VALGRIND_MAKE_VEC_UNDEFINED( std::vector< T >& v )
00067 {
00068     (void)VALGRIND_MAKE_MEM_UNDEFINED( (T*)&v[0], v.size() * sizeof( T ) );
00069 }
00070 
00071 #else
00072 #ifndef VALGRIND_CHECK_MEM_IS_DEFINED
00073 #define VALGRIND_CHECK_MEM_IS_DEFINED( a, b ) ( (void)0 )
00074 #endif
00075 #ifndef VALGRIND_CHECK_MEM_IS_ADDRESSABLE
00076 #define VALGRIND_CHECK_MEM_IS_ADDRESSABLE( a, b ) ( (void)0 )
00077 #endif
00078 #ifndef VALGRIND_MAKE_MEM_UNDEFINED
00079 #define VALGRIND_MAKE_MEM_UNDEFINED( a, b ) ( (void)0 )
00080 #endif
00081 
00082 template < typename T >
00083 inline void VALGRIND_MAKE_VEC_UNDEFINED( std::vector< T >& )
00084 {
00085     (void)VALGRIND_MAKE_MEM_UNDEFINED( 0, 0 );
00086 }
00087 
00088 #endif
00089 
00090 namespace moab
00091 {
00092 
00093 #define WRITE_HDF5_BUFFER_SIZE ( 40 * 1024 * 1024 )
00094 
00095 static hid_t get_id_type()
00096 {
00097     if( 8 == sizeof( WriteHDF5::wid_t ) )
00098     {
00099         if( 8 == sizeof( long ) )
00100             return H5T_NATIVE_ULONG;
00101         else
00102             return H5T_NATIVE_UINT64;
00103     }
00104     else if( 4 == sizeof( WriteHDF5::wid_t ) )
00105     {
00106         if( 4 == sizeof( int ) )
00107             return H5T_NATIVE_UINT;
00108         else
00109             return H5T_NATIVE_UINT32;
00110     }
00111     else
00112     {
00113         assert( 0 );
00114         return (hid_t)-1;
00115     }
00116 }
00117 
00118 // This is the HDF5 type used to store file IDs
00119 const hid_t WriteHDF5::id_type = get_id_type();
00120 
00121 // This function doesn't do anything useful. It's just a nice
00122 // place to set a break point to determine why the writer fails.
00123 static inline ErrorCode error( ErrorCode rval )
00124 {
00125     return rval;
00126 }
00127 
00128 // Call \c error function during HDF5 library errors to make
00129 // it easier to trap such errors in the debugger. This function
00130 // gets registered with the HDF5 library as a callback. It
00131 // works the same as the default (H5Eprint), except that it
00132 // also calls the \c error function as a no-op.
00133 #if defined( H5E_auto_t_vers ) && H5E_auto_t_vers > 1
00134 static herr_t handle_hdf5_error( hid_t stack, void* data )
00135 {
00136     WriteHDF5::HDF5ErrorHandler* h = reinterpret_cast< WriteHDF5::HDF5ErrorHandler* >( data );
00137     herr_t result                  = 0;
00138     if( h->func ) result = ( *h->func )( stack, h->data );
00139     error( MB_FAILURE );
00140     return result;
00141 }
00142 #else
00143 static herr_t handle_hdf5_error( void* data )
00144 {
00145     WriteHDF5::HDF5ErrorHandler* h = reinterpret_cast< WriteHDF5::HDF5ErrorHandler* >( data );
00146     herr_t result                  = 0;
00147     if( h->func ) result = ( *h->func )( h->data );
00148     error( MB_FAILURE );
00149     return result;
00150 }
00151 #endif
00152 
00153 // Some macros to handle error checking. The
00154 // CHK_MHDF__ERR* macros check the value of an mhdf_Status
00155 // object. The CHK_MB_ERR_* check the value of an ErrorCode.
00156 // The *_0 macros accept no other arguments. The *_1
00157 // macros accept a single hdf5 handle to close on error.
00158 // The *_2 macros accept an array of two hdf5 handles to
00159 // close on error. The _*2C macros accept one hdf5 handle
00160 // to close on error and a bool and an hdf5 handle where
00161 // the latter handle is conditionally closed depending on
00162 // the value of the bool. All macros contain a "return"
00163 // statement.
00164 #define CHK_MHDF_ERR_0( A )                            \
00165     do                                                 \
00166     {                                                  \
00167         if( mhdf_isError( &( A ) ) )                   \
00168         {                                              \
00169             MB_SET_ERR_CONT( mhdf_message( &( A ) ) ); \
00170             assert( 0 );                               \
00171             return error( MB_FAILURE );                \
00172         }                                              \
00173     } while( false )
00174 
00175 #define CHK_MHDF_ERR_1( A, B )                         \
00176     do                                                 \
00177     {                                                  \
00178         if( mhdf_isError( &( A ) ) )                   \
00179         {                                              \
00180             MB_SET_ERR_CONT( mhdf_message( &( A ) ) ); \
00181             assert( 0 );                               \
00182             mhdf_closeData( filePtr, ( B ), &( A ) );  \
00183             return error( MB_FAILURE );                \
00184         }                                              \
00185     } while( false )
00186 
00187 #define CHK_MHDF_ERR_2( A, B )                           \
00188     do                                                   \
00189     {                                                    \
00190         if( mhdf_isError( &( A ) ) )                     \
00191         {                                                \
00192             MB_SET_ERR_CONT( mhdf_message( &( A ) ) );   \
00193             assert( 0 );                                 \
00194             mhdf_closeData( filePtr, ( B )[0], &( A ) ); \
00195             mhdf_closeData( filePtr, ( B )[1], &( A ) ); \
00196             return error( MB_FAILURE );                  \
00197         }                                                \
00198     } while( false )
00199 
00200 #define CHK_MHDF_ERR_3( A, B )                           \
00201     do                                                   \
00202     {                                                    \
00203         if( mhdf_isError( &( A ) ) )                     \
00204         {                                                \
00205             MB_SET_ERR_CONT( mhdf_message( &( A ) ) );   \
00206             assert( 0 );                                 \
00207             mhdf_closeData( filePtr, ( B )[0], &( A ) ); \
00208             mhdf_closeData( filePtr, ( B )[1], &( A ) ); \
00209             mhdf_closeData( filePtr, ( B )[2], &( A ) ); \
00210             return error( MB_FAILURE );                  \
00211         }                                                \
00212     } while( false )
00213 
00214 #define CHK_MHDF_ERR_2C( A, B, C, D )                         \
00215     do                                                        \
00216     {                                                         \
00217         if( mhdf_isError( &( A ) ) )                          \
00218         {                                                     \
00219             MB_SET_ERR_CONT( mhdf_message( &( A ) ) );        \
00220             assert( 0 );                                      \
00221             mhdf_closeData( filePtr, ( B ), &( A ) );         \
00222             if( C ) mhdf_closeData( filePtr, ( D ), &( A ) ); \
00223             return error( MB_FAILURE );                       \
00224         }                                                     \
00225     } while( false )
00226 
00227 #define CHK_MB_ERR_0( A )             \
00228     do                                \
00229     {                                 \
00230         if( MB_SUCCESS != ( A ) )     \
00231         {                             \
00232             MB_CHK_ERR_CONT( ( A ) ); \
00233             return error( A );        \
00234         }                             \
00235     } while( false )
00236 
00237 #define CHK_MB_ERR_1( A, B, C )                       \
00238     do                                                \
00239     {                                                 \
00240         if( MB_SUCCESS != ( A ) )                     \
00241         {                                             \
00242             MB_CHK_ERR_CONT( ( A ) );                 \
00243             mhdf_closeData( filePtr, ( B ), &( C ) ); \
00244             assert( 0 );                              \
00245             return error( A );                        \
00246         }                                             \
00247     } while( false )
00248 
00249 #define CHK_MB_ERR_2( A, B, C )                          \
00250     do                                                   \
00251     {                                                    \
00252         if( MB_SUCCESS != ( A ) )                        \
00253         {                                                \
00254             MB_CHK_ERR_CONT( ( A ) );                    \
00255             mhdf_closeData( filePtr, ( B )[0], &( C ) ); \
00256             mhdf_closeData( filePtr, ( B )[1], &( C ) ); \
00257             write_finished();                            \
00258             assert( 0 );                                 \
00259             return error( A );                           \
00260         }                                                \
00261     } while( false )
00262 
00263 #define CHK_MB_ERR_3( A, B, C )                          \
00264     do                                                   \
00265     {                                                    \
00266         if( MB_SUCCESS != ( A ) )                        \
00267         {                                                \
00268             MB_CHK_ERR_CONT( ( A ) );                    \
00269             mhdf_closeData( filePtr, ( B )[0], &( C ) ); \
00270             mhdf_closeData( filePtr, ( B )[1], &( C ) ); \
00271             mhdf_closeData( filePtr, ( B )[2], &( C ) ); \
00272             write_finished();                            \
00273             assert( 0 );                                 \
00274             return error( A );                           \
00275         }                                                \
00276     } while( false )
00277 
00278 #define CHK_MB_ERR_2C( A, B, C, D, E )                        \
00279     do                                                        \
00280     {                                                         \
00281         if( MB_SUCCESS != ( A ) )                             \
00282         {                                                     \
00283             MB_CHK_ERR_CONT( ( A ) );                         \
00284             mhdf_closeData( filePtr, ( B ), &( E ) );         \
00285             if( C ) mhdf_closeData( filePtr, ( D ), &( E ) ); \
00286             write_finished();                                 \
00287             assert( 0 );                                      \
00288             return error( A );                                \
00289         }                                                     \
00290     } while( false )
00291 
00292 #define debug_barrier() debug_barrier_line( __LINE__ )
00293 void WriteHDF5::debug_barrier_line( int ) {}
00294 
00295 class CheckOpenWriteHDF5Handles
00296 {
00297     int fileline;
00298     mhdf_FileHandle handle;
00299     int enter_count;
00300 
00301   public:
00302     CheckOpenWriteHDF5Handles( mhdf_FileHandle file, int line )
00303         : fileline( line ), handle( file ), enter_count( mhdf_countOpenHandles( file ) )
00304     {
00305     }
00306 
00307     ~CheckOpenWriteHDF5Handles()
00308     {
00309         int new_count = mhdf_countOpenHandles( handle );
00310         if( new_count != enter_count )
00311         {
00312             std::cout << "Leaked HDF5 object handle in function at " << __FILE__ << ":" << fileline << std::endl
00313                       << "Open at entrance: " << enter_count << std::endl
00314                       << "Open at exit:     " << new_count << std::endl;
00315         }
00316     }
00317 };
00318 
00319 MPEState WriteHDF5::topState;
00320 MPEState WriteHDF5::subState;
00321 
00322 #ifdef NDEBUG
00323 #define CHECK_OPEN_HANDLES
00324 #else
00325 #define CHECK_OPEN_HANDLES CheckOpenWriteHDF5Handles check_open_handles_( filePtr, __LINE__ )
00326 #endif
00327 
00328 bool WriteHDF5::convert_handle_tag( const EntityHandle* source, EntityHandle* dest, size_t count ) const
00329 {
00330     bool some_valid = false;
00331     for( size_t i = 0; i < count; ++i )
00332     {
00333         if( !source[i] )
00334             dest[i] = 0;
00335         else
00336         {
00337             dest[i] = idMap.find( source[i] );
00338             if( dest[i] ) some_valid = true;
00339         }
00340     }
00341 
00342     return some_valid;
00343 }
00344 
00345 bool WriteHDF5::convert_handle_tag( EntityHandle* data, size_t count ) const
00346 {
00347     assert( sizeof( EntityHandle ) == sizeof( wid_t ) );
00348     return convert_handle_tag( data, data, count );
00349 }
00350 
00351 ErrorCode WriteHDF5::assign_ids( const Range& entities, wid_t id )
00352 {
00353     Range::const_pair_iterator pi;
00354     for( pi = entities.const_pair_begin(); pi != entities.const_pair_end(); ++pi )
00355     {
00356         const EntityHandle n = pi->second - pi->first + 1;
00357         dbgOut.printf( 3, "Assigning %s %lu to %lu to file IDs [%lu,%lu]\n",
00358                        CN::EntityTypeName( TYPE_FROM_HANDLE( pi->first ) ),
00359                        (unsigned long)( ID_FROM_HANDLE( pi->first ) ),
00360                        (unsigned long)( ID_FROM_HANDLE( pi->first ) + n - 1 ), (unsigned long)id,
00361                        (unsigned long)( id + n - 1 ) );
00362         if( TYPE_FROM_HANDLE( pi->first ) == MBPOLYGON || TYPE_FROM_HANDLE( pi->first ) == MBPOLYHEDRON )
00363         {
00364             int num_vertices         = 0;
00365             const EntityHandle* conn = 0;
00366             iFace->get_connectivity( pi->first, conn, num_vertices );
00367             dbgOut.printf( 3, "  poly with %d verts/faces \n", num_vertices );
00368         }
00369         if( !idMap.insert( pi->first, id, n ).second ) return error( MB_FAILURE );
00370         id += n;
00371     }
00372 
00373     return MB_SUCCESS;
00374 }
00375 
00376 const char* WriteHDF5::ExportSet::name() const
00377 {
00378     static char buffer[128];
00379     switch( type )
00380     {
00381         case MBVERTEX:
00382             return mhdf_node_type_handle();
00383         case MBENTITYSET:
00384             return mhdf_set_type_handle();
00385         default:
00386             sprintf( buffer, "%s%d", CN::EntityTypeName( type ), num_nodes );
00387             return buffer;
00388     }
00389 }
00390 
00391 WriterIface* WriteHDF5::factory( Interface* iface )
00392 {
00393     return new WriteHDF5( iface );
00394 }
00395 
00396 WriteHDF5::WriteHDF5( Interface* iface )
00397     : bufferSize( WRITE_HDF5_BUFFER_SIZE ), dataBuffer( 0 ), iFace( iface ), writeUtil( 0 ), filePtr( 0 ),
00398       setContentsOffset( 0 ), setChildrenOffset( 0 ), setParentsOffset( 0 ), maxNumSetContents( 0 ),
00399       maxNumSetChildren( 0 ), maxNumSetParents( 0 ), writeSets( false ), writeSetContents( false ),
00400       writeSetChildren( false ), writeSetParents( false ), parallelWrite( false ), collectiveIO( false ),
00401       writeTagDense( false ), writeProp( H5P_DEFAULT ), dbgOut( "H5M", stderr ), debugTrack( false )
00402 {
00403 }
00404 
00405 ErrorCode WriteHDF5::init()
00406 {
00407     ErrorCode rval;
00408 
00409     if( writeUtil )  // init has already been called
00410         return MB_SUCCESS;
00411     /*
00412     #ifdef DEBUG
00413       H5Eset_auto(&hdf_error_handler, writeUtil); // HDF5 callback for errors
00414     #endif
00415     */
00416     // For known tag types, store the corresponding HDF5 in which
00417     // the tag data is to be written in the file.
00418     // register_known_tag_types(iFace);
00419 
00420     // Get the util interface
00421     rval = iFace->query_interface( writeUtil );
00422     CHK_MB_ERR_0( rval );
00423 
00424     idMap.clear();
00425 
00426 #if defined( H5Eget_auto_vers ) && H5Eget_auto_vers > 1
00427     herr_t err = H5Eget_auto( H5E_DEFAULT, &errorHandler.func, &errorHandler.data );
00428 #else
00429     herr_t err = H5Eget_auto( &errorHandler.func, &errorHandler.data );
00430 #endif
00431     if( err < 0 )
00432     {
00433         errorHandler.func = 0;
00434         errorHandler.data = 0;
00435     }
00436     else
00437     {
00438 #if defined( H5Eset_auto_vers ) && H5Eset_auto_vers > 1
00439         err = H5Eset_auto( H5E_DEFAULT, &handle_hdf5_error, &errorHandler );
00440 #else
00441         err = H5Eset_auto( &handle_hdf5_error, &errorHandler );
00442 #endif
00443         if( err < 0 )
00444         {
00445             errorHandler.func = 0;
00446             errorHandler.data = 0;
00447         }
00448     }
00449 
00450     if( !topState.valid() ) topState = MPEState( "WriteHDF5", "yellow" );
00451     if( !subState.valid() ) subState = MPEState( "WriteHDF5 subevent", "cyan" );
00452 
00453     return MB_SUCCESS;
00454 }
00455 
00456 ErrorCode WriteHDF5::write_finished()
00457 {
00458     // Release memory allocated in lists
00459     exportList.clear();
00460     nodeSet.range.clear();
00461     setSet.range.clear();
00462     tagList.clear();
00463     idMap.clear();
00464 
00465     HDF5ErrorHandler handler;
00466 #if defined( H5Eget_auto_vers ) && H5Eget_auto_vers > 1
00467     herr_t err = H5Eget_auto( H5E_DEFAULT, &handler.func, &handler.data );
00468 #else
00469     herr_t err = H5Eget_auto( &handler.func, &handler.data );
00470 #endif
00471     if( err >= 0 && handler.func == &handle_hdf5_error )
00472     {
00473         assert( handler.data == &errorHandler );
00474 #if defined( H5Eget_auto_vers ) && H5Eget_auto_vers > 1
00475         H5Eset_auto( H5E_DEFAULT, errorHandler.func, errorHandler.data );
00476 #else
00477         H5Eset_auto( errorHandler.func, errorHandler.data );
00478 #endif
00479     }
00480 
00481     return MB_SUCCESS;
00482 }
00483 
00484 WriteHDF5::~WriteHDF5()
00485 {
00486     if( !writeUtil )  // init() failed.
00487         return;
00488 
00489     iFace->release_interface( writeUtil );
00490 }
00491 
00492 ErrorCode WriteHDF5::write_file( const char* filename,
00493                                  bool overwrite,
00494                                  const FileOptions& opts,
00495                                  const EntityHandle* set_array,
00496                                  const int num_sets,
00497                                  const std::vector< std::string >& qa_records,
00498                                  const Tag* tag_list,
00499                                  int num_tags,
00500                                  int user_dimension )
00501 {
00502     mhdf_Status status;
00503 
00504     parallelWrite = false;
00505     collectiveIO  = false;
00506 
00507     // Enable debug output
00508     int tmpval = 0;
00509     if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) ) dbgOut.set_verbosity( tmpval );
00510 
00511     // writeTagDense = (MB_SUCCESS == opts.get_null_option("DENSE_TAGS"));
00512     writeTagDense = true;
00513 
00514     // Enable some extra checks for reads.  Note: amongst other things this
00515     // will print errors if the entire file is not read, so if doing a
00516     // partial read that is not a parallel read, this should be disabled.
00517     debugTrack = ( MB_SUCCESS == opts.get_null_option( "DEBUG_BINIO" ) );
00518 
00519     bufferSize = WRITE_HDF5_BUFFER_SIZE;
00520     int buf_size;
00521     ErrorCode rval = opts.get_int_option( "BUFFER_SIZE", buf_size );
00522     if( MB_SUCCESS == rval && buf_size >= 24 ) bufferSize = buf_size;
00523 
00524     // Allocate internal buffer to use when gathering data to write.
00525     dataBuffer = (char*)malloc( bufferSize );
00526     if( !dataBuffer ) return error( MB_MEMORY_ALLOCATION_FAILED );
00527 
00528     // Clear filePtr so we know if it is open upon failure
00529     filePtr = 0;
00530 
00531     // Do actual write.
00532     writeProp        = H5P_DEFAULT;
00533     ErrorCode result = write_file_impl( filename, overwrite, opts, set_array, num_sets, qa_records, tag_list, num_tags,
00534                                         user_dimension );
00535     // Close writeProp if it was opened
00536     if( writeProp != H5P_DEFAULT ) H5Pclose( writeProp );
00537 
00538     // Free memory buffer
00539     free( dataBuffer );
00540     dataBuffer = 0;
00541 
00542     // Close file
00543     bool created_file = false;
00544     if( filePtr )
00545     {
00546         created_file = true;
00547         mhdf_closeFile( filePtr, &status );
00548         filePtr = 0;
00549         if( mhdf_isError( &status ) )
00550         {
00551             MB_SET_ERR_CONT( mhdf_message( &status ) );
00552             if( MB_SUCCESS == result ) result = MB_FAILURE;
00553         }
00554     }
00555 
00556     // Release other resources
00557     if( MB_SUCCESS == result )
00558         result = write_finished();
00559     else
00560         write_finished();
00561 
00562     // If write failed, remove file unless KEEP option was specified
00563     if( MB_SUCCESS != result && created_file && MB_ENTITY_NOT_FOUND == opts.get_null_option( "KEEP" ) )
00564         remove( filename );
00565 
00566     return result;
00567 }
00568 
00569 ErrorCode WriteHDF5::write_file_impl( const char* filename,
00570                                       bool overwrite,
00571                                       const FileOptions& opts,
00572                                       const EntityHandle* set_array,
00573                                       const int num_sets,
00574                                       const std::vector< std::string >& qa_records,
00575                                       const Tag* tag_list,
00576                                       int num_tags,
00577                                       int user_dimension )
00578 {
00579     ErrorCode result;
00580     std::list< TagDesc >::const_iterator t_itor;
00581     std::list< ExportSet >::iterator ex_itor;
00582     EntityHandle elem_count, max_id;
00583     double times[NUM_TIMES] = { 0 };
00584 
00585     if( MB_SUCCESS != init() ) return error( MB_FAILURE );
00586 
00587     // See if we need to report times
00588     bool cputime = false;
00589     result       = opts.get_null_option( "CPUTIME" );
00590     if( MB_SUCCESS == result ) cputime = true;
00591 
00592     CpuTimer timer;
00593 
00594     dbgOut.tprint( 1, "Gathering Mesh\n" );
00595     topState.start( "gathering mesh" );
00596 
00597     // Gather mesh to export
00598     exportList.clear();
00599     if( 0 == num_sets || ( 1 == num_sets && set_array[0] == 0 ) )
00600     {
00601         result = gather_all_mesh();
00602         topState.end( result );
00603         CHK_MB_ERR_0( result );
00604     }
00605     else
00606     {
00607         std::vector< EntityHandle > passed_export_list( set_array, set_array + num_sets );
00608         result = gather_mesh_info( passed_export_list );
00609         topState.end( result );
00610         CHK_MB_ERR_0( result );
00611     }
00612 
00613     times[GATHER_TIME] = timer.time_elapsed();
00614 
00615     // if (nodeSet.range.size() == 0)
00616     //  return error(MB_ENTITY_NOT_FOUND);
00617 
00618     dbgOut.tprint( 1, "Checking ID space\n" );
00619 
00620     // Make sure ID space is sufficient
00621     elem_count = nodeSet.range.size() + setSet.range.size();
00622     for( ex_itor = exportList.begin(); ex_itor != exportList.end(); ++ex_itor )
00623         elem_count += ex_itor->range.size();
00624     max_id = (EntityHandle)1 << ( 8 * sizeof( wid_t ) - 1 );
00625     if( elem_count > max_id )
00626     {
00627         MB_SET_ERR_CONT( "ID space insufficient for mesh size" );
00628         return error( result );
00629     }
00630 
00631     dbgOut.tprint( 1, "Creating File\n" );
00632 
00633     // Figure out the dimension in which to write the mesh.
00634     int mesh_dim;
00635     result = iFace->get_dimension( mesh_dim );
00636     CHK_MB_ERR_0( result );
00637 
00638     if( user_dimension < 1 ) user_dimension = mesh_dim;
00639     user_dimension = user_dimension > mesh_dim ? mesh_dim : user_dimension;
00640 
00641     // Create the file layout, including all tables (zero-ed) and
00642     // all structure and meta information.
00643     const char* optnames[] = { "WRITE_PART", "FORMAT", 0 };
00644     int junk;
00645     parallelWrite = ( MB_SUCCESS == opts.match_option( "PARALLEL", optnames, junk ) );
00646     if( parallelWrite )
00647     {
00648         // Just store Boolean value based on string option here.
00649         // parallel_create_file will set writeProp accordingly.
00650         // collectiveIO = (MB_SUCCESS == opts.get_null_option("COLLECTIVE"));
00651         // dbgOut.printf(2, "'COLLECTIVE' option = %s\n", collectiveIO ? "YES" : "NO");
00652         // Do this all the time, as it appears to be much faster than indep in some cases
00653         collectiveIO = true;
00654         result =
00655             parallel_create_file( filename, overwrite, qa_records, opts, tag_list, num_tags, user_dimension, times );
00656     }
00657     else
00658     {
00659         result = serial_create_file( filename, overwrite, qa_records, tag_list, num_tags, user_dimension );
00660     }
00661     if( MB_SUCCESS != result ) return error( result );
00662 
00663     times[CREATE_TIME] = timer.time_elapsed();
00664 
00665     dbgOut.tprint( 1, "Writing Nodes.\n" );
00666     // Write node coordinates
00667     if( !nodeSet.range.empty() || parallelWrite )
00668     {
00669         topState.start( "writing coords" );
00670         result = write_nodes();
00671         topState.end( result );
00672         if( MB_SUCCESS != result ) return error( result );
00673     }
00674 
00675     times[COORD_TIME] = timer.time_elapsed();
00676 
00677     dbgOut.tprint( 1, "Writing connectivity.\n" );
00678 
00679     // Write element connectivity
00680     for( ex_itor = exportList.begin(); ex_itor != exportList.end(); ++ex_itor )
00681     {
00682         topState.start( "writing connectivity for ", ex_itor->name() );
00683         result = write_elems( *ex_itor );
00684         topState.end( result );
00685         if( MB_SUCCESS != result ) return error( result );
00686     }
00687     times[CONN_TIME] = timer.time_elapsed();
00688 
00689     dbgOut.tprint( 1, "Writing sets.\n" );
00690 
00691     // Write meshsets
00692     result = write_sets( times );
00693     if( MB_SUCCESS != result ) return error( result );
00694     debug_barrier();
00695 
00696     times[SET_TIME] = timer.time_elapsed();
00697     dbgOut.tprint( 1, "Writing adjacencies.\n" );
00698 
00699     // Write adjacencies
00700     // Tim says don't save node adjacencies!
00701 #ifdef MB_H5M_WRITE_NODE_ADJACENCIES
00702     result = write_adjacencies( nodeSet );
00703     if( MB_SUCCESS != result ) return error( result );
00704 #endif
00705     for( ex_itor = exportList.begin(); ex_itor != exportList.end(); ++ex_itor )
00706     {
00707         topState.start( "writing adjacencies for ", ex_itor->name() );
00708         result = write_adjacencies( *ex_itor );
00709         topState.end( result );
00710         if( MB_SUCCESS != result ) return error( result );
00711     }
00712     times[ADJ_TIME] = timer.time_elapsed();
00713 
00714     dbgOut.tprint( 1, "Writing tags.\n" );
00715 
00716     // Write tags
00717     for( t_itor = tagList.begin(); t_itor != tagList.end(); ++t_itor )
00718     {
00719         std::string name;
00720         iFace->tag_get_name( t_itor->tag_id, name );
00721         topState.start( "writing tag: ", name.c_str() );
00722         result = write_tag( *t_itor, times );
00723         topState.end( result );
00724         if( MB_SUCCESS != result ) return error( result );
00725     }
00726     times[TAG_TIME] = timer.time_elapsed();
00727 
00728     times[TOTAL_TIME] = timer.time_since_birth();
00729 
00730     if( cputime )
00731     {
00732         print_times( times );
00733     }
00734 
00735     return MB_SUCCESS;
00736 }
00737 
00738 ErrorCode WriteHDF5::initialize_mesh( const Range ranges[5] )
00739 {
00740     ErrorCode rval;
00741 
00742     if( !ranges[0].all_of_type( MBVERTEX ) ) return error( MB_FAILURE );
00743     nodeSet.range        = ranges[0];
00744     nodeSet.type         = MBVERTEX;
00745     nodeSet.num_nodes    = 1;
00746     nodeSet.max_num_ents = nodeSet.max_num_adjs = 0;
00747 
00748     if( !ranges[4].all_of_type( MBENTITYSET ) ) return error( MB_FAILURE );
00749     setSet.range        = ranges[4];
00750     setSet.type         = MBENTITYSET;
00751     setSet.num_nodes    = 0;
00752     setSet.max_num_ents = setSet.max_num_adjs = 0;
00753     maxNumSetContents = maxNumSetChildren = maxNumSetParents = 0;
00754 
00755     exportList.clear();
00756     std::vector< Range > bins( 1024 );  // Sort entities by connectivity length
00757                                         // Resize is expensive due to Range copy, so start big
00758     for( EntityType type = MBEDGE; type < MBENTITYSET; ++type )
00759     {
00760         ExportSet set;
00761         set.max_num_ents = set.max_num_adjs = 0;
00762         const int dim                       = CN::Dimension( type );
00763 
00764         // Group entities by connectivity length
00765         bins.clear();
00766         assert( dim >= 0 && dim <= 4 );
00767         std::pair< Range::const_iterator, Range::const_iterator > p = ranges[dim].equal_range( type );
00768         Range::const_iterator i                                     = p.first;
00769         while( i != p.second )
00770         {
00771             Range::const_iterator first = i;
00772             EntityHandle const* conn;
00773             int len, firstlen;
00774 
00775             // Dummy storage vector for structured mesh "get_connectivity" function
00776             std::vector< EntityHandle > storage;
00777 
00778             rval = iFace->get_connectivity( *i, conn, firstlen, false, &storage );
00779             if( MB_SUCCESS != rval ) return error( rval );
00780 
00781             for( ++i; i != p.second; ++i )
00782             {
00783                 rval = iFace->get_connectivity( *i, conn, len, false, &storage );
00784                 if( MB_SUCCESS != rval ) return error( rval );
00785 
00786                 if( len != firstlen ) break;
00787             }
00788 
00789             if( firstlen >= (int)bins.size() ) bins.resize( firstlen + 1 );
00790             bins[firstlen].merge( first, i );
00791         }
00792         // Create ExportSet for each group
00793         for( std::vector< Range >::iterator j = bins.begin(); j != bins.end(); ++j )
00794         {
00795             if( j->empty() ) continue;
00796 
00797             set.range.clear();
00798             set.type      = type;
00799             set.num_nodes = j - bins.begin();
00800             exportList.push_back( set );
00801             exportList.back().range.swap( *j );
00802         }
00803     }
00804 
00805     return MB_SUCCESS;
00806 }
00807 
00808 // Gather the mesh to be written from a list of owning meshsets.
00809 ErrorCode WriteHDF5::gather_mesh_info( const std::vector< EntityHandle >& export_sets )
00810 {
00811     ErrorCode rval;
00812 
00813     int dim;
00814     Range range;      // Temporary storage
00815     Range ranges[5];  // Lists of entities to export, grouped by dimension
00816 
00817     // Gather list of all related sets
00818     std::vector< EntityHandle > stack( export_sets );
00819     std::copy( export_sets.begin(), export_sets.end(), stack.begin() );
00820     std::vector< EntityHandle > set_children;
00821     while( !stack.empty() )
00822     {
00823         EntityHandle meshset = stack.back();
00824         stack.pop_back();
00825         ranges[4].insert( meshset );
00826 
00827         // Get contained sets
00828         range.clear();
00829         rval = iFace->get_entities_by_type( meshset, MBENTITYSET, range );
00830         CHK_MB_ERR_0( rval );
00831         for( Range::iterator ritor = range.begin(); ritor != range.end(); ++ritor )
00832         {
00833             if( ranges[4].find( *ritor ) == ranges[4].end() ) stack.push_back( *ritor );
00834         }
00835 
00836         // Get child sets
00837         set_children.clear();
00838         rval = iFace->get_child_meshsets( meshset, set_children, 1 );
00839         CHK_MB_ERR_0( rval );
00840         for( std::vector< EntityHandle >::iterator vitor = set_children.begin(); vitor != set_children.end(); ++vitor )
00841         {
00842             if( ranges[4].find( *vitor ) == ranges[4].end() ) stack.push_back( *vitor );
00843         }
00844     }
00845 
00846     // Gather list of all mesh entities from list of sets,
00847     // grouped by dimension.
00848     for( Range::iterator setitor = ranges[4].begin(); setitor != ranges[4].end(); ++setitor )
00849     {
00850         for( dim = 0; dim < 4; ++dim )
00851         {
00852             range.clear();
00853             rval = iFace->get_entities_by_dimension( *setitor, dim, range, false );
00854             CHK_MB_ERR_0( rval );
00855 
00856             ranges[dim].merge( range );
00857         }
00858     }
00859 
00860     // For each list of elements, append adjacent children and
00861     // nodes to lists.
00862     for( dim = 3; dim > 0; --dim )
00863     {
00864         for( int cdim = 1; cdim < dim; ++cdim )
00865         {
00866             range.clear();
00867             rval = iFace->get_adjacencies( ranges[dim], cdim, false, range );
00868             CHK_MB_ERR_0( rval );
00869             ranges[cdim].merge( range );
00870         }
00871         range.clear();
00872         rval = writeUtil->gather_nodes_from_elements( ranges[dim], 0, range );
00873         CHK_MB_ERR_0( rval );
00874         ranges[0].merge( range );
00875     }
00876 
00877     return initialize_mesh( ranges );
00878 }
00879 
00880 // Gather all the mesh and related information to be written.
00881 ErrorCode WriteHDF5::gather_all_mesh()
00882 {
00883     ErrorCode rval;
00884     Range ranges[5];
00885 
00886     rval = iFace->get_entities_by_type( 0, MBVERTEX, ranges[0] );
00887     if( MB_SUCCESS != rval ) return error( rval );
00888 
00889     rval = iFace->get_entities_by_dimension( 0, 1, ranges[1] );
00890     if( MB_SUCCESS != rval ) return error( rval );
00891 
00892     rval = iFace->get_entities_by_dimension( 0, 2, ranges[2] );
00893     if( MB_SUCCESS != rval ) return error( rval );
00894 
00895     rval = iFace->get_entities_by_dimension( 0, 3, ranges[3] );
00896     if( MB_SUCCESS != rval ) return error( rval );
00897 
00898     rval = iFace->get_entities_by_type( 0, MBENTITYSET, ranges[4] );
00899     if( MB_SUCCESS != rval ) return error( rval );
00900 
00901     return initialize_mesh( ranges );
00902 }
00903 
00904 ErrorCode WriteHDF5::write_nodes()
00905 {
00906     mhdf_Status status;
00907     int dim, mesh_dim;
00908     ErrorCode rval;
00909     hid_t node_table;
00910     long first_id, num_nodes;
00911 
00912     if( !nodeSet.total_num_ents ) return MB_SUCCESS;  // No nodes!
00913 
00914     CHECK_OPEN_HANDLES;
00915 
00916     rval = iFace->get_dimension( mesh_dim );
00917     CHK_MB_ERR_0( rval );
00918 
00919     debug_barrier();
00920     dbgOut.print( 3, "Opening Node Coords\n" );
00921     node_table = mhdf_openNodeCoords( filePtr, &num_nodes, &dim, &first_id, &status );
00922     CHK_MHDF_ERR_0( status );
00923     IODebugTrack track( debugTrack, "nodes", num_nodes );
00924 
00925     double* buffer = (double*)dataBuffer;
00926 #ifdef BLOCKED_COORD_IO
00927     int chunk_size = bufferSize / sizeof( double );
00928 #else
00929     int chunk_size = bufferSize / ( 3 * sizeof( double ) );
00930 #endif
00931 
00932     long remaining  = nodeSet.range.size();
00933     long num_writes = ( remaining + chunk_size - 1 ) / chunk_size;
00934     if( nodeSet.max_num_ents )
00935     {
00936         assert( nodeSet.max_num_ents >= remaining );
00937         num_writes = ( nodeSet.max_num_ents + chunk_size - 1 ) / chunk_size;
00938     }
00939     long remaining_writes = num_writes;
00940 
00941     long offset                = nodeSet.offset;
00942     Range::const_iterator iter = nodeSet.range.begin();
00943     dbgOut.printf( 3, "Writing %ld nodes in %ld blocks of %d\n", remaining, ( remaining + chunk_size - 1 ) / chunk_size,
00944                    chunk_size );
00945     while( remaining )
00946     {
00947         (void)VALGRIND_MAKE_MEM_UNDEFINED( dataBuffer, bufferSize );
00948         long count = chunk_size < remaining ? chunk_size : remaining;
00949         remaining -= count;
00950         Range::const_iterator end = iter;
00951         end += count;
00952 
00953 #ifdef BLOCKED_COORD_IO
00954         for( int d = 0; d < dim; d++ )
00955         {
00956             if( d < mesh_dim )
00957             {
00958                 rval = writeUtil->get_node_coords( d, iter, end, count, buffer );
00959                 CHK_MB_ERR_1( rval, node_table, status );
00960             }
00961             else
00962                 memset( buffer, 0, count * sizeof( double ) );
00963 
00964             dbgOut.printf( 3, " writing %c node chunk %ld of %ld, %ld values at %ld\n", (char)( 'X' + d ),
00965                            num_writes - remaining_writes + 1, num_writes, count, offset );
00966             mhdf_writeNodeCoordWithOpt( node_table, offset, count, d, buffer, writeProp, &status );
00967             CHK_MHDF_ERR_1( status, node_table );
00968         }
00969 #else
00970         rval = writeUtil->get_node_coords( -1, iter, end, 3 * count, buffer );
00971         CHK_MB_ERR_1( rval, node_table, status );
00972         dbgOut.printf( 3, " writing node chunk %ld of %ld, %ld values at %ld\n", num_writes - remaining_writes + 1,
00973                        num_writes, count, offset );
00974         mhdf_writeNodeCoordsWithOpt( node_table, offset, count, buffer, writeProp, &status );
00975         CHK_MHDF_ERR_1( status, node_table );
00976 #endif
00977         track.record_io( offset, count );
00978 
00979         iter = end;
00980         offset += count;
00981         --remaining_writes;
00982     }
00983 
00984     // Do empty writes if necessary for parallel collective IO
00985     if( collectiveIO )
00986     {
00987         while( remaining_writes-- )
00988         {
00989             assert( writeProp != H5P_DEFAULT );
00990 #ifdef BLOCKED_COORD_IO
00991             for( int d = 0; d < dim; ++d )
00992             {
00993                 dbgOut.printf( 3, " writing (empty) %c node chunk %ld of %ld.\n", (char)( 'X' + d ),
00994                                num_writes - remaining_writes, num_writes );
00995                 mhdf_writeNodeCoordWithOpt( node_table, offset, 0, d, 0, writeProp, &status );
00996                 CHK_MHDF_ERR_1( status, node_table );
00997             }
00998 #else
00999             dbgOut.printf( 3, " writing (empty) node chunk %ld of %ld.\n", num_writes - remaining_writes, num_writes );
01000             mhdf_writeNodeCoordsWithOpt( node_table, offset, 0, 0, writeProp, &status );
01001             CHK_MHDF_ERR_1( status, node_table );
01002 #endif
01003         }
01004     }
01005 
01006     mhdf_closeData( filePtr, node_table, &status );
01007     CHK_MHDF_ERR_0( status );
01008 
01009     track.all_reduce();
01010     return MB_SUCCESS;
01011 }
01012 
01013 ErrorCode WriteHDF5::write_elems( ExportSet& elems )
01014 {
01015     mhdf_Status status;
01016     ErrorCode rval;
01017     long first_id;
01018     int nodes_per_elem;
01019     long table_size;
01020 
01021     CHECK_OPEN_HANDLES;
01022 
01023     debug_barrier();
01024     dbgOut.printf( 2, "Writing %lu elements of type %s%d\n", (unsigned long)elems.range.size(),
01025                    CN::EntityTypeName( elems.type ), elems.num_nodes );
01026     dbgOut.print( 3, "Writing elements", elems.range );
01027 
01028     hid_t elem_table = mhdf_openConnectivity( filePtr, elems.name(), &nodes_per_elem, &table_size, &first_id, &status );
01029     CHK_MHDF_ERR_0( status );
01030     IODebugTrack track( debugTrack, elems.name() && strlen( elems.name() ) ? elems.name() : "<ANONYMOUS ELEM SET?>",
01031                         table_size );
01032 
01033     assert( (unsigned long)first_id <= elems.first_id );
01034     assert( (unsigned long)table_size >= elems.offset + elems.range.size() );
01035 
01036     EntityHandle* buffer = (EntityHandle*)dataBuffer;
01037     int chunk_size       = bufferSize / ( elems.num_nodes * sizeof( wid_t ) );
01038     long offset          = elems.offset;
01039     long remaining       = elems.range.size();
01040     long num_writes      = ( remaining + chunk_size - 1 ) / chunk_size;
01041     if( elems.max_num_ents )
01042     {
01043         assert( elems.max_num_ents >= remaining );
01044         num_writes = ( elems.max_num_ents + chunk_size - 1 ) / chunk_size;
01045     }
01046     long remaining_writes = num_writes;
01047     Range::iterator iter  = elems.range.begin();
01048 
01049     while( remaining )
01050     {
01051         (void)VALGRIND_MAKE_MEM_UNDEFINED( dataBuffer, bufferSize );
01052         long count = chunk_size < remaining ? chunk_size : remaining;
01053         remaining -= count;
01054 
01055         Range::iterator next = iter;
01056         next += count;
01057         rval = writeUtil->get_element_connect( iter, next, elems.num_nodes, count * elems.num_nodes, buffer );
01058         CHK_MB_ERR_1( rval, elem_table, status );
01059         iter = next;
01060 
01061         for( long i = 0; i < count * nodes_per_elem; ++i )
01062         {
01063             buffer[i] = idMap.find( buffer[i] );
01064             if( 0 == buffer[i] )
01065             {
01066                 MB_SET_ERR_CONT( "Invalid " << elems.name() << " element connectivity. Write Aborted" );
01067                 mhdf_closeData( filePtr, elem_table, &status );
01068                 return error( MB_FAILURE );
01069             }
01070         }
01071 
01072         dbgOut.printf( 3, " writing node connectivity %ld of %ld, %ld values at %ld\n",
01073                        num_writes - remaining_writes + 1, num_writes, count, offset );
01074         track.record_io( offset, count );
01075         mhdf_writeConnectivityWithOpt( elem_table, offset, count, id_type, buffer, writeProp, &status );
01076         CHK_MHDF_ERR_1( status, elem_table );
01077 
01078         offset += count;
01079         --remaining_writes;
01080     }
01081 
01082     // Do empty writes if necessary for parallel collective IO
01083     if( collectiveIO )
01084     {
01085         while( remaining_writes-- )
01086         {
01087             assert( writeProp != H5P_DEFAULT );
01088             dbgOut.printf( 3, " writing (empty) connectivity chunk %ld of %ld.\n", num_writes - remaining_writes + 1,
01089                            num_writes );
01090             mhdf_writeConnectivityWithOpt( elem_table, offset, 0, id_type, 0, writeProp, &status );
01091             CHK_MHDF_ERR_1( status, elem_table );
01092         }
01093     }
01094 
01095     mhdf_closeData( filePtr, elem_table, &status );
01096     CHK_MHDF_ERR_0( status );
01097 
01098     track.all_reduce();
01099     return MB_SUCCESS;
01100 }
01101 
01102 ErrorCode WriteHDF5::get_set_info( EntityHandle set,
01103                                    long& num_entities,
01104                                    long& num_children,
01105                                    long& num_parents,
01106                                    unsigned long& flags )
01107 {
01108     ErrorCode rval;
01109     int i;
01110     unsigned int u;
01111 
01112     rval = iFace->get_number_entities_by_handle( set, i, false );
01113     CHK_MB_ERR_0( rval );
01114     num_entities = i;
01115 
01116     rval = iFace->num_child_meshsets( set, &i );
01117     CHK_MB_ERR_0( rval );
01118     num_children = i;
01119 
01120     rval = iFace->num_parent_meshsets( set, &i );
01121     CHK_MB_ERR_0( rval );
01122     num_parents = i;
01123 
01124     rval = iFace->get_meshset_options( set, u );
01125     CHK_MB_ERR_0( rval );
01126     flags = u;
01127 
01128     return MB_SUCCESS;
01129 }
01130 
01131 ErrorCode WriteHDF5::write_set_data( const WriteUtilIface::EntityListType which_data,
01132                                      const hid_t handle,
01133                                      IODebugTrack& track,
01134                                      Range* ranged,
01135                                      Range* null_stripped,
01136                                      std::vector< long >* set_sizes )
01137 {
01138     // ranged must be non-null for CONTENTS and null for anything else
01139     assert( ( which_data == WriteUtilIface::CONTENTS ) == ( 0 != ranged ) );
01140     ErrorCode rval;
01141     mhdf_Status status;
01142 
01143     debug_barrier();
01144 
01145     // Function pointer type used to write set data
01146     void ( *write_func )( hid_t, long, long, hid_t, const void*, hid_t, mhdf_Status* );
01147     long max_vals;  // Max over all procs of number of values to write to data set
01148     long offset;    // Offset in HDF5 dataset at which to write next block of data
01149     switch( which_data )
01150     {
01151         case WriteUtilIface::CONTENTS:
01152             assert( ranged != 0 && null_stripped != 0 && set_sizes != 0 );
01153             write_func = &mhdf_writeSetDataWithOpt;
01154             max_vals   = maxNumSetContents;
01155             offset     = setContentsOffset;
01156             dbgOut.print( 2, "Writing set contents\n" );
01157             break;
01158         case WriteUtilIface::CHILDREN:
01159             assert( !ranged && !null_stripped && !set_sizes );
01160             write_func = &mhdf_writeSetParentsChildrenWithOpt;
01161             max_vals   = maxNumSetChildren;
01162             offset     = setChildrenOffset;
01163             dbgOut.print( 2, "Writing set child lists\n" );
01164             break;
01165         case WriteUtilIface::PARENTS:
01166             assert( !ranged && !null_stripped && !set_sizes );
01167             write_func = &mhdf_writeSetParentsChildrenWithOpt;
01168             max_vals   = maxNumSetParents;
01169             offset     = setParentsOffset;
01170             dbgOut.print( 2, "Writing set parent lists\n" );
01171             break;
01172         default:
01173             assert( false );
01174             return MB_FAILURE;
01175     }
01176     // assert(max_vals > 0); // Should have skipped this function otherwise
01177 
01178     // buffer to use for IO
01179     wid_t* buffer = reinterpret_cast< wid_t* >( dataBuffer );
01180     // number of handles that will fit in the buffer
01181     const size_t buffer_size = bufferSize / sizeof( EntityHandle );
01182     // the total number of write calls that must be made, including no-ops for collective io
01183     const size_t num_total_writes = ( max_vals + buffer_size - 1 ) / buffer_size;
01184 
01185     std::vector< SpecialSetData >::iterator si = specialSets.begin();
01186 
01187     std::vector< wid_t > remaining;         // data left over from prev iteration because it didn't fit in buffer
01188     size_t remaining_offset           = 0;  // avoid erasing from front of 'remaining'
01189     const EntityHandle* remaining_ptr = 0;  // remaining for non-ranged data
01190     size_t remaining_count            = 0;
01191     const wid_t* special_rem_ptr      = 0;
01192     Range::const_iterator i           = setSet.range.begin(), j, rhint, nshint;
01193     if( ranged ) rhint = ranged->begin();
01194     if( null_stripped ) nshint = null_stripped->begin();
01195     for( size_t w = 0; w < num_total_writes; ++w )
01196     {
01197         if( i == setSet.range.end() && !remaining.empty() && !remaining_ptr )
01198         {
01199             // If here, then we've written everything but we need to
01200             // make more write calls because we're doing collective IO
01201             // in parallel
01202             ( *write_func )( handle, 0, 0, id_type, 0, writeProp, &status );
01203             CHK_MHDF_ERR_0( status );
01204             continue;
01205         }
01206 
01207         // If we had some left-over data from a range-compacted set
01208         // from the last iteration, add it to the buffer now
01209         size_t count = 0;
01210         if( !remaining.empty() )
01211         {
01212             count = remaining.size() - remaining_offset;
01213             if( count > buffer_size )
01214             {
01215                 memcpy( buffer, &remaining[remaining_offset], buffer_size * sizeof( wid_t ) );
01216                 count = buffer_size;
01217                 remaining_offset += buffer_size;
01218             }
01219             else
01220             {
01221                 memcpy( buffer, &remaining[remaining_offset], count * sizeof( wid_t ) );
01222                 remaining_offset = 0;
01223                 remaining.clear();
01224             }
01225         }
01226         // If we had some left-over data from a non-range-compacted set
01227         // from the last iteration, add it to the buffer now
01228         else if( remaining_ptr )
01229         {
01230             if( remaining_count > buffer_size )
01231             {
01232                 rval = vector_to_id_list( remaining_ptr, buffer, buffer_size );
01233                 CHK_MB_ERR_0( rval );
01234                 count = buffer_size;
01235                 remaining_ptr += count;
01236                 remaining_count -= count;
01237             }
01238             else
01239             {
01240                 rval = vector_to_id_list( remaining_ptr, buffer, remaining_count );
01241                 CHK_MB_ERR_0( rval );
01242                 count           = remaining_count;
01243                 remaining_ptr   = 0;
01244                 remaining_count = 0;
01245             }
01246         }
01247         // If we had some left-over data from a "special" (i.e. parallel shared)
01248         // set.
01249         else if( special_rem_ptr )
01250         {
01251             if( remaining_count > buffer_size )
01252             {
01253                 memcpy( buffer, special_rem_ptr, buffer_size * sizeof( wid_t ) );
01254                 count = buffer_size;
01255                 special_rem_ptr += count;
01256                 remaining_count -= count;
01257             }
01258             else
01259             {
01260                 memcpy( buffer, special_rem_ptr, remaining_count * sizeof( wid_t ) );
01261                 count           = remaining_count;
01262                 special_rem_ptr = 0;
01263                 remaining_count = 0;
01264             }
01265         }
01266 
01267         // While there is both space remaining in the buffer and
01268         // more sets to write, append more set data to buffer.
01269 
01270         while( count < buffer_size && i != setSet.range.end() )
01271         {
01272             // Special case for "special" (i.e. parallel shared) sets:
01273             // we already have the data in a vector, just copy it.
01274             if( si != specialSets.end() && si->setHandle == *i )
01275             {
01276                 std::vector< wid_t >& list = ( which_data == WriteUtilIface::CONTENTS )  ? si->contentIds
01277                                              : ( which_data == WriteUtilIface::PARENTS ) ? si->parentIds
01278                                                                                          : si->childIds;
01279                 size_t append              = list.size();
01280                 if( count + list.size() > buffer_size )
01281                 {
01282                     append          = buffer_size - count;
01283                     special_rem_ptr = &list[append];
01284                     remaining_count = list.size() - append;
01285                 }
01286                 memcpy( buffer + count, &list[0], append * sizeof( wid_t ) );
01287                 ++i;
01288                 ++si;
01289                 count += append;
01290                 continue;
01291             }
01292 
01293             j = i;
01294             ++i;
01295             const EntityHandle* ptr;
01296             int len;
01297             unsigned char flags;
01298             rval = writeUtil->get_entity_list_pointers( j, i, &ptr, which_data, &len, &flags );
01299             if( MB_SUCCESS != rval ) return rval;
01300             if( which_data == WriteUtilIface::CONTENTS && !( flags & MESHSET_ORDERED ) )
01301             {
01302                 bool compacted;
01303                 remaining.clear();
01304                 if( len == 0 )
01305                     compacted = false;
01306                 else
01307                 {
01308                     assert( !( len % 2 ) );
01309                     rval = range_to_blocked_list( ptr, len / 2, remaining, compacted );
01310                     if( MB_SUCCESS != rval ) return rval;
01311                 }
01312                 if( compacted )
01313                 {
01314                     rhint = ranged->insert( rhint, *j );
01315                     set_sizes->push_back( remaining.size() );
01316                 }
01317                 else if( remaining.size() != (unsigned)len )
01318                 {
01319                     nshint = null_stripped->insert( nshint, *j );
01320                     set_sizes->push_back( remaining.size() );
01321                 }
01322 
01323                 if( count + remaining.size() <= buffer_size )
01324                 {
01325                     if( !remaining.empty() )
01326                         memcpy( buffer + count, &remaining[0], sizeof( wid_t ) * remaining.size() );
01327                     count += remaining.size();
01328                     remaining.clear();
01329                     remaining_offset = 0;
01330                 }
01331                 else
01332                 {
01333                     remaining_offset = buffer_size - count;
01334                     memcpy( buffer + count, &remaining[0], sizeof( wid_t ) * remaining_offset );
01335                     count += remaining_offset;
01336                 }
01337             }
01338             else
01339             {
01340                 if( count + len > buffer_size )
01341                 {
01342                     size_t append   = buffer_size - count;
01343                     remaining_ptr   = ptr + append;
01344                     remaining_count = len - append;
01345                     len             = append;
01346                 }
01347 
01348                 rval = vector_to_id_list( ptr, buffer + count, len );
01349                 count += len;
01350             }
01351         }
01352 
01353         // Write the buffer.
01354         ( *write_func )( handle, offset, count, id_type, buffer, writeProp, &status );
01355         CHK_MHDF_ERR_0( status );
01356         track.record_io( offset, count );
01357         offset += count;
01358     }
01359 
01360     return MB_SUCCESS;
01361 }
01362 
01363 ErrorCode WriteHDF5::write_sets( double* times )
01364 {
01365     mhdf_Status status;
01366     ErrorCode rval;
01367     long first_id, size;
01368     hid_t table;
01369     CpuTimer timer;
01370 
01371     CHECK_OPEN_HANDLES;
01372     /* If no sets, just return success */
01373     if( !writeSets ) return MB_SUCCESS;
01374 
01375     debug_barrier();
01376     dbgOut.printf( 2, "Writing %lu non-shared sets\n", (unsigned long)setSet.range.size() );
01377     dbgOut.print( 3, "Non-shared sets", setSet.range );
01378 
01379     /* Write set parents */
01380     if( writeSetParents )
01381     {
01382         topState.start( "writing parent lists for local sets" );
01383         table = mhdf_openSetParents( filePtr, &size, &status );
01384         CHK_MHDF_ERR_0( status );
01385         IODebugTrack track( debugTrack, "SetParents", size );
01386 
01387         rval = write_set_data( WriteUtilIface::PARENTS, table, track );
01388         topState.end( rval );
01389         CHK_MB_ERR_1( rval, table, status );
01390 
01391         mhdf_closeData( filePtr, table, &status );
01392         CHK_MHDF_ERR_0( status );
01393 
01394         times[SET_PARENT] = timer.time_elapsed();
01395         track.all_reduce();
01396     }
01397 
01398     /* Write set children */
01399     if( writeSetChildren )
01400     {
01401         topState.start( "writing child lists for local sets" );
01402         table = mhdf_openSetChildren( filePtr, &size, &status );
01403         CHK_MHDF_ERR_0( status );
01404         IODebugTrack track( debugTrack, "SetChildren", size );
01405 
01406         rval = write_set_data( WriteUtilIface::CHILDREN, table, track );
01407         topState.end( rval );
01408         CHK_MB_ERR_1( rval, table, status );
01409 
01410         mhdf_closeData( filePtr, table, &status );
01411         CHK_MHDF_ERR_0( status );
01412 
01413         times[SET_CHILD] = timer.time_elapsed();
01414         track.all_reduce();
01415     }
01416 
01417     /* Write set contents */
01418     Range ranged_sets, null_stripped_sets;
01419     std::vector< long > set_sizes;
01420     if( writeSetContents )
01421     {
01422         topState.start( "writing content lists for local sets" );
01423         table = mhdf_openSetData( filePtr, &size, &status );
01424         CHK_MHDF_ERR_0( status );
01425         IODebugTrack track( debugTrack, "SetContents", size );
01426 
01427         rval = write_set_data( WriteUtilIface::CONTENTS, table, track, &ranged_sets, &null_stripped_sets, &set_sizes );
01428         topState.end( rval );
01429         CHK_MB_ERR_1( rval, table, status );
01430 
01431         mhdf_closeData( filePtr, table, &status );
01432         CHK_MHDF_ERR_0( status );
01433 
01434         times[SET_CONTENT] = timer.time_elapsed();
01435         track.all_reduce();
01436     }
01437     assert( ranged_sets.size() + null_stripped_sets.size() == set_sizes.size() );
01438 
01439     /* Write set description table */
01440 
01441     debug_barrier();
01442     topState.start( "writing descriptions of local sets" );
01443     dbgOut.printf( 2, "Writing %lu non-shared sets\n", (unsigned long)setSet.range.size() );
01444     dbgOut.print( 3, "Non-shared sets", setSet.range );
01445 
01446     /* Open the table */
01447     table = mhdf_openSetMeta( filePtr, &size, &first_id, &status );
01448     CHK_MHDF_ERR_0( status );
01449     IODebugTrack track_meta( debugTrack, "SetMeta", size );
01450 
01451     /* Some debug stuff */
01452     debug_barrier();
01453     dbgOut.printf( 2, "Writing %lu non-shared sets\n", (unsigned long)setSet.range.size() );
01454     dbgOut.print( 3, "Non-shared sets", setSet.range );
01455 
01456     /* Counts and buffers and such */
01457     mhdf_index_t* const buffer     = reinterpret_cast< mhdf_index_t* >( dataBuffer );
01458     const size_t buffer_size       = bufferSize / ( 4 * sizeof( mhdf_index_t ) );
01459     const size_t num_local_writes  = ( setSet.range.size() + buffer_size - 1 ) / buffer_size;
01460     const size_t num_global_writes = ( setSet.max_num_ents + buffer_size - 1 ) / buffer_size;
01461     assert( num_local_writes <= num_global_writes );
01462     assert( num_global_writes > 0 );
01463 
01464     /* data about sets for which number of handles written is
01465      * not the same as the number of handles in the set
01466      * (range-compacted or null handles stripped out)
01467      */
01468     Range::const_iterator i                       = setSet.range.begin();
01469     Range::const_iterator r                       = ranged_sets.begin();
01470     Range::const_iterator s                       = null_stripped_sets.begin();
01471     std::vector< mhdf_index_t >::const_iterator n = set_sizes.begin();
01472     assert( ranged_sets.size() + null_stripped_sets.size() == set_sizes.size() );
01473 
01474     /* We write the end index for each list, rather than the count */
01475     mhdf_index_t prev_contents_end = setContentsOffset - 1;
01476     mhdf_index_t prev_children_end = setChildrenOffset - 1;
01477     mhdf_index_t prev_parents_end  = setParentsOffset - 1;
01478 
01479     /* While there is more data to write */
01480     size_t offset                                    = setSet.offset;
01481     std::vector< SpecialSetData >::const_iterator si = specialSets.begin();
01482     for( size_t w = 0; w < num_local_writes; ++w )
01483     {
01484         // Get a buffer full of data
01485         size_t count = 0;
01486         while( count < buffer_size && i != setSet.range.end() )
01487         {
01488             // Get set properties
01489             long num_ent, num_child, num_parent;
01490             unsigned long flags;
01491             if( si != specialSets.end() && si->setHandle == *i )
01492             {
01493                 flags      = si->setFlags;
01494                 num_ent    = si->contentIds.size();
01495                 num_child  = si->childIds.size();
01496                 num_parent = si->parentIds.size();
01497                 ++si;
01498                 if( r != ranged_sets.end() && *i == *r )
01499                 {
01500                     assert( flags & mhdf_SET_RANGE_BIT );
01501                     ++r;
01502                     ++n;
01503                 }
01504                 else if( s != null_stripped_sets.end() && *i == *s )
01505                 {
01506                     ++s;
01507                     ++n;
01508                 }
01509             }
01510             else
01511             {
01512                 assert( si == specialSets.end() || si->setHandle > *i );
01513 
01514                 // Get set properties
01515                 rval = get_set_info( *i, num_ent, num_child, num_parent, flags );
01516                 CHK_MB_ERR_1( rval, table, status );
01517 
01518                 // Check if size is something other than num handles in set
01519                 if( r != ranged_sets.end() && *i == *r )
01520                 {
01521                     num_ent = *n;
01522                     ++r;
01523                     ++n;
01524                     flags |= mhdf_SET_RANGE_BIT;
01525                 }
01526                 else if( s != null_stripped_sets.end() && *i == *s )
01527                 {
01528                     num_ent = *n;
01529                     ++s;
01530                     ++n;
01531                 }
01532             }
01533 
01534             // Put data in buffer
01535             mhdf_index_t* local = buffer + 4 * count;
01536             prev_contents_end += num_ent;
01537             prev_children_end += num_child;
01538             prev_parents_end += num_parent;
01539             local[0] = prev_contents_end;
01540             local[1] = prev_children_end;
01541             local[2] = prev_parents_end;
01542             local[3] = flags;
01543 
01544             // Iterate
01545             ++count;
01546             ++i;
01547         }
01548 
01549         // Write the data
01550         mhdf_writeSetMetaWithOpt( table, offset, count, MHDF_INDEX_TYPE, buffer, writeProp, &status );
01551         CHK_MHDF_ERR_1( status, table );
01552         track_meta.record_io( offset, count );
01553         offset += count;
01554     }
01555     assert( r == ranged_sets.end() );
01556     assert( s == null_stripped_sets.end() );
01557     assert( n == set_sizes.end() );
01558 
01559     /* If doing parallel write with collective IO, do null write
01560      * calls because other procs aren't done yet and write calls
01561      * are collective */
01562     for( size_t w = num_local_writes; w != num_global_writes; ++w )
01563     {
01564         mhdf_writeSetMetaWithOpt( table, 0, 0, MHDF_INDEX_TYPE, 0, writeProp, &status );
01565         CHK_MHDF_ERR_1( status, table );
01566     }
01567 
01568     topState.end();
01569     mhdf_closeData( filePtr, table, &status );
01570     CHK_MHDF_ERR_0( status );
01571 
01572     times[SET_META] = timer.time_elapsed();
01573     track_meta.all_reduce();
01574 
01575     return MB_SUCCESS;
01576 }
01577 
01578 template < class HandleRangeIter >
01579 inline size_t count_num_handles( HandleRangeIter iter, HandleRangeIter end )
01580 {
01581     size_t result = 0;
01582     for( ; iter != end; ++iter )
01583         result += iter->second - iter->first + 1;
01584 
01585     return result;
01586 }
01587 
01588 template < class HandleRangeIter >
01589 inline ErrorCode range_to_id_list_templ( HandleRangeIter begin,
01590                                          HandleRangeIter end,
01591                                          const RangeMap< EntityHandle, WriteHDF5::wid_t >& idMap,
01592                                          WriteHDF5::wid_t* array )
01593 {
01594     ErrorCode rval                                          = MB_SUCCESS;
01595     RangeMap< EntityHandle, WriteHDF5::wid_t >::iterator ri = idMap.begin();
01596     WriteHDF5::wid_t* i                                     = array;
01597     for( HandleRangeIter pi = begin; pi != end; ++pi )
01598     {
01599         EntityHandle h = pi->first;
01600         while( h <= pi->second )
01601         {
01602             ri = idMap.lower_bound( ri, idMap.end(), h );
01603             if( ri == idMap.end() || ri->begin > h )
01604             {
01605                 rval = MB_ENTITY_NOT_FOUND;
01606                 *i   = 0;
01607                 ++i;
01608                 ++h;
01609                 continue;
01610             }
01611 
01612             // compute the last available value of the found target range (ri iterator)
01613             WriteHDF5::wid_t last_valid_input_value_in_current_map_range = ri->begin + ri->count - 1;
01614             // limit the number of steps we do on top of h so we do not overflow the output range
01615             // span
01616             WriteHDF5::wid_t step_until = std::min( last_valid_input_value_in_current_map_range, pi->second );
01617             WriteHDF5::wid_t n          = step_until - h + 1;
01618             assert( n > 0 );  // We must at least step 1
01619 
01620             WriteHDF5::wid_t id = ri->value + ( h - ri->begin );
01621             for( WriteHDF5::wid_t j = 0; j < n; ++i, ++j )
01622                 *i = id + j;
01623             h += n;
01624         }
01625     }
01626 
01627     assert( i == array + count_num_handles( begin, end ) );
01628     return rval;
01629 }
01630 
01631 template < class HandleRangeIter >
01632 inline ErrorCode range_to_blocked_list_templ( HandleRangeIter begin,
01633                                               HandleRangeIter end,
01634                                               const RangeMap< EntityHandle, WriteHDF5::wid_t >& idMap,
01635                                               std::vector< WriteHDF5::wid_t >& output_id_list,
01636                                               bool& ranged_list )
01637 {
01638     output_id_list.clear();
01639     if( begin == end )
01640     {
01641         ranged_list = false;
01642         return MB_SUCCESS;
01643     }
01644 
01645     // First try ranged format, but give up if we reach the
01646     // non-range format size.
01647     RangeMap< EntityHandle, WriteHDF5::wid_t >::iterator ri = idMap.begin();
01648 
01649     const size_t num_handles = count_num_handles( begin, end );
01650     // If we end up with more than this many range blocks, then
01651     // we're better off just writing the set as a simple list
01652     size_t pairs_remaining = num_handles / 2;
01653     for( HandleRangeIter pi = begin; pi != end; ++pi )
01654     {
01655         EntityHandle h                              = pi->first;
01656         WriteHDF5::wid_t local_mapped_from_subrange = 0;
01657         while( h <= pi->second )
01658         {
01659             ri = idMap.lower_bound( ri, idMap.end(), h );
01660             if( ri == idMap.end() || ri->begin > h )
01661             {
01662                 ++h;
01663                 continue;
01664             }
01665 
01666             WriteHDF5::wid_t n = pi->second - pi->first + 1 - local_mapped_from_subrange;
01667             if( n > ri->count ) n = ri->count;
01668 
01669             WriteHDF5::wid_t id = ri->value + ( h - ri->begin );
01670             // see if we can go to the end of the range
01671             if( id + n > ri->value + ri->count )  // we have to reduce n, because we cannot go over next subrange
01672             {
01673                 if( ri->value + ri->count - id > 0 ) n = ri->value + ri->count - id;
01674             }
01675 
01676             // See if we can append it to the previous range
01677             if( !output_id_list.empty() && output_id_list[output_id_list.size() - 2] + output_id_list.back() == id )
01678             {
01679                 output_id_list.back() += n;
01680             }
01681 
01682             // If we ran out of space, (or set is empty) just do list format
01683             else if( !pairs_remaining )
01684             {
01685                 ranged_list = false;
01686                 output_id_list.resize( num_handles );
01687                 range_to_id_list_templ( begin, end, idMap, &output_id_list[0] );
01688                 output_id_list.erase( std::remove( output_id_list.begin(), output_id_list.end(), 0u ),
01689                                       output_id_list.end() );
01690                 return MB_SUCCESS;
01691             }
01692 
01693             //
01694             else
01695             {
01696                 --pairs_remaining;
01697                 output_id_list.push_back( id );
01698                 output_id_list.push_back( n );
01699             }
01700             local_mapped_from_subrange += n;  // we already mapped so many
01701             h += n;
01702         }
01703     }
01704 
01705     ranged_list = true;
01706     return MB_SUCCESS;
01707 }
01708 
01709 ErrorCode WriteHDF5::range_to_blocked_list( const Range& input_range,
01710                                             std::vector< wid_t >& output_id_list,
01711                                             bool& ranged_list )
01712 {
01713     return range_to_blocked_list_templ( input_range.const_pair_begin(), input_range.const_pair_end(), idMap,
01714                                         output_id_list, ranged_list );
01715 }
01716 
01717 ErrorCode WriteHDF5::range_to_blocked_list( const EntityHandle* array,
01718                                             size_t num_input_ranges,
01719                                             std::vector< wid_t >& output_id_list,
01720                                             bool& ranged_list )
01721 {
01722     // We assume this in the cast on the following line
01723     typedef std::pair< EntityHandle, EntityHandle > mtype;
01724     assert( sizeof( mtype ) == 2 * sizeof( EntityHandle ) );
01725     const mtype* arr = reinterpret_cast< const mtype* >( array );
01726     return range_to_blocked_list_templ( arr, arr + num_input_ranges, idMap, output_id_list, ranged_list );
01727 }
01728 
01729 ErrorCode WriteHDF5::range_to_id_list( const Range& range, wid_t* array )
01730 {
01731     return range_to_id_list_templ( range.const_pair_begin(), range.const_pair_end(), idMap, array );
01732 }
01733 
01734 ErrorCode WriteHDF5::vector_to_id_list( const EntityHandle* input,
01735                                         size_t input_len,
01736                                         wid_t* output,
01737                                         size_t& output_len,
01738                                         bool remove_zeros )
01739 {
01740     const EntityHandle* i_iter = input;
01741     const EntityHandle* i_end  = input + input_len;
01742     wid_t* o_iter              = output;
01743     for( ; i_iter != i_end; ++i_iter )
01744     {
01745         wid_t id = idMap.find( *i_iter );
01746         if( !remove_zeros || id != 0 )
01747         {
01748             *o_iter = id;
01749             ++o_iter;
01750         }
01751     }
01752     output_len = o_iter - output;
01753 
01754     return MB_SUCCESS;
01755 }
01756 
01757 ErrorCode WriteHDF5::vector_to_id_list( const std::vector< EntityHandle >& input,
01758                                         std::vector< wid_t >& output,
01759                                         bool remove_zeros )
01760 {
01761     output.resize( input.size() );
01762     size_t output_size = 0;
01763     ErrorCode rval     = vector_to_id_list( &input[0], input.size(), &output[0], output_size, remove_zeros );
01764     output.resize( output_size );
01765     return rval;
01766 }
01767 
01768 ErrorCode WriteHDF5::vector_to_id_list( const EntityHandle* input, wid_t* output, size_t count )
01769 {
01770     size_t output_len;
01771     return vector_to_id_list( input, count, output, output_len, false );
01772 }
01773 
01774 inline ErrorCode WriteHDF5::get_adjacencies( EntityHandle entity, std::vector< wid_t >& adj )
01775 {
01776     const EntityHandle* adj_array;
01777     int num_adj;
01778     ErrorCode rval = writeUtil->get_adjacencies( entity, adj_array, num_adj );
01779     if( MB_SUCCESS != rval ) return error( rval );
01780 
01781     size_t j = 0;
01782     adj.resize( num_adj );
01783     for( int i = 0; i < num_adj; ++i )
01784         if( wid_t id = idMap.find( adj_array[i] ) ) adj[j++] = id;
01785     adj.resize( j );
01786 
01787     return MB_SUCCESS;
01788 }
01789 
01790 ErrorCode WriteHDF5::write_adjacencies( const ExportSet& elements )
01791 {
01792     ErrorCode rval;
01793     mhdf_Status status;
01794     Range::const_iterator iter;
01795     const Range::const_iterator end = elements.range.end();
01796     std::vector< wid_t > adj_list;
01797 
01798     CHECK_OPEN_HANDLES;
01799 
01800     debug_barrier();
01801 
01802     /* Count Adjacencies */
01803     long count = 0;
01804     // for (iter = elements.range.begin(); iter != end; ++iter) {
01805     //  adj_list.clear();
01806     //  rval = get_adjacencies(*iter, adj_list);CHK_MB_ERR_0(rval);
01807     //
01808     //  if (adj_list.size() > 0)
01809     //    count += adj_list.size() + 2;
01810     //}
01811 
01812     // if (count == 0)
01813     //  return MB_SUCCESS;
01814 
01815     long offset = elements.adj_offset;
01816     if( elements.max_num_adjs == 0 ) return MB_SUCCESS;
01817 
01818     /* Create data list */
01819     hid_t table = mhdf_openAdjacency( filePtr, elements.name(), &count, &status );
01820     CHK_MHDF_ERR_0( status );
01821     IODebugTrack track( debugTrack, "Adjacencies", count );
01822 
01823     /* Write data */
01824     wid_t* buffer   = (wid_t*)dataBuffer;
01825     long chunk_size = bufferSize / sizeof( wid_t );
01826     long num_writes = ( elements.max_num_adjs + chunk_size - 1 ) / chunk_size;
01827     (void)VALGRIND_MAKE_MEM_UNDEFINED( dataBuffer, bufferSize );
01828     count = 0;
01829     for( iter = elements.range.begin(); iter != end; ++iter )
01830     {
01831         adj_list.clear();
01832         rval = get_adjacencies( *iter, adj_list );
01833         CHK_MB_ERR_1( rval, table, status );
01834         if( adj_list.size() == 0 ) continue;
01835 
01836         // If buffer is full, flush it
01837         if( count + adj_list.size() + 2 > (unsigned long)chunk_size )
01838         {
01839             dbgOut.print( 3, " writing adjacency chunk.\n" );
01840             track.record_io( offset, count );
01841             mhdf_writeAdjacencyWithOpt( table, offset, count, id_type, buffer, writeProp, &status );
01842             CHK_MHDF_ERR_1( status, table );
01843             (void)VALGRIND_MAKE_MEM_UNDEFINED( dataBuffer, bufferSize );
01844 
01845             offset += count;
01846             count = 0;
01847         }
01848 
01849         buffer[count++] = idMap.find( *iter );
01850         buffer[count++] = adj_list.size();
01851 
01852         assert( adj_list.size() + 2 < (unsigned long)chunk_size );
01853         memcpy( buffer + count, &adj_list[0], adj_list.size() * sizeof( wid_t ) );
01854         count += adj_list.size();
01855     }
01856 
01857     if( count )
01858     {
01859         dbgOut.print( 2, " writing final adjacency chunk.\n" );
01860         mhdf_writeAdjacencyWithOpt( table, offset, count, id_type, buffer, writeProp, &status );
01861         CHK_MHDF_ERR_1( status, table );
01862 
01863         offset += count;
01864         count = 0;
01865         --num_writes;
01866     }
01867 
01868     // Do empty writes if necessary for parallel collective IO
01869     if( collectiveIO )
01870     {
01871         while( num_writes > 0 )
01872         {
01873             --num_writes;
01874             assert( writeProp != H5P_DEFAULT );
01875             dbgOut.print( 2, " writing empty adjacency chunk.\n" );
01876             mhdf_writeAdjacencyWithOpt( table, offset, 0, id_type, 0, writeProp, &status );
01877             CHK_MHDF_ERR_1( status, table );
01878         }
01879     }
01880 
01881     mhdf_closeData( filePtr, table, &status );
01882     CHK_MHDF_ERR_0( status );
01883 
01884     track.all_reduce();
01885     return MB_SUCCESS;
01886 }
01887 
01888 ErrorCode WriteHDF5::write_tag( const TagDesc& tag_data, double* times )
01889 {
01890     std::string name;
01891     ErrorCode rval = iFace->tag_get_name( tag_data.tag_id, name );
01892     if( MB_SUCCESS != rval ) return error( rval );
01893 
01894     CHECK_OPEN_HANDLES;
01895     debug_barrier();
01896     dbgOut.tprintf( 1, "Writing tag: \"%s\"\n", name.c_str() );
01897 
01898     int moab_size, elem_size, array_len;
01899     DataType moab_type;
01900     mhdf_TagDataType mhdf_type;
01901     hid_t hdf5_type;
01902     rval = get_tag_size( tag_data.tag_id, moab_type, moab_size, elem_size, array_len, mhdf_type, hdf5_type );
01903     if( MB_SUCCESS != rval ) return error( rval );
01904 
01905     CpuTimer timer;
01906     if( array_len == MB_VARIABLE_LENGTH && tag_data.write_sparse )
01907     {
01908         dbgOut.printf( 2, "Writing sparse data for var-len tag: \"%s\"\n", name.c_str() );
01909         rval = write_var_len_tag( tag_data, name, moab_type, hdf5_type, elem_size );
01910         times[VARLEN_TAG_TIME] += timer.time_elapsed();
01911     }
01912     else
01913     {
01914         int data_len = elem_size;
01915         if( moab_type != MB_TYPE_BIT ) data_len *= array_len;
01916         if( tag_data.write_sparse )
01917         {
01918             dbgOut.printf( 2, "Writing sparse data for tag: \"%s\"\n", name.c_str() );
01919             rval = write_sparse_tag( tag_data, name, moab_type, hdf5_type, data_len );
01920             times[SPARSE_TAG_TIME] += timer.time_elapsed();
01921         }
01922         for( size_t i = 0; MB_SUCCESS == rval && i < tag_data.dense_list.size(); ++i )
01923         {
01924             const ExportSet* set = find( tag_data.dense_list[i] );
01925             assert( 0 != set );
01926             debug_barrier();
01927             dbgOut.printf( 2, "Writing dense data for tag: \"%s\" on group \"%s\"\n", name.c_str(), set->name() );
01928             subState.start( "writing dense data for tag: ", ( name + ":" + set->name() ).c_str() );
01929             rval = write_dense_tag( tag_data, *set, name, moab_type, hdf5_type, data_len );
01930             subState.end( rval );
01931         }
01932         times[DENSE_TAG_TIME] += timer.time_elapsed();
01933     }
01934 
01935     H5Tclose( hdf5_type );
01936     return MB_SUCCESS == rval ? MB_SUCCESS : error( rval );
01937 }
01938 
01939 ErrorCode WriteHDF5::write_sparse_ids( const TagDesc& tag_data,
01940                                        const Range& range,
01941                                        hid_t id_table,
01942                                        size_t table_size,
01943                                        const char* name )
01944 {
01945     ErrorCode rval;
01946     mhdf_Status status;
01947 
01948     CHECK_OPEN_HANDLES;
01949 
01950     std::string tname( name ? name : "<UNKNOWN TAG?>" );
01951     tname += " - Ids";
01952     IODebugTrack track( debugTrack, tname, table_size );
01953 
01954     // Set up data buffer for writing IDs
01955     size_t chunk_size = bufferSize / sizeof( wid_t );
01956     wid_t* id_buffer  = (wid_t*)dataBuffer;
01957 
01958     // Write IDs of tagged entities.
01959     long remaining  = range.size();
01960     long offset     = tag_data.sparse_offset;
01961     long num_writes = ( remaining + chunk_size - 1 ) / chunk_size;
01962     if( tag_data.max_num_ents )
01963     {
01964         assert( tag_data.max_num_ents >= (unsigned long)remaining );
01965         num_writes = ( tag_data.max_num_ents + chunk_size - 1 ) / chunk_size;
01966     }
01967     Range::const_iterator iter = range.begin();
01968     while( remaining )
01969     {
01970         (void)VALGRIND_MAKE_MEM_UNDEFINED( dataBuffer, bufferSize );
01971 
01972         // Write "chunk_size" blocks of data
01973         long count = (unsigned long)remaining > chunk_size ? chunk_size : remaining;
01974         remaining -= count;
01975         Range::const_iterator stop = iter;
01976         stop += count;
01977         Range tmp;
01978         ;
01979         tmp.merge( iter, stop );
01980         iter = stop;
01981         assert( tmp.size() == (unsigned)count );
01982 
01983         rval = range_to_id_list( tmp, id_buffer );
01984         CHK_MB_ERR_0( rval );
01985 
01986         // Write the data
01987         dbgOut.print( 3, " writing sparse tag entity chunk.\n" );
01988         track.record_io( offset, count );
01989         mhdf_writeSparseTagEntitiesWithOpt( id_table, offset, count, id_type, id_buffer, writeProp, &status );
01990         CHK_MHDF_ERR_0( status );
01991 
01992         offset += count;
01993         --num_writes;
01994     }  // while (remaining)
01995 
01996     // Do empty writes if necessary for parallel collective IO
01997     if( collectiveIO )
01998     {
01999         while( num_writes-- )
02000         {
02001             assert( writeProp != H5P_DEFAULT );
02002             dbgOut.print( 3, " writing empty sparse tag entity chunk.\n" );
02003             mhdf_writeSparseTagEntitiesWithOpt( id_table, offset, 0, id_type, 0, writeProp, &status );
02004             CHK_MHDF_ERR_0( status );
02005         }
02006     }
02007 
02008     track.all_reduce();
02009     return MB_SUCCESS;
02010 }
02011 
02012 ErrorCode WriteHDF5::write_sparse_tag( const TagDesc& tag_data,
02013                                        const std::string& name,
02014                                        DataType mb_data_type,
02015                                        hid_t value_type,
02016                                        int value_type_size )
02017 {
02018     ErrorCode rval;
02019     mhdf_Status status;
02020     hid_t tables[3];
02021     long table_size, data_size;
02022 
02023     CHECK_OPEN_HANDLES;
02024 
02025     // Get entities for which to write tag values
02026     Range range;
02027     rval = get_sparse_tagged_entities( tag_data, range );
02028 
02029     // Open tables to write info
02030     mhdf_openSparseTagData( filePtr, name.c_str(), &table_size, &data_size, tables, &status );
02031     CHK_MHDF_ERR_0( status );
02032     assert( range.size() + tag_data.sparse_offset <= (unsigned long)table_size );
02033     // Fixed-length tag
02034     assert( table_size == data_size );
02035 
02036     // Write IDs for tagged entities
02037     subState.start( "writing sparse ids for tag: ", name.c_str() );
02038     rval = write_sparse_ids( tag_data, range, tables[0], table_size, name.c_str() );
02039     subState.end( rval );
02040     CHK_MB_ERR_2( rval, tables, status );
02041     mhdf_closeData( filePtr, tables[0], &status );
02042     CHK_MHDF_ERR_1( status, tables[1] );
02043 
02044     // Set up data buffer for writing tag values
02045     IODebugTrack track( debugTrack, name + " Data", data_size );
02046     subState.start( "writing sparse values for tag: ", name.c_str() );
02047     rval = write_tag_values( tag_data.tag_id, tables[1], tag_data.sparse_offset, range, mb_data_type, value_type,
02048                              value_type_size, tag_data.max_num_ents, track );
02049     subState.end( rval );
02050     CHK_MB_ERR_0( rval );
02051     mhdf_closeData( filePtr, tables[1], &status );
02052     CHK_MHDF_ERR_0( status );
02053 
02054     track.all_reduce();
02055     return MB_SUCCESS;
02056 }
02057 
02058 ErrorCode WriteHDF5::write_var_len_indices( const TagDesc& tag_data,
02059                                             const Range& range,
02060                                             hid_t idx_table,
02061                                             size_t table_size,
02062                                             int /*type_size*/,
02063                                             const char* name )
02064 {
02065     ErrorCode rval;
02066     mhdf_Status status;
02067 
02068     CHECK_OPEN_HANDLES;
02069 
02070     std::string tname( name ? name : "<UNKNOWN TAG?>" );
02071     tname += " - End Indices";
02072     IODebugTrack track( debugTrack, tname, table_size );
02073 
02074     // Set up data buffer for writing indices
02075     size_t chunk_size        = bufferSize / ( std::max( sizeof( void* ), sizeof( long ) ) + sizeof( int ) );
02076     mhdf_index_t* idx_buffer = (mhdf_index_t*)dataBuffer;
02077     const void** junk        = (const void**)dataBuffer;
02078     int* size_buffer         = (int*)( dataBuffer + chunk_size * std::max( sizeof( void* ), sizeof( mhdf_index_t ) ) );
02079 
02080     // Write IDs of tagged entities.
02081     long data_offset  = tag_data.var_data_offset - 1;  // Offset at which to write data buffer
02082     size_t remaining  = range.size();
02083     size_t offset     = tag_data.sparse_offset;
02084     size_t num_writes = ( remaining + chunk_size - 1 ) / chunk_size;
02085     if( tag_data.max_num_ents )
02086     {
02087         assert( tag_data.max_num_ents >= (unsigned long)remaining );
02088         num_writes = ( tag_data.max_num_ents + chunk_size - 1 ) / chunk_size;
02089     }
02090     Range::const_iterator iter = range.begin();
02091     while( remaining )
02092     {
02093         (void)VALGRIND_MAKE_MEM_UNDEFINED( dataBuffer, bufferSize );
02094 
02095         // Write "chunk_size" blocks of data
02096         size_t count = remaining > chunk_size ? chunk_size : remaining;
02097         remaining -= count;
02098         Range::const_iterator stop = iter;
02099         stop += count;
02100         Range tmp;
02101         tmp.merge( iter, stop );
02102         iter = stop;
02103         assert( tmp.size() == (unsigned)count );
02104 
02105         rval = iFace->tag_get_by_ptr( tag_data.tag_id, tmp, junk, size_buffer );
02106         CHK_MB_ERR_0( rval );
02107 
02108         // Calculate end indices
02109         dbgOut.print( 3, " writing var-len tag offset chunk.\n" );
02110         track.record_io( offset, count );
02111         for( size_t i = 0; i < count; ++i )
02112         {
02113             data_offset += size_buffer[i];
02114             idx_buffer[i] = data_offset;
02115         }
02116 
02117         // Write
02118         mhdf_writeSparseTagIndicesWithOpt( idx_table, offset, count, MHDF_INDEX_TYPE, idx_buffer, writeProp, &status );
02119         CHK_MHDF_ERR_0( status );
02120 
02121         offset += count;
02122         --num_writes;
02123     }  // while (remaining)
02124 
02125     // Do empty writes if necessary for parallel collective IO
02126     if( collectiveIO )
02127     {
02128         while( num_writes-- )
02129         {
02130             assert( writeProp != H5P_DEFAULT );
02131             dbgOut.print( 3, " writing empty sparse tag entity chunk.\n" );
02132             mhdf_writeSparseTagIndicesWithOpt( idx_table, offset, 0, id_type, 0, writeProp, &status );
02133             CHK_MHDF_ERR_0( status );
02134         }
02135     }
02136 
02137     track.all_reduce();
02138     return MB_SUCCESS;
02139 }
02140 
02141 ErrorCode WriteHDF5::write_var_len_data( const TagDesc& tag_data,
02142                                          const Range& range,
02143                                          hid_t table,
02144                                          size_t table_size,
02145                                          bool handle_tag,
02146                                          hid_t hdf_type,
02147                                          int type_size,
02148                                          const char* name )
02149 {
02150     ErrorCode rval;
02151     mhdf_Status status;
02152 
02153     CHECK_OPEN_HANDLES;
02154     assert( !handle_tag || sizeof( EntityHandle ) == type_size );
02155 
02156     std::string tname( name ? name : "<UNKNOWN TAG?>" );
02157     tname += " - Values";
02158     IODebugTrack track( debugTrack, tname, table_size );
02159 
02160     const size_t buffer_size = bufferSize / type_size;
02161 
02162     size_t num_writes = ( table_size + buffer_size - 1 ) / buffer_size;
02163     if( collectiveIO )
02164     {
02165         assert( tag_data.max_num_vals > 0 );
02166         num_writes = ( tag_data.max_num_vals + buffer_size - 1 ) / buffer_size;
02167     }
02168 
02169     unsigned char* buffer      = (unsigned char*)dataBuffer;
02170     const void* prev_data      = 0;  // Data left over from prev iteration
02171     size_t prev_len            = 0;
02172     Range::const_iterator iter = range.begin();
02173     long offset                = tag_data.var_data_offset;
02174     while( prev_data || iter != range.end() )
02175     {
02176         size_t count = 0;
02177         if( prev_data )
02178         {
02179             size_t len;
02180             const void* ptr = prev_data;
02181             if( prev_len <= buffer_size )
02182             {
02183                 len       = prev_len;
02184                 prev_data = 0;
02185                 prev_len  = 0;
02186             }
02187             else
02188             {
02189                 len       = buffer_size;
02190                 prev_data = ( (const char*)prev_data ) + buffer_size * type_size;
02191                 prev_len -= buffer_size;
02192             }
02193 
02194             if( handle_tag )
02195                 convert_handle_tag( (const EntityHandle*)ptr, (EntityHandle*)buffer, len );
02196             else
02197                 memcpy( buffer, ptr, len * type_size );
02198             count = len;
02199         }
02200 
02201         for( ; count < buffer_size && iter != range.end(); ++iter )
02202         {
02203             int len;
02204             const void* ptr;
02205             rval = iFace->tag_get_by_ptr( tag_data.tag_id, &*iter, 1, &ptr, &len );
02206             CHK_MB_ERR_0( rval );
02207             if( len + count > buffer_size )
02208             {
02209                 prev_len  = len + count - buffer_size;
02210                 len       = buffer_size - count;
02211                 prev_data = ( (const char*)ptr ) + len * type_size;
02212             }
02213 
02214             if( handle_tag )
02215                 convert_handle_tag( (const EntityHandle*)ptr, ( (EntityHandle*)buffer ) + count, len );
02216             else
02217                 memcpy( buffer + count * type_size, ptr, len * type_size );
02218             count += len;
02219         }
02220 
02221         track.record_io( offset, count );
02222         mhdf_writeTagValuesWithOpt( table, offset, count, hdf_type, buffer, writeProp, &status );
02223         offset += count;
02224         CHK_MHDF_ERR_0( status );
02225         --num_writes;
02226     }
02227 
02228     // Do empty writes if necessary for parallel collective IO
02229     if( collectiveIO )
02230     {
02231         while( num_writes-- )
02232         {
02233             assert( writeProp != H5P_DEFAULT );
02234             dbgOut.print( 3, " writing empty var-len tag data chunk.\n" );
02235             mhdf_writeTagValuesWithOpt( table, 0, 0, hdf_type, 0, writeProp, &status );
02236             CHK_MHDF_ERR_0( status );
02237         }
02238     }
02239 
02240     track.all_reduce();
02241     return MB_SUCCESS;
02242 }
02243 
02244 ErrorCode WriteHDF5::write_var_len_tag( const TagDesc& tag_data,
02245                                         const std::string& name,
02246                                         DataType mb_data_type,
02247                                         hid_t hdf_type,
02248                                         int type_size )
02249 {
02250     ErrorCode rval;
02251     mhdf_Status status;
02252     hid_t tables[3];
02253     long table_size;
02254     long data_table_size;
02255 
02256     CHECK_OPEN_HANDLES;
02257 
02258     // Get entities for which to write tag values
02259     Range range;
02260     rval = get_sparse_tagged_entities( tag_data, range );
02261 
02262     // Open tables to write info
02263     mhdf_openSparseTagData( filePtr, name.c_str(), &table_size, &data_table_size, tables, &status );
02264     CHK_MHDF_ERR_0( status );
02265     assert( range.size() + tag_data.sparse_offset <= (unsigned long)table_size );
02266 
02267     // Write IDs for tagged entities
02268     subState.start( "writing ids for var-len tag: ", name.c_str() );
02269     rval = write_sparse_ids( tag_data, range, tables[0], table_size, name.c_str() );
02270     subState.end( rval );
02271     CHK_MB_ERR_2( rval, tables, status );
02272     mhdf_closeData( filePtr, tables[0], &status );
02273     CHK_MHDF_ERR_2( status, tables + 1 );
02274 
02275     // Write offsets for tagged entities
02276     subState.start( "writing indices for var-len tag: ", name.c_str() );
02277     rval = write_var_len_indices( tag_data, range, tables[2], table_size, type_size, name.c_str() );
02278     subState.end( rval );
02279     CHK_MB_ERR_1( rval, tables[1], status );
02280     mhdf_closeData( filePtr, tables[2], &status );
02281     CHK_MHDF_ERR_1( status, tables[1] );
02282 
02283     // Write the actual tag data
02284     subState.start( "writing values for var-len tag: ", name.c_str() );
02285     rval = write_var_len_data( tag_data, range, tables[1], data_table_size, mb_data_type == MB_TYPE_HANDLE, hdf_type,
02286                                type_size, name.c_str() );
02287     subState.end( rval );
02288     CHK_MB_ERR_0( rval );
02289     mhdf_closeData( filePtr, tables[1], &status );
02290     CHK_MHDF_ERR_0( status );
02291 
02292     return MB_SUCCESS;
02293 }
02294 
02295 ErrorCode WriteHDF5::write_dense_tag( const TagDesc& tag_data,
02296                                       const ExportSet& elem_data,
02297                                       const std::string& name,
02298                                       DataType mb_data_type,
02299                                       hid_t value_type,
02300                                       int value_type_size )
02301 {
02302     CHECK_OPEN_HANDLES;
02303 
02304     // Open tables to write info
02305     mhdf_Status status;
02306     long table_size;
02307     hid_t table = mhdf_openDenseTagData( filePtr, name.c_str(), elem_data.name(), &table_size, &status );
02308     CHK_MHDF_ERR_0( status );
02309     assert( elem_data.range.size() + elem_data.offset <= (unsigned long)table_size );
02310 
02311     IODebugTrack track( debugTrack, name + " " + elem_data.name() + " Data", table_size );
02312     ErrorCode rval = write_tag_values( tag_data.tag_id, table, elem_data.offset, elem_data.range, mb_data_type,
02313                                        value_type, value_type_size, elem_data.max_num_ents, track );
02314     CHK_MB_ERR_0( rval );
02315     mhdf_closeData( filePtr, table, &status );
02316     CHK_MHDF_ERR_0( status );
02317 
02318     return MB_SUCCESS;
02319 }
02320 
02321 ErrorCode WriteHDF5::write_tag_values( Tag tag_id,
02322                                        hid_t data_table,
02323                                        unsigned long offset_in,
02324                                        const Range& range_in,
02325                                        DataType mb_data_type,
02326                                        hid_t value_type,
02327                                        int value_type_size,
02328                                        unsigned long max_num_ents,
02329                                        IODebugTrack& track )
02330 {
02331     mhdf_Status status;
02332 
02333     CHECK_OPEN_HANDLES;
02334 
02335     // Set up data buffer for writing tag values
02336     size_t chunk_size = bufferSize / value_type_size;
02337     assert( chunk_size > 0 );
02338     char* tag_buffer = (char*)dataBuffer;
02339 
02340     // Write the tag values
02341     size_t remaining           = range_in.size();
02342     size_t offset              = offset_in;
02343     Range::const_iterator iter = range_in.begin();
02344     long num_writes            = ( remaining + chunk_size - 1 ) / chunk_size;
02345     if( max_num_ents )
02346     {
02347         assert( max_num_ents >= remaining );
02348         num_writes = ( max_num_ents + chunk_size - 1 ) / chunk_size;
02349     }
02350     while( remaining )
02351     {
02352         (void)VALGRIND_MAKE_MEM_UNDEFINED( dataBuffer, bufferSize );
02353 
02354         // Write "chunk_size" blocks of data
02355         long count = (unsigned long)remaining > chunk_size ? chunk_size : remaining;
02356         remaining -= count;
02357         memset( tag_buffer, 0, count * value_type_size );
02358         Range::const_iterator stop = iter;
02359         stop += count;
02360         Range range;
02361         range.merge( iter, stop );
02362         iter = stop;
02363         assert( range.size() == (unsigned)count );
02364 
02365         ErrorCode rval = iFace->tag_get_data( tag_id, range, tag_buffer );
02366         CHK_MB_ERR_0( rval );
02367 
02368         // Convert EntityHandles to file ids
02369         if( mb_data_type == MB_TYPE_HANDLE )
02370             convert_handle_tag( reinterpret_cast< EntityHandle* >( tag_buffer ),
02371                                 count * value_type_size / sizeof( EntityHandle ) );
02372 
02373         // Write the data
02374         dbgOut.print( 2, " writing tag value chunk.\n" );
02375         track.record_io( offset, count );
02376         assert( value_type > 0 );
02377         mhdf_writeTagValuesWithOpt( data_table, offset, count, value_type, tag_buffer, writeProp, &status );
02378         CHK_MHDF_ERR_0( status );
02379 
02380         offset += count;
02381         --num_writes;
02382     }  // while (remaining)
02383 
02384     // Do empty writes if necessary for parallel collective IO
02385     if( collectiveIO )
02386     {
02387         while( num_writes-- )
02388         {
02389             assert( writeProp != H5P_DEFAULT );
02390             dbgOut.print( 2, " writing empty tag value chunk.\n" );
02391             assert( value_type > 0 );
02392             mhdf_writeTagValuesWithOpt( data_table, offset, 0, value_type, 0, writeProp, &status );
02393             CHK_MHDF_ERR_0( status );
02394         }
02395     }
02396 
02397     track.all_reduce();
02398     return MB_SUCCESS;
02399 }
02400 
02401 ErrorCode WriteHDF5::write_qa( const std::vector< std::string >& list )
02402 {
02403     const char* app  = "MOAB";
02404     const char* vers = MOAB_VERSION;
02405     char date_str[64];
02406     char time_str[64];
02407 
02408     CHECK_OPEN_HANDLES;
02409 
02410     std::vector< const char* > strs( list.size() ? list.size() : 4 );
02411     if( list.size() == 0 )
02412     {
02413         time_t t = time( NULL );
02414         tm* lt   = localtime( &t );
02415 #ifdef WIN32
02416         strftime( date_str, sizeof( date_str ), "%m/%d/%y", lt );  // VS 2008 does not support %D
02417         strftime( time_str, sizeof( time_str ), "%H:%M:%S", lt );  // VS 2008 does not support %T
02418 #else
02419         strftime( date_str, sizeof( date_str ), "%D", lt );
02420         strftime( time_str, sizeof( time_str ), "%T", lt );
02421 #endif
02422 
02423         strs[0] = app;
02424         strs[1] = vers;
02425         strs[2] = date_str;
02426         strs[3] = time_str;
02427     }
02428     else
02429     {
02430         for( unsigned int i = 0; i < list.size(); ++i )
02431             strs[i] = list[i].c_str();
02432     }
02433 
02434     mhdf_Status status;
02435     dbgOut.print( 2, " writing QA history.\n" );
02436     mhdf_writeHistory( filePtr, &strs[0], strs.size(), &status );
02437     CHK_MHDF_ERR_0( status );
02438 
02439     return MB_SUCCESS;
02440 }
02441 
02442 /*
02443 ErrorCode WriteHDF5::register_known_tag_types(Interface* iface)
02444 {
02445   hid_t int4, double16;
02446   hsize_t dim[1];
02447   int error = 0;
02448   ErrorCode rval;
02449 
02450   dim[0] = 4;
02451   int4 = H5Tarray_create(H5T_NATIVE_INT, 1, dim, NULL);
02452 
02453   dim[0] = 16;
02454   double16 = H5Tarray_create(H5T_NATIVE_DOUBLE, 1, dim, NULL);
02455 
02456   if (int4 < 0 || double16 < 0)
02457     error = 1;
02458 
02459   struct { const char* name; hid_t type; } list[] = {
02460     { GLOBAL_ID_TAG_NAME, H5T_NATIVE_INT } ,
02461     { MATERIAL_SET_TAG_NAME, H5T_NATIVE_INT },
02462     { DIRICHLET_SET_TAG_NAME, H5T_NATIVE_INT },
02463     { NEUMANN_SET_TAG_NAME, H5T_NATIVE_INT },
02464     { HAS_MID_NODES_TAG_NAME, int4 },
02465     { GEOM_DIMENSION_TAG_NAME, H5T_NATIVE_INT },
02466     { MESH_TRANSFORM_TAG_NAME, double16 },
02467     { 0, 0 } };
02468 
02469   for (int i = 0; list[i].name; ++i) {
02470     if (list[i].type < 1) {
02471       ++error;
02472       continue;
02473     }
02474 
02475     Tag handle;
02476 
02477     std::string name("__hdf5_tag_type_");
02478     name += list[i].name;
02479 
02480     rval = iface->tag_get_handle(name.c_str(), handle);
02481     if (MB_TAG_NOT_FOUND == rval) {
02482       rval = iface->tag_create(name.c_str(), sizeof(hid_t), MB_TAG_SPARSE, handle, NULL);
02483       if (MB_SUCCESS != rval) {
02484         ++error;
02485         continue;
02486       }
02487 
02488       hid_t copy_id = H5Tcopy(list[i].type);
02489       const EntityHandle mesh = 0;
02490       rval = iface->tag_set_data(handle, &mesh, 1, &copy_id);
02491       if (MB_SUCCESS != rval) {
02492         ++error;
02493         continue;
02494       }
02495     }
02496   }
02497 
02498   H5Tclose(int4);
02499   H5Tclose(double16);
02500   return error ? MB_FAILURE : MB_SUCCESS;
02501 }
02502 */
02503 
02504 ErrorCode WriteHDF5::gather_tags( const Tag* user_tag_list, int num_tags )
02505 {
02506     ErrorCode result;
02507     std::vector< Tag > tag_list;
02508     std::vector< Tag >::iterator t_itor;
02509     Range range;
02510 
02511     // Get list of Tags to write
02512     result = writeUtil->get_tag_list( tag_list, user_tag_list, num_tags );
02513     CHK_MB_ERR_0( result );
02514 
02515     // Get list of tags
02516     for( t_itor = tag_list.begin(); t_itor != tag_list.end(); ++t_itor )
02517     {
02518         // Add tag to export list
02519         TagDesc tag_data;
02520         tag_data.write_sparse    = false;
02521         tag_data.tag_id          = *t_itor;
02522         tag_data.sparse_offset   = 0;
02523         tag_data.var_data_offset = 0;
02524         tag_data.max_num_ents    = 0;
02525         tag_data.max_num_vals    = 0;
02526         tagList.push_back( tag_data );
02527     }
02528 
02529     return MB_SUCCESS;
02530 }
02531 
02532 // If we support parallel, then this function will have been
02533 // overridden with an alternate version in WriteHDF5Parallel
02534 // that supports parallel I/O.  If we're here
02535 // then MOAB was not built with support for parallel HDF5 I/O.
02536 ErrorCode WriteHDF5::parallel_create_file( const char* /* filename */,
02537                                            bool /* overwrite */,
02538                                            const std::vector< std::string >& /* qa_records */,
02539                                            const FileOptions& /* opts */,
02540                                            const Tag* /* tag_list */,
02541                                            int /* num_tags */,
02542                                            int /* dimension */,
02543                                            double* /* times */ )
02544 {
02545     MB_SET_ERR( MB_NOT_IMPLEMENTED, "WriteHDF5 does not support parallel writing" );
02546 }
02547 
02548 ErrorCode WriteHDF5::serial_create_file( const char* filename,
02549                                          bool overwrite,
02550                                          const std::vector< std::string >& qa_records,
02551                                          const Tag* user_tag_list,
02552                                          int num_user_tags,
02553                                          int dimension )
02554 {
02555     long first_id;
02556     mhdf_Status status;
02557     hid_t handle;
02558     std::list< ExportSet >::iterator ex_itor;
02559     ErrorCode rval;
02560 
02561     topState.start( "creating file" );
02562 
02563     const char* type_names[MBMAXTYPE];
02564     memset( type_names, 0, MBMAXTYPE * sizeof( char* ) );
02565     for( EntityType i = MBEDGE; i < MBENTITYSET; ++i )
02566         type_names[i] = CN::EntityTypeName( i );
02567 
02568     // Create the file
02569     filePtr = mhdf_createFile( filename, overwrite, type_names, MBMAXTYPE, id_type, &status );
02570     CHK_MHDF_ERR_0( status );
02571     assert( !!filePtr );
02572 
02573     rval = write_qa( qa_records );
02574     CHK_MB_ERR_0( rval );
02575 
02576     // Create node table
02577     if( nodeSet.range.size() )
02578     {
02579         nodeSet.total_num_ents = nodeSet.range.size();
02580         handle = mhdf_createNodeCoords( filePtr, dimension, nodeSet.total_num_ents, &first_id, &status );
02581         CHK_MHDF_ERR_0( status );
02582         mhdf_closeData( filePtr, handle, &status );
02583         CHK_MHDF_ERR_0( status );
02584         nodeSet.first_id = (wid_t)first_id;
02585         rval             = assign_ids( nodeSet.range, nodeSet.first_id );
02586         CHK_MB_ERR_0( rval );
02587     }
02588     else
02589     {
02590         nodeSet.first_id = std::numeric_limits< wid_t >::max();
02591     }
02592     nodeSet.offset = 0;
02593 
02594     // Create element tables
02595     for( ex_itor = exportList.begin(); ex_itor != exportList.end(); ++ex_itor )
02596     {
02597         ex_itor->total_num_ents = ex_itor->range.size();
02598         rval                    = create_elem_table( *ex_itor, ex_itor->total_num_ents, first_id );
02599         CHK_MB_ERR_0( rval );
02600 
02601         ex_itor->first_id = (wid_t)first_id;
02602         ex_itor->offset   = 0;
02603         rval              = assign_ids( ex_itor->range, ex_itor->first_id );
02604         CHK_MB_ERR_0( rval );
02605     }
02606     // Create set tables
02607     writeSets = !setSet.range.empty();
02608     if( writeSets )
02609     {
02610         long contents_len, children_len, parents_len;
02611 
02612         setSet.total_num_ents = setSet.range.size();
02613         setSet.max_num_ents   = setSet.total_num_ents;
02614         rval                  = create_set_meta( setSet.total_num_ents, first_id );
02615         CHK_MB_ERR_0( rval );
02616 
02617         setSet.first_id = (wid_t)first_id;
02618         rval            = assign_ids( setSet.range, setSet.first_id );
02619         CHK_MB_ERR_0( rval );
02620 
02621         rval = count_set_size( setSet.range, contents_len, children_len, parents_len );
02622         CHK_MB_ERR_0( rval );
02623 
02624         rval = create_set_tables( contents_len, children_len, parents_len );
02625         CHK_MB_ERR_0( rval );
02626 
02627         setSet.offset     = 0;
02628         setContentsOffset = 0;
02629         setChildrenOffset = 0;
02630         setParentsOffset  = 0;
02631         writeSetContents  = !!contents_len;
02632         writeSetChildren  = !!children_len;
02633         writeSetParents   = !!parents_len;
02634 
02635         maxNumSetContents = contents_len;
02636         maxNumSetChildren = children_len;
02637         maxNumSetParents  = parents_len;
02638     }  // if (!setSet.range.empty())
02639 
02640     // Create adjacency table after set table, because sets do not have yet an id
02641     // some entities are adjacent to sets (exodus?)
02642     // Create node adjacency table
02643     wid_t num_adjacencies;
02644 #ifdef MB_H5M_WRITE_NODE_ADJACENCIES
02645     rval = count_adjacencies( nodeSet.range, num_adjacencies );
02646     CHK_MB_ERR_0( rval );
02647     nodeSet.adj_offset   = 0;
02648     nodeSet.max_num_adjs = num_adjacencies;
02649     if( num_adjacencies > 0 )
02650     {
02651         handle = mhdf_createAdjacency( filePtr, mhdf_node_type_handle(), num_adjacencies, &status );
02652         CHK_MHDF_ERR_0( status );
02653         mhdf_closeData( filePtr, handle, &status );
02654     }
02655 #endif
02656 
02657     // Create element adjacency tables
02658     for( ex_itor = exportList.begin(); ex_itor != exportList.end(); ++ex_itor )
02659     {
02660         rval = count_adjacencies( ex_itor->range, num_adjacencies );
02661         CHK_MB_ERR_0( rval );
02662 
02663         ex_itor->adj_offset   = 0;
02664         ex_itor->max_num_adjs = num_adjacencies;
02665         if( num_adjacencies > 0 )
02666         {
02667             handle = mhdf_createAdjacency( filePtr, ex_itor->name(), num_adjacencies, &status );
02668             CHK_MHDF_ERR_0( status );
02669             mhdf_closeData( filePtr, handle, &status );
02670         }
02671     }
02672 
02673     dbgOut.tprint( 1, "Gathering Tags\n" );
02674 
02675     rval = gather_tags( user_tag_list, num_user_tags );
02676     CHK_MB_ERR_0( rval );
02677 
02678     // Create the tags and tag data tables
02679     std::list< TagDesc >::iterator tag_iter = tagList.begin();
02680     for( ; tag_iter != tagList.end(); ++tag_iter )
02681     {
02682         // As we haven't yet added any ExportSets for which to write
02683         // dense tag data to the TagDesc struct pointed to by
02684         // tag_iter, this call will initially return all tagged entities
02685         // in the set of entities to be written.
02686         Range range;
02687         rval = get_sparse_tagged_entities( *tag_iter, range );
02688         CHK_MB_ERR_0( rval );
02689 
02690         int s;
02691         bool var_len = ( MB_VARIABLE_DATA_LENGTH == iFace->tag_get_length( tag_iter->tag_id, s ) );
02692 
02693         // Determine which ExportSets we want to write dense
02694         // data for. We never write dense data for variable-length
02695         // tag data.
02696         if( !var_len && writeTagDense )
02697         {
02698             // Check if we want to write this tag in dense format even if not
02699             // all of the entities have a tag value.  The criterion of this
02700             // is that the tag be dense, have a default value, and have at
02701             // least 2/3 of the entities tagged.
02702             bool prefer_dense = false;
02703             TagType type;
02704             rval = iFace->tag_get_type( tag_iter->tag_id, type );
02705             CHK_MB_ERR_0( rval );
02706             if( MB_TAG_DENSE == type )
02707             {
02708                 const void* defval = 0;
02709                 rval               = iFace->tag_get_default_value( tag_iter->tag_id, defval, s );
02710                 if( MB_SUCCESS == rval ) prefer_dense = true;
02711             }
02712 
02713             if( check_dense_format_tag( nodeSet, range, prefer_dense ) )
02714             {
02715                 range -= nodeSet.range;
02716                 tag_iter->dense_list.push_back( nodeSet );
02717             }
02718 
02719             std::list< ExportSet >::const_iterator ex = exportList.begin();
02720             for( ; ex != exportList.end(); ++ex )
02721             {
02722                 if( check_dense_format_tag( *ex, range, prefer_dense ) )
02723                 {
02724                     range -= ex->range;
02725                     tag_iter->dense_list.push_back( *ex );
02726                 }
02727             }
02728 
02729             if( check_dense_format_tag( setSet, range, prefer_dense ) )
02730             {
02731                 range -= setSet.range;
02732                 tag_iter->dense_list.push_back( setSet );
02733             }
02734         }
02735 
02736         tag_iter->write_sparse = !range.empty();
02737 
02738         unsigned long var_len_total = 0;
02739         if( var_len )
02740         {
02741             rval = get_tag_data_length( *tag_iter, range, var_len_total );
02742             CHK_MB_ERR_0( rval );
02743         }
02744 
02745         rval = create_tag( *tag_iter, range.size(), var_len_total );
02746         CHK_MB_ERR_0( rval );
02747     }  // for (tags)
02748 
02749     topState.end();
02750     return MB_SUCCESS;
02751 }
02752 
02753 bool WriteHDF5::check_dense_format_tag( const ExportSet& ents, const Range& all_tagged, bool prefer_dense )
02754 {
02755     // If there are no tagged entities, then don't write anything
02756     if( ents.range.empty() ) return false;
02757 
02758     // If all of the entities are tagged, then write in dense format
02759     if( all_tagged.contains( ents.range ) ) return true;
02760 
02761     // Unless asked for more lenient choice of dense format, return false
02762     if( !prefer_dense ) return false;
02763 
02764     // If we're being lenient about choosing dense format, then
02765     // return true if at least 2/3 of the entities are tagged.
02766     Range xsect = intersect( setSet.range, all_tagged );
02767     if( 3 * xsect.size() >= 2 * setSet.range.size() ) return true;
02768 
02769     return false;
02770 }
02771 
02772 ErrorCode WriteHDF5::count_adjacencies( const Range& set, wid_t& result )
02773 {
02774     ErrorCode rval;
02775     std::vector< wid_t > adj_list;
02776     Range::const_iterator iter      = set.begin();
02777     const Range::const_iterator end = set.end();
02778     result                          = 0;
02779     for( ; iter != end; ++iter )
02780     {
02781         adj_list.clear();
02782         rval = get_adjacencies( *iter, adj_list );
02783         CHK_MB_ERR_0( rval );
02784 
02785         if( adj_list.size() > 0 ) result += 2 + adj_list.size();
02786     }
02787 
02788     return MB_SUCCESS;
02789 }
02790 
02791 ErrorCode WriteHDF5::create_elem_table( const ExportSet& block, long num_entities, long& first_id_out )
02792 {
02793     mhdf_Status status;
02794     hid_t handle;
02795 
02796     CHECK_OPEN_HANDLES;
02797 
02798     mhdf_addElement( filePtr, block.name(), block.type, &status );
02799     CHK_MHDF_ERR_0( status );
02800 
02801     handle = mhdf_createConnectivity( filePtr, block.name(), block.num_nodes, num_entities, &first_id_out, &status );
02802     CHK_MHDF_ERR_0( status );
02803     mhdf_closeData( filePtr, handle, &status );
02804     CHK_MHDF_ERR_0( status );
02805 
02806     return MB_SUCCESS;
02807 }
02808 
02809 ErrorCode WriteHDF5::count_set_size( const Range& sets,
02810                                      long& contents_length_out,
02811                                      long& children_length_out,
02812                                      long& parents_length_out )
02813 {
02814     ErrorCode rval;
02815     Range set_contents;
02816     long contents_length_set, children_length_set, parents_length_set;
02817     unsigned long flags;
02818     std::vector< wid_t > set_contents_ids;
02819     std::vector< SpecialSetData >::const_iterator si = specialSets.begin();
02820 
02821     contents_length_out = 0;
02822     children_length_out = 0;
02823     parents_length_out  = 0;
02824 
02825     for( Range::const_iterator iter = sets.begin(); iter != sets.end(); ++iter )
02826     {
02827         while( si != specialSets.end() && si->setHandle < *iter )
02828             ++si;
02829 
02830         if( si != specialSets.end() && si->setHandle == *iter )
02831         {
02832             contents_length_out += si->contentIds.size();
02833             children_length_out += si->childIds.size();
02834             parents_length_out += si->parentIds.size();
02835             ++si;
02836             continue;
02837         }
02838 
02839         rval = get_set_info( *iter, contents_length_set, children_length_set, parents_length_set, flags );
02840         CHK_MB_ERR_0( rval );
02841 
02842         // Check if can and should compress as ranges
02843         if( !( flags & MESHSET_ORDERED ) && contents_length_set )
02844         {
02845             set_contents.clear();
02846             rval = iFace->get_entities_by_handle( *iter, set_contents, false );
02847             CHK_MB_ERR_0( rval );
02848 
02849             bool blocked_list;
02850             rval = range_to_blocked_list( set_contents, set_contents_ids, blocked_list );
02851             CHK_MB_ERR_0( rval );
02852 
02853             if( blocked_list )
02854             {
02855                 assert( set_contents_ids.size() % 2 == 0 );
02856                 contents_length_set = set_contents_ids.size();
02857             }
02858         }
02859 
02860         contents_length_out += contents_length_set;
02861         children_length_out += children_length_set;
02862         parents_length_out += parents_length_set;
02863     }
02864 
02865     return MB_SUCCESS;
02866 }
02867 
02868 ErrorCode WriteHDF5::create_set_meta( long num_sets, long& first_id_out )
02869 {
02870     hid_t handle;
02871     mhdf_Status status;
02872 
02873     CHECK_OPEN_HANDLES;
02874 
02875     handle = mhdf_createSetMeta( filePtr, num_sets, &first_id_out, &status );
02876     CHK_MHDF_ERR_0( status );
02877     mhdf_closeData( filePtr, handle, &status );
02878 
02879     return MB_SUCCESS;
02880 }
02881 
02882 WriteHDF5::SpecialSetData* WriteHDF5::find_set_data( EntityHandle h )
02883 {
02884     SpecialSetData tmp;
02885     tmp.setHandle = h;
02886     std::vector< SpecialSetData >::iterator i;
02887     i = std::lower_bound( specialSets.begin(), specialSets.end(), tmp, SpecSetLess() );
02888     return ( i == specialSets.end() || i->setHandle != h ) ? 0 : &*i;
02889 }
02890 
02891 ErrorCode WriteHDF5::create_set_tables( long num_set_contents, long num_set_children, long num_set_parents )
02892 {
02893     hid_t handle;
02894     mhdf_Status status;
02895 
02896     CHECK_OPEN_HANDLES;
02897 
02898     if( num_set_contents > 0 )
02899     {
02900         handle = mhdf_createSetData( filePtr, num_set_contents, &status );
02901         CHK_MHDF_ERR_0( status );
02902         mhdf_closeData( filePtr, handle, &status );
02903     }
02904 
02905     if( num_set_children > 0 )
02906     {
02907         handle = mhdf_createSetChildren( filePtr, num_set_children, &status );
02908         CHK_MHDF_ERR_0( status );
02909         mhdf_closeData( filePtr, handle, &status );
02910     }
02911 
02912     if( num_set_parents > 0 )
02913     {
02914         handle = mhdf_createSetParents( filePtr, num_set_parents, &status );
02915         CHK_MHDF_ERR_0( status );
02916         mhdf_closeData( filePtr, handle, &status );
02917     }
02918 
02919     return MB_SUCCESS;
02920 }
02921 
02922 ErrorCode WriteHDF5::get_tag_size( Tag tag,
02923                                    DataType& moab_type,
02924                                    int& num_bytes,
02925                                    int& type_size,
02926                                    int& array_length,
02927                                    mhdf_TagDataType& file_type,
02928                                    hid_t& hdf_type )
02929 {
02930     ErrorCode rval;
02931     Tag type_handle;
02932     std::string tag_name, tag_type_name;
02933 
02934     CHECK_OPEN_HANDLES;
02935 
02936     // We return NULL for hdf_type if it can be determined from
02937     // the file_type.  The only case where it is non-zero is
02938     // if the user specified a specific type via a mesh tag.
02939     hdf_type            = (hid_t)0;
02940     bool close_hdf_type = false;
02941 
02942     rval = iFace->tag_get_data_type( tag, moab_type );
02943     CHK_MB_ERR_0( rval );
02944     rval = iFace->tag_get_length( tag, array_length );
02945     if( MB_VARIABLE_DATA_LENGTH == rval )
02946     {
02947         array_length = MB_VARIABLE_LENGTH;
02948     }
02949     else if( MB_SUCCESS != rval )
02950         return error( rval );
02951     rval = iFace->tag_get_bytes( tag, num_bytes );
02952     if( MB_VARIABLE_DATA_LENGTH == rval )
02953         num_bytes = MB_VARIABLE_LENGTH;
02954     else if( MB_SUCCESS != rval )
02955         return error( rval );
02956 
02957     switch( moab_type )
02958     {
02959         case MB_TYPE_INTEGER:
02960             type_size      = sizeof( int );
02961             file_type      = mhdf_INTEGER;
02962             hdf_type       = H5T_NATIVE_INT;
02963             close_hdf_type = false;
02964             break;
02965         case MB_TYPE_DOUBLE:
02966             type_size      = sizeof( double );
02967             file_type      = mhdf_FLOAT;
02968             hdf_type       = H5T_NATIVE_DOUBLE;
02969             close_hdf_type = false;
02970             break;
02971         case MB_TYPE_BIT:
02972             type_size = sizeof( bool );
02973             file_type = mhdf_BITFIELD;
02974             assert( array_length <= 8 );
02975             hdf_type = H5Tcopy( H5T_NATIVE_B8 );
02976             H5Tset_precision( hdf_type, array_length );
02977             close_hdf_type = true;
02978             break;
02979         case MB_TYPE_HANDLE:
02980             type_size      = sizeof( EntityHandle );
02981             file_type      = mhdf_ENTITY_ID;
02982             hdf_type       = id_type;
02983             close_hdf_type = false;
02984             break;
02985         case MB_TYPE_OPAQUE:
02986             file_type = mhdf_OPAQUE;
02987             rval      = iFace->tag_get_name( tag, tag_name );
02988             CHK_MB_ERR_0( rval );
02989             tag_type_name = "__hdf5_tag_type_";
02990             tag_type_name += tag_name;
02991             rval = iFace->tag_get_handle( tag_type_name.c_str(), 0, MB_TYPE_OPAQUE, type_handle, MB_TAG_ANY );
02992             if( MB_TAG_NOT_FOUND == rval )
02993             {
02994                 if( num_bytes == MB_VARIABLE_LENGTH )
02995                     type_size = 1;
02996                 else
02997                     type_size = num_bytes;
02998                 hdf_type       = H5Tcreate( H5T_OPAQUE, type_size );
02999                 close_hdf_type = true;
03000             }
03001             else if( MB_SUCCESS == rval )
03002             {
03003                 int hsize;
03004                 rval = iFace->tag_get_bytes( type_handle, hsize );
03005                 if( hsize != sizeof( hid_t ) ) return error( MB_FAILURE );
03006 
03007                 const EntityHandle root = 0;
03008                 rval                    = iFace->tag_get_data( type_handle, &root, 1, &hdf_type );
03009                 if( rval != MB_SUCCESS ) return error( rval );
03010 
03011                 type_size = H5Tget_size( hdf_type );
03012                 if( type_size != num_bytes ) return error( MB_FAILURE );
03013 
03014                 close_hdf_type = false;
03015             }
03016             else
03017                 return error( rval );
03018             num_bytes    = array_length;
03019             array_length = ( num_bytes == MB_VARIABLE_LENGTH ) ? MB_VARIABLE_LENGTH : 1;
03020             break;
03021         default:
03022             break;
03023     }
03024 
03025     assert( num_bytes == MB_VARIABLE_LENGTH || ( moab_type == MB_TYPE_BIT && num_bytes == 1 ) ||
03026             array_length * type_size == num_bytes );
03027 
03028     if( num_bytes == MB_VARIABLE_LENGTH )
03029     {
03030         array_length = MB_VARIABLE_LENGTH;
03031         if( !close_hdf_type )
03032         {
03033             hdf_type = H5Tcopy( hdf_type );
03034             // close_hdf_type = true;
03035         }
03036     }
03037     else if( array_length > 1 && moab_type != MB_TYPE_BIT )
03038     {
03039         hsize_t len = array_length;
03040 #if defined( H5Tarray_create_vers ) && ( H5Tarray_create_vers > 1 )
03041         hid_t temp_id = H5Tarray_create2( hdf_type, 1, &len );
03042 #else
03043         hid_t temp_id = H5Tarray_create( hdf_type, 1, &len, NULL );
03044 #endif
03045         if( close_hdf_type ) H5Tclose( hdf_type );
03046         hdf_type = temp_id;
03047     }
03048     else if( !close_hdf_type )
03049     {
03050         hdf_type = H5Tcopy( hdf_type );
03051         // close_hdf_type = true;
03052     }
03053 
03054     return MB_SUCCESS;
03055 }
03056 
03057 ErrorCode WriteHDF5::get_tag_data_length( const TagDesc& tag_info, const Range& range, unsigned long& result )
03058 {
03059     ErrorCode rval;
03060     result = 0;
03061 
03062     // Split buffer into two pieces, one for pointers and one for sizes
03063     size_t step, remaining;
03064     step                    = bufferSize / ( sizeof( int ) + sizeof( void* ) );
03065     const void** ptr_buffer = reinterpret_cast< const void** >( dataBuffer );
03066     int* size_buffer        = reinterpret_cast< int* >( ptr_buffer + step );
03067     Range subrange;
03068     Range::const_iterator iter = range.begin();
03069     for( remaining = range.size(); remaining >= step; remaining -= step )
03070     {
03071         // Get subset of range containing 'count' entities
03072         Range::const_iterator end = iter;
03073         end += step;
03074         subrange.clear();
03075         subrange.merge( iter, end );
03076         iter = end;
03077         // Get tag sizes for entities
03078         rval = iFace->tag_get_by_ptr( tag_info.tag_id, subrange, ptr_buffer, size_buffer );
03079         if( MB_SUCCESS != rval ) return error( rval );
03080         // Sum lengths
03081         for( size_t i = 0; i < step; ++i )
03082             result += size_buffer[i];
03083     }
03084     // Process remaining
03085     subrange.clear();
03086     subrange.merge( iter, range.end() );
03087     assert( subrange.size() == remaining );
03088     rval = iFace->tag_get_by_ptr( tag_info.tag_id, subrange, ptr_buffer, size_buffer );
03089     if( MB_SUCCESS != rval ) return error( rval );
03090     for( size_t i = 0; i < remaining; ++i )
03091         result += size_buffer[i];
03092 
03093     return MB_SUCCESS;
03094 }
03095 
03096 ErrorCode WriteHDF5::create_tag( const TagDesc& tag_data,
03097                                  unsigned long num_sparse_entities,
03098                                  unsigned long data_table_size )
03099 {
03100     TagType mb_storage;
03101     DataType mb_type;
03102     mhdf_TagDataType mhdf_type;
03103     int tag_bytes, type_size, num_vals, storage;
03104     hid_t hdf_type = (hid_t)0;
03105     hid_t handles[3];
03106     std::string tag_name;
03107     ErrorCode rval;
03108     mhdf_Status status;
03109 
03110     CHECK_OPEN_HANDLES;
03111 
03112     // Get tag properties
03113     rval = iFace->tag_get_type( tag_data.tag_id, mb_storage );
03114     CHK_MB_ERR_0( rval );
03115     switch( mb_storage )
03116     {
03117         case MB_TAG_DENSE:
03118             storage = mhdf_DENSE_TYPE;
03119             break;
03120         case MB_TAG_SPARSE:
03121             storage = mhdf_SPARSE_TYPE;
03122             break;
03123         case MB_TAG_BIT:
03124             storage = mhdf_BIT_TYPE;
03125             break;
03126         case MB_TAG_MESH:
03127             storage = mhdf_MESH_TYPE;
03128             break;
03129         default:
03130             return error( MB_FAILURE );
03131     }
03132     rval = iFace->tag_get_name( tag_data.tag_id, tag_name );
03133     CHK_MB_ERR_0( rval );
03134     rval = get_tag_size( tag_data.tag_id, mb_type, tag_bytes, type_size, num_vals, mhdf_type, hdf_type );
03135     CHK_MB_ERR_0( rval );
03136 
03137     // Get default value
03138     const void *def_value, *mesh_value;
03139     int def_val_len, mesh_val_len;
03140     rval = iFace->tag_get_default_value( tag_data.tag_id, def_value, def_val_len );
03141     if( MB_ENTITY_NOT_FOUND == rval )
03142     {
03143         def_value   = 0;
03144         def_val_len = 0;
03145     }
03146     else if( MB_SUCCESS != rval )
03147     {
03148         H5Tclose( hdf_type );
03149         return error( rval );
03150     }
03151 
03152     // Get mesh value
03153     unsigned char byte;
03154     const EntityHandle root = 0;
03155     if( mb_storage == MB_TAG_BIT )
03156     {
03157         rval         = iFace->tag_get_data( tag_data.tag_id, &root, 1, &byte );
03158         mesh_value   = &byte;
03159         mesh_val_len = 1;
03160     }
03161     else
03162     {
03163         rval = iFace->tag_get_by_ptr( tag_data.tag_id, &root, 1, &mesh_value, &mesh_val_len );
03164     }
03165     if( MB_TAG_NOT_FOUND == rval )
03166     {
03167         mesh_value   = 0;
03168         mesh_val_len = 0;
03169     }
03170     else if( MB_SUCCESS != rval )
03171     {
03172         H5Tclose( hdf_type );
03173         return error( rval );
03174     }
03175 
03176     // For handle-type tags, need to convert from handles to file ids
03177     if( MB_TYPE_HANDLE == mb_type )
03178     {
03179         // Make sure there's room in the buffer for both
03180         assert( ( def_val_len + mesh_val_len ) * sizeof( long ) < (size_t)bufferSize );
03181 
03182         // Convert default value
03183         if( def_value )
03184         {
03185             memcpy( dataBuffer, def_value, def_val_len * sizeof( EntityHandle ) );
03186             convert_handle_tag( reinterpret_cast< EntityHandle* >( dataBuffer ), def_val_len );
03187             def_value = dataBuffer;
03188         }
03189 
03190         // Convert mesh value
03191         if( mesh_value )
03192         {
03193             EntityHandle* ptr = reinterpret_cast< EntityHandle* >( dataBuffer ) + def_val_len;
03194             memcpy( ptr, mesh_value, mesh_val_len * sizeof( EntityHandle ) );
03195             if( convert_handle_tag( ptr, mesh_val_len ) )
03196                 mesh_value = ptr;
03197             else
03198                 mesh_value = 0;
03199         }
03200     }
03201 
03202     if( MB_VARIABLE_LENGTH != tag_bytes )
03203     {
03204         // Write the tag description to the file
03205         mhdf_createTag( filePtr, tag_name.c_str(), mhdf_type, num_vals, storage, def_value, mesh_value, hdf_type,
03206                         mb_type == MB_TYPE_HANDLE ? id_type : 0, &status );
03207         CHK_MHDF_ERR_0( status );
03208         H5Tclose( hdf_type );
03209 
03210         // Create empty table for tag data
03211         if( num_sparse_entities )
03212         {
03213             mhdf_createSparseTagData( filePtr, tag_name.c_str(), num_sparse_entities, handles, &status );
03214             CHK_MHDF_ERR_0( status );
03215             mhdf_closeData( filePtr, handles[0], &status );
03216             mhdf_closeData( filePtr, handles[1], &status );
03217         }
03218 
03219         for( size_t i = 0; i < tag_data.dense_list.size(); ++i )
03220         {
03221             const ExportSet* ex = find( tag_data.dense_list[i] );
03222             assert( 0 != ex );
03223             handles[0] = mhdf_createDenseTagData( filePtr, tag_name.c_str(), ex->name(), ex->total_num_ents, &status );
03224             CHK_MHDF_ERR_0( status );
03225             mhdf_closeData( filePtr, handles[0], &status );
03226         }
03227     }
03228     else
03229     {
03230         mhdf_createVarLenTag( filePtr, tag_name.c_str(), mhdf_type, storage, def_value, def_val_len, mesh_value,
03231                               mesh_val_len, hdf_type, mb_type == MB_TYPE_HANDLE ? id_type : 0, &status );
03232         CHK_MHDF_ERR_0( status );
03233         H5Tclose( hdf_type );
03234 
03235         // Create empty table for tag data
03236         if( num_sparse_entities )
03237         {
03238             mhdf_createVarLenTagData( filePtr, tag_name.c_str(), num_sparse_entities, data_table_size, handles,
03239                                       &status );
03240             CHK_MHDF_ERR_0( status );
03241             mhdf_closeData( filePtr, handles[0], &status );
03242             mhdf_closeData( filePtr, handles[1], &status );
03243             mhdf_closeData( filePtr, handles[2], &status );
03244         }
03245     }
03246 
03247     return MB_SUCCESS;
03248 }
03249 
03250 ErrorCode WriteHDF5::get_num_sparse_tagged_entities( const TagDesc& tag, size_t& count )
03251 {
03252     Range tmp;
03253     ErrorCode rval = get_sparse_tagged_entities( tag, tmp );
03254     count          = tmp.size();
03255     return rval;
03256 }
03257 
03258 ErrorCode WriteHDF5::get_sparse_tagged_entities( const TagDesc& tag, Range& results )
03259 {
03260     results.clear();
03261     if( !tag.have_dense( setSet ) ) results.merge( setSet.range );
03262     std::list< ExportSet >::reverse_iterator e;
03263     for( e = exportList.rbegin(); e != exportList.rend(); ++e )
03264     {
03265         if( !tag.have_dense( *e ) ) results.merge( e->range );
03266     }
03267     if( !tag.have_dense( nodeSet ) ) results.merge( nodeSet.range );
03268     if( results.empty() ) return MB_SUCCESS;
03269 
03270     return iFace->get_entities_by_type_and_tag( 0, MBMAXTYPE, &tag.tag_id, 0, 1, results, Interface::INTERSECT );
03271 }
03272 
03273 void WriteHDF5::get_write_entities( Range& range )
03274 {
03275     range.clear();
03276     range.merge( setSet.range );
03277     std::list< ExportSet >::reverse_iterator e;
03278     for( e = exportList.rbegin(); e != exportList.rend(); ++e )
03279         range.merge( e->range );
03280     range.merge( nodeSet.range );
03281 }
03282 
03283 void WriteHDF5::print_id_map() const
03284 {
03285     print_id_map( std::cout, "" );
03286 }
03287 
03288 void WriteHDF5::print_id_map( std::ostream& s, const char* pfx ) const
03289 {
03290     RangeMap< EntityHandle, wid_t >::const_iterator i;
03291     for( i = idMap.begin(); i != idMap.end(); ++i )
03292     {
03293         const char* n1 = CN::EntityTypeName( TYPE_FROM_HANDLE( i->begin ) );
03294         EntityID id    = ID_FROM_HANDLE( i->begin );
03295         if( 1 == i->count )
03296         {
03297             s << pfx << n1 << " " << id << " -> " << i->value << std::endl;
03298         }
03299         else
03300         {
03301             const char* n2 = CN::EntityTypeName( TYPE_FROM_HANDLE( i->begin + i->count - 1 ) );
03302             if( n1 == n2 )
03303             {
03304                 s << pfx << n1 << " " << id << "-" << id + i->count - 1 << " -> " << i->value << "-"
03305                   << i->value + i->count - 1 << std::endl;
03306             }
03307             else
03308             {
03309                 s << pfx << n1 << " " << id << "-" << n1 << " " << ID_FROM_HANDLE( i->begin + i->count - 1 ) << " -> "
03310                   << i->value << "-" << i->value + i->count - 1 << std::endl;
03311             }
03312         }
03313     }
03314 }
03315 
03316 void WriteHDF5::print_times( const double* t ) const
03317 {
03318     std::cout << "WriteHDF5:           " << t[TOTAL_TIME] << std::endl
03319               << "  gather mesh:       " << t[GATHER_TIME] << std::endl
03320               << "  create file:       " << t[CREATE_TIME] << std::endl
03321               << "    create nodes:    " << t[CREATE_NODE_TIME] << std::endl
03322               << "    negotiate types: " << t[NEGOTIATE_TYPES_TIME] << std::endl
03323               << "    create elem:     " << t[CREATE_ELEM_TIME] << std::endl
03324               << "    file id exch:    " << t[FILEID_EXCHANGE_TIME] << std::endl
03325               << "    create adj:      " << t[CREATE_ADJ_TIME] << std::endl
03326               << "    create set:      " << t[CREATE_SET_TIME] << std::endl
03327               << "      shared ids:    " << t[SHARED_SET_IDS] << std::endl
03328               << "      shared data:   " << t[SHARED_SET_CONTENTS] << std::endl
03329               << "      set offsets:   " << t[SET_OFFSET_TIME] << std::endl
03330               << "    create tags:     " << t[CREATE_TAG_TIME] << std::endl
03331               << "  coordinates:       " << t[COORD_TIME] << std::endl
03332               << "  connectivity:      " << t[CONN_TIME] << std::endl
03333               << "  sets:              " << t[SET_TIME] << std::endl
03334               << "    set descrip:     " << t[SET_META] << std::endl
03335               << "    set content:     " << t[SET_CONTENT] << std::endl
03336               << "    set parent:      " << t[SET_PARENT] << std::endl
03337               << "    set child:       " << t[SET_CHILD] << std::endl
03338               << "  adjacencies:       " << t[ADJ_TIME] << std::endl
03339               << "  tags:              " << t[TAG_TIME] << std::endl
03340               << "    dense data:      " << t[DENSE_TAG_TIME] << std::endl
03341               << "    sparse data:     " << t[SPARSE_TAG_TIME] << std::endl
03342               << "    var-len data:    " << t[VARLEN_TAG_TIME] << std::endl;
03343 }
03344 
03345 }  // namespace moab
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines