seqperf.cpp

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#include <time.h>
#include <assert.h>
#include <iostream>
#include <sstream>
#include "moab/Core.hpp"
#include "moab/ReadUtilIface.hpp"

#define PRINT_SEQUENCE_COUNT

#ifdef PRINT_SEQUENCE_COUNT
#ifndef IS_BUILDING_MB
#define IS_BUILDING_MB
#endif
#include "EntitySequence.hpp"
#ifdef MB_ENTITY_SEQUENCE_HPP
#include "EntitySequenceManager.hpp"
#else
#include "SequenceManager.hpp"
#endif
#endif

using namespace moab;

// constants
const bool dump_mesh          = false;  //!< write mesh to vtk file
const int default_intervals   = 25;     //!< defaul interval count for cubic structured hex mesh
const int default_query_count = 100;    //!< number of times to do each query set
const int default_order[]     = { 0, 1, 2 };
const int default_create[]    = { 0, 1 };
const int default_delete[]    = { 0, 10, 30, 50, 70, 90 };
#define ARRSIZE( A ) ( sizeof( A ) / sizeof( A[0] ) )

// input parameters
long numSideInt, numVert, numElem;  //!< total counts;
int queryCount;                     //!< number of times to do each query set

// misc globals
Core mb_core;                       //!< moab instance
Interface& mb = mb_core;            //!< moab instance
EntityHandle vertStart, elemStart;  //!< first handle
ReadUtilIface* readTool    = 0;
long* queryVertPermutation = 0;  //!< pupulated by init(): "random" order for vertices
long* queryElemPermutation = 0;  //!< pupulated by init(): "random" order for elements

//! Generate random permutation of values in [0,count-1]
long* permutation( long count )
{
    srand( count );
    long* array = new long[count];
    for( long i = 0; i < count; ++i )
        array[i] = i;

    for( long i = 0; i < count; ++i )
    {
        long r = rand();
        if( count > RAND_MAX )
        {
            r += RAND_MAX * rand();
            if( count / RAND_MAX > RAND_MAX )
            {
                long t = (long)RAND_MAX * rand();
                r += (long)RAND_MAX * t;
            }
        }
        std::swap( array[i], array[r % count] );
    }

    return array;
}

//! Initialize global variables
void init()
{
    ErrorCode rval = mb.query_interface( readTool );
    if( rval || !readTool )
    {
        assert( false );
        abort();
    }

    queryVertPermutation = permutation( numVert );
    queryElemPermutation = permutation( numElem );
}

void create_vertices_single();  //!< create vertices one at a time
void create_vertices_block();   //!< create vertices in block using ReadUtilIface
void create_elements_single();  //!< create elements one at a time
void create_elements_block();   //!< create elements in block using ReadUtilIface

void forward_order_query_vertices( int percent );  //!< calculate mean of all vertex coordinates
void reverse_order_query_vertices( int percent );  //!< calculate mean of all vertex coordinates
void random_order_query_vertices( int percent );   //!< calculate mean of all vertex coordinates

void forward_order_query_elements( int percent );  //!< check all element connectivity for valid vertex handles
void reverse_order_query_elements( int percent );  //!< check all element connectivity for valid vertex handles
void random_order_query_elements( int percent );   //!< check all element connectivity for valid vertex handles

void forward_order_query_element_verts( int percent );  //!< calculate centroid
void reverse_order_query_element_verts( int percent );  //!< calculate centroid
void random_order_query_element_verts( int percent );   //!< calculate centroid

void forward_order_delete_vertices( int percent );  //!< delete x% of vertices
void reverse_order_delete_vertices( int percent );  //!< delete x% of vertices
void random_order_delete_vertices( int percent );   //!< delete x% of vertices

void forward_order_delete_elements( int percent );  //!< delete x% of elements
void reverse_order_delete_elements( int percent );  //!< delete x% of elements
void random_order_delete_elements( int percent );   //!< delete x% of elements

void create_missing_vertices( int percent );  //!< re-create deleted vertices
void create_missing_elements( int percent );  //!< re-create deleted elements

#ifdef PRINT_SEQUENCE_COUNT
unsigned get_number_sequences( EntityType type );
#endif

/* Build arrays of function pointers, indexed by the order the entities are traversed in */

typedef void ( *naf_t )();
typedef void ( *iaf_t )( int );

iaf_t query_verts[3] = { &forward_order_query_vertices, &reverse_order_query_vertices, &random_order_query_vertices };

iaf_t query_elems[3] = { &forward_order_query_elements, &reverse_order_query_elements, &random_order_query_elements };

iaf_t query_elem_verts[3] = { &forward_order_query_element_verts, &reverse_order_query_element_verts,
                              &random_order_query_element_verts };

iaf_t delete_verts[3] = { &forward_order_delete_vertices, &reverse_order_delete_vertices,
                          &random_order_delete_vertices };

iaf_t delete_elems[3] = { &forward_order_delete_elements, &reverse_order_delete_elements,
                          &random_order_delete_elements };

const char* order_strs[] = { "Forward", "Reverse", "Random" };

//! Coordinates for ith vertex in structured hex mesh
inline void vertex_coords( long vert_index, double& x, double& y, double& z );
//! Connectivity for ith hex in structured hex mesh
inline void element_conn( long elem_index, EntityHandle conn[8] );
//! True if passed index is one of the x% to be deleted
inline bool deleted_vert( long index, int percent );
//! True if passed index is one of the x% to be deleted
inline bool deleted_elem( long index, int percent );
//! if (deleted_vert(index,percent)) delete vertex
inline void delete_vert( long index, int percent );
//! if (deleted_elem(index,percent)) delete element
inline void delete_elem( long index, int percent );

//! print usage and exit
void usage()
{
    std::cerr << "Usage: seqperf [-i <intervals>] [-o <order>] [-d <percent>] [-b|-s] [-q <count>]" << std::endl;
    std::cerr << " -i specify size of cubic structured hex mesh in intervals.  Default: " << default_intervals
              << std::endl;
    std::cerr << " -o one of \"forward\", \"reverse\", or \"random\".  May be specified multiple "
                 "times.  Default is all."
              << std::endl;
    std::cerr << " -d percent of entities to delete.  May be specified multiple times.  Default is {";
    for( unsigned i = 0; i < ARRSIZE( default_delete ) - 1; ++i )
        std::cerr << default_delete[i] << ",";
    std::cerr << default_delete[ARRSIZE( default_delete ) - 1] << "}" << std::endl;
    std::cerr << " -b block creation of mesh" << std::endl;
    std::cerr << " -s single entity mesh creation" << std::endl;
    std::cerr << " -q number of times to repeat queries.  Default: " << default_query_count << std::endl;
    exit( 1 );
}

//! convert CPU time to string
std::string ts( clock_t t )
{
    std::ostringstream s;
    s << ( (double)t ) / CLOCKS_PER_SEC << 's';
    return s.str();
}

//! run function, printing time spent
void TIME( const char* str, void ( *func )() )
{
    std::cout << str << "... " << std::flush;
    clock_t t = clock();
    ( *func )();
    std::cout << ts( clock() - t ) << std::endl;
}

//! run function query_repeat times, printing time spent
void TIME_QRY( const char* str, void ( *func )( int percent ), int percent )
{
    std::cout << str << "... " << std::flush;
    clock_t t = clock();
    for( int i = 0; i < queryCount; ++i )
        ( *func )( percent );
    std::cout << ts( clock() - t ) << std::endl;
}

//! run function with integer argument, printing time spent
void TIME_DEL( const char* str, void ( *func )( int ), int percent )
{
    std::cout << str << "... " << std::flush;
    clock_t t = clock();
    ( *func )( percent );
    std::cout << ts( clock() - t ) << std::endl;
}

//! call MB::delete_mesh().  function so can be passed to TIME
void delete_mesh()
{
    mb.delete_mesh();
}

//! Run a single combination of test parameters
void do_test( int create_mode,  //!< 0 == single, 1 == block
              int order,        //!< 0 == forward, 1 == reverse, 2 == random
              int percent )     //!< percent of entities to delete
{
    clock_t t = clock();
    if( create_mode )
    {
        std::cout << "Block Entity Creation (all entities in single block of memory)" << std::endl;
        TIME( "  Creating initial vertices", create_vertices_block );
        TIME( "  Creating initial elements", create_elements_block );
        if( dump_mesh && !percent && mb.write_file( "seqperf.vtk" ) == MB_SUCCESS )
            std::cout << "Wrote mesh to file: seqperf.vtk" << std::endl;
    }
    else
    {
        std::cout << "Single Entity Creation (entities grouped in memory blocks of constant size)" << std::endl;
        TIME( "  Creating initial vertices", create_vertices_single );
        TIME( "  Creating initial elements", create_elements_single );
    }

    std::cout << order_strs[order] << " order with deletion of " << percent << "% of vertices and elements"
              << std::endl;

    TIME_DEL( "  Deleting elements", delete_elems[order], percent );
    TIME_DEL( "  Deleting vertices", delete_verts[order], percent );

    int num_vert = 0;
    int num_elem = 0;
    mb.get_number_entities_by_type( 0, MBVERTEX, num_vert );
    mb.get_number_entities_by_type( 0, MBHEX, num_elem );
    std::cout << "  " << num_vert << " vertices and " << num_elem << " elements remaining" << std::endl;
#ifdef PRINT_SEQUENCE_COUNT
    std::cout << "  " << get_number_sequences( MBVERTEX ) << " vertex sequences and " << get_number_sequences( MBHEX )
              << " element sequences." << std::endl;
#endif

    TIME_QRY( "  Querying vertex coordinates", query_verts[order], percent );
    TIME_QRY( "  Querying element connectivity", query_elems[order], percent );
    TIME_QRY( "  Querying element coordinates", query_elem_verts[order], percent );

    TIME_DEL( "  Re-creating vertices", create_missing_vertices, percent );
    TIME_DEL( "  Re-creating elements", create_missing_elements, percent );

    TIME( "  Clearing mesh instance", delete_mesh );

    std::cout << "Total time for test: " << ts( clock() - t ) << std::endl << std::endl;
}

void parse_order( const char* str, std::vector< int >& list )
{
    if( str[0] == 'f' )
    {
        if( strncmp( str, "forward", strlen( str ) ) ) usage();
        list.push_back( 0 );
    }
    else if( str[0] != 'r' )
        usage();
    else if( str[1] == 'e' )
    {
        if( strncmp( str, "reverse", strlen( str ) ) ) usage();
        list.push_back( 0 );
    }
    else
    {
        if( strncmp( str, "random", strlen( str ) ) ) usage();
        list.push_back( 0 );
    }
}

void parse_percent( const char* str, std::vector< int >& list )
{
    char* endptr;
    long p = strtol( str, &endptr, 0 );
    if( !endptr || *endptr || p < 0 || p > 100 ) usage();

    list.push_back( (int)p );
}

int parse_positive_int( const char* str )
{
    char* endptr;
    long p = strtol( str, &endptr, 0 );
    if( !endptr || *endptr || p < 1 ) usage();
    int result = p;
    if( p != (long)result )  // overflow
        usage();

    return result;
}

void check_default( std::vector< int >& list, const int* array, size_t array_len )
{
    if( list.empty() ) std::copy( array, array + array_len, std::back_inserter( list ) );
}

int main( int argc, char* argv[] )
{
    // Parse arguments
    std::vector< int > createList, orderList, deleteList;
    numSideInt = default_intervals;
    queryCount = default_query_count;

    for( int i = 1; i < argc; ++i )
    {
        // check that arg is a '-' followed by a single character
        if( argv[i][0] != '-' || argv[i][1] == '\0' || argv[i][2] != '\0' ) usage();

        const char flag = argv[i][1];
        switch( flag )
        {
            case 'b':
                createList.push_back( 1 );
                break;
            case 's':
                createList.push_back( 0 );
                break;
            default:
                if( ++i == argc ) usage();
                switch( flag )
                {
                    case 'i':
                        numSideInt = parse_positive_int( argv[i] );
                        break;
                    case 'o':
                        parse_order( argv[i], orderList );
                        break;
                    case 'd':
                        parse_percent( argv[i], deleteList );
                        break;
                    case 'q':
                        queryCount = parse_positive_int( argv[i] );
                        break;
                    default:
                        usage();
                }
        }
    }
    check_default( createList, default_create, ARRSIZE( default_create ) );
    check_default( orderList, default_order, ARRSIZE( default_order ) );
    check_default( deleteList, default_delete, ARRSIZE( default_delete ) );

    // Do some initialization.

    int numSideVert = numSideInt + 1;
    numVert         = numSideVert * numSideVert * numSideVert;
    numElem         = numSideInt * numSideInt * numSideInt;
    if( numVert / numSideVert / numSideVert != numSideVert )  // overflow
        usage();
    init();

    // Echo input args

    std::cout << numSideInt << "x" << numSideInt << "x" << numSideInt << " hex grid: " << numElem << " elements and "
              << numVert << " vertices" << std::endl;

    // Run tests

    std::vector< int >::const_iterator i, j, k;
    clock_t t = clock();
    for( i = createList.begin(); i != createList.end(); ++i )
    {
        for( j = deleteList.begin(); j != deleteList.end(); ++j )
        {
            for( k = orderList.begin(); k != orderList.end(); ++k )
            {
                do_test( *i, *k, *j );
            }
        }
    }

    // Clean up

    std::cout << "TOTAL: " << ts( clock() - t ) << std::endl << std::endl;
    delete[] queryVertPermutation;
    delete[] queryElemPermutation;
    return 0;
}

inline void vertex_coords( long vert_index, double& x, double& y, double& z )
{
    const long vs = numSideInt + 1;
    x             = vert_index % vs;
    y             = ( vert_index / vs ) % vs;
    z             = ( vert_index / vs / vs );
}

inline long vert_index( long x, long y, long z )
{
    const long vs = numSideInt + 1;
    return x + vs * ( y + vs * z );
}

inline void element_conn( long elem_index, EntityHandle conn[8] )
{
    const long x = elem_index % numSideInt;
    const long y = ( elem_index / numSideInt ) % numSideInt;
    const long z = ( elem_index / numSideInt / numSideInt );
    conn[0]      = vertStart + vert_index( x, y, z );
    conn[1]      = vertStart + vert_index( x + 1, y, z );
    conn[2]      = vertStart + vert_index( x + 1, y + 1, z );
    conn[3]      = vertStart + vert_index( x, y + 1, z );
    conn[4]      = vertStart + vert_index( x, y, z + 1 );
    conn[5]      = vertStart + vert_index( x + 1, y, z + 1 );
    conn[6]      = vertStart + vert_index( x + 1, y + 1, z + 1 );
    conn[7]      = vertStart + vert_index( x, y + 1, z + 1 );
}

inline bool deleted_vert( long index, int percent )
{
    return index % ( numSideInt + 1 ) >= ( numSideInt + 1 ) * ( 100 - percent ) / 100;
}

inline bool deleted_elem( long index, int percent )
{
    return index % numSideInt + 1 >= ( numSideInt + 1 ) * ( 100 - percent ) / 100;
}

void create_vertices_single()
{
    double coords[3];
    vertex_coords( 0, coords[0], coords[1], coords[2] );
    ErrorCode rval = mb.create_vertex( coords, vertStart );
    assert( !rval );
    if( rval ) {}  // empty line to remove compiler warning

    EntityHandle h;
    for( long i = 1; i < numVert; ++i )
    {
        vertex_coords( i, coords[0], coords[1], coords[2] );
        rval = mb.create_vertex( coords, h );
        assert( !rval );
        assert( h - vertStart == (EntityHandle)i );
    }
}

void create_vertices_block()
{
    std::vector< double* > arrays;
    ErrorCode rval = readTool->get_node_coords( 3, numVert, 0, vertStart, arrays );
    if( rval || arrays.size() != 3 )
    {
        assert( false );
        abort();
    }
    double *x = arrays[0], *y = arrays[1], *z = arrays[2];
    assert( x && y && z );

    for( long i = 0; i < numVert; ++i )
        vertex_coords( i, *x++, *y++, *z++ );
}

void create_elements_single()
{
    EntityHandle conn[8];
    element_conn( 0, conn );
    ErrorCode rval = mb.create_element( MBHEX, conn, 8, elemStart );
    if( rval )
    {
        assert( false );
        abort();
    }

    EntityHandle h;
    for( long i = 1; i < numElem; ++i )
    {
        element_conn( i, conn );
        rval = mb.create_element( MBHEX, conn, 8, h );
        assert( !rval );
        assert( h - elemStart == (EntityHandle)i );
    }
}

void create_elements_block()
{
    EntityHandle* conn = 0;
    ErrorCode rval     = readTool->get_element_connect( numElem, 8, MBHEX, 0, elemStart, conn );
    if( rval && !conn )
    {
        assert( false );
        abort();
    }

    for( long i = 0; i < numElem; ++i )
        element_conn( i, conn + 8 * i );
}

void forward_order_query_vertices( int percent )
{
    ErrorCode r;
    double coords[3];
    long x, y, z;
    const long vert_per_edge = numSideInt + 1;
    const long deleted_x     = ( numSideInt + 1 ) * ( 100 - percent ) / 100;
    EntityHandle h           = vertStart;
    for( z = 0; z < vert_per_edge; ++z )
    {
        for( y = 0; y < vert_per_edge; ++y )
        {
            for( x = 0; x < deleted_x; ++x, ++h )
            {
                r = mb.get_coords( &h, 1, coords );
                if( MB_SUCCESS != r )
                {
                    assert( false );
                    abort();
                }
            }
            h += ( vert_per_edge - deleted_x );
        }
    }
}

void reverse_order_query_vertices( int percent )
{
    ErrorCode r;
    double coords[3];
    long x, y, z;
    const long vert_per_edge = numSideInt + 1;
    const long deleted_x     = ( numSideInt + 1 ) * ( 100 - percent ) / 100;
    EntityHandle h           = vertStart + numVert - 1;
    ;
    for( z = vert_per_edge - 1; z >= 0; --z )
    {
        for( y = vert_per_edge - 1; y >= 0; --y )
        {
            h -= ( vert_per_edge - deleted_x );
            for( x = deleted_x - 1; x >= 0; --x, --h )
            {
                r = mb.get_coords( &h, 1, coords );
                assert( MB_SUCCESS == r );
                if( r ) {}  // empty line to remove compiler warning
            }
        }
    }
}

void random_order_query_vertices( int percent )
{
    ErrorCode r;
    EntityHandle h;
    double coords[3];
    for( long i = 0; i < numVert; ++i )
    {
        if( !deleted_vert( queryVertPermutation[i], percent ) )
        {
            h = vertStart + queryVertPermutation[i];
            r = mb.get_coords( &h, 1, coords );
            assert( MB_SUCCESS == r );
            if( r ) {}  // empty line to remove compiler warning
        }
    }
}

void forward_order_query_elements( int percent )
{
    ErrorCode r;
    const EntityHandle* conn;
    int len;
    long x, y, z;
    const long elem_per_edge = numSideInt;
    const long deleted_x     = ( numSideInt + 1 ) * ( 100 - percent ) / 100 - 1;
    EntityHandle h           = elemStart;
    for( z = 0; z < elem_per_edge; ++z )
    {
        for( y = 0; y < elem_per_edge; ++y )
        {
            for( x = 0; x < deleted_x; ++x, ++h )
            {
                r = mb.get_connectivity( h, conn, len );
                assert( MB_SUCCESS == r );
                if( r ) {}  // empty line to remove compiler warning
                assert( conn && 8 == len );
            }
            h += ( elem_per_edge - deleted_x );
        }
    }
}

void reverse_order_query_elements( int percent )
{
    ErrorCode r;
    const EntityHandle* conn;
    int len;
    long x, y, z;
    const long elem_per_edge = numSideInt;
    const long deleted_x     = ( numSideInt + 1 ) * ( 100 - percent ) / 100 - 1;
    EntityHandle h           = elemStart + numElem - 1;
    ;
    for( z = elem_per_edge - 1; z >= 0; --z )
    {
        for( y = elem_per_edge - 1; y >= 0; --y )
        {
            h -= ( elem_per_edge - deleted_x );
            for( x = deleted_x - 1; x >= 0; --x, --h )
            {
                r = mb.get_connectivity( h, conn, len );
                assert( MB_SUCCESS == r );
                if( r ) {}  // empty line to remove compiler warning
                assert( conn && 8 == len );
            }
        }
    }
}

void random_order_query_elements( int percent )
{
    ErrorCode r;
    const EntityHandle* conn;
    int len;
    for( long i = 0; i < numElem; ++i )
    {
        if( !deleted_elem( queryElemPermutation[i], percent ) )
        {
            r = mb.get_connectivity( elemStart + queryElemPermutation[i], conn, len );
            assert( MB_SUCCESS == r );
            if( r ) {}  // empty line to remove compiler warning
            assert( conn && 8 == len );
        }
    }
}

/*
static double hex_centroid( double coords[24], double cent[3] )
{
  double a[3], b[3], c[3], vol;
  cent[0] += 0.125*(coords[0] + coords[3] + coords[6] + coords[ 9] + coords[12] + coords[15] +
coords[18] + coords[21]); cent[1] += 0.125*(coords[1] + coords[4] + coords[7] + coords[10] +
coords[13] + coords[16] + coords[19] + coords[22]); cent[2] += 0.125*(coords[2] + coords[5] +
coords[8] + coords[11] + coords[14] + coords[17] + coords[20] + coords[23]); a[0] = coords[0] +
coords[3] + coords[15] + coords[12] - coords[ 9] - coords[6] - coords[18] - coords[21]; a[1] =
coords[1] + coords[4] + coords[16] + coords[13] - coords[10] - coords[7] - coords[19] - coords[22];
  a[2] = coords[2] + coords[5] + coords[17] + coords[14] - coords[11] - coords[8] - coords[20] -
coords[23]; b[0] = coords[0] + coords[ 9] + coords[21] + coords[12] - coords[3] - coords[6] -
coords[18] - coords[15]; b[1] = coords[1] + coords[10] + coords[22] + coords[13] - coords[4] -
coords[7] - coords[19] - coords[16]; b[2] = coords[2] + coords[11] + coords[23] + coords[14] -
coords[5] - coords[8] - coords[20] - coords[17]; c[0] = coords[0] + coords[3] + coords[6] + coords[
9] - coords[12] - coords[15] - coords[18] - coords[21]; c[1] = coords[1] + coords[4] + coords[7] +
coords[10] - coords[13] - coords[16] - coords[19] - coords[22]; c[2] = coords[2] + coords[5] +
coords[8] + coords[11] - coords[14] - coords[17] - coords[20] - coords[23]; vol = c[0]*(a[1]*b[2] -
a[2]*b[1]) + c[1]*(a[2]*b[0] - a[0]*b[2]) + c[2]*(a[0]*b[1] - a[1]*b[0]); return (1./64.) * vol;
}
*/

void forward_order_query_element_verts( int percent )
{
    ErrorCode r = MB_SUCCESS;
    if( r ) {}  // empty line to remove compiler warning
    const EntityHandle* conn;
    int len;
    long x, y, z;
    double coords[24];
    const long elem_per_edge = numSideInt;
    const long deleted_x     = ( numSideInt + 1 ) * ( 100 - percent ) / 100 - 1;
    EntityHandle h           = elemStart;
    for( z = 0; z < elem_per_edge; ++z )
    {
        for( y = 0; y < elem_per_edge; ++y )
        {
            for( x = 0; x < deleted_x; ++x, ++h )
            {
                r = mb.get_connectivity( h, conn, len );
                assert( MB_SUCCESS == r );
                assert( conn && 8 == len );
                r = mb.get_coords( conn, len, coords );
                assert( MB_SUCCESS == r );
            }
            h += ( elem_per_edge - deleted_x );
        }
    }
}

void reverse_order_query_element_verts( int percent )
{
    ErrorCode r = MB_SUCCESS;
    if( r ) {}  // empty statement to remove compiler warning

    const EntityHandle* conn;
    int len;
    long x, y, z;
    double coords[24];
    const long elem_per_edge = numSideInt;
    const long deleted_x     = ( numSideInt + 1 ) * ( 100 - percent ) / 100 - 1;
    EntityHandle h           = elemStart + numElem - 1;
    ;
    for( z = elem_per_edge - 1; z >= 0; --z )
    {
        for( y = elem_per_edge - 1; y >= 0; --y )
        {
            h -= ( elem_per_edge - deleted_x );
            for( x = deleted_x - 1; x >= 0; --x, --h )
            {
                r = mb.get_connectivity( h, conn, len );
                assert( MB_SUCCESS == r );
                assert( conn && 8 == len );
                r = mb.get_coords( conn, len, coords );
                assert( MB_SUCCESS == r );
            }
        }
    }
}

void random_order_query_element_verts( int percent )
{
    ErrorCode r = MB_SUCCESS;
    if( r ) {}  // empty line to remove compiler warning
    const EntityHandle* conn;
    int len;
    double coords[24];
    for( long i = 0; i < numElem; ++i )
    {
        if( !deleted_elem( queryElemPermutation[i], percent ) )
        {
            r = mb.get_connectivity( elemStart + queryElemPermutation[i], conn, len );
            assert( MB_SUCCESS == r );
            assert( conn && 8 == len );
            r = mb.get_coords( conn, len, coords );
            assert( MB_SUCCESS == r );
        }
    }
}

void forward_order_delete_vertices( int percent )
{
    for( long i = 0; i < numVert; ++i )
        delete_vert( i, percent );
}

void reverse_order_delete_vertices( int percent )
{
    for( long i = numVert - 1; i >= 0; --i )
        delete_vert( i, percent );
}

void random_order_delete_vertices( int percent )
{
    for( long i = 0; i < numVert; ++i )
        delete_vert( queryVertPermutation[i], percent );
}

void forward_order_delete_elements( int percent )
{
    for( long i = 0; i < numElem; ++i )
        delete_elem( i, percent );
}

void reverse_order_delete_elements( int percent )
{
    for( long i = numElem - 1; i >= 0; --i )
        delete_elem( i, percent );
}

void random_order_delete_elements( int percent )
{
    for( long i = 0; i < numElem; ++i )
        delete_elem( queryElemPermutation[i], percent );
}

void create_missing_vertices( int percent )
{
    EntityHandle h;
    ErrorCode rval = MB_SUCCESS;
    if( rval ) {}  // empty line to remove compiler warning
    double coords[3];
    for( long i = 0; i < numVert; ++i )
        if( deleted_vert( i, percent ) )
        {
            vertex_coords( i, coords[0], coords[1], coords[2] );
            rval = mb.create_vertex( coords, h );
            assert( !rval );
        }
}

void create_missing_elements( int percent )
{
    EntityHandle h;
    ErrorCode rval;
    EntityHandle conn[8];
    for( long i = 0; i < numElem; ++i )
        if( deleted_elem( i, percent ) )
        {
            element_conn( i, conn );
            rval = mb.create_element( MBHEX, conn, 8, h );
            if( rval )
            {
                assert( false );
                abort();
            }
        }
}

inline void delete_vert( long index, int percent )
{
    if( deleted_vert( index, percent ) )
    {
        EntityHandle h = index + vertStart;
        ErrorCode rval = mb.delete_entities( &h, 1 );
        if( rval )
        {
            assert( false );
            abort();
        }
    }
}

inline void delete_elem( long index, int percent )
{
    if( deleted_elem( index, percent ) )
    {
        EntityHandle h = index + elemStart;
        ErrorCode rval = mb.delete_entities( &h, 1 );
        if( rval )
        {
            assert( false );
            abort();
        }
    }
}

#ifdef PRINT_SEQUENCE_COUNT
unsigned get_number_sequences( EntityType type )
{
#ifdef MB_ENTITY_SEQUENCE_HPP
    return mb_core.sequence_manager()->entity_map( type )->size();
#else
    return mb_core.sequence_manager()->entity_map( type ).get_sequence_count();
#endif
}
#endif