GenLargeMesh.cpp

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/** @example GenLargeMesh.cpp \n
 * \brief Create a large structured mesh, partitioned \n
 *
 *  It shows how to create a mesh on the fly, on multiple processors
 *  Each processor will create its version of a block mesh, partitioned
 *  as AxBxC blocks. Each block will be with blockSize^3 hexahedrons, and
 *  will get a different PARALLEL_PARTITION tag
 *
 *  The number of tasks will be MxNxK, and it must match the mpi size
 *  Each task p will generate its mesh at location (m,n,k), and it is
 *  lexicographic ordering: rank = m + n * M + k * M * N
 *
 *  By default M=1, N=1, K=1, so by default it should be launched on 1 proc
 *  By default, blockSize is 4, and A=2, B=2, C=2, so each task will generate locally
 *  blockSize^3 x A x B x C hexahedrons (value = 64x8 = 512 hexas, in 8 partitions)
 *  (if -t, multiple by 6 for total number of cells/tets)
 *  The total number of partitions will be A*B*C*M*N*K (default 8)
 *
 *  Each part in partition will get a proper tag, and the numbering is in
 *  lexicographic ordering; x direction varies first, then y, then z.
 *  The same principle is used for global id numbering of the nodes and cells.
 *  (x varies first)
 *
 *  The vertices will get a proper global id, which will be used to resolve the
 *  shared entities
 *  The output will be written in parallel, and we will try sizes as big as we can
 *  (up to a billion vertices, because we use int for global ids)
 *
 *  Within each partition, the hexas entity handles will be contiguous, and also the
 *  vertices; The global id will be determined easily, for a vertex, but the entity
 *  handle space will be more interesting to handle, within a partition (we want
 *  contiguous handles within a partition). After merging the vertices, some fragmentation
 *  will occur in the vertices handle space, within each partition.
 *
 *  To run: ./GenLargeMesh
 *
 *  When launched on more procs, you have to make sure
 *  num procs = M*N*K
 *
 *  So you can launch with
 *  mpiexec -np 8 ./GenLargeMesh -M 2 -N 2 -K 2
 *
 *  We also added -q option; it works now only for hexa mesh, it will generate
 *  quadratic hex27 elements
 *
 *  -t option will generate tetrahedrons instead of hexahedra. Each hexahedra is
 *  decomposed into 6 tetrahedrons.
 *
 *  -f option will also generate all edges and faces in the model.
 *  -w will use a newer merging method locally. Merging is necessary to merge
 *  vertices on the local task, and the new method does not use a searching tree,
 *  but rather the global id set on the vertices in a consistent manner
 *
 *  -d and -i options can be used to add some artificial tags on the model;
 *  you can have multiple -d and -i options; -i <tag_name> will set an integer
 *  tag with name tag_name on the vertices; -d < tag_name2> will generate
 *  double tags on cells (3d elements). You can have multiple tags, like
 *  -i tag1 -i tag2 -i tag3 -d tag4
 *
 *  -x, -y, -z options will control the geometric dimensions of the final mesh, in
 *  x, y and z directions.
 *
 *  -o <out_file> controls the name of the output file; it needs to have extension h5m,
 *  because the file is written in parallel.
 *
 *  -k will keep the edges and faces that are generated as part of resolving shared entities
 *  (by default these edges and faces are removed); when -f option is used, the -k option is
 *  enabled too (so no faces and edges are deleted)
 *
 */
 
#include "moab/Core.hpp"
#include "moab/ProgOptions.hpp"
#include "moab/MeshGeneration.hpp"
#ifdef MOAB_HAVE_MPI
#include "moab/ParallelComm.hpp"
#include "MBParallelConventions.h"
#endif
 
#include <ctime>
#include <iostream>
#include <vector>
 
using namespace moab;
using namespace std;
 
int main( int argc, char** argv )
{
 
    bool nosave = false;
 
#ifdef MOAB_HAVE_MPI
    MPI_Init( &argc, &argv );
#endif
    MeshGeneration::BrickOpts bopts;
    // default options
    bopts.A = bopts.B = bopts.C = 2;
    bopts.M = bopts.N = bopts.K = 1;
    bopts.blockSize             = 4;
    bopts.xsize = bopts.ysize = bopts.zsize = 1.;
    bopts.ui                                = CartVect( 1., 0, 0. );
    bopts.uj                                = CartVect( 0., 1., 0. );
    bopts.uk                                = CartVect( 0., 0., 1. );
    bopts.newMergeMethod = bopts.quadratic = bopts.keep_skins = bopts.tetra = false;
    bopts.adjEnts = bopts.parmerge = false;
    bopts.GL                       = 0;
 
    ProgOptions opts;
 
    opts.addOpt< int >( string( "blockSize,b" ), string( "Block size of mesh (default=4)" ), &bopts.blockSize );
    opts.addOpt< int >( string( "xproc,M" ), string( "Number of processors in x dir (default=1)" ), &bopts.M );
    opts.addOpt< int >( string( "yproc,N" ), string( "Number of processors in y dir (default=1)" ), &bopts.N );
    opts.addOpt< int >( string( "zproc,K" ), string( "Number of processors in z dir (default=1)" ), &bopts.K );
 
    opts.addOpt< int >( string( "xblocks,A" ), string( "Number of blocks on a task in x dir (default=2)" ), &bopts.A );
    opts.addOpt< int >( string( "yblocks,B" ), string( "Number of blocks on a task in y dir (default=2)" ), &bopts.B );
    opts.addOpt< int >( string( "zblocks,C" ), string( "Number of blocks on a task in x dir (default=2)" ), &bopts.C );
 
    opts.addOpt< double >( string( "xsize,x" ), string( "Total size in x direction (default=1.)" ), &bopts.xsize );
    opts.addOpt< double >( string( "ysize,y" ), string( "Total size in y direction (default=1.)" ), &bopts.ysize );
    opts.addOpt< double >( string( "zsize,z" ), string( "Total size in z direction (default=1.)" ), &bopts.zsize );
 
    opts.addOpt< void >( "newMerge,w", "use new merging method", &bopts.newMergeMethod );
 
    opts.addOpt< void >( "quadratic,q", "use hex 27 elements", &bopts.quadratic );
 
    opts.addOpt< void >( "keep_skins,k", "keep skins with shared entities", &bopts.keep_skins );
 
    opts.addOpt< void >( "tetrahedrons,t", "generate tetrahedrons", &bopts.tetra );
 
    opts.addOpt< void >( "faces_edges,f", "create all faces and edges", &bopts.adjEnts );
 
    opts.addOpt< int >( string( "ghost_layers,g" ), string( "Number of ghost layers (default=0)" ), &bopts.GL );
 
    vector< string > intTagNames;
    string firstIntTag;
    opts.addOpt< string >( "int_tag_vert,i", "add integer tag on vertices", &firstIntTag );
 
    vector< string > doubleTagNames;
    string firstDoubleTag;
    opts.addOpt< string >( "double_tag_cell,d", "add double tag on cells", &firstDoubleTag );
 
    string outFileName = "GenLargeMesh.h5m";
    opts.addOpt< string >( "outFile,o", "Specify the output file name string (default GenLargeMesh.h5m)",
                           &outFileName );
 
#ifdef MOAB_HAVE_HDF5_PARALLEL
    bool readb = false;
    opts.addOpt< void >( "readback,r", "read back the generated mesh", &readb );
 
    bool readAndGhost = false;
    opts.addOpt< void >( "readAndGhost,G", "read back the generated mesh and ghost one layer", &readAndGhost );
#endif
 
    opts.addOpt< void >( "parallel_merge,p", "use parallel mesh merge, not vertex ID based merge", &bopts.parmerge );
 
    opts.addOpt< void >( "no_save,n", "do not save the file", &nosave );
 
    opts.parseCommandLine( argc, argv );
 
    opts.getOptAllArgs( "int_tag_vert,i", intTagNames );
    opts.getOptAllArgs( "double_tag_cell,d", doubleTagNames );
 
    if( bopts.adjEnts ) bopts.keep_skins = true;  // Do not delete anything
 
    Interface* mb = new( std::nothrow ) Core;
    if( NULL == mb )
    {
#ifdef MOAB_HAVE_MPI
        MPI_Finalize();
#endif
        return 1;
    }
 
    int rank = 0, size = 1;
 
#ifdef MOAB_HAVE_MPI
    MPI_Comm_rank( MPI_COMM_WORLD, &rank );
    MPI_Comm_size( MPI_COMM_WORLD, &size );
#endif
 
    EntityHandle fileset;
    ErrorCode rval = mb->create_meshset( MESHSET_SET, fileset );MB_CHK_ERR( rval );
#ifdef MOAB_HAVE_MPI
    ParallelComm* pc     = new ParallelComm( mb, MPI_COMM_WORLD );
    MeshGeneration* mgen = new MeshGeneration( mb, pc, fileset );
#else
    MeshGeneration* mgen = new MeshGeneration( mb, 0, fileset );
#endif
 
    clock_t tt = clock();
 
    rval = mgen->BrickInstance( bopts );MB_CHK_ERR( rval );
 
    Range all3dcells;
    rval = mb->get_entities_by_dimension( fileset, 3, all3dcells );MB_CHK_ERR( rval );
 
    if( 0 == rank )
    {
        cout << "generate local mesh: " << ( clock() - tt ) / (double)CLOCKS_PER_SEC << " seconds" << endl;
        tt = clock();
        cout << "number of elements on rank 0: " << all3dcells.size() << endl;
        cout << "Total number of elements " << all3dcells.size() * size << endl;
        cout << "Element type: " << ( bopts.tetra ? "MBTET" : "MBHEX" )
             << " order:" << ( bopts.quadratic ? "quadratic" : "linear" ) << endl;
    }
    Range verts;
    rval = mb->get_entities_by_dimension( 0, 0, verts );MB_CHK_SET_ERR( rval, "Can't get all vertices" );
 
    if( !nosave )
    {
#ifdef MOAB_HAVE_HDF5_PARALLEL
        rval = mb->write_file( outFileName.c_str(), 0, ";;PARALLEL=WRITE_PART;CPUTIME;", &fileset, 1 );MB_CHK_SET_ERR( rval, "Can't write in parallel" );
#else
        // should be a vtk file, actually, maybe make sure of that
        rval = mb->write_file( outFileName.c_str(), 0, "", &fileset, 1 );MB_CHK_SET_ERR( rval, "Can't write in serial" );
#endif
        if( 0 == rank )
        {
            cout << "write file " << outFileName << " in " << ( clock() - tt ) / (double)CLOCKS_PER_SEC << " seconds"
                 << endl;
            tt = clock();
        }
    }
    // delete the mesh that we already have in-memory
    size_t nLocalVerts = verts.size();
    size_t nLocalCells = all3dcells.size();
 
    mb->delete_mesh();
 
#ifdef MOAB_HAVE_HDF5_PARALLEL
    if( !nosave && readb )
    {
        // now recreate a core instance and load the file we just wrote out to verify
        Core mb2;
        std::string read_opts( "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARALLEL_RESOLVE_"
                               "SHARED_ENTS;CPUTIME;" );
        if( readAndGhost ) read_opts += "PARALLEL_GHOSTS=3.0.1;";
        rval = mb2.load_file( outFileName.c_str(), 0, read_opts.c_str() );MB_CHK_SET_ERR( rval, "Can't read in parallel" );
        if( 0 == rank )
        {
            cout << "read back file " << outFileName << " with options: \n"
                 << read_opts << " in " << ( clock() - tt ) / (double)CLOCKS_PER_SEC << " seconds" << endl;
            tt = clock();
        }
        moab::Range nverts, ncells;
        rval = mb2.get_entities_by_dimension( 0, 0, nverts );MB_CHK_SET_ERR( rval, "Can't get all vertices" );
        rval = mb2.get_entities_by_dimension( 0, 3, ncells );MB_CHK_SET_ERR( rval, "Can't get all 3d cells elements" );
 
        if( readAndGhost && size > 1 )
        {
            // filter out the ghost nodes and elements, for comparison with original mesh
            // first get the parallel comm
            ParallelComm* pcomm2 = ParallelComm::get_pcomm( &mb2, 0 );
            if( NULL == pcomm2 ) MB_SET_ERR( MB_FAILURE, "can't get parallel comm." );
            rval = pcomm2->filter_pstatus( nverts, PSTATUS_GHOST, PSTATUS_NOT );MB_CHK_SET_ERR( rval, "Can't filter ghost vertices" );
            rval = pcomm2->filter_pstatus( ncells, PSTATUS_GHOST, PSTATUS_NOT );MB_CHK_SET_ERR( rval, "Can't filter ghost cells" );
        }
        if( nverts.size() != nLocalVerts && ncells.size() != nLocalCells )
        {
            MB_SET_ERR( MB_FAILURE, "Reading back the output file led to inconsistent number of entities." );
        }
 
        // delete the mesh that we already have in-memory
        mb2.delete_mesh();
    }
#endif
 
#ifdef MOAB_HAVE_MPI
    MPI_Finalize();
#endif
    return 0;
}