mbaddchunk.cpp

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/*
 * addncdata.cpp
 * this tool will take an existing h5m file and add data from some chunk description files
 *  generated from e3sm runs;
 * will support mainly showing the chunks in ViSit
 *
 * example of usage:
 * ./mbaddchunk -i penta3d.h5m -n chunks_on_proc.txt -o penta3d_ch.h5m
 *
 *
 * Basically, will output a new h5m file (penta3d_ch.h5m), which has 2 extra tags, corresponding to
 * the chunks number and processors it sits on
 *
 *
 *  file  penta3d.h5m is obtained from the pentagons file, with a python script
 *
 */
 
#include "moab/ProgOptions.hpp"
#include "moab/Core.hpp"
 
#include <cmath>
#include <sstream>
#include <iostream>
#include <iomanip>
#include <fstream>
 
using namespace moab;
using namespace std;
 
int main( int argc, char* argv[] )
{
    ProgOptions opts;
 
    std::string inputfile( "penta3d.h5m" ), outfile( "penta3d_ch.h5m" ), chunkfile_name, gsmapfile;
    opts.addOpt< std::string >( "input,i", "input mesh filename", &inputfile );
    opts.addOpt< std::string >( "chunkFile,n", "chunk file from cam run", &chunkfile_name );
    opts.addOpt< std::string >( "gsMAPfile,g", "gsmap file", &gsmapfile );
    opts.addOpt< std::string >( "output,o", "output mesh filename", &outfile );
 
    opts.parseCommandLine( argc, argv );
 
    Core* mb = new Core();
 
    // open the netcdf file, and see if it has that variable we are looking for
    MB_CHK_SET_ERR( mb->load_file( inputfile.c_str() ), "can't load input file" );
    std::cout << " opened " << inputfile << " with initial h5m data.\n";
 
    Range nodes;
    MB_CHK_SET_ERR( mb->get_entities_by_dimension( 0, 0, nodes ), "can't get nodes" );
 
    Range edges;
    MB_CHK_SET_ERR( mb->get_entities_by_dimension( 0, 1, edges ), "can't get edges" );
 
    Range cells;
    MB_CHK_SET_ERR( mb->get_entities_by_dimension( 0, 2, cells ), "can't get cells" );
 
    std::cout << " it has " << nodes.size() << " vertices " << edges.size() << " edges " << cells.size() << " cells\n";
 
    // construct maps between global id and handles
    std::map< int, EntityHandle > vGidHandle;
    std::map< int, EntityHandle > eGidHandle;
    std::map< int, EntityHandle > cGidHandle;
    std::vector< int > gids;
    Tag gid = mb->globalId_tag();
    
    gids.resize( nodes.size() );
    MB_CHK_SET_ERR( mb->tag_get_data( gid, nodes, &gids[0] ), "can't get global id on vertices" );
    int i = 0;
    for( Range::iterator vit = nodes.begin(); vit != nodes.end(); vit++ )
    {
        vGidHandle[gids[i++]] = *vit;
    }
 
    gids.resize( edges.size() );
    MB_CHK_SET_ERR( mb->tag_get_data( gid, edges, &gids[0] ), "can't get global id on edges" );
    i = 0;
    for( Range::iterator vit = edges.begin(); vit != edges.end(); vit++ )
    {
        eGidHandle[gids[i++]] = *vit;
    }
 
    gids.resize( cells.size() );
    MB_CHK_SET_ERR( mb->tag_get_data( gid, cells, &gids[0] ), "can't get global id on cells" );
    i = 0;
    for( Range::iterator vit = cells.begin(); vit != cells.end(); vit++ )
    {
        cGidHandle[gids[i++]] = *vit;
    }
 
    if( chunkfile_name.length() > 0 )
    {
        // Open chunk file
        ifstream inFile;
        inFile.open( chunkfile_name.c_str() );
        if( !inFile )
        {
            cout << "Unable to open chunk file";
            exit( 1 );  // terminate with error
        }
 
        Tag pTag, cTag;
        int def_val = -1;
        MB_CHK_SET_ERR( mb->tag_get_handle( "ProcID", 1, MB_TYPE_INTEGER, pTag, MB_TAG_CREAT | MB_TAG_DENSE, &def_val ),
                        "can't define processor tag" );
        MB_CHK_SET_ERR( mb->tag_get_handle( "ChunkID", 1, MB_TYPE_INTEGER, cTag, MB_TAG_CREAT | MB_TAG_DENSE,
                                            &def_val ),
                        "can't define chunk tag" );
 
        int proc, lcid, ncols;
        while( inFile >> proc )
        {
            inFile >> lcid >> ncols;
            int Gid;
            for( i = 0; i < ncols; i++ )
            {
                inFile >> Gid;
                EntityHandle cell = cGidHandle[Gid];
                MB_CHK_SET_ERR( mb->tag_set_data( pTag, &cell, 1, &proc ), "can't set proc tag" );
                MB_CHK_SET_ERR( mb->tag_set_data( cTag, &cell, 1, &lcid ), "can't set chunk tag" );
            }
        }
 
        inFile.close();
    }
 
    if( gsmapfile.length() > 0 )
    {
        // Open chunk file
        ifstream inFile;
 
        inFile.open( gsmapfile.c_str() );
        if( !inFile )
        {
            cout << "Unable to open gsmap file";
            exit( 1 );  // terminate with error
        }
 
        Tag pTag, cTag;
        int def_val             = -1;
        std::string procTagName = gsmapfile + "_proc";
        MB_CHK_SET_ERR( mb->tag_get_handle( procTagName.c_str(), 1, MB_TYPE_INTEGER, pTag, MB_TAG_CREAT | MB_TAG_DENSE,
                                            &def_val ),
                        "can't define processor tag" );
        std::string segTagName = gsmapfile + "_seg";
        MB_CHK_SET_ERR( mb->tag_get_handle( segTagName.c_str(), 1, MB_TYPE_INTEGER, cTag, MB_TAG_CREAT | MB_TAG_DENSE,
                                            &def_val ),
                        "can't define segment tag" );
 
        int compid, ngseg, gsize;
        inFile >> compid >> ngseg >> gsize;
        for( i = 1; i <= ngseg; i++ )
        {
            int start, len, pe;
            inFile >> start >> len >> pe;
            int Gid;
            for( int j = 0; j < len; j++ )
            {
                Gid               = start + j;
                EntityHandle cell = cGidHandle[Gid];
                MB_CHK_SET_ERR( mb->tag_set_data( pTag, &cell, 1, &pe ), "can't set proc tag" );
                MB_CHK_SET_ERR( mb->tag_set_data( cTag, &cell, 1, &i ), "can't set segment tag" );
            }
        }
 
        inFile.close();
    }
 
    MB_CHK_SET_ERR( mb->write_file( outfile.c_str() ), "can't write file" );
    std::cout << " wrote file " << outfile << "\n";
    return 0;
}