read_gcrm_nc.cpp

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#include "TestUtil.hpp"
#include "moab/Core.hpp"
#include "moab/ReadUtilIface.hpp"
#include "MBTagConventions.hpp"

using namespace moab;

std::string example = TestDir + "unittest/io/gcrm_r3.nc";

#ifdef MOAB_HAVE_MPI
#include "moab_mpi.h"
#include "moab/ParallelComm.hpp"
#endif

void test_read_all();
void test_read_onevar();
void test_read_onetimestep();
void test_read_nomesh();
void test_read_novars();
void test_read_no_edges();  // Test read option NO_EDGES
void test_gather_onevar();  // Test gather set with one variable

void get_options( std::string& opts );

const double eps     = 1e-6;
const int layers     = 3;
const int interfaces = 3;

int main( int argc, char* argv[] )
{
    int result = 0;

#ifdef MOAB_HAVE_MPI
    int fail = MPI_Init( &argc, &argv );
    if( fail ) return 1;
#else
    argv[0]   = argv[argc - argc];  // To remove the warnings in serial mode about unused variables
#endif

    result += RUN_TEST( test_read_all );
    result += RUN_TEST( test_read_onevar );
    result += RUN_TEST( test_read_onetimestep );
    result += RUN_TEST( test_read_nomesh );
    result += RUN_TEST( test_read_novars );
    result += RUN_TEST( test_read_no_edges );
    result += RUN_TEST( test_gather_onevar );

#ifdef MOAB_HAVE_MPI
    fail = MPI_Finalize();
    if( fail ) return 1;
#endif

    return result;
}

void test_read_all()
{
    Core moab;
    Interface& mb = moab;

    std::string opts;
    get_options( opts );

    // Read mesh and read all variables at all timesteps
    ErrorCode rval = mb.load_file( example.c_str(), 0, opts.c_str() );CHECK_ERR( rval );

#ifdef MOAB_HAVE_MPI
    ParallelComm* pcomm = ParallelComm::get_pcomm( &mb, 0 );
    int procs           = pcomm->proc_config().proc_size();
#else
    int procs = 1;
#endif

    // Make check runs this test on one processor
    if( 1 == procs )
    {
        // For u, wind and vorticity, check tag values on two entities
        double val[2 * layers];

        // Check tags for vertex variable u
        Tag u_tag0, u_tag1;
        rval = mb.tag_get_handle( "u0", layers, MB_TYPE_DOUBLE, u_tag0 );CHECK_ERR( rval );
        rval = mb.tag_get_handle( "u1", layers, MB_TYPE_DOUBLE, u_tag1 );CHECK_ERR( rval );

        // Get vertices (1280 vertices)
        Range verts;
        rval = mb.get_entities_by_type( 0, MBVERTEX, verts );CHECK_ERR( rval );
        CHECK_EQUAL( (size_t)1280, verts.size() );
        CHECK_EQUAL( (size_t)1, verts.psize() );

        // Check u tag values on first and last vertices
        EntityHandle vert_ents[] = { verts[0], verts[1279] };

        // Only check first two layers
        // Timestep 0
        rval = mb.tag_get_data( u_tag0, vert_ents, 2, val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( -4.839992, val[0 * layers], eps );
        CHECK_REAL_EQUAL( -3.699257, val[1 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( -4.839925, val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( -3.699206, val[1 * layers + 1], eps );

        // Timestep 1
        rval = mb.tag_get_data( u_tag1, vert_ents, 2, val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( -4.712473, val[0 * layers], eps );
        CHECK_REAL_EQUAL( -3.601793, val[1 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( -4.712409, val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( -3.601743, val[1 * layers + 1], eps );

        // Check tags for edge variable wind
        Tag wind_tag0, wind_tag1;
        rval = mb.tag_get_handle( "wind0", layers, MB_TYPE_DOUBLE, wind_tag0 );CHECK_ERR( rval );
        rval = mb.tag_get_handle( "wind1", layers, MB_TYPE_DOUBLE, wind_tag1 );CHECK_ERR( rval );

        // Get edges (1920 edges)
        Range edges;
        rval = mb.get_entities_by_type( 0, MBEDGE, edges );CHECK_ERR( rval );
        CHECK_EQUAL( (size_t)1920, edges.size() );
        CHECK_EQUAL( (size_t)1, edges.psize() );

        // Check wind tag values on first and last edges
        EntityHandle edge_ents[] = { edges[0], edges[1919] };

        // Only check first two layers
        // Timestep 0
        rval = mb.tag_get_data( wind_tag0, edge_ents, 2, val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( -5.081991, val[0 * layers], eps );
        CHECK_REAL_EQUAL( -6.420274, val[1 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( -5.081781, val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( -6.419831, val[1 * layers + 1], eps );

        // Timestep 1
        rval = mb.tag_get_data( wind_tag1, edge_ents, 2, val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( -4.948097, val[0 * layers], eps );
        CHECK_REAL_EQUAL( -6.251121, val[1 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( -4.947892, val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( -6.250690, val[1 * layers + 1], eps );

        // Check tags for cell variable vorticity
        Tag vorticity_tag0, vorticity_tag1;
        rval = mb.tag_get_handle( "vorticity0", layers, MB_TYPE_DOUBLE, vorticity_tag0 );CHECK_ERR( rval );
        rval = mb.tag_get_handle( "vorticity1", layers, MB_TYPE_DOUBLE, vorticity_tag1 );CHECK_ERR( rval );

        // Get cells (12 pentagons and 630 hexagons)
        Range cells;
        rval = mb.get_entities_by_type( 0, MBPOLYGON, cells );CHECK_ERR( rval );
        CHECK_EQUAL( (size_t)642, cells.size() );

        // GCRM pentagons are always padded to hexagons
        CHECK_EQUAL( (size_t)1, cells.psize() );

        // Check vorticity tag values on first and last cells
        EntityHandle cell_ents[] = { cells[0], cells[641] };

        // Only check first two layers
        // Timestep 0
        rval = mb.tag_get_data( vorticity_tag0, cell_ents, 2, val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( 3.629994, val[0 * layers], eps );
        CHECK_REAL_EQUAL( -0.554888, val[1 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( 3.629944, val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.554881, val[1 * layers + 1], eps );

        // Timestep 1
        rval = mb.tag_get_data( vorticity_tag1, cell_ents, 2, val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( 3.534355, val[0 * layers], eps );
        CHECK_REAL_EQUAL( -0.540269, val[1 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( 3.534306, val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.540262, val[1 * layers + 1], eps );

        // Check tags for cell variable pressure
        Tag pressure_tag0, pressure_tag1;
        rval = mb.tag_get_handle( "pressure0", interfaces, MB_TYPE_DOUBLE, pressure_tag0 );CHECK_ERR( rval );
        rval = mb.tag_get_handle( "pressure1", interfaces, MB_TYPE_DOUBLE, pressure_tag1 );CHECK_ERR( rval );

        // For pressure, check tag values on two cells
        double pressure_val[2 * interfaces];

        // Check pressure tag values on first and last cells
        // Only check first two interfaces
        // Timestep 0
        rval = mb.tag_get_data( pressure_tag0, cell_ents, 2, pressure_val );CHECK_ERR( rval );
        // Interface 0
        CHECK_REAL_EQUAL( 4.44234e-06, pressure_val[0 * interfaces], 1e-11 );
        CHECK_REAL_EQUAL( 0.2486804, pressure_val[1 * interfaces], 1e-7 );
        // Interface 1
        CHECK_REAL_EQUAL( 4.44234e-06, pressure_val[0 * interfaces + 1], 1e-11 );
        CHECK_REAL_EQUAL( 0.2486804, pressure_val[1 * interfaces + 1], 1e-7 );

        // Timestep 1
        rval = mb.tag_get_data( pressure_tag1, cell_ents, 2, pressure_val );CHECK_ERR( rval );
        // Interface 0
        CHECK_REAL_EQUAL( 2.365176e-07, pressure_val[0 * interfaces], 1e-13 );
        CHECK_REAL_EQUAL( 0.02234409, pressure_val[1 * interfaces], 1e-8 );
        // Interface 1
        CHECK_REAL_EQUAL( 2.365176e-07, pressure_val[0 * interfaces + 1], 1e-13 );
        CHECK_REAL_EQUAL( 0.02234409, pressure_val[1 * interfaces + 1], 1e-8 );
    }
}

void test_read_onevar()
{
    Core moab;
    Interface& mb = moab;

    std::string opts;
    get_options( opts );

    // Read mesh and read cell variable vorticity at all timesteps
    opts += ";VARIABLE=vorticity";
    ErrorCode rval = mb.load_file( example.c_str(), NULL, opts.c_str() );CHECK_ERR( rval );

#ifdef MOAB_HAVE_MPI
    ParallelComm* pcomm = ParallelComm::get_pcomm( &mb, 0 );
    int procs           = pcomm->proc_config().proc_size();
#else
    int procs = 1;
#endif

    // Make check runs this test on one processor
    if( 1 == procs )
    {
        // Check vorticity tags
        Tag vorticity_tag0, vorticity_tag1;
        rval = mb.tag_get_handle( "vorticity0", layers, MB_TYPE_DOUBLE, vorticity_tag0 );CHECK_ERR( rval );
        rval = mb.tag_get_handle( "vorticity1", layers, MB_TYPE_DOUBLE, vorticity_tag1 );CHECK_ERR( rval );

        // Get cells (12 pentagons and 630 hexagons)
        Range cells;
        rval = mb.get_entities_by_type( 0, MBPOLYGON, cells );CHECK_ERR( rval );
        CHECK_EQUAL( (size_t)642, cells.size() );

        // GCRM pentagons are always padded to hexagons
        CHECK_EQUAL( (size_t)1, cells.psize() );

        // Check vorticity tag values on 4 cells: first cell, two median cells, and last cell
        EntityHandle cell_ents[] = { cells[0], cells[320], cells[321], cells[641] };
        double vorticity_val[4 * layers];

        // Only check first two layers
        // Timestep 0
        rval = mb.tag_get_data( vorticity_tag0, cell_ents, 4, vorticity_val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( 3.629994, vorticity_val[0 * layers], eps );
        CHECK_REAL_EQUAL( 0.131688, vorticity_val[1 * layers], eps );
        CHECK_REAL_EQUAL( -0.554888, vorticity_val[2 * layers], eps );
        CHECK_REAL_EQUAL( -0.554888, vorticity_val[3 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( 3.629944, vorticity_val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( 0.131686, vorticity_val[1 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.554881, vorticity_val[2 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.554881, vorticity_val[3 * layers + 1], eps );

        // Timestep 1
        rval = mb.tag_get_data( vorticity_tag1, cell_ents, 4, vorticity_val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( 3.534355, vorticity_val[0 * layers], eps );
        CHECK_REAL_EQUAL( 0.128218, vorticity_val[1 * layers], eps );
        CHECK_REAL_EQUAL( -0.540269, vorticity_val[2 * layers], eps );
        CHECK_REAL_EQUAL( -0.540269, vorticity_val[3 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( 3.534306, vorticity_val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( 0.128216, vorticity_val[1 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.540262, vorticity_val[2 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.540262, vorticity_val[3 * layers + 1], eps );
    }
}

void test_read_onetimestep()
{
    Core moab;
    Interface& mb = moab;

    std::string opts;
    get_options( opts );

    // Read mesh and read all variables at 2nd timestep
    opts += ";TIMESTEP=1";
    ErrorCode rval = mb.load_file( example.c_str(), NULL, opts.c_str() );CHECK_ERR( rval );

    // Check vorticity tags
    Tag vorticity_tag0, vorticity_tag1;
    rval = mb.tag_get_handle( "vorticity0", layers, MB_TYPE_DOUBLE, vorticity_tag0 );
    // Tag vorticity0 should not exist
    CHECK_EQUAL( rval, MB_TAG_NOT_FOUND );
    rval = mb.tag_get_handle( "vorticity1", layers, MB_TYPE_DOUBLE, vorticity_tag1 );CHECK_ERR( rval );
}

void test_read_nomesh()
{
    Core moab;
    Interface& mb = moab;

    // Need a file set for nomesh to work right
    EntityHandle file_set;
    ErrorCode rval = mb.create_meshset( MESHSET_SET, file_set );CHECK_ERR( rval );

    std::string orig, opts;
    get_options( orig );

    // Read mesh and read all variables at 1st timestep
    opts = orig + ";TIMESTEP=0";
    rval = mb.load_file( example.c_str(), &file_set, opts.c_str() );CHECK_ERR( rval );

    // Check u tags
    Tag u_tag0, u_tag1;
    rval = mb.tag_get_handle( "u0", layers, MB_TYPE_DOUBLE, u_tag0 );CHECK_ERR( rval );
    // Tag u1 should not exist
    rval = mb.tag_get_handle( "u1", layers, MB_TYPE_DOUBLE, u_tag1 );
    CHECK_EQUAL( rval, MB_TAG_NOT_FOUND );

    // Read all variables at 2nd timestep 0, no need to read mesh
    opts = orig + ";TIMESTEP=1;NOMESH";
    rval = mb.load_file( example.c_str(), &file_set, opts.c_str() );CHECK_ERR( rval );

    // Check tag u1 again
    rval = mb.tag_get_handle( "u1", layers, MB_TYPE_DOUBLE, u_tag1 );
    // Tag u1 should exist at this time
    CHECK_ERR( rval );
}

void test_read_novars()
{
    Core moab;
    Interface& mb = moab;

    // Need a file set for nomesh to work right
    EntityHandle file_set;
    ErrorCode rval = mb.create_meshset( MESHSET_SET, file_set );CHECK_ERR( rval );

    std::string orig, opts;
    get_options( orig );CHECK_ERR( rval );

    // Read header info only, no mesh, no variables
    opts = orig + ";NOMESH;VARIABLE=";
    rval = mb.load_file( example.c_str(), &file_set, opts.c_str() );CHECK_ERR( rval );

    // Read mesh, but still no variables
    opts = orig + ";VARIABLE=";
    rval = mb.load_file( example.c_str(), &file_set, opts.c_str() );CHECK_ERR( rval );

    // Check vorticity tags
    Tag vorticity_tag0, vorticity_tag1;
    rval = mb.tag_get_handle( "vorticity0", layers, MB_TYPE_DOUBLE, vorticity_tag0 );
    // Tag vorticity0 should not exist
    CHECK_EQUAL( rval, MB_TAG_NOT_FOUND );
    rval = mb.tag_get_handle( "vorticity1", layers, MB_TYPE_DOUBLE, vorticity_tag1 );
    // Tag vorticity1 should not exist
    CHECK_EQUAL( rval, MB_TAG_NOT_FOUND );

    // Read vorticity at 1st timestep, no need to read mesh
    opts = orig + ";VARIABLE=vorticity;TIMESTEP=0;NOMESH";
    rval = mb.load_file( example.c_str(), &file_set, opts.c_str() );CHECK_ERR( rval );

    // Check vorticity tags again
    rval = mb.tag_get_handle( "vorticity0", layers, MB_TYPE_DOUBLE, vorticity_tag0 );
    // Tag vorticity0 should exist at this time
    CHECK_ERR( rval );
    // Tag vorticity1 should still not exist
    rval = mb.tag_get_handle( "vorticity1", layers, MB_TYPE_DOUBLE, vorticity_tag1 );
    CHECK_EQUAL( rval, MB_TAG_NOT_FOUND );

    // Read vorticity at 2nd timestep, no need to read mesh
    opts = orig + ";VARIABLE=vorticity;TIMESTEP=1;NOMESH";
    rval = mb.load_file( example.c_str(), &file_set, opts.c_str() );CHECK_ERR( rval );

    // Check tag vorticity1 again
    rval = mb.tag_get_handle( "vorticity1", layers, MB_TYPE_DOUBLE, vorticity_tag1 );
    // Tag vorticity1 should exist at this time
    CHECK_ERR( rval );

#ifdef MOAB_HAVE_MPI
    ParallelComm* pcomm = ParallelComm::get_pcomm( &mb, 0 );
    int procs           = pcomm->proc_config().proc_size();
#else
    int procs = 1;
#endif

    // Make check runs this test on one processor
    if( 1 == procs )
    {
        // Get cells (12 pentagons and 630 hexagons)
        Range cells;
        rval = mb.get_entities_by_type( file_set, MBPOLYGON, cells );CHECK_ERR( rval );
        CHECK_EQUAL( (size_t)642, cells.size() );

        // GCRM pentagons are always padded to hexagons
        CHECK_EQUAL( (size_t)1, cells.psize() );

        // Check vorticity tag values on 4 cells: first cell, two median cells, and last cell
        EntityHandle cell_ents[] = { cells[0], cells[320], cells[321], cells[641] };
        double vorticity_val[4 * layers];

        // Only check first two layers
        // Timestep 0
        rval = mb.tag_get_data( vorticity_tag0, cell_ents, 4, vorticity_val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( 3.629994, vorticity_val[0 * layers], eps );
        CHECK_REAL_EQUAL( 0.131688, vorticity_val[1 * layers], eps );
        CHECK_REAL_EQUAL( -0.554888, vorticity_val[2 * layers], eps );
        CHECK_REAL_EQUAL( -0.554888, vorticity_val[3 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( 3.629944, vorticity_val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( 0.131686, vorticity_val[1 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.554881, vorticity_val[2 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.554881, vorticity_val[3 * layers + 1], eps );

        // Timestep 1
        rval = mb.tag_get_data( vorticity_tag1, cell_ents, 4, vorticity_val );CHECK_ERR( rval );
        // Layer 0
        CHECK_REAL_EQUAL( 3.534355, vorticity_val[0 * layers], eps );
        CHECK_REAL_EQUAL( 0.128218, vorticity_val[1 * layers], eps );
        CHECK_REAL_EQUAL( -0.540269, vorticity_val[2 * layers], eps );
        CHECK_REAL_EQUAL( -0.540269, vorticity_val[3 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( 3.534306, vorticity_val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( 0.128216, vorticity_val[1 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.540262, vorticity_val[2 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.540262, vorticity_val[3 * layers + 1], eps );
    }
}

void test_read_no_edges()
{
    Core moab;
    Interface& mb = moab;

    std::string opts;
    get_options( opts );

    opts += ";NO_EDGES;VARIABLE=";
    ErrorCode rval = mb.load_file( example.c_str(), NULL, opts.c_str() );CHECK_ERR( rval );

    // Get edges
    Range edges;
    rval = mb.get_entities_by_type( 0, MBEDGE, edges );CHECK_ERR( rval );
    CHECK_EQUAL( (size_t)0, edges.size() );
}

void test_gather_onevar()
{
    Core moab;
    Interface& mb = moab;

    EntityHandle file_set;
    ErrorCode rval = mb.create_meshset( MESHSET_SET, file_set );CHECK_ERR( rval );

    std::string opts;
    get_options( opts );

    // Read cell variable vorticity and create gather set on processor 0
    opts += ";VARIABLE=vorticity;GATHER_SET=0";
    rval = mb.load_file( example.c_str(), &file_set, opts.c_str() );CHECK_ERR( rval );

#ifdef MOAB_HAVE_MPI
    ParallelComm* pcomm = ParallelComm::get_pcomm( &mb, 0 );
    int rank            = pcomm->proc_config().proc_rank();

    Range cells, cells_owned;
    rval = mb.get_entities_by_type( file_set, MBPOLYGON, cells );CHECK_ERR( rval );

    // Get local owned cells
    rval = pcomm->filter_pstatus( cells, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &cells_owned );CHECK_ERR( rval );

    EntityHandle gather_set = 0;
    if( 0 == rank )
    {
        // Get gather set
        ReadUtilIface* readUtilIface;
        mb.query_interface( readUtilIface );
        rval = readUtilIface->get_gather_set( gather_set );CHECK_ERR( rval );
        assert( gather_set != 0 );
    }

    Tag vorticity_tag0, gid_tag;
    rval = mb.tag_get_handle( "vorticity0", layers, MB_TYPE_DOUBLE, vorticity_tag0, MB_TAG_DENSE );CHECK_ERR( rval );

    gid_tag = mb.globalId_tag();

    pcomm->gather_data( cells_owned, vorticity_tag0, gid_tag, gather_set, 0 );

    if( 0 == rank )
    {
        // Get gather set cells
        Range gather_set_cells;
        rval = mb.get_entities_by_type( gather_set, MBPOLYGON, gather_set_cells );CHECK_ERR( rval );
        CHECK_EQUAL( (size_t)642, gather_set_cells.size() );
        CHECK_EQUAL( (size_t)1, gather_set_cells.psize() );

        // Check vorticity0 tag values on 4 gather set cells: first cell, two median cells, and last
        // cell
        EntityHandle cell_ents[] = { gather_set_cells[0], gather_set_cells[320], gather_set_cells[321],
                                     gather_set_cells[641] };
        double vorticity0_val[4 * layers];
        rval = mb.tag_get_data( vorticity_tag0, cell_ents, 4, vorticity0_val );CHECK_ERR( rval );

        // Only check first two layers
        // Layer 0
        CHECK_REAL_EQUAL( 3.629994, vorticity0_val[0 * layers], eps );
        CHECK_REAL_EQUAL( 0.131688, vorticity0_val[1 * layers], eps );
        CHECK_REAL_EQUAL( -0.554888, vorticity0_val[2 * layers], eps );
        CHECK_REAL_EQUAL( -0.554888, vorticity0_val[3 * layers], eps );
        // Layer 1
        CHECK_REAL_EQUAL( 3.629944, vorticity0_val[0 * layers + 1], eps );
        CHECK_REAL_EQUAL( 0.131686, vorticity0_val[1 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.554881, vorticity0_val[2 * layers + 1], eps );
        CHECK_REAL_EQUAL( -0.554881, vorticity0_val[3 * layers + 1], eps );
    }
#endif
}

void get_options( std::string& opts )
{
#ifdef MOAB_HAVE_MPI
    // Use parallel options
    opts = std::string( ";;PARALLEL=READ_PART;PARTITION_METHOD=TRIVIAL" );
#else
    opts      = std::string( ";;" );
#endif
}