imoab_test.c File Reference

#include "moab/MOABConfig.h"
#include "moab/iMOAB.h"
#include <string.h>

Include dependency graph for imoab_test.c:

Go to the source code of this file.

Macros
#define	CHECKRC(rc, message)

Functions
int	main (int argc, char *argv[])

Macro Definition Documentation

CHECKRC

#define CHECKRC	(		rc,
			message
	)

Value:

 if( 0 != ( rc ) ) \
 { \
 printf( "Error: %s.\n", message ); \
 return 1; \
 }

Definition at line 10 of file imoab_test.c.

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 17 of file imoab_test.c.

{
 /* Declarations */
 ErrCode rc;
 int nprocs = 1, rank = 0;
 char filen[1024] = "";
 int i, j, k;
 
 int irank = 0, num_tags_to_sync = 1;
 int* ranks;
 
 int appID, appDupID;
 iMOAB_AppID pid;
 iMOAB_AppID pidDup;
 int compid = 11, compdupid = 12;
 
 int num_global_vertices = 0, num_global_elements = 0, num_dimension = 0, num_parts = 0;
 int nverts[3], nelem[3], nblocks[3], nsbc[3], ndbc[3];
 
 iMOAB_GlobalID* vGlobalID;
 int* vranks;
 double* coords;
 int size_coords;
 
#ifdef MOAB_HAVE_MPI
 const char* read_opts = "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARALLEL_RESOLVE_SHARED_ENTS";
 int num_ghost_layers[1] = { 1 };
#else
 const char* read_opts = "";
 int num_ghost_layers[1] = { 0 };
#endif
 
 iMOAB_GlobalID* gbIDs;
 int tagIndex[2];
 int entTypes[2] = { 0, 1 }; /* first is on vertex, second is on elements; */
 int tagTypes[2] = { DENSE_INTEGER, DENSE_DOUBLE };
 int num_components = 1;
 
 iMOAB_GlobalID *element_global_IDs, *block_IDs;
 int vertices_per_element, num_elements_in_block;
 int conn[27], nv, eindex;
 
 int* int_tag_vals;
 double* double_tag_vals;
 
 int local_index = 0; /* test element with local index 0 */
 int num_adjacent_elements = 10; /* we can have maximum 6 actually */
 iMOAB_LocalID adjacent_element_IDs[10], *element_connectivity, *local_element_ID;
 int size_conn, *element_ownership;
 iMOAB_GlobalID* global_element_ID;
 
 iMOAB_LocalID *vertBC_ID, *surfBC_ID;
 int *vertBC_value, *ref_surf, *bc_value;
 
 char *outputFile, *writeOptions;
 
#ifdef MOAB_HAVE_MPI
 MPI_Comm comm;
 MPI_Init( &argc, &argv );
 
 comm = MPI_COMM_WORLD;
 MPI_Comm_size( comm, &nprocs );
 MPI_Comm_rank( comm, &rank );
#endif
 
#ifdef MOAB_HAVE_HDF5
 strcpy( filen, MOAB_MESH_DIR );
 strcat( filen, "unittest/io/p8ex1.h5m" );
#endif
 
 if( argc > 1 ) strcpy( filen, argv[1] );
 
 if( !strlen( filen ) )
 {
 printf( "Invalid filename specified at command line.\n" );
 return 1;
 }
 /*
 * MOAB needs to be initialized; A MOAB instance will be created, and will be used by each
 * application in this framework. There is no parallel context yet.
 */
 rc = iMOAB_Initialize( argc, argv );
 CHECKRC( rc, "failed to initialize MOAB" );
 
 /*
 * Header information is cheap to retrieve from an hdf5 file; it can be called by each process
 * or can be called by one master task and broadcasted. The hdf5 file has to be in MOAB native
 * format, and has to be partitioned in advance. There should be at least as many partitions in
 * the file as number of tasks in the communicator.
 */
 rc = iMOAB_ReadHeaderInfo( filen, &num_global_vertices, &num_global_elements, &num_dimension, &num_parts );
 CHECKRC( rc, "failed to read header info" );
 
 if( 0 == rank )
 {
 printf( "file %s has %d vertices, %d elements, %d parts in partition\n", filen, num_global_vertices,
 num_global_elements, num_parts );
 }
 
 pid = &appID;
 pidDup = &appDupID;
 
 /*
 * Each application has to be registered once. A mesh set and a parallel communicator will be
 * associated with each application. A unique application id will be returned, and will be used
 * for all future mesh operations/queries.
 */
 rc = iMOAB_RegisterApplication( "MBAPP",
#ifdef MOAB_HAVE_MPI
 &comm,
#endif
 &compid, pid );
 CHECKRC( rc, "failed to register application" );
 
 rc = iMOAB_RegisterApplication( "MBDUPAPP",
#ifdef MOAB_HAVE_MPI
 &comm,
#endif
 &compdupid, pidDup );
 CHECKRC( rc, "failed to register duplicate application" );
 
 /*
 * Loading the mesh is a parallel IO operation. Ghost layers can be exchanged too, and default
 * MOAB sets are augmented with ghost elements. By convention, blocks correspond to MATERIAL_SET
 * sets, side sets with NEUMANN_SET sets, node sets with DIRICHLET_SET sets. Each element and
 * vertex entity should have a GLOBAL ID tag in the file, which will be available for visible
 * entities
 */
 rc = iMOAB_LoadMesh( pid, filen, read_opts, num_ghost_layers );
 CHECKRC( rc, "failed to load mesh" );
 
 rc = iMOAB_LoadMesh( pidDup, filen, read_opts, num_ghost_layers );
 CHECKRC( rc, "failed to load mesh" );
 
 rc = iMOAB_SetGlobalInfo( pid, &num_global_vertices, &num_global_elements );
 CHECKRC( rc, "failed to set global info" );
 
 /*
 * Each process in the communicator will have access to a local mesh instance, which will
 * contain the original cells in the local partition and ghost entities. Number of vertices,
 * primary cells, visible blocks, number of sidesets and nodesets boundary conditions will be
 * returned in size 3 arrays, for local, ghost and total numbers.
 */
 rc = iMOAB_GetMeshInfo( pid, nverts, nelem, nblocks, nsbc, ndbc );
 CHECKRC( rc, "failed to get mesh info" );
 
 vGlobalID = (iMOAB_GlobalID*)malloc( nverts[2] * sizeof( iMOAB_GlobalID ) );
 /*
 * All visible vertices have a unique global ID. All arrays are allocated by client.
 * Currently, global ID is a 32 bit integer, total number of visible vertices was returned by
 * iMOAB_GetMeshInfo
 */
 rc = iMOAB_GetVertexID( pid, &nverts[2], vGlobalID );
 CHECKRC( rc, "failed to get vertex id info" );
 
 vranks = (int*)malloc( nverts[2] * sizeof( int ) );
 /*
 * In MOAB terminology, a vertex can be owned, shared or ghost. An owned vertex will be
 * owned by the current process. A shared vertex appears at the interface between partitions, it
 * can be owned by another process, while a ghost vertex is owned by another process always. All
 * vertex arrays have a natural local order, in which the ghost vertices are at the end of the
 * arrays. The local index of the vertex will vary from 0 to number of visible vertices (in this
 * example nverts[2]-1)
 */
 rc = iMOAB_GetVertexOwnership( pid, &nverts[2], vranks );
 CHECKRC( rc, "failed to get vertex ranks" );
 
 coords = (double*)malloc( 3 * nverts[2] * sizeof( double ) );
 size_coords = 3 * nverts[2];
 /*
 * Coordinates are returned interleaved, for all visible vertices. Size is dimension times
 * number of visible vertices
 */
 rc = iMOAB_GetVisibleVerticesCoordinates( pid, &size_coords, coords );
 CHECKRC( rc, "failed to get coordinates" );
 
 /*
 * Block IDs correspond to MATERIAL_SET tag values in hdf5 file
 * They also correspond to block IDs in a Cubit model.
 * Local visible blocks might contain ghost cells, owned by other
 * processes.
 * 
 * Inside MOAB, a block will correspond to a meshset with a MATERIAL_SET tag,
 * with value the block ID.
 * A MATERIAL_SET tag in moab if SPARSE and type INTEGER.
 */
 gbIDs = (iMOAB_GlobalID*)malloc( nblocks[2] * sizeof( iMOAB_GlobalID ) );
 rc = iMOAB_GetBlockID( pid, &nblocks[2], gbIDs );
 CHECKRC( rc, "failed to get block info" );
 
 /*
 * The 2 tags used in this example exist in the file, already.
 * If a user needs a new tag, it can be defined with the same call as this one
 * this method, iMOAB_DefineTagStorage, will return a local index for the tag.
 * The name of the tag is case sensitive.
 * This method is collective.
 */
 rc = iMOAB_DefineTagStorage( pid, "INTFIELD", &tagTypes[0], &num_components, &tagIndex[0] );
 CHECKRC( rc, "failed to get tag INTFIELD " );
 rc = iMOAB_DefineTagStorage( pid, "DFIELD", &tagTypes[1], &num_components, &tagIndex[1] );
 CHECKRC( rc, "failed to get tag DFIELD " );
 
 /*
 * Synchronize one of the tags only, just to see what happens;
 * Tags are not exchanged for ghost entities by default. The user has to explicitly
 * synchronize them with a call like this one. The tags to synchronize are referenced by the
 * index returned at their "definition" with iMOAB_DefineTagStorage method.
 */
 rc = iMOAB_SynchronizeTags( pid, &num_tags_to_sync, &tagIndex[0], &tagTypes[0] );
 CHECKRC( rc, "failed to sync tag INTFIELD " );
 
 for( irank = 0; irank < nprocs; irank++ )
 {
 if( irank == rank )
 {
 /* printf some of the block info */
 printf( "on rank %d, there are \n"
 " %3d visible vertices of which %3d local %3d ghost \n"
 " %3d visible elements of which %3d owned %3d ghost \n"
 " %3d visible blocks\n"
 " %3d visible neumann BCs\n"
 " %3d visible dirichlet BCs\n",
 rank, nverts[2], nverts[0], nverts[1], nelem[2], nelem[0], nelem[1], nblocks[2], nsbc[2], ndbc[2] );
 
 /* print some of the vertex id infos */
 printf( "on rank %d vertex info:\n", rank );
 for( i = 0; i < nverts[2]; i++ )
 printf( " vertex local id: %3d, rank ID:%d global ID: %3d coords: %g, %g, %g\n", i, vranks[i],
 vGlobalID[i], coords[3 * i], coords[3 * i + 1], coords[3 * i + 2] );
 
 element_global_IDs = (iMOAB_GlobalID*)malloc( nelem[2] * sizeof( iMOAB_GlobalID ) );
 block_IDs = (iMOAB_GlobalID*)malloc( nelem[2] * sizeof( iMOAB_GlobalID ) );
 ranks = (int*)malloc( nelem[2] * sizeof( int ) );
 /*
 * Visible elements info is available for all visible elements, with this call. Similar
 * information can be retrieved by looping over visible blocks
 */
 rc = iMOAB_GetVisibleElementsInfo( pid, &nelem[2], element_global_IDs, ranks, block_IDs );
 CHECKRC( rc, "failed to get all elem info" );
 for( i = 0; i < nelem[2]; i++ )
 printf( " element local id: %3d, global ID: %3d rank:%d block ID: %2d \n", i, element_global_IDs[i],
 ranks[i], block_IDs[i] );
 free( element_global_IDs );
 free( ranks );
 free( block_IDs );
 
 /* Get first element connectivity */
 nv = 27;
 eindex = 0;
 /*
 * Element connectivity can be retrieved for a single element. Local vertex indices are returned.
 */
 rc = iMOAB_GetElementConnectivity( pid, &eindex, &nv, conn );
 CHECKRC( rc, "failed to get first element connectivity" );
 printf( " conn for first element: \n" );
 for( i = 0; i < nv; i++ )
 printf( " %3d", conn[i] );
 printf( "\n" );
 
 /*
 * Test neighbors:
 * Neighbor elements that share a face with current element can be determined with this
 * call Elements are identified by their local index
 */
 rc = iMOAB_GetNeighborElements( pid, &local_index, &num_adjacent_elements, adjacent_element_IDs );
 CHECKRC( rc, "failed to get first element neighbors" );
 printf( " neighbors for first element:\n" );
 for( i = 0; i < num_adjacent_elements; i++ )
 {
 printf( " %4d", adjacent_element_IDs[i] );
 }
 printf( "\n" );
 
 for( i = 0; i < nblocks[2]; i++ )
 {
 printf( " block index: %3d, block ID: %3d \n", i, gbIDs[i] );
 /*
 * Blocks should have the same type of primary elements. Number of elements in block
 * and number of vertices per element are found with this call. The method refers
 * only to the visible elements on the process. The block is identified with its
 * block ID. Should it be identified with its local index in the list of visible
 * blocks?
 */
 rc = iMOAB_GetBlockInfo( pid, &gbIDs[i], &vertices_per_element, &num_elements_in_block );
 CHECKRC( rc, "failed to elem block info" );
 printf( " has %4d elements with %d vertices per element\n", num_elements_in_block,
 vertices_per_element );
 
 size_conn = num_elements_in_block * vertices_per_element;
 element_connectivity = (iMOAB_LocalID*)malloc( sizeof( iMOAB_LocalID ) * size_conn );
 /*
 * Connectivity for all elements in the block can be determined with this method.
 * Vertices are identified by their local index (from 0 to number of visible
 * vertices -1)
 */
 rc = iMOAB_GetBlockElementConnectivities( pid, &gbIDs[i], &size_conn, element_connectivity );
 CHECKRC( rc, "failed to get block elem connectivity" );
 element_ownership = (int*)malloc( sizeof( int ) * num_elements_in_block );
 
 /*
 * Each element is owned by a particular process. Ownership can be returned for all
 * elements in a block with this call.
 */
 rc = iMOAB_GetElementOwnership( pid, &gbIDs[i], &num_elements_in_block, element_ownership );
 CHECKRC( rc, "failed to get block elem ownership" );
 global_element_ID = (iMOAB_GlobalID*)malloc( sizeof( iMOAB_GlobalID ) * num_elements_in_block );
 local_element_ID = (iMOAB_LocalID*)malloc( sizeof( iMOAB_LocalID ) * num_elements_in_block );
 
 /*
 * Global element IDs are determined with this call. Local indices within the
 * process are returned too.
 */
 rc = iMOAB_GetElementID( pid, &gbIDs[i], &num_elements_in_block, global_element_ID, local_element_ID );
 CHECKRC( rc, "failed to get block elem IDs" );
 for( j = 0; j < num_elements_in_block; j++ )
 {
 printf( " elem %3d owned by %d gid: %4d lid: %4d -- ", j, element_ownership[j],
 global_element_ID[j], local_element_ID[j] );
 for( k = 0; k < vertices_per_element; k++ )
 printf( " %5d", element_connectivity[j * vertices_per_element + k] );
 printf( "\n" );
 }
 free( global_element_ID );
 free( local_element_ID );
 free( element_connectivity );
 free( element_ownership );
 }
 /*
 * Query integer tag values on vertices.
 * this tag was synchronized (see iMOAB_SynchronizeTags above)
 * Being a dense tag, all visible vertices have a value.
 * As usual, the client allocates the returned array, which is filled with data with
 * this call (deep copy)
 */
 int_tag_vals = (int*)malloc( sizeof( int ) * nverts[2] ); /* for all visible vertices on the rank */
 rc = iMOAB_GetIntTagStorage( pid, "INTFIELD", &nverts[2], &entTypes[0], int_tag_vals );
 CHECKRC( rc, "failed to get INTFIELD tag" );
 printf( "INTFIELD tag values:\n" );
 for( i = 0; i < nverts[2]; i++ )
 {
 printf( " %4d", int_tag_vals[i] );
 if( i % 20 == 19 ) printf( "\n" );
 }
 printf( "\n" );
 free( int_tag_vals );
 
 /*
 * Query double tag values on elements.
 * This tag was not synchronized, so ghost elements have a default value of 0.
 */
 double_tag_vals = (double*)malloc( sizeof( double ) * nelem[2] ); /* for all visible elements on the rank */
 rc = iMOAB_GetDoubleTagStorage( pid, "DFIELD", &nelem[2], &entTypes[1], double_tag_vals );
 CHECKRC( rc, "failed to get DFIELD tag" );
 printf( "DFIELD tag values: (not exchanged) \n" );
 for( i = 0; i < nelem[2]; i++ )
 {
 printf( " %f", double_tag_vals[i] );
 if( i % 8 == 7 ) printf( "\n" );
 }
 printf( "\n" );
 free( double_tag_vals );
 
 /* query surface BCs */
 surfBC_ID = (iMOAB_LocalID*)malloc( sizeof( iMOAB_LocalID ) * nsbc[2] );
 ref_surf = (int*)malloc( sizeof( int ) * nsbc[2] );
 bc_value = (int*)malloc( sizeof( int ) * nsbc[2] );
 /*
 * Surface boundary condition information is returned for all visible Neumann conditions
 * the reference surfaces are indexed from 1 to 6 for hexahedrons, 1 to 4 to
 * tetrahedrons, in the MOAB canonical ordering convention
 */
 rc = iMOAB_GetPointerToSurfaceBC( pid, &nsbc[2], surfBC_ID, ref_surf, bc_value );
 CHECKRC( rc, "failed to get surf boundary conditions" );
 printf( " Surface boundary conditions:\n" );
 for( i = 0; i < nsbc[2]; i++ )
 {
 printf( " elem_localID %4d side:%d BC:%2d\n", surfBC_ID[i], ref_surf[i], bc_value[i] );
 }
 free( surfBC_ID );
 free( ref_surf );
 free( bc_value );
 
 /* Query vertex BCs */
 vertBC_ID = (iMOAB_LocalID*)malloc( sizeof( iMOAB_LocalID ) * ndbc[2] );
 vertBC_value = (int*)malloc( sizeof( int ) * ndbc[2] );
 rc = iMOAB_GetPointerToVertexBC( pid, &ndbc[2], vertBC_ID, vertBC_value );
 CHECKRC( rc, "failed to get vertex boundary conditions" );
 printf( " Vertex boundary conditions:\n" );
 for( i = 0; i < ndbc[2]; i++ )
 {
 printf( " vertex %4d BC:%2d\n", vertBC_ID[i], vertBC_value[i] );
 }
 free( vertBC_ID );
 free( vertBC_value );
 }
#ifdef MOAB_HAVE_MPI
 MPI_Barrier( comm ); /* to avoid printing problems */
#endif
 }
 
 /* free allocated data */
 free( coords );
 free( vGlobalID );
 free( vranks );
 outputFile = "fnew.h5m";
#ifdef MOAB_HAVE_MPI
 writeOptions = "PARALLEL=WRITE_PART";
#else
 writeOptions = "";
#endif
 /*
 * The file can be written in parallel, and it will contain additional tags defined by the user
 * we may extend the method to write only desired tags to the file
 */
 rc = iMOAB_WriteMesh( pid, outputFile, writeOptions );
 CHECKRC( rc, "failed to write output file" );
 
 /*
 * Deregistering application will delete all mesh entities associated with the application and
 * will free allocated tag storage.
 */
 rc = iMOAB_DeregisterApplication( pid );
 CHECKRC( rc, "failed to de-register application" );
 
 rc = iMOAB_DeregisterApplication( pidDup );
 CHECKRC( rc, "failed to de-register application" );
 
 /*
 * This method will delete MOAB instance
 */
 rc = iMOAB_Finalize();
 CHECKRC( rc, "failed to finalize MOAB" );
#ifdef MOAB_HAVE_MPI
 MPI_Finalize();
#endif
 
 return 0;
}

References CHECKRC, DENSE_DOUBLE, DENSE_INTEGER, ErrCode, iMOAB_AppID, iMOAB_DefineTagStorage(), iMOAB_DeregisterApplication(), iMOAB_Finalize(), iMOAB_GetBlockElementConnectivities(), iMOAB_GetBlockID(), iMOAB_GetBlockInfo(), iMOAB_GetDoubleTagStorage(), iMOAB_GetElementConnectivity(), iMOAB_GetElementID(), iMOAB_GetElementOwnership(), iMOAB_GetIntTagStorage(), iMOAB_GetMeshInfo(), iMOAB_GetNeighborElements(), iMOAB_GetPointerToSurfaceBC(), iMOAB_GetPointerToVertexBC(), iMOAB_GetVertexID(), iMOAB_GetVertexOwnership(), iMOAB_GetVisibleElementsInfo(), iMOAB_GetVisibleVerticesCoordinates(), iMOAB_GlobalID, iMOAB_Initialize(), iMOAB_LoadMesh(), iMOAB_LocalID, iMOAB_ReadHeaderInfo(), iMOAB_RegisterApplication(), iMOAB_SetGlobalInfo(), iMOAB_SynchronizeTags(), iMOAB_WriteMesh(), MOAB_MESH_DIR, MPI_COMM_WORLD, and rank.