[cig-commits] commit:

[Mercurial]

changeset:   66:4626dfedc2b1
user:        LukeHodkinson
date:        Mon Mar 31 05:28:57 2008 +0000
files:       Utils/src/dump_discretisation.c
description:
Adding a routine to dump a combined mesh/particle
discretisation file for later visualisation.


diff -r 28d99eb7b300 -r 4626dfedc2b1 Utils/src/dump_discretisation.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Utils/src/dump_discretisation.c	Mon Mar 31 05:28:57 2008 +0000
@@ -0,0 +1,151 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <hdf5.h>
+#include <StGermain/StGermain.h>
+#include <StgDomain/StgDomain.h>
+
+
+#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR < 8
+#define H5DCREATE( file, path, type, space, props1, props2, props3 )	\
+   H5Dcreate( file, path, type, space, props1 )
+#else
+#define H5DCREATE( file, path, type, space, props1, props2, props3 )	\
+   H5Dcreate( file, path, type, space, props1, props2, props3 )
+#endif
+
+
+void dump_discretisation( Mesh *mesh, Swarm *swarm, const char *filename ) {
+#ifdef HAVE_HDF5
+   hid_t file, fileSpace, fileData;
+   hid_t memSpace;
+   hid_t props;
+   hid_t particleType;
+   hsize_t size[2];
+   int intSize[2];
+   int rank, nRanks, offset;
+   hsize_t start[2], count[2];
+   int nDims, nLocals, nGlobals;
+   char dataName[13];
+   int nTrashBytes;
+   int nParticles;
+   int ii;
+
+   /* Create parallel file property list. */
+   props = H5Pcreate( H5P_FILE_ACCESS );
+   H5Pset_fapl_mpio( props, MPI_COMM_WORLD, MPI_INFO_NULL );
+
+   /* Open the HDF5 output file. */
+   file = H5Fcreate( filename, H5F_ACC_TRUNC, H5P_DEFAULT, props );
+   assert( file );
+   H5Pclose( props );
+
+   /* Dump the size so we don't have to do any divisions later on. */
+   props = H5Pcreate( H5P_DATASET_XFER );
+   H5Pset_dxpl_mpio( props, H5FD_MPIO_COLLECTIVE );
+   size[0] = 1;
+   fileSpace = H5Screate_simple( 1, size, NULL );
+   fileData = H5Dcreate( file, "/numDims", H5T_NATIVE_INT, fileSpace,
+                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
+   nDims = Mesh_GetDimSize( mesh );
+   H5Dwrite( fileData, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, props, &nDims );
+   H5Dclose( fileData );
+   nLocals = Mesh_GetLocalSize( mesh, 0 );
+   MPI_Allreduce( &nLocals, &nGlobals, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
+   fileData = H5Dcreate( file, "/numMeshGlobals", H5T_NATIVE_INT, fileSpace,
+                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
+   H5Dwrite( fileData, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, props, &nGlobals );
+   H5Dclose( fileData );
+   MPI_Allreduce( &swarm->particleLocalCount, &nParticles, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
+   fileData = H5Dcreate( file, "/numParticles", H5T_NATIVE_INT, fileSpace,
+                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
+   H5Dwrite( fileData, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, props, &nParticles );
+   H5Dclose( fileData );
+   H5Sclose( fileSpace );
+   H5Pclose( props );
+
+   /* Dump mesh vertices */
+   size[0] = nGlobals;
+   size[1] = nDims;
+   fileSpace = H5Screate_simple( 2, size, NULL );
+   fileData = H5Dcreate( file, "/meshVertices", H5T_NATIVE_CHAR, fileSpace,
+                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
+
+   MPI_Comm_rank( MPI_COMM_WORLD, &rank );
+   MPI_Comm_size( MPI_COMM_WORLD, &nRanks );
+   offset = 0;
+   if( rank > 0 ) {
+      MPI_Status status;
+      MPI_Recv( &offset, 1, MPI_INT, rank - 1, 455, MPI_COMM_WORLD, &status );
+   }
+   start[0] = offset;  start[1] = 0;
+   count[0] = nLocals; count[1] = nDims;
+   offset += nLocals;
+   if( rank < nRanks - 1 )
+      MPI_Send( &offset, 1, MPI_INT, rank + 1, 455, MPI_COMM_WORLD );
+   H5Sselect_hyperslab( fileSpace, H5S_SELECT_SET, start, NULL, count, NULL );
+
+   memSpace = H5Screate_simple( 2, count, NULL );
+
+   props = H5Pcreate( H5P_DATASET_XFER );
+   H5Pset_dxpl_mpio( props, H5FD_MPIO_INDEPENDENT );
+   H5Dwrite( fileData, H5T_NATIVE_CHAR, memSpace, fileSpace, props, mesh->verts );
+
+   H5Pclose( props );
+   H5Sclose( memSpace );
+   H5Dclose( fileData );
+   H5Sclose( fileSpace );
+
+   /* Dump particle coordinates. */
+   particleType = H5Tcreate( H5T_COMPOUND, swarm->particleExtensionMgr->finalSize );
+   offset = 0;
+   H5Tinsert( particleType, "owning cell", 0, H5T_NATIVE_INT );
+   offset += sizeof(int);
+   for( ii = 0; ii < nDims; ii++ ) {
+      sprintf( dataName, "coordinate %d", ii );
+      H5Tinsert( particleType, dataName, offset, H5T_NATIVE_DOUBLE );
+      offset += sizeof(double);
+   }
+   nTrashBytes = swarm->particleExtensionMgr->finalSize - sizeof(int) - nDims * sizeof(double);
+   for( ii = 0; ii < nTrashBytes; ii++ ) {
+      sprintf( dataName, "trash %d", ii );
+      H5Tinsert( particleType, dataName, offset, H5T_NATIVE_CHAR );
+      offset++;
+   }
+
+   size[0] = nParticles;
+   fileSpace = H5Screate_simple( 1, size, NULL );
+   fileData = H5Dcreate( file, "/particles", particleType, fileSpace,
+                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
+
+   MPI_Comm_rank( MPI_COMM_WORLD, &rank );
+   MPI_Comm_size( MPI_COMM_WORLD, &nRanks );
+   offset = 0;
+   if( rank > 0 ) {
+      MPI_Status status;
+      MPI_Recv( &offset, 1, MPI_INT, rank - 1, 455, MPI_COMM_WORLD, &status );
+   }
+   start[0] = offset;                    start[1] = 0;
+   count[0] = swarm->particleLocalCount; count[1] = 1;
+   offset += swarm->particleLocalCount;
+   if( rank < nRanks - 1 )
+      MPI_Send( &offset, 1, MPI_INT, rank + 1, 455, MPI_COMM_WORLD );
+   H5Sselect_hyperslab( fileSpace, H5S_SELECT_SET, start, NULL, count, NULL );
+
+   size[0] = swarm->particleLocalCount;
+   memSpace = H5Screate_simple( 1, size, NULL );
+
+   props = H5Pcreate( H5P_DATASET_XFER );
+   H5Pset_dxpl_mpio( props, H5FD_MPIO_INDEPENDENT );
+   H5Dwrite( fileData, particleType, memSpace, fileSpace, props, mesh->verts );
+
+   H5Pclose( props );
+   H5Sclose( memSpace );
+   H5Dclose( fileData );
+   H5Sclose( fileSpace );
+
+   /* Close off all our handles. */
+   H5Fclose( file );
+#else
+   printf( "*** Warning: cannot dump discretisation, not configured with HDF5.\n" );
+#endif
+}