Actual source code: densehdf5.c


  2: /* TODO change to
  3: #include <../src/mat/impls/dense/seq/dense.h>
  4: */
  5: #include <../src/mat/impls/dense/mpi/mpidense.h>
  6: #include <petsc/private/isimpl.h>
  7: #include <petsc/private/vecimpl.h>
  8: #include <petsc/private/viewerhdf5impl.h>
  9: #include <petsclayouthdf5.h>

 11: #if defined(PETSC_HAVE_HDF5)
 12: PetscErrorCode MatLoad_Dense_HDF5(Mat mat, PetscViewer viewer)
 13: {
 14:   PetscViewer_HDF5    *hdf5;
 15:   hid_t               scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
 16:   PetscLayout         vmap;
 17:   PetscViewerFormat   format;
 18:   PetscScalar         *a = NULL;
 19:   const char          *mat_name = NULL;
 20:   MPI_Comm            comm;
 21:   PetscMPIInt         rank, size;
 22:   PetscErrorCode      ierr;

 25:   PetscViewerGetFormat(viewer, &format);
 26:   switch (format) {
 27:     case PETSC_VIEWER_HDF5_PETSC:
 28:     case PETSC_VIEWER_DEFAULT:
 29:     case PETSC_VIEWER_NATIVE:
 30:     case PETSC_VIEWER_HDF5_MAT:
 31:       break;
 32:     default:
 33:       SETERRQ1(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"PetscViewerFormat %s not supported for HDF5 input.",PetscViewerFormats[format]);
 34:   }
 35:   hdf5 = (PetscViewer_HDF5*) viewer->data;
 36:   /* we store dense matrix columns as blocks, like MATLAB save(filename,variables,'-v7.3') does */
 37:   hdf5->horizontal = PETSC_TRUE;

 39:   if (!((PetscObject)mat)->name) SETERRQ(PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "Mat name must be set with PetscObjectSetName() before MatLoad()");
 40: #if defined(PETSC_USE_REAL_SINGLE)
 41:   scalartype = H5T_NATIVE_FLOAT;
 42: #elif defined(PETSC_USE_REAL___FLOAT128)
 43: #error "HDF5 output with 128 bit floats not supported."
 44: #elif defined(PETSC_USE_REAL___FP16)
 45: #error "HDF5 output with 16 bit floats not supported."
 46: #else
 47:   scalartype = H5T_NATIVE_DOUBLE;
 48: #endif

 50:   PetscObjectGetComm((PetscObject)mat,&comm);
 51:   MPI_Comm_rank(comm,&rank);
 52:   MPI_Comm_size(comm,&size);
 53:   PetscObjectGetName((PetscObject)mat,&mat_name);

 55:   /* Convert user-defined rmap and cmap to the dataset layout */
 56:   PetscLayoutCreate(PetscObjectComm((PetscObject)mat),&vmap);
 57:   if (mat->rmap->n >= 0 && mat->cmap->N < 0) {
 58:     /* We need to know mat->cmap->N if user specifies custom mat->rmap->n, otherwise the latter would get ignored below */
 59:     PetscViewerHDF5ReadSizes(viewer, mat_name, &mat->cmap->N, NULL);
 60:   }
 61:   vmap->bs = mat->cmap->N;
 62:   vmap->n = (mat->rmap->n < 0 || mat->cmap->N < 0) ? -1 : mat->rmap->n * mat->cmap->N;
 63:   vmap->N = (mat->rmap->N < 0 || mat->cmap->N < 0) ? -1 : mat->rmap->N * mat->cmap->N;

 65:   /* Read the dataset and setup its layout */
 66:   /* Note: PetscViewerHDF5ReadSizes_Private takes into account that the dataset is transposed for MATLAB MAT files */
 67:   PetscViewerHDF5Load(viewer, mat_name, vmap, scalartype, (void**)&a);

 69:   /* Convert the dataset layout back to rmap and cmap */
 70:   mat->cmap->N = vmap->bs;
 71:   mat->rmap->n = vmap->n / mat->cmap->N;
 72:   mat->rmap->N = vmap->N / mat->cmap->N;
 73:   PetscLayoutSetUp(mat->rmap);
 74:   PetscLayoutSetUp(mat->cmap);
 75:   PetscLayoutDestroy(&vmap);

 77:   /* TODO adding PetscCopyMode flag to MatSeqDenseSetPreallocation would make this code cleaner and simpler */
 78:   {
 79:     PetscBool flg;
 80:     Mat_SeqDense *impl;
 81:     PetscObjectTypeCompare((PetscObject)mat,MATSEQDENSE,&flg);
 82:     if (flg) {
 83:       impl = (Mat_SeqDense*)mat->data;
 84:       MatSeqDenseSetPreallocation(mat,a);
 85:     } else {
 86:       Mat_MPIDense *implm = (Mat_MPIDense*)mat->data;
 87:       MatMPIDenseSetPreallocation(mat,a);
 88:       impl = (Mat_SeqDense*)implm->A->data;
 89:     }
 90:     impl->user_alloc = PETSC_FALSE;
 91:   }

 93:   MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
 94:   MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
 95:   return(0);
 96: }
 97: #endif