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;
23: PetscFunctionBegin;
24: PetscCall(PetscViewerGetFormat(viewer, &format));
25: switch (format) {
26: case PETSC_VIEWER_HDF5_PETSC:
27: case PETSC_VIEWER_DEFAULT:
28: case PETSC_VIEWER_NATIVE:
29: case PETSC_VIEWER_HDF5_MAT:
30: break;
31: default:
32: SETERRQ(PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
33: }
34: hdf5 = (PetscViewer_HDF5 *)viewer->data;
35: /* we store dense matrix columns as blocks, like MATLAB save(filename,variables,'-v7.3') does */
36: hdf5->horizontal = PETSC_TRUE;
38: PetscCheck(((PetscObject)mat)->name, PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "Mat name must be set with PetscObjectSetName() before MatLoad()");
39: #if defined(PETSC_USE_REAL_SINGLE)
40: scalartype = H5T_NATIVE_FLOAT;
41: #elif defined(PETSC_USE_REAL___FLOAT128)
42: #error "HDF5 output with 128 bit floats not supported."
43: #elif defined(PETSC_USE_REAL___FP16)
44: #error "HDF5 output with 16 bit floats not supported."
45: #else
46: scalartype = H5T_NATIVE_DOUBLE;
47: #endif
49: PetscCall(PetscObjectGetComm((PetscObject)mat, &comm));
50: PetscCallMPI(MPI_Comm_rank(comm, &rank));
51: PetscCallMPI(MPI_Comm_size(comm, &size));
52: PetscCall(PetscObjectGetName((PetscObject)mat, &mat_name));
54: /* Convert user-defined rmap and cmap to the dataset layout */
55: PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)mat), &vmap));
56: if (mat->rmap->n >= 0 && mat->cmap->N < 0) {
57: /* We need to know mat->cmap->N if user specifies custom mat->rmap->n, otherwise the latter would get ignored below */
58: PetscCall(PetscViewerHDF5ReadSizes(viewer, mat_name, &mat->cmap->N, NULL));
59: }
60: vmap->bs = mat->cmap->N;
61: vmap->n = (mat->rmap->n < 0 || mat->cmap->N < 0) ? -1 : mat->rmap->n * mat->cmap->N;
62: vmap->N = (mat->rmap->N < 0 || mat->cmap->N < 0) ? -1 : mat->rmap->N * mat->cmap->N;
64: /* Read the dataset and setup its layout */
65: /* Note: PetscViewerHDF5ReadSizes_Private takes into account that the dataset is transposed for MATLAB MAT files */
66: PetscCall(PetscViewerHDF5Load(viewer, mat_name, vmap, scalartype, (void **)&a));
68: /* Convert the dataset layout back to rmap and cmap */
69: mat->cmap->N = vmap->bs;
70: mat->rmap->n = vmap->n / mat->cmap->N;
71: mat->rmap->N = vmap->N / mat->cmap->N;
72: PetscCall(PetscLayoutSetUp(mat->rmap));
73: PetscCall(PetscLayoutSetUp(mat->cmap));
74: PetscCall(PetscLayoutDestroy(&vmap));
76: /* TODO adding PetscCopyMode flag to MatSeqDenseSetPreallocation would make this code cleaner and simpler */
77: {
78: PetscBool flg;
79: Mat_SeqDense *impl;
80: PetscCall(PetscObjectTypeCompare((PetscObject)mat, MATSEQDENSE, &flg));
81: if (flg) {
82: impl = (Mat_SeqDense *)mat->data;
83: PetscCall(MatSeqDenseSetPreallocation(mat, a));
84: } else {
85: Mat_MPIDense *implm = (Mat_MPIDense *)mat->data;
86: PetscCall(MatMPIDenseSetPreallocation(mat, a));
87: impl = (Mat_SeqDense *)implm->A->data;
88: }
89: impl->user_alloc = PETSC_FALSE;
90: }
92: PetscCall(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY));
93: PetscCall(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY));
94: PetscFunctionReturn(PETSC_SUCCESS);
95: }
96: #endif