Actual source code: aijhdf5.c
1: #include <../src/mat/impls/aij/seq/aij.h>
2: #include <petsc/private/isimpl.h>
3: #include <petsc/private/vecimpl.h>
4: #include <petsclayouthdf5.h>
6: PetscErrorCode MatLoad_AIJ_HDF5(Mat mat, PetscViewer viewer)
7: {
8: PetscViewerFormat format;
9: const PetscInt *i_glob = NULL;
10: PetscInt *i = NULL;
11: const PetscInt *j = NULL;
12: const PetscScalar *a = NULL;
13: char *a_name = NULL, *i_name = NULL, *j_name = NULL, *c_name = NULL;
14: const char *mat_name = NULL;
15: PetscInt p, m, M, N;
16: PetscInt bs = mat->rmap->bs;
17: PetscInt *range;
18: PetscBool flg;
19: IS is_i = NULL, is_j = NULL;
20: Vec vec_a = NULL;
21: PetscLayout jmap = NULL;
22: MPI_Comm comm;
23: PetscMPIInt rank, size;
25: PetscFunctionBegin;
26: PetscCall(PetscViewerGetFormat(viewer, &format));
27: switch (format) {
28: case PETSC_VIEWER_HDF5_PETSC:
29: case PETSC_VIEWER_DEFAULT:
30: case PETSC_VIEWER_NATIVE:
31: case PETSC_VIEWER_HDF5_MAT:
32: break;
33: default:
34: SETERRQ(PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
35: }
37: PetscCall(PetscObjectGetComm((PetscObject)mat, &comm));
38: PetscCallMPI(MPI_Comm_rank(comm, &rank));
39: PetscCallMPI(MPI_Comm_size(comm, &size));
40: PetscCall(PetscObjectGetName((PetscObject)mat, &mat_name));
41: if (format == PETSC_VIEWER_HDF5_MAT) {
42: PetscCall(PetscStrallocpy("jc", &i_name));
43: PetscCall(PetscStrallocpy("ir", &j_name));
44: PetscCall(PetscStrallocpy("data", &a_name));
45: PetscCall(PetscStrallocpy("MATLAB_sparse", &c_name));
46: } else {
47: /* TODO Once corresponding MatView is implemented, change the names to i,j,a */
48: /* TODO Maybe there could be both namings in the file, using "symbolic link" features of HDF5. */
49: PetscCall(PetscStrallocpy("jc", &i_name));
50: PetscCall(PetscStrallocpy("ir", &j_name));
51: PetscCall(PetscStrallocpy("data", &a_name));
52: PetscCall(PetscStrallocpy("MATLAB_sparse", &c_name));
53: }
55: PetscOptionsBegin(comm, NULL, "Options for loading matrix from HDF5", "Mat");
56: PetscCall(PetscOptionsInt("-matload_block_size", "Set the blocksize used to store the matrix", "MatLoad", bs, &bs, &flg));
57: PetscOptionsEnd();
58: if (flg) PetscCall(MatSetBlockSize(mat, bs));
60: PetscCall(PetscViewerHDF5PushGroup(viewer, mat_name));
61: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, c_name, PETSC_INT, NULL, &N));
62: PetscCall(PetscViewerHDF5ReadSizes(viewer, i_name, NULL, &M));
63: --M; /* i has size M+1 as there is global number of nonzeros stored at the end */
65: if (format == PETSC_VIEWER_HDF5_MAT && mat->symmetric != PETSC_BOOL3_TRUE) {
66: /* Swap row and columns layout for unallocated matrix. I want to avoid calling MatTranspose() just to transpose sparsity pattern and layout. */
67: if (!mat->preallocated) {
68: PetscLayout tmp;
69: tmp = mat->rmap;
70: mat->rmap = mat->cmap;
71: mat->cmap = tmp;
72: } else SETERRQ(comm, PETSC_ERR_SUP, "Not for preallocated matrix - we would need to transpose it here which we want to avoid");
73: }
75: /* If global sizes are set, check if they are consistent with that given in the file */
76: PetscCheck(mat->rmap->N < 0 || mat->rmap->N == M, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows: Matrix in file has (%" PetscInt_FMT ") and input matrix has (%" PetscInt_FMT ")", mat->rmap->N, M);
77: PetscCheck(mat->cmap->N < 0 || mat->cmap->N == N, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of cols: Matrix in file has (%" PetscInt_FMT ") and input matrix has (%" PetscInt_FMT ")", mat->cmap->N, N);
79: /* Determine ownership of all (block) rows and columns */
80: mat->rmap->N = M;
81: mat->cmap->N = N;
82: PetscCall(PetscLayoutSetUp(mat->rmap));
83: PetscCall(PetscLayoutSetUp(mat->cmap));
84: m = mat->rmap->n;
86: /* Read array i (array of row indices) */
87: PetscCall(PetscMalloc1(m + 1, &i)); /* allocate i with one more position for local number of nonzeros on each rank */
88: i[0] = i[m] = 0; /* make the last entry always defined - the code block below overwrites it just on last rank */
89: if (rank == size - 1) m++; /* in the loaded array i_glob, only the last rank has one more position with the global number of nonzeros */
90: M++;
91: PetscCall(ISCreate(comm, &is_i));
92: PetscCall(PetscObjectSetName((PetscObject)is_i, i_name));
93: PetscCall(PetscLayoutSetLocalSize(is_i->map, m));
94: PetscCall(PetscLayoutSetSize(is_i->map, M));
95: PetscCall(ISLoad(is_i, viewer));
96: PetscCall(ISGetIndices(is_i, &i_glob));
97: PetscCall(PetscArraycpy(i, i_glob, m));
99: /* Reset m and M to the matrix sizes */
100: m = mat->rmap->n;
101: M--;
103: /* Create PetscLayout for j and a vectors; construct ranges first */
104: PetscCall(PetscMalloc1(size + 1, &range));
105: PetscCallMPI(MPI_Allgather(i, 1, MPIU_INT, range, 1, MPIU_INT, comm));
106: /* Last rank has global number of nonzeros (= length of j and a arrays) in i[m] (last i entry) so broadcast it */
107: range[size] = i[m];
108: PetscCallMPI(MPI_Bcast(&range[size], 1, MPIU_INT, size - 1, comm));
109: for (p = size - 1; p > 0; p--) {
110: if (!range[p]) range[p] = range[p + 1]; /* for ranks with 0 rows, take the value from the next processor */
111: }
112: i[m] = range[rank + 1]; /* i[m] (last i entry) is equal to next rank's offset */
113: /* Deduce rstart, rend, n and N from the ranges */
114: PetscCall(PetscLayoutCreateFromRanges(comm, range, PETSC_OWN_POINTER, 1, &jmap));
116: /* Convert global to local indexing of rows */
117: for (p = 1; p < m + 1; ++p) i[p] -= i[0];
118: i[0] = 0;
120: /* Read array j (array of column indices) */
121: PetscCall(ISCreate(comm, &is_j));
122: PetscCall(PetscObjectSetName((PetscObject)is_j, j_name));
123: PetscCall(PetscLayoutDuplicate(jmap, &is_j->map));
124: PetscCall(ISLoad(is_j, viewer));
125: PetscCall(ISGetIndices(is_j, &j));
127: /* Read array a (array of values) */
128: PetscCall(VecCreate(comm, &vec_a));
129: PetscCall(PetscObjectSetName((PetscObject)vec_a, a_name));
130: PetscCall(PetscLayoutDuplicate(jmap, &vec_a->map));
131: PetscCall(VecLoad(vec_a, viewer));
132: PetscCall(VecGetArrayRead(vec_a, &a));
134: /* populate matrix */
135: if (!((PetscObject)mat)->type_name) PetscCall(MatSetType(mat, MATAIJ));
136: PetscCall(MatSeqAIJSetPreallocationCSR(mat, i, j, a));
137: PetscCall(MatMPIAIJSetPreallocationCSR(mat, i, j, a));
138: /*
139: PetscCall(MatSeqBAIJSetPreallocationCSR(mat,bs,i,j,a));
140: PetscCall(MatMPIBAIJSetPreallocationCSR(mat,bs,i,j,a));
141: */
143: if (format == PETSC_VIEWER_HDF5_MAT && mat->symmetric != PETSC_BOOL3_TRUE) {
144: /* Transpose the input matrix back */
145: PetscCall(MatTranspose(mat, MAT_INPLACE_MATRIX, &mat));
146: }
148: PetscCall(PetscViewerHDF5PopGroup(viewer));
149: PetscCall(PetscFree(i_name));
150: PetscCall(PetscFree(j_name));
151: PetscCall(PetscFree(a_name));
152: PetscCall(PetscFree(c_name));
153: PetscCall(PetscLayoutDestroy(&jmap));
154: PetscCall(PetscFree(i));
155: PetscCall(ISRestoreIndices(is_i, &i_glob));
156: PetscCall(ISRestoreIndices(is_j, &j));
157: PetscCall(VecRestoreArrayRead(vec_a, &a));
158: PetscCall(ISDestroy(&is_i));
159: PetscCall(ISDestroy(&is_j));
160: PetscCall(VecDestroy(&vec_a));
161: PetscFunctionReturn(PETSC_SUCCESS);
162: }