Actual source code: aijhdf5.c
petsc-3.12.5 2020-03-29
2: #include <../src/mat/impls/aij/seq/aij.h>
3: #include <petsc/private/isimpl.h>
4: #include <petsc/private/vecimpl.h>
5: #include <petsclayouthdf5.h>
7: #if defined(PETSC_HAVE_HDF5)
8: PetscErrorCode MatLoad_AIJ_HDF5(Mat mat, PetscViewer viewer)
9: {
10: PetscViewerFormat format;
11: const PetscInt *i_glob = NULL;
12: PetscInt *i = NULL;
13: const PetscInt *j = NULL;
14: const PetscScalar *a = NULL;
15: char *a_name = NULL, *i_name = NULL, *j_name = NULL, *c_name = NULL;
16: const char *mat_name = NULL;
17: PetscInt p, m, M, N;
18: PetscInt bs = mat->rmap->bs;
19: PetscInt *range;
20: PetscBool flg;
21: IS is_i = NULL, is_j = NULL;
22: Vec vec_a = NULL;
23: PetscLayout jmap = NULL;
24: MPI_Comm comm;
25: PetscMPIInt rank, size;
26: PetscErrorCode ierr;
29: PetscViewerGetFormat(viewer, &format);
30: switch (format) {
31: case PETSC_VIEWER_HDF5_PETSC:
32: case PETSC_VIEWER_DEFAULT:
33: case PETSC_VIEWER_NATIVE:
34: case PETSC_VIEWER_HDF5_MAT:
35: break;
36: default:
37: SETERRQ1(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"PetscViewerFormat %s not supported for HDF5 input.",PetscViewerFormats[format]);
38: }
40: PetscObjectGetComm((PetscObject)mat,&comm);
41: MPI_Comm_rank(comm,&rank);
42: MPI_Comm_size(comm,&size);
43: PetscObjectGetName((PetscObject)mat,&mat_name);
44: if (format==PETSC_VIEWER_HDF5_MAT) {
45: PetscStrallocpy("jc",&i_name);
46: PetscStrallocpy("ir",&j_name);
47: PetscStrallocpy("data",&a_name);
48: PetscStrallocpy("MATLAB_sparse",&c_name);
49: } else {
50: /* TODO Once corresponding MatView is implemented, change the names to i,j,a */
51: /* TODO Maybe there could be both namings in the file, using "symbolic link" features of HDF5. */
52: PetscStrallocpy("jc",&i_name);
53: PetscStrallocpy("ir",&j_name);
54: PetscStrallocpy("data",&a_name);
55: PetscStrallocpy("MATLAB_sparse",&c_name);
56: }
58: PetscOptionsBegin(comm,NULL,"Options for loading matrix from HDF5","Mat");
59: PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,&flg);
60: PetscOptionsEnd();
61: if (flg) {
62: MatSetBlockSize(mat, bs);
63: }
65: PetscViewerHDF5PushGroup(viewer,mat_name);
66: PetscViewerHDF5ReadAttribute(viewer,NULL,c_name,PETSC_INT,&N);
67: PetscViewerHDF5ReadSizes(viewer, i_name, NULL, &M);
68: --M; /* i has size M+1 as there is global number of nonzeros stored at the end */
70: if (format==PETSC_VIEWER_HDF5_MAT && !mat->symmetric) {
71: /* Swap row and columns layout for unallocated matrix. I want to avoid calling MatTranspose() just to transpose sparsity pattern and layout. */
72: if (!mat->preallocated) {
73: PetscLayout tmp;
74: tmp = mat->rmap; mat->rmap = mat->cmap; mat->cmap = tmp;
75: } else SETERRQ(comm,PETSC_ERR_SUP,"Not for preallocated matrix - we would need to transpose it here which we want to avoid");
76: }
78: /* If global sizes are set, check if they are consistent with that given in the file */
79: if (mat->rmap->N >= 0 && mat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows: Matrix in file has (%D) and input matrix has (%D)",mat->rmap->N,M);
80: if (mat->cmap->N >= 0 && mat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols: Matrix in file has (%D) and input matrix has (%D)",mat->cmap->N,N);
82: /* Determine ownership of all (block) rows and columns */
83: mat->rmap->N = M;
84: mat->cmap->N = N;
85: PetscLayoutSetUp(mat->rmap);
86: PetscLayoutSetUp(mat->cmap);
87: m = mat->rmap->n;
89: /* Read array i (array of row indices) */
90: PetscMalloc1(m+1, &i); /* allocate i with one more position for local number of nonzeros on each rank */
91: i[0] = i[m] = 0; /* make the last entry always defined - the code block below overwrites it just on last rank */
92: 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 */
93: M++;
94: ISCreate(comm,&is_i);
95: PetscObjectSetName((PetscObject)is_i,i_name);
96: PetscLayoutSetLocalSize(is_i->map,m);
97: PetscLayoutSetSize(is_i->map,M);
98: ISLoad(is_i,viewer);
99: ISGetIndices(is_i,&i_glob);
100: PetscArraycpy(i,i_glob,m);
102: /* Reset m and M to the matrix sizes */
103: m = mat->rmap->n;
104: M--;
106: /* Create PetscLayout for j and a vectors; construct ranges first */
107: PetscMalloc1(size+1, &range);
108: MPI_Allgather(i, 1, MPIU_INT, range, 1, MPIU_INT, comm);
109: /* Last rank has global number of nonzeros (= length of j and a arrays) in i[m] (last i entry) so broadcast it */
110: range[size] = i[m];
111: MPI_Bcast(&range[size], 1, MPIU_INT, size-1, comm);
112: for (p=size-1; p>0; p--) {
113: if (!range[p]) range[p] = range[p+1]; /* for ranks with 0 rows, take the value from the next processor */
114: }
115: i[m] = range[rank+1]; /* i[m] (last i entry) is equal to next rank's offset */
116: /* Deduce rstart, rend, n and N from the ranges */
117: PetscLayoutCreateFromRanges(comm,range,PETSC_OWN_POINTER,1,&jmap);
119: /* Convert global to local indexing of rows */
120: for (p=1; p<m+1; ++p) i[p] -= i[0];
121: i[0] = 0;
123: /* Read array j (array of column indices) */
124: ISCreate(comm,&is_j);
125: PetscObjectSetName((PetscObject)is_j,j_name);
126: PetscLayoutDuplicate(jmap,&is_j->map);
127: ISLoad(is_j,viewer);
128: ISGetIndices(is_j,&j);
130: /* Read array a (array of values) */
131: VecCreate(comm,&vec_a);
132: PetscObjectSetName((PetscObject)vec_a,a_name);
133: PetscLayoutDuplicate(jmap,&vec_a->map);
134: VecLoad(vec_a,viewer);
135: VecGetArrayRead(vec_a,&a);
137: /* populate matrix */
138: if (!((PetscObject)mat)->type_name) {
139: MatSetType(mat,MATAIJ);
140: }
141: MatSeqAIJSetPreallocationCSR(mat,i,j,a);
142: MatMPIAIJSetPreallocationCSR(mat,i,j,a);
143: /*
144: MatSeqBAIJSetPreallocationCSR(mat,bs,i,j,a);
145: MatMPIBAIJSetPreallocationCSR(mat,bs,i,j,a);
146: */
148: if (format==PETSC_VIEWER_HDF5_MAT && !mat->symmetric) {
149: /* Transpose the input matrix back */
150: MatTranspose(mat,MAT_INPLACE_MATRIX,&mat);
151: }
153: PetscViewerHDF5PopGroup(viewer);
154: PetscFree(i_name);
155: PetscFree(j_name);
156: PetscFree(a_name);
157: PetscFree(c_name);
158: PetscLayoutDestroy(&jmap);
159: PetscFree(i);
160: ISRestoreIndices(is_i,&i_glob);
161: ISRestoreIndices(is_j,&j);
162: VecRestoreArrayRead(vec_a,&a);
163: ISDestroy(&is_i);
164: ISDestroy(&is_j);
165: VecDestroy(&vec_a);
166: return(0);
167: }
168: #endif