Actual source code: hdf5io.c
1: #include <petsc/private/viewerhdf5impl.h>
2: #include <petsclayouthdf5.h>
4: struct _n_HDF5ReadCtx {
5: const char *name;
6: hid_t file, group, dataset, dataspace;
7: int lenInd, bsInd, complexInd, rdim;
8: hsize_t *dims;
9: PetscBool complexVal, dim2;
11: // Needed for compression
12: PetscInt runs;
13: PetscInt *cind;
14: };
15: typedef struct _n_HDF5ReadCtx *HDF5ReadCtx;
17: PetscErrorCode PetscViewerHDF5CheckTimestepping_Internal(PetscViewer viewer, const char name[])
18: {
19: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
20: PetscBool timestepping = PETSC_FALSE;
22: PetscFunctionBegin;
23: PetscCall(PetscViewerHDF5ReadAttribute(viewer, name, "timestepping", PETSC_BOOL, &hdf5->defTimestepping, ×tepping));
24: if (timestepping != hdf5->timestepping) {
25: char *group;
27: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &group));
28: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Dataset %s/%s stored with timesteps? %s Timestepping pushed? %s", group, name, PetscBools[timestepping], PetscBools[hdf5->timestepping]);
29: }
30: PetscFunctionReturn(PETSC_SUCCESS);
31: }
33: static PetscErrorCode PetscViewerHDF5ReadInitialize_Private(PetscViewer viewer, const char name[], HDF5ReadCtx *ctx)
34: {
35: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
36: HDF5ReadCtx h = NULL;
38: PetscFunctionBegin;
39: PetscCall(PetscViewerHDF5CheckTimestepping_Internal(viewer, name));
40: PetscCall(PetscNew(&h));
41: h->name = name;
42: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &h->file, &h->group));
43: PetscCallHDF5Return(h->dataset, H5Dopen2, (h->group, name, H5P_DEFAULT));
44: PetscCallHDF5Return(h->dataspace, H5Dget_space, (h->dataset));
45: PetscCall(PetscViewerHDF5ReadAttribute(viewer, name, "complex", PETSC_BOOL, &h->complexVal, &h->complexVal));
46: if (!hdf5->horizontal) {
47: /* MATLAB stores column vectors horizontally */
48: PetscCall(PetscViewerHDF5HasAttribute(viewer, name, "MATLAB_class", &hdf5->horizontal));
49: }
50: h->runs = 0;
51: h->cind = NULL;
52: *ctx = h;
53: PetscFunctionReturn(PETSC_SUCCESS);
54: }
56: static PetscErrorCode PetscViewerHDF5ReadFinalize_Private(PetscViewer viewer, HDF5ReadCtx *ctx)
57: {
58: HDF5ReadCtx h;
60: PetscFunctionBegin;
61: h = *ctx;
62: PetscCallHDF5(H5Gclose, (h->group));
63: PetscCallHDF5(H5Sclose, (h->dataspace));
64: PetscCallHDF5(H5Dclose, (h->dataset));
65: PetscCall(PetscFree((*ctx)->dims));
66: PetscCall(PetscFree((*ctx)->cind));
67: PetscCall(PetscFree(*ctx));
68: PetscFunctionReturn(PETSC_SUCCESS);
69: }
71: // Need forward declaration because we have a cyclic call chain
72: static PetscErrorCode PetscViewerHDF5Load_Internal(PetscViewer, const char[], PetscBool, PetscLayout, hid_t, void **);
74: static PetscErrorCode PetscViewerHDF5ReadSizes_Private(PetscViewer viewer, HDF5ReadCtx ctx, PetscBool uncompress, PetscBool setup, PetscLayout *map_)
75: {
76: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
77: PetscInt bs, N;
78: PetscLayout map;
79: PetscBool compressed;
81: PetscFunctionBegin;
82: if (!*map_) PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)viewer), map_));
83: map = *map_;
85: PetscCall(PetscViewerHDF5HasAttribute(viewer, ctx->name, "compressed", &compressed));
86: if (compressed && uncompress) {
87: hid_t inttype;
88: PetscLayout cmap;
89: PetscInt *lcind, N = 0;
90: PetscMPIInt *counts, *displs, size, n;
91: const PetscInt *range;
92: MPI_Comm comm;
94: #if defined(PETSC_USE_64BIT_INDICES)
95: inttype = H5T_NATIVE_LLONG;
96: #else
97: inttype = H5T_NATIVE_INT;
98: #endif
99: PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));
100: PetscCall(PetscLayoutCreate(PetscObjectComm((PetscObject)viewer), &cmap));
101: cmap->bs = 3;
102: PetscCall(PetscViewerHDF5Load_Internal(viewer, ctx->name, PETSC_FALSE, cmap, inttype, (void **)&lcind));
103: PetscCheck(!(cmap->n % 3), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Compressed IS must have an even number of entries, not %" PetscInt_FMT, cmap->n);
104: for (PetscInt i = 0; i < cmap->n / 3; ++i) N += lcind[i * 3 + 0];
105: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &N, 1, MPIU_INT, MPIU_SUM, comm));
106: ctx->runs = cmap->N / 3;
107: PetscCall(PetscMalloc1(cmap->N, &ctx->cind));
108: PetscCallMPI(MPI_Comm_size(comm, &size));
109: PetscCall(PetscLayoutGetRanges(cmap, &range));
110: PetscCall(PetscMalloc2(size, &counts, size, &displs));
111: for (PetscInt r = 0; r < size; ++r) {
112: PetscCall(PetscMPIIntCast(range[r + 1] - range[r], &counts[r]));
113: PetscCall(PetscMPIIntCast(range[r], &displs[r]));
114: }
115: PetscCall(PetscMPIIntCast(cmap->n, &n));
116: PetscCallMPI(MPI_Allgatherv(lcind, n, MPIU_INT, ctx->cind, counts, displs, MPIU_INT, comm));
117: PetscCall(PetscFree2(counts, displs));
118: PetscCall(PetscFree(lcind));
119: PetscCall(PetscLayoutDestroy(&cmap));
121: ctx->dim2 = PETSC_FALSE;
122: ctx->rdim = 1;
123: ctx->lenInd = 0;
124: PetscCall(PetscMalloc1(ctx->rdim, &ctx->dims));
125: ctx->dims[0] = N;
126: bs = 1;
127: goto layout;
128: }
130: /* Get actual number of dimensions in dataset */
131: PetscCallHDF5Return(ctx->rdim, H5Sget_simple_extent_dims, (ctx->dataspace, NULL, NULL));
132: PetscCall(PetscMalloc1(ctx->rdim, &ctx->dims));
133: PetscCallHDF5Return(ctx->rdim, H5Sget_simple_extent_dims, (ctx->dataspace, ctx->dims, NULL));
135: /*
136: Dimensions are in this order:
137: [0] timesteps (optional)
138: [lenInd] entries (numbers or blocks)
139: ...
140: [bsInd] entries of blocks (optional)
141: [bsInd+1] real & imaginary part (optional)
142: = rdim-1
143: */
145: /* Get entries dimension index */
146: ctx->lenInd = 0;
147: if (hdf5->timestepping) ++ctx->lenInd;
149: /* Get block dimension index */
150: if (ctx->complexVal) {
151: ctx->bsInd = ctx->rdim - 2;
152: ctx->complexInd = ctx->rdim - 1;
153: } else {
154: ctx->bsInd = ctx->rdim - 1;
155: ctx->complexInd = -1;
156: }
157: PetscCheck(ctx->lenInd <= ctx->bsInd, PetscObjectComm((PetscObject)viewer), PETSC_ERR_PLIB, "Calculated block dimension index = %d < %d = length dimension index.", ctx->bsInd, ctx->lenInd);
158: PetscCheck(ctx->bsInd <= ctx->rdim - 1, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Calculated block dimension index = %d > %d = total number of dimensions - 1.", ctx->bsInd, ctx->rdim - 1);
159: PetscCheck(!ctx->complexVal || ctx->dims[ctx->complexInd] == 2, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Complex numbers must have exactly 2 parts (%" PRIuHSIZE ")", ctx->dims[ctx->complexInd]);
161: if (hdf5->horizontal) {
162: /* support horizontal 1D arrays (MATLAB vectors) - swap meaning of blocks and entries */
163: int t = ctx->lenInd;
164: ctx->lenInd = ctx->bsInd;
165: ctx->bsInd = t;
166: }
168: /* Get block size */
169: ctx->dim2 = PETSC_FALSE;
170: if (ctx->lenInd == ctx->bsInd) {
171: bs = 1; /* support vectors stored as 1D array */
172: } else {
173: bs = (PetscInt)ctx->dims[ctx->bsInd];
174: if (bs == 1) ctx->dim2 = PETSC_TRUE; /* vector with blocksize of 1, still stored as 2D array */
175: }
177: layout:
178: /* Get global size */
179: PetscCall(PetscIntCast(bs * ctx->dims[ctx->lenInd], &N));
181: /* Set global size, blocksize and type if not yet set */
182: if (map->bs < 0) {
183: PetscCall(PetscLayoutSetBlockSize(map, bs));
184: } else PetscCheck(map->bs == bs, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Block size of array in file is %" PetscInt_FMT ", not %" PetscInt_FMT " as expected", bs, map->bs);
185: if (map->N < 0) {
186: PetscCall(PetscLayoutSetSize(map, N));
187: } else PetscCheck(map->N == N, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Global size of array %s in file is %" PetscInt_FMT ", not %" PetscInt_FMT " as expected", ctx->name, N, map->N);
188: if (setup) PetscCall(PetscLayoutSetUp(map));
189: PetscFunctionReturn(PETSC_SUCCESS);
190: }
192: static PetscErrorCode PetscViewerHDF5ReadSelectHyperslab_Private(PetscViewer viewer, HDF5ReadCtx ctx, PetscLayout map, hid_t *memspace)
193: {
194: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
195: hsize_t *count, *offset;
196: PetscInt bs, n, low;
197: int i;
199: PetscFunctionBegin;
200: /* Compute local size and ownership range */
201: PetscCall(PetscLayoutSetUp(map));
202: PetscCall(PetscLayoutGetBlockSize(map, &bs));
203: PetscCall(PetscLayoutGetLocalSize(map, &n));
204: PetscCall(PetscLayoutGetRange(map, &low, NULL));
206: /* Each process defines a dataset and reads it from the hyperslab in the file */
207: PetscCall(PetscMalloc2(ctx->rdim, &count, ctx->rdim, &offset));
208: for (i = 0; i < ctx->rdim; i++) {
209: /* By default, select all entries with no offset */
210: offset[i] = 0;
211: count[i] = ctx->dims[i];
212: }
213: if (hdf5->timestepping) {
214: count[0] = 1;
215: offset[0] = hdf5->timestep;
216: }
217: {
218: PetscCall(PetscHDF5IntCast(n / bs, &count[ctx->lenInd]));
219: PetscCall(PetscHDF5IntCast(low / bs, &offset[ctx->lenInd]));
220: }
221: PetscCallHDF5Return(*memspace, H5Screate_simple, (ctx->rdim, count, NULL));
222: PetscCallHDF5(H5Sselect_hyperslab, (ctx->dataspace, H5S_SELECT_SET, offset, NULL, count, NULL));
223: PetscCall(PetscFree2(count, offset));
224: PetscFunctionReturn(PETSC_SUCCESS);
225: }
227: static PetscErrorCode PetscViewerHDF5ReadArray_Private(PetscViewer viewer, HDF5ReadCtx h, hid_t datatype, hid_t memspace, void *arr)
228: {
229: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
231: PetscFunctionBegin;
232: PetscCallHDF5(H5Dread, (h->dataset, datatype, memspace, h->dataspace, hdf5->dxpl_id, arr));
233: PetscFunctionReturn(PETSC_SUCCESS);
234: }
236: static PetscErrorCode PetscViewerHDF5Load_Internal(PetscViewer viewer, const char name[], PetscBool uncompress, PetscLayout map, hid_t datatype, void **newarr)
237: {
238: PetscBool has;
239: char *group;
240: HDF5ReadCtx h = NULL;
241: hid_t memspace = 0;
242: size_t unitsize;
243: void *arr;
245: PetscFunctionBegin;
246: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &group));
247: PetscCall(PetscViewerHDF5HasDataset(viewer, name, &has));
248: PetscCheck(has, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", name, group);
249: PetscCall(PetscViewerHDF5ReadInitialize_Private(viewer, name, &h));
250: #if defined(PETSC_USE_COMPLEX)
251: if (!h->complexVal) {
252: H5T_class_t clazz = H5Tget_class(datatype);
253: PetscCheck(clazz != H5T_FLOAT, PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Dataset %s/%s is marked as real but PETSc is configured for complex scalars. The conversion is not yet implemented. Configure with --with-scalar-type=real to read this dataset", group ? group : "", name);
254: }
255: #else
256: PetscCheck(!h->complexVal, PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Dataset %s/%s is marked as complex but PETSc is configured for real scalars. Configure with --with-scalar-type=complex to read this dataset", group, name);
257: #endif
259: PetscCall(PetscViewerHDF5ReadSizes_Private(viewer, h, uncompress, PETSC_TRUE, &map));
260: PetscCall(PetscViewerHDF5ReadSelectHyperslab_Private(viewer, h, map, &memspace));
262: if (h->runs && uncompress) {
263: PetscInt *ind;
265: PetscCall(PetscInfo(viewer, "Read compressed object with name %s of size %" PetscInt_FMT ":%" PetscInt_FMT "\n", name, map->n, map->N));
266: // Each process stores the whole compression, so skip any leading parts
267: PetscCall(PetscMalloc1(map->n, &ind));
268: for (PetscInt i = 0, off = 0; i < h->runs; ++i) {
269: for (PetscInt j = 0, inc = 0; j < h->cind[i * 3 + 0]; ++j, ++off, inc += h->cind[i * 3 + 1]) {
270: if (off >= map->rend) {
271: i = h->runs;
272: break;
273: }
274: if (off >= map->rstart) ind[off - map->rstart] = h->cind[i * 3 + 2] + inc;
275: }
276: }
277: *newarr = ind;
278: goto cleanup;
279: }
281: unitsize = H5Tget_size(datatype);
282: if (h->complexVal) unitsize *= 2;
283: /* unitsize is size_t i.e. always unsigned, so the negative check is pointless? */
284: PetscCheck(unitsize > 0 && unitsize <= PetscMax(sizeof(PetscInt), sizeof(PetscScalar)), PETSC_COMM_SELF, PETSC_ERR_LIB, "Sanity check failed: HDF5 function H5Tget_size(datatype) returned suspicious value %zu", unitsize);
285: PetscCall(PetscMalloc(map->n * unitsize, &arr));
287: PetscCall(PetscViewerHDF5ReadArray_Private(viewer, h, datatype, memspace, arr));
288: *newarr = arr;
290: cleanup:
291: PetscCallHDF5(H5Sclose, (memspace));
292: PetscCall(PetscViewerHDF5ReadFinalize_Private(viewer, &h));
293: PetscCall(PetscFree(group));
294: PetscFunctionReturn(PETSC_SUCCESS);
295: }
297: /*@C
298: PetscViewerHDF5Load - Read a raw array from the `PETSCVIEWERHDF5` dataset in parallel
300: Collective; No Fortran Support
302: Input Parameters:
303: + viewer - The `PETSCVIEWERHDF5` viewer
304: . name - The dataset name
305: - datatype - The HDF5 datatype of the items in the dataset
307: Input/Output Parameter:
308: . map - The layout which specifies array partitioning, on output the
309: set up layout (with global size and blocksize according to dataset)
311: Output Parameter:
312: . newarr - The partitioned array, a memory image of the given dataset
314: Level: developer
316: Notes:
317: This is intended mainly for internal use; users should use higher level routines such as `ISLoad()`, `VecLoad()`, `DMLoad()`.
319: The array is partitioned according to the given `PetscLayout` which is converted to an HDF5 hyperslab.
321: This name is relative to the current group returned by `PetscViewerHDF5OpenGroup()`.
323: .seealso: `PetscViewer`, `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5OpenGroup()`, `PetscViewerHDF5ReadSizes()`,
324: `VecLoad()`, `ISLoad()`, `PetscLayout`
325: @*/
326: PetscErrorCode PetscViewerHDF5Load(PetscViewer viewer, const char name[], PetscLayout map, hid_t datatype, void **newarr)
327: {
328: PetscFunctionBegin;
329: PetscCall(PetscViewerHDF5Load_Internal(viewer, name, PETSC_TRUE, map, datatype, newarr));
330: PetscFunctionReturn(PETSC_SUCCESS);
331: }
333: /*@
334: PetscViewerHDF5ReadSizes - Read block size and global size of a `Vec` or `IS` stored in an HDF5 file.
336: Input Parameters:
337: + viewer - The `PETSCVIEWERHDF5` viewer
338: - name - The dataset name
340: Output Parameters:
341: + bs - block size
342: - N - global size
344: Level: advanced
346: Notes:
347: The dataset is stored as an HDF5 dataspace with 1-4 dimensions in the order
348: 1) # timesteps (optional), 2) # blocks, 3) # elements per block (optional), 4) real and imaginary part (only for complex).
350: The dataset can be stored as a 2D dataspace even if its blocksize is 1; see `PetscViewerHDF5SetBaseDimension2()`.
352: .seealso: `PetscViewer`, `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `VecLoad()`, `ISLoad()`, `VecGetSize()`, `ISGetSize()`, `PetscViewerHDF5SetBaseDimension2()`
353: @*/
354: PetscErrorCode PetscViewerHDF5ReadSizes(PetscViewer viewer, const char name[], PetscInt *bs, PetscInt *N)
355: {
356: HDF5ReadCtx h = NULL;
357: PetscLayout map = NULL;
359: PetscFunctionBegin;
361: PetscCall(PetscViewerHDF5ReadInitialize_Private(viewer, name, &h));
362: PetscCall(PetscViewerHDF5ReadSizes_Private(viewer, h, PETSC_TRUE, PETSC_FALSE, &map));
363: PetscCall(PetscViewerHDF5ReadFinalize_Private(viewer, &h));
364: if (bs) *bs = map->bs;
365: if (N) *N = map->N;
366: PetscCall(PetscLayoutDestroy(&map));
367: PetscFunctionReturn(PETSC_SUCCESS);
368: }