Actual source code: vecio.c
1: /*
2: This file contains simple binary input routines for vectors. The
3: analogous output routines are within each vector implementation's
4: VecView (with viewer types PETSCVIEWERBINARY)
5: */
7: #include <petscsys.h>
8: #include <petscvec.h>
9: #include <petsc/private/vecimpl.h>
10: #include <petsc/private/viewerimpl.h>
11: #include <petsclayouthdf5.h>
13: PetscErrorCode VecView_Binary(Vec vec, PetscViewer viewer)
14: {
15: PetscBool skipHeader;
16: PetscLayout map;
17: PetscInt tr[2], n, s, N;
18: const PetscScalar *xarray;
20: PetscFunctionBegin;
21: PetscCheckSameComm(vec, 1, viewer, 2);
22: PetscCall(PetscViewerSetUp(viewer));
23: PetscCall(PetscViewerBinaryGetSkipHeader(viewer, &skipHeader));
25: PetscCall(VecGetLayout(vec, &map));
26: PetscCall(PetscLayoutGetLocalSize(map, &n));
27: PetscCall(PetscLayoutGetRange(map, &s, NULL));
28: PetscCall(PetscLayoutGetSize(map, &N));
30: tr[0] = VEC_FILE_CLASSID;
31: tr[1] = N;
32: if (!skipHeader) PetscCall(PetscViewerBinaryWrite(viewer, tr, 2, PETSC_INT));
34: PetscCall(VecGetArrayRead(vec, &xarray));
35: PetscCall(PetscViewerBinaryWriteAll(viewer, xarray, n, s, N, PETSC_SCALAR));
36: PetscCall(VecRestoreArrayRead(vec, &xarray));
38: { /* write to the viewer's .info file */
39: FILE *info;
40: PetscMPIInt rank;
41: PetscViewerFormat format;
42: const char *name, *pre;
44: PetscCall(PetscViewerBinaryGetInfoPointer(viewer, &info));
45: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)vec), &rank));
47: PetscCall(PetscViewerGetFormat(viewer, &format));
48: if (format == PETSC_VIEWER_BINARY_MATLAB) {
49: PetscCall(PetscObjectGetName((PetscObject)vec, &name));
50: if (rank == 0 && info) {
51: PetscCall(PetscFPrintf(PETSC_COMM_SELF, info, "#--- begin code written by PetscViewerBinary for MATLAB format ---#\n"));
52: PetscCall(PetscFPrintf(PETSC_COMM_SELF, info, "#$$ Set.%s = PetscBinaryRead(fd);\n", name));
53: PetscCall(PetscFPrintf(PETSC_COMM_SELF, info, "#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n"));
54: }
55: }
57: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)vec, &pre));
58: if (rank == 0 && info) PetscCall(PetscFPrintf(PETSC_COMM_SELF, info, "-%svecload_block_size %" PetscInt_FMT "\n", pre ? pre : "", PetscAbs(vec->map->bs)));
59: }
60: PetscFunctionReturn(PETSC_SUCCESS);
61: }
63: static PetscErrorCode VecLoad_Binary(Vec vec, PetscViewer viewer)
64: {
65: PetscBool skipHeader, flg;
66: uint32_t tr[2];
67: PetscInt token, rows, N, n, s, bs;
68: PetscScalar *array;
69: PetscLayout map;
71: PetscFunctionBegin;
72: PetscCall(PetscViewerSetUp(viewer));
73: PetscCall(PetscViewerBinaryGetSkipHeader(viewer, &skipHeader));
75: PetscCall(VecGetLayout(vec, &map));
76: PetscCall(PetscLayoutGetSize(map, &N));
78: /* read vector header */
79: if (!skipHeader) {
80: PetscCall(PetscViewerBinaryRead(viewer, tr, 2, NULL, PETSC_INT32));
81: if (tr[0] == VEC_FILE_CLASSID) { // File was written with 32-bit ints
82: rows = tr[1];
83: } else { // Assume file was written with 64-bit ints so reconstruct token and read number of rows
84: PetscInt64 rows64;
85: token = (PetscInt)((uint64_t)tr[0] << 32) + tr[1];
86: PetscCheck(token == VEC_FILE_CLASSID, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Not a vector next in file");
87: PetscCall(PetscViewerBinaryRead(viewer, &rows64, 1, NULL, PETSC_INT64));
88: PetscCall(PetscIntCast(rows64, &rows));
89: }
90: PetscCheck(rows >= 0, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Vector size (%" PetscInt_FMT ") in file is negative", rows);
91: PetscCheck(N < 0 || N == rows, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Vector in file different size (%" PetscInt_FMT ") than input vector (%" PetscInt_FMT ")", rows, N);
92: } else {
93: PetscCheck(N >= 0, PETSC_COMM_SELF, PETSC_ERR_USER, "Vector binary file header was skipped, thus the user must specify the global size of input vector");
94: rows = N;
95: }
97: /* set vector size, blocksize, and type if not already set; block size first so that local sizes will be compatible. */
98: PetscCall(PetscLayoutGetBlockSize(map, &bs));
99: PetscCall(PetscOptionsGetInt(((PetscObject)viewer)->options, ((PetscObject)vec)->prefix, "-vecload_block_size", &bs, &flg));
100: if (flg) PetscCall(VecSetBlockSize(vec, bs));
101: PetscCall(PetscLayoutGetLocalSize(map, &n));
102: if (N < 0) PetscCall(VecSetSizes(vec, n, rows));
103: PetscCall(VecSetUp(vec));
105: /* get vector sizes and check global size */
106: PetscCall(VecGetSize(vec, &N));
107: PetscCall(VecGetLocalSize(vec, &n));
108: PetscCall(VecGetOwnershipRange(vec, &s, NULL));
109: PetscCheck(N == rows, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Vector in file different size (%" PetscInt_FMT ") than input vector (%" PetscInt_FMT ")", rows, N);
111: /* read vector values */
112: PetscCall(VecGetArray(vec, &array));
113: PetscCall(PetscViewerBinaryReadAll(viewer, array, n, s, N, PETSC_SCALAR));
114: PetscCall(VecRestoreArray(vec, &array));
115: PetscFunctionReturn(PETSC_SUCCESS);
116: }
118: #if defined(PETSC_HAVE_HDF5)
119: static PetscErrorCode VecLoad_HDF5(Vec xin, PetscViewer viewer)
120: {
121: hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
122: PetscScalar *x, *arr;
123: const char *vecname;
125: PetscFunctionBegin;
126: PetscCheck(((PetscObject)xin)->name, PetscObjectComm((PetscObject)xin), PETSC_ERR_SUP, "Vec name must be set with PetscObjectSetName() before VecLoad()");
127: #if defined(PETSC_USE_REAL_SINGLE)
128: scalartype = H5T_NATIVE_FLOAT;
129: #elif defined(PETSC_USE_REAL___FLOAT128)
130: #error "HDF5 output with 128 bit floats not supported."
131: #elif defined(PETSC_USE_REAL___FP16)
132: #error "HDF5 output with 16 bit floats not supported."
133: #else
134: scalartype = H5T_NATIVE_DOUBLE;
135: #endif
136: PetscCall(PetscObjectGetName((PetscObject)xin, &vecname));
137: PetscCall(PetscViewerHDF5Load(viewer, vecname, xin->map, scalartype, (void **)&x));
138: PetscCall(VecSetUp(xin)); /* VecSetSizes might have not been called so ensure ops->create has been called */
139: if (!xin->ops->replacearray) {
140: PetscCall(VecGetArray(xin, &arr));
141: PetscCall(PetscArraycpy(arr, x, xin->map->n));
142: PetscCall(PetscFree(x));
143: PetscCall(VecRestoreArray(xin, &arr));
144: } else {
145: PetscCall(VecReplaceArray(xin, x));
146: }
147: PetscFunctionReturn(PETSC_SUCCESS);
148: }
149: #endif
151: #if defined(PETSC_HAVE_ADIOS)
152: #include <adios.h>
153: #include <adios_read.h>
154: #include <petsc/private/vieweradiosimpl.h>
155: #include <petsc/private/viewerimpl.h>
157: static PetscErrorCode VecLoad_ADIOS(Vec xin, PetscViewer viewer)
158: {
159: PetscViewer_ADIOS *adios = (PetscViewer_ADIOS *)viewer->data;
160: PetscScalar *x;
161: PetscInt Nfile, N, rstart, n;
162: uint64_t N_t, rstart_t;
163: const char *vecname;
164: ADIOS_VARINFO *v;
165: ADIOS_SELECTION *sel;
167: PetscFunctionBegin;
168: PetscCall(PetscObjectGetName((PetscObject)xin, &vecname));
170: v = adios_inq_var(adios->adios_fp, vecname);
171: PetscCheck(v->ndim == 1, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Vector in file is not of dimension 1 (%" PetscInt_FMT ")", v->ndim);
172: Nfile = (PetscInt)v->dims[0];
174: /* Set Vec sizes,blocksize,and type if not already set */
175: if ((xin)->map->n < 0 && (xin)->map->N < 0) PetscCall(VecSetSizes(xin, PETSC_DECIDE, Nfile));
176: /* If sizes and type already set,check if the vector global size is correct */
177: PetscCall(VecGetSize(xin, &N));
178: PetscCall(VecGetLocalSize(xin, &n));
179: PetscCheck(N == Nfile, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Vector in file different length (%" PetscInt_FMT ") then input vector (%" PetscInt_FMT ")", Nfile, N);
181: PetscCall(VecGetOwnershipRange(xin, &rstart, NULL));
182: rstart_t = rstart;
183: N_t = n;
184: sel = adios_selection_boundingbox(v->ndim, &rstart_t, &N_t);
185: PetscCall(VecGetArray(xin, &x));
186: adios_schedule_read(adios->adios_fp, sel, vecname, 0, 1, x);
187: adios_perform_reads(adios->adios_fp, 1);
188: PetscCall(VecRestoreArray(xin, &x));
189: adios_selection_delete(sel);
190: PetscFunctionReturn(PETSC_SUCCESS);
191: }
192: #endif
194: PetscErrorCode VecLoad_Default(Vec newvec, PetscViewer viewer)
195: {
196: PetscBool isbinary;
197: #if defined(PETSC_HAVE_HDF5)
198: PetscBool ishdf5;
199: #endif
200: #if defined(PETSC_HAVE_ADIOS)
201: PetscBool isadios;
202: #endif
204: PetscFunctionBegin;
205: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary));
206: #if defined(PETSC_HAVE_HDF5)
207: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5));
208: #endif
209: #if defined(PETSC_HAVE_ADIOS)
210: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERADIOS, &isadios));
211: #endif
213: #if defined(PETSC_HAVE_HDF5)
214: if (ishdf5) {
215: if (!((PetscObject)newvec)->name) {
216: PetscCall(PetscLogEventEnd(VEC_Load, viewer, 0, 0, 0));
217: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Since HDF5 format gives ASCII name for each object in file; must use VecLoad() after setting name of Vec with PetscObjectSetName()");
218: }
219: PetscCall(VecLoad_HDF5(newvec, viewer));
220: } else
221: #endif
222: #if defined(PETSC_HAVE_ADIOS)
223: if (isadios) {
224: if (!((PetscObject)newvec)->name) {
225: PetscCall(PetscLogEventEnd(VEC_Load, viewer, 0, 0, 0));
226: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Since ADIOS format gives ASCII name for each object in file; must use VecLoad() after setting name of Vec with PetscObjectSetName()");
227: }
228: PetscCall(VecLoad_ADIOS(newvec, viewer));
229: } else
230: #endif
231: {
232: PetscCall(VecLoad_Binary(newvec, viewer));
233: }
234: PetscFunctionReturn(PETSC_SUCCESS);
235: }
237: /*@
238: VecFilter - Set all values in the vector with an absolute value less than or equal to the tolerance to zero
240: Input Parameters:
241: + v - The vector
242: - tol - The zero tolerance
244: Output Parameter:
245: . v - The filtered vector
247: Level: intermediate
249: .seealso: `VecCreate()`, `VecSet()`, `MatFilter()`
250: @*/
251: PetscErrorCode VecFilter(Vec v, PetscReal tol)
252: {
253: PetscScalar *a;
254: PetscInt n;
256: PetscFunctionBegin;
257: PetscCall(VecGetLocalSize(v, &n));
258: PetscCall(VecGetArray(v, &a));
259: for (PetscInt i = 0; i < n; ++i) {
260: if (PetscAbsScalar(a[i]) < tol) a[i] = 0.0;
261: }
262: PetscCall(VecRestoreArray(v, &a));
263: PetscFunctionReturn(PETSC_SUCCESS);
264: }