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: }