Actual source code: vecio.c


  2: /*
  3:    This file contains simple binary input routines for vectors.  The
  4:    analogous output routines are within each vector implementation's
  5:    VecView (with viewer types PETSCVIEWERBINARY)
  6:  */

  8: #include <petscsys.h>
  9: #include <petscvec.h>
 10: #include <petsc/private/vecimpl.h>
 11: #include <petsc/private/viewerimpl.h>
 12: #include <petsclayouthdf5.h>

 14: PetscErrorCode VecView_Binary(Vec vec, PetscViewer viewer)
 15: {
 16:   PetscBool          skipHeader;
 17:   PetscLayout        map;
 18:   PetscInt           tr[2], n, s, N;
 19:   const PetscScalar *xarray;

 21:   PetscFunctionBegin;
 22:   PetscCheckSameComm(vec, 1, viewer, 2);
 23:   PetscCall(PetscViewerSetUp(viewer));
 24:   PetscCall(PetscViewerBinaryGetSkipHeader(viewer, &skipHeader));

 26:   PetscCall(VecGetLayout(vec, &map));
 27:   PetscCall(PetscLayoutGetLocalSize(map, &n));
 28:   PetscCall(PetscLayoutGetRange(map, &s, NULL));
 29:   PetscCall(PetscLayoutGetSize(map, &N));

 31:   tr[0] = VEC_FILE_CLASSID;
 32:   tr[1] = N;
 33:   if (!skipHeader) PetscCall(PetscViewerBinaryWrite(viewer, tr, 2, PETSC_INT));

 35:   PetscCall(VecGetArrayRead(vec, &xarray));
 36:   PetscCall(PetscViewerBinaryWriteAll(viewer, xarray, n, s, N, PETSC_SCALAR));
 37:   PetscCall(VecRestoreArrayRead(vec, &xarray));

 39:   { /* write to the viewer's .info file */
 40:     FILE             *info;
 41:     PetscMPIInt       rank;
 42:     PetscViewerFormat format;
 43:     const char       *name, *pre;

 45:     PetscCall(PetscViewerBinaryGetInfoPointer(viewer, &info));
 46:     PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)vec), &rank));

 48:     PetscCall(PetscViewerGetFormat(viewer, &format));
 49:     if (format == PETSC_VIEWER_BINARY_MATLAB) {
 50:       PetscCall(PetscObjectGetName((PetscObject)vec, &name));
 51:       if (rank == 0 && info) {
 52:         PetscCall(PetscFPrintf(PETSC_COMM_SELF, info, "#--- begin code written by PetscViewerBinary for MATLAB format ---#\n"));
 53:         PetscCall(PetscFPrintf(PETSC_COMM_SELF, info, "#$$ Set.%s = PetscBinaryRead(fd);\n", name));
 54:         PetscCall(PetscFPrintf(PETSC_COMM_SELF, info, "#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n"));
 55:       }
 56:     }

 58:     PetscCall(PetscObjectGetOptionsPrefix((PetscObject)vec, &pre));
 59:     if (rank == 0 && info) PetscCall(PetscFPrintf(PETSC_COMM_SELF, info, "-%svecload_block_size %" PetscInt_FMT "\n", pre ? pre : "", PetscAbs(vec->map->bs)));
 60:   }
 61:   PetscFunctionReturn(PETSC_SUCCESS);
 62: }

 64: PetscErrorCode VecLoad_Binary(Vec vec, PetscViewer viewer)
 65: {
 66:   PetscBool    skipHeader, flg;
 67:   PetscInt     tr[2], 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_INT));
 81:     PetscCheck(tr[0] == VEC_FILE_CLASSID, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Not a vector next in file");
 82:     PetscCheck(tr[1] >= 0, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Vector size (%" PetscInt_FMT ") in file is negative", tr[1]);
 83:     PetscCheck(N < 0 || N == tr[1], PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Vector in file different size (%" PetscInt_FMT ") than input vector (%" PetscInt_FMT ")", tr[1], N);
 84:     rows = tr[1];
 85:   } else {
 86:     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");
 87:     rows = N;
 88:   }

 90:   /* set vector size, blocksize, and type if not already set; block size first so that local sizes will be compatible. */
 91:   PetscCall(PetscLayoutGetBlockSize(map, &bs));
 92:   PetscCall(PetscOptionsGetInt(((PetscObject)viewer)->options, ((PetscObject)vec)->prefix, "-vecload_block_size", &bs, &flg));
 93:   if (flg) PetscCall(VecSetBlockSize(vec, bs));
 94:   PetscCall(PetscLayoutGetLocalSize(map, &n));
 95:   if (N < 0) PetscCall(VecSetSizes(vec, n, rows));
 96:   PetscCall(VecSetUp(vec));

 98:   /* get vector sizes and check global size */
 99:   PetscCall(VecGetSize(vec, &N));
100:   PetscCall(VecGetLocalSize(vec, &n));
101:   PetscCall(VecGetOwnershipRange(vec, &s, NULL));
102:   PetscCheck(N == rows, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Vector in file different size (%" PetscInt_FMT ") than input vector (%" PetscInt_FMT ")", rows, N);

104:   /* read vector values */
105:   PetscCall(VecGetArray(vec, &array));
106:   PetscCall(PetscViewerBinaryReadAll(viewer, array, n, s, N, PETSC_SCALAR));
107:   PetscCall(VecRestoreArray(vec, &array));
108:   PetscFunctionReturn(PETSC_SUCCESS);
109: }

111: #if defined(PETSC_HAVE_HDF5)
112: PetscErrorCode VecLoad_HDF5(Vec xin, PetscViewer viewer)
113: {
114:   hid_t        scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
115:   PetscScalar *x, *arr;
116:   const char  *vecname;

118:   PetscFunctionBegin;
119:   PetscCheck(((PetscObject)xin)->name, PetscObjectComm((PetscObject)xin), PETSC_ERR_SUP, "Vec name must be set with PetscObjectSetName() before VecLoad()");
120:   #if defined(PETSC_USE_REAL_SINGLE)
121:   scalartype = H5T_NATIVE_FLOAT;
122:   #elif defined(PETSC_USE_REAL___FLOAT128)
123:     #error "HDF5 output with 128 bit floats not supported."
124:   #elif defined(PETSC_USE_REAL___FP16)
125:     #error "HDF5 output with 16 bit floats not supported."
126:   #else
127:   scalartype = H5T_NATIVE_DOUBLE;
128:   #endif
129:   PetscCall(PetscObjectGetName((PetscObject)xin, &vecname));
130:   PetscCall(PetscViewerHDF5Load(viewer, vecname, xin->map, scalartype, (void **)&x));
131:   PetscCall(VecSetUp(xin)); /* VecSetSizes might have not been called so ensure ops->create has been called */
132:   if (!xin->ops->replacearray) {
133:     PetscCall(VecGetArray(xin, &arr));
134:     PetscCall(PetscArraycpy(arr, x, xin->map->n));
135:     PetscCall(PetscFree(x));
136:     PetscCall(VecRestoreArray(xin, &arr));
137:   } else {
138:     PetscCall(VecReplaceArray(xin, x));
139:   }
140:   PetscFunctionReturn(PETSC_SUCCESS);
141: }
142: #endif

144: #if defined(PETSC_HAVE_ADIOS)
145:   #include <adios.h>
146:   #include <adios_read.h>
147: #include <petsc/private/vieweradiosimpl.h>
148: #include <petsc/private/viewerimpl.h>

150: PetscErrorCode VecLoad_ADIOS(Vec xin, PetscViewer viewer)
151: {
152:   PetscViewer_ADIOS *adios = (PetscViewer_ADIOS *)viewer->data;
153:   PetscScalar       *x;
154:   PetscInt           Nfile, N, rstart, n;
155:   uint64_t           N_t, rstart_t;
156:   const char        *vecname;
157:   ADIOS_VARINFO     *v;
158:   ADIOS_SELECTION   *sel;

160:   PetscFunctionBegin;
161:   PetscCall(PetscObjectGetName((PetscObject)xin, &vecname));

163:   v = adios_inq_var(adios->adios_fp, vecname);
164:   PetscCheck(v->ndim == 1, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Vector in file is not of dimension 1 (%" PetscInt_FMT ")", v->ndim);
165:   Nfile = (PetscInt)v->dims[0];

167:   /* Set Vec sizes,blocksize,and type if not already set */
168:   if ((xin)->map->n < 0 && (xin)->map->N < 0) PetscCall(VecSetSizes(xin, PETSC_DECIDE, Nfile));
169:   /* If sizes and type already set,check if the vector global size is correct */
170:   PetscCall(VecGetSize(xin, &N));
171:   PetscCall(VecGetLocalSize(xin, &n));
172:   PetscCheck(N == Nfile, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Vector in file different length (%" PetscInt_FMT ") then input vector (%" PetscInt_FMT ")", Nfile, N);

174:   PetscCall(VecGetOwnershipRange(xin, &rstart, NULL));
175:   rstart_t = rstart;
176:   N_t      = n;
177:   sel      = adios_selection_boundingbox(v->ndim, &rstart_t, &N_t);
178:   PetscCall(VecGetArray(xin, &x));
179:   adios_schedule_read(adios->adios_fp, sel, vecname, 0, 1, x);
180:   adios_perform_reads(adios->adios_fp, 1);
181:   PetscCall(VecRestoreArray(xin, &x));
182:   adios_selection_delete(sel);

184:   PetscFunctionReturn(PETSC_SUCCESS);
185: }
186: #endif

188: PetscErrorCode VecLoad_Default(Vec newvec, PetscViewer viewer)
189: {
190:   PetscBool isbinary;
191: #if defined(PETSC_HAVE_HDF5)
192:   PetscBool ishdf5;
193: #endif
194: #if defined(PETSC_HAVE_ADIOS)
195:   PetscBool isadios;
196: #endif

198:   PetscFunctionBegin;
199:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary));
200: #if defined(PETSC_HAVE_HDF5)
201:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5));
202: #endif
203: #if defined(PETSC_HAVE_ADIOS)
204:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERADIOS, &isadios));
205: #endif

207: #if defined(PETSC_HAVE_HDF5)
208:   if (ishdf5) {
209:     if (!((PetscObject)newvec)->name) {
210:       PetscCall(PetscLogEventEnd(VEC_Load, viewer, 0, 0, 0));
211:       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()");
212:     }
213:     PetscCall(VecLoad_HDF5(newvec, viewer));
214:   } else
215: #endif
216: #if defined(PETSC_HAVE_ADIOS)
217:     if (isadios) {
218:     if (!((PetscObject)newvec)->name) {
219:       PetscCall(PetscLogEventEnd(VEC_Load, viewer, 0, 0, 0));
220:       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()");
221:     }
222:     PetscCall(VecLoad_ADIOS(newvec, viewer));
223:   } else
224: #endif
225:   {
226:     PetscCall(VecLoad_Binary(newvec, viewer));
227:   }
228:   PetscFunctionReturn(PETSC_SUCCESS);
229: }

231: /*@
232:   VecChop - Set all values in the vector with an absolute value less than the tolerance to zero

234:   Input Parameters:
235: + v   - The vector
236: - tol - The zero tolerance

238:   Output Parameter:
239: . v - The chopped vector

241:   Level: intermediate

243: .seealso: `VecCreate()`, `VecSet()`
244: @*/
245: PetscErrorCode VecChop(Vec v, PetscReal tol)
246: {
247:   PetscScalar *a;
248:   PetscInt     n, i;

250:   PetscFunctionBegin;
251:   PetscCall(VecGetLocalSize(v, &n));
252:   PetscCall(VecGetArray(v, &a));
253:   for (i = 0; i < n; ++i) {
254:     if (PetscAbsScalar(a[i]) < tol) a[i] = 0.0;
255:   }
256:   PetscCall(VecRestoreArray(v, &a));
257:   PetscFunctionReturn(PETSC_SUCCESS);
258: }