Actual source code: vecio.c

petsc-3.5.1 2014-07-24
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  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>         /*I  "petscvec.h"  I*/
 10: #include <petsc-private/vecimpl.h>
 11: #include <petscmat.h> /* so that MAT_FILE_CLASSID is defined */
 12: #include <petscviewerhdf5.h>

 16: static PetscErrorCode PetscViewerBinaryReadVecHeader_Private(PetscViewer viewer,PetscInt *rows)
 17: {
 19:   MPI_Comm       comm;
 20:   PetscInt       tr[2],type;

 23:   PetscObjectGetComm((PetscObject)viewer,&comm);
 24:   /* Read vector header */
 25:   PetscViewerBinaryRead(viewer,tr,2,PETSC_INT);
 26:   type = tr[0];
 27:   if (type != VEC_FILE_CLASSID) {
 28:     PetscLogEventEnd(VEC_Load,viewer,0,0,0);
 29:     if (type == MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Matrix is next in file, not a vector as you requested");
 30:     else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Not a vector next in file");
 31:   }
 32:   *rows = tr[1];
 33:   return(0);
 34: }

 36: #if defined(PETSC_HAVE_MPIIO)
 39: static PetscErrorCode VecLoad_Binary_MPIIO(Vec vec, PetscViewer viewer)
 40: {
 42:   PetscMPIInt    lsize;
 43:   PetscScalar    *avec;
 44:   MPI_File       mfdes;
 45:   MPI_Offset     off;

 48:   VecGetArray(vec,&avec);
 49:   PetscMPIIntCast(vec->map->n,&lsize);

 51:   PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);
 52:   PetscViewerBinaryGetMPIIOOffset(viewer,&off);
 53:   off += vec->map->rstart*sizeof(PetscScalar);
 54:   MPI_File_set_view(mfdes,off,MPIU_SCALAR,MPIU_SCALAR,(char*)"native",MPI_INFO_NULL);
 55:   MPIU_File_read_all(mfdes,avec,lsize,MPIU_SCALAR,MPI_STATUS_IGNORE);
 56:   PetscViewerBinaryAddMPIIOOffset(viewer,vec->map->N*sizeof(PetscScalar));

 58:   VecRestoreArray(vec,&avec);
 59:   VecAssemblyBegin(vec);
 60:   VecAssemblyEnd(vec);
 61:   return(0);
 62: }
 63: #endif

 67: PetscErrorCode VecLoad_Binary(Vec vec, PetscViewer viewer)
 68: {
 69:   PetscMPIInt    size,rank,tag;
 70:   int            fd;
 71:   PetscInt       i,rows = 0,n,*range,N,bs;
 73:   PetscBool      flag;
 74:   PetscScalar    *avec,*avecwork;
 75:   MPI_Comm       comm;
 76:   MPI_Request    request;
 77:   MPI_Status     status;
 78: #if defined(PETSC_HAVE_MPIIO)
 79:   PetscBool      useMPIIO;
 80: #endif

 83:   PetscObjectGetComm((PetscObject)viewer,&comm);
 84:   MPI_Comm_rank(comm,&rank);
 85:   MPI_Comm_size(comm,&size);

 87:   PetscViewerBinaryGetDescriptor(viewer,&fd);
 88:   PetscViewerBinaryReadVecHeader_Private(viewer,&rows);
 89:   /* Set Vec sizes,blocksize,and type if not already set. Block size first so that local sizes will be compatible. */
 90:   PetscOptionsGetInt(((PetscObject)vec)->prefix, "-vecload_block_size", &bs, &flag);
 91:   if (flag) {
 92:     VecSetBlockSize(vec, bs);
 93:   }
 94:   if (vec->map->n < 0 && vec->map->N < 0) {
 95:     VecSetSizes(vec,PETSC_DECIDE,rows);
 96:   }

 98:   /* If sizes and type already set,check if the vector global size is correct */
 99:   VecGetSize(vec, &N);
100:   if (N != rows) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Vector in file different length (%d) then input vector (%d)", rows, N);

102: #if defined(PETSC_HAVE_MPIIO)
103:   PetscViewerBinaryGetMPIIO(viewer,&useMPIIO);
104:   if (useMPIIO) {
105:     VecLoad_Binary_MPIIO(vec, viewer);
106:     return(0);
107:   }
108: #endif

110:   VecGetLocalSize(vec,&n);
111:   PetscObjectGetNewTag((PetscObject)viewer,&tag);
112:   VecGetArray(vec,&avec);
113:   if (!rank) {
114:     PetscBinaryRead(fd,avec,n,PETSC_SCALAR);

116:     if (size > 1) {
117:       /* read in other chuncks and send to other processors */
118:       /* determine maximum chunck owned by other */
119:       range = vec->map->range;
120:       n = 1;
121:       for (i=1; i<size; i++) n = PetscMax(n,range[i+1] - range[i]);

123:       PetscMalloc1(n,&avecwork);
124:       for (i=1; i<size; i++) {
125:         n    = range[i+1] - range[i];
126:         PetscBinaryRead(fd,avecwork,n,PETSC_SCALAR);
127:         MPI_Isend(avecwork,n,MPIU_SCALAR,i,tag,comm,&request);
128:         MPI_Wait(&request,&status);
129:       }
130:       PetscFree(avecwork);
131:     }
132:   } else {
133:     MPI_Recv(avec,n,MPIU_SCALAR,0,tag,comm,&status);
134:   }

136:   VecRestoreArray(vec,&avec);
137:   VecAssemblyBegin(vec);
138:   VecAssemblyEnd(vec);
139:   return(0);
140: }

142: #if defined(PETSC_HAVE_HDF5)
145: PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId)
146: {
147:   hid_t          file_id, group;
148:   htri_t         found;
149:   const char     *groupName = NULL;

153:   PetscViewerHDF5GetFileId(viewer, &file_id);
154:   PetscViewerHDF5GetGroup(viewer, &groupName);
155:   /* Open group */
156:   if (groupName) {
157:     PetscBool root;

159:     PetscStrcmp(groupName, "/", &root);
160:     found = H5Lexists(file_id, groupName, H5P_DEFAULT);
161:     if (!root && (found <= 0)) {
162: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
163:       group = H5Gcreate2(file_id, groupName, 0, H5P_DEFAULT, H5P_DEFAULT);
164: #else /* deprecated HDF5 1.6 API */
165:       group = H5Gcreate(file_id, groupName, 0);
166: #endif
167:       if (group < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Could not create group %s", groupName);
168:       H5Gclose(group);
169:     }
170: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
171:     group = H5Gopen2(file_id, groupName, H5P_DEFAULT);
172: #else
173:     group = H5Gopen(file_id, groupName);
174: #endif
175:     if (group < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Could not open group %s", groupName);
176:   } else group = file_id;

178:   *fileId  = file_id;
179:   *groupId = group;
180:   return(0);
181: }

185: PetscErrorCode PetscViewerHDF5ReadSizes(PetscViewer viewer, const char name[], PetscInt *bs, PetscInt *N)
186: {
187:   hid_t          file_id, group, dset_id, filespace;
188:   hsize_t        rdim, dim;
189:   hsize_t        dims[4];
190:   herr_t         status;
191:   PetscInt       bsInd, lenInd, timestep;

195:   PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
196:   PetscViewerHDF5GetTimestep(viewer, &timestep);
197: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
198:   dset_id = H5Dopen2(group, name, H5P_DEFAULT);
199: #else
200:   dset_id = H5Dopen(group, name);
201: #endif
202:   if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Could not H5Dopen() with PetscObject named %s", name);
203:   filespace = H5Dget_space(dset_id);
204:   if (filespace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Could not H5Dget_space()");
205:   dim = 0;
206:   if (timestep >= 0) ++dim;
207:   ++dim; /* length in blocks */
208:   ++dim; /* block size */
209: #if defined(PETSC_USE_COMPLEX)
210:   ++dim;
211: #endif
212:   rdim = H5Sget_simple_extent_dims(filespace, dims, NULL);
213: #if defined(PETSC_USE_COMPLEX)
214:   bsInd = rdim-2;
215: #else
216:   bsInd = rdim-1;
217: #endif
218:   lenInd = timestep >= 0 ? 1 : 0;
219:   if (rdim != dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file %d not %d as expected", rdim, dim);
220:   /* Close/release resources */
221:   status = H5Sclose(filespace);CHKERRQ(status);
222:   status = H5Dclose(dset_id);CHKERRQ(status);
223:   if (group != file_id) {status = H5Gclose(group);CHKERRQ(status);}
224:   if (bs) *bs = (PetscInt) dims[bsInd];
225:   if (N)  *N  = (PetscInt) dims[lenInd]*dims[bsInd];
226:   return(0);
227: }

231: /*
232:      This should handle properly the cases where PetscInt is 32 or 64 and hsize_t is 32 or 64. These means properly casting with
233:    checks back and forth between the two types of variables.
234: */
235: PetscErrorCode VecLoad_HDF5(Vec xin, PetscViewer viewer)
236: {
237:   hid_t          file_id, group, dset_id, filespace, memspace, plist_id;
238:   hsize_t        rdim, dim;
239:   hsize_t        dims[4], count[4], offset[4];
240:   herr_t         status;
241:   PetscInt       n, N, bs = 1, bsInd, lenInd, low, timestep;
242:   PetscScalar    *x;
243:   const char     *vecname;

247:   PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
248:   PetscViewerHDF5GetTimestep(viewer, &timestep);
249:   VecGetBlockSize(xin,&bs);
250:   /* Create the dataset with default properties and close filespace */
251:   PetscObjectGetName((PetscObject)xin,&vecname);
252: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
253:   dset_id = H5Dopen2(group, vecname, H5P_DEFAULT);
254: #else
255:   dset_id = H5Dopen(group, vecname);
256: #endif
257:   if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Dopen() with Vec named %s",vecname);
258:   /* Retrieve the dataspace for the dataset */
259:   filespace = H5Dget_space(dset_id);
260:   if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Dget_space()");
261:   dim = 0;
262:   if (timestep >= 0) ++dim;
263:   ++dim;
264:   if (bs >= 1) ++dim;
265: #if defined(PETSC_USE_COMPLEX)
266:   ++dim;
267: #endif
268:   rdim = H5Sget_simple_extent_dims(filespace, dims, NULL);
269: #if defined(PETSC_USE_COMPLEX)
270:   bsInd = rdim-2;
271: #else
272:   bsInd = rdim-1;
273: #endif
274:   lenInd = timestep >= 0 ? 1 : 0;
275:   if (rdim != dim) {
276:     if (rdim == dim+1 && bs == -1) bs = dims[bsInd];
277:     else SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file %d not %d as expected",rdim,dim);
278:   } else if (bs >= 1 && bs != (PetscInt) dims[bsInd]) {
279:     VecSetBlockSize(xin, dims[bsInd]);
280:     if (ierr) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Block size %d specified for vector does not match blocksize in file %d",bs,dims[bsInd]);
281:     bs = dims[bsInd];
282:   }

284:   /* Set Vec sizes,blocksize,and type if not already set */
285:   if ((xin)->map->n < 0 && (xin)->map->N < 0) {
286:     VecSetSizes(xin, PETSC_DECIDE, dims[lenInd]*bs);
287:   }
288:   /* If sizes and type already set,check if the vector global size is correct */
289:   VecGetSize(xin, &N);
290:   if (N/bs != (PetscInt) dims[lenInd]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Vector in file different length (%d) then input vector (%d)", (PetscInt) dims[lenInd], N/bs);

292:   /* Each process defines a dataset and reads it from the hyperslab in the file */
293:   VecGetLocalSize(xin, &n);
294:   dim  = 0;
295:   if (timestep >= 0) {
296:     count[dim] = 1;
297:     ++dim;
298:   }
299:   PetscHDF5IntCast(n/bs,count + dim);
300:   ++dim;
301:   if (bs >= 1) {
302:     count[dim] = bs;
303:     ++dim;
304:   }
305: #if defined(PETSC_USE_COMPLEX)
306:   count[dim] = 2;
307:   ++dim;
308: #endif
309:   memspace = H5Screate_simple(dim, count, NULL);
310:   if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Screate_simple()");

312:   /* Select hyperslab in the file */
313:   VecGetOwnershipRange(xin, &low, NULL);
314:   dim  = 0;
315:   if (timestep >= 0) {
316:     offset[dim] = timestep;
317:     ++dim;
318:   }
319:   PetscHDF5IntCast(low/bs,offset + dim);
320:   ++dim;
321:   if (bs >= 1) {
322:     offset[dim] = 0;
323:     ++dim;
324:   }
325: #if defined(PETSC_USE_COMPLEX)
326:   offset[dim] = 0;
327:   ++dim;
328: #endif
329:   status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);

331:   /* Create property list for collective dataset read */
332:   plist_id = H5Pcreate(H5P_DATASET_XFER);
333:   if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Pcreate()");
334: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
335:   status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
336: #endif
337:   /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */

339:   VecGetArray(xin, &x);
340:   status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, plist_id, x);CHKERRQ(status);
341:   VecRestoreArray(xin, &x);

343:   /* Close/release resources */
344:   if (group != file_id) {
345:     status = H5Gclose(group);CHKERRQ(status);
346:   }
347:   status = H5Pclose(plist_id);CHKERRQ(status);
348:   status = H5Sclose(filespace);CHKERRQ(status);
349:   status = H5Sclose(memspace);CHKERRQ(status);
350:   status = H5Dclose(dset_id);CHKERRQ(status);

352:   VecAssemblyBegin(xin);
353:   VecAssemblyEnd(xin);
354:   return(0);
355: }
356: #endif


361: PetscErrorCode  VecLoad_Default(Vec newvec, PetscViewer viewer)
362: {
364:   PetscBool      isbinary;
365: #if defined(PETSC_HAVE_HDF5)
366:   PetscBool      ishdf5;
367: #endif

370:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
371: #if defined(PETSC_HAVE_HDF5)
372:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
373: #endif

375: #if defined(PETSC_HAVE_HDF5)
376:   if (ishdf5) {
377:     if (!((PetscObject)newvec)->name) {
378:       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()");
379:       PetscLogEventEnd(VEC_Load,viewer,0,0,0);
380:     }
381:     VecLoad_HDF5(newvec, viewer);
382:   } else
383: #endif
384:   {
385:     VecLoad_Binary(newvec, viewer);
386:   }
387:   return(0);
388: }

392: /*@
393:   VecChop - Set all values in the vector less than the tolerance to zero

395:   Input Parameters:
396: + v   - The vector
397: - tol - The zero tolerance

399:   Output Parameters:
400: . v - The chopped vector

402:   Level: intermediate

404: .seealso: VecCreate(), VecSet()
405: @*/
406: PetscErrorCode VecChop(Vec v, PetscReal tol)
407: {
408:   PetscScalar    *a;
409:   PetscInt       n, i;

413:   VecGetLocalSize(v, &n);
414:   VecGetArray(v, &a);
415:   for (i = 0; i < n; ++i) {
416:     if (PetscAbsScalar(a[i]) < tol) a[i] = 0.0;
417:   }
418:   VecRestoreArray(v, &a);
419:   return(0);
420: }