Actual source code: vecio.c
petsc-3.7.1 2016-05-15
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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 <petscviewerhdf5.h>

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

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

     34: #if defined(PETSC_HAVE_MPIIO)
     37: static PetscErrorCode VecLoad_Binary_MPIIO(Vec vec, PetscViewer viewer)
     38: {
     40:   PetscMPIInt    lsize;
     41:   PetscScalar    *avec;
     42:   MPI_File       mfdes;
     43:   MPI_Offset     off;

     46:   VecGetArray(vec,&avec);
     47:   PetscMPIIntCast(vec->map->n,&lsize);

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

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

     65: PetscErrorCode VecLoad_Binary(Vec vec, PetscViewer viewer)
     66: {
     67:   PetscMPIInt    size,rank,tag;
     68:   int            fd;
     69:   PetscInt       i,rows = 0,n,*range,N,bs;
     71:   PetscBool      flag,skipheader;
     72:   PetscScalar    *avec,*avecwork;
     73:   MPI_Comm       comm;
     74:   MPI_Request    request;
     75:   MPI_Status     status;
     76: #if defined(PETSC_HAVE_MPIIO)
     77:   PetscBool      useMPIIO;
     78: #endif

     81:   /* force binary viewer to load .info file if it has not yet done so */
     82:   PetscViewerSetUp(viewer);
     83:   PetscObjectGetComm((PetscObject)viewer,&comm);
     84:   MPI_Comm_rank(comm,&rank);
     85:   MPI_Comm_size(comm,&size);

     87:   PetscViewerBinaryGetDescriptor(viewer,&fd);
     88:   PetscViewerBinaryGetSkipHeader(viewer,&skipheader);
     89:   if (!skipheader) {
     90:     PetscViewerBinaryReadVecHeader_Private(viewer,&rows);
     91:   } else {
     92:     VecType vtype;
     93:     VecGetType(vec,&vtype);
     94:     if (!vtype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER, "Vector binary file header was skipped, thus the user must specify the type and length of input vector");
     95:     VecGetSize(vec,&N);
     96:     if (!N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER, "Vector binary file header was skipped, thus the user must specify the length of input vector");
     97:     rows = N;
     98:   }
     99:   /* Set Vec sizes,blocksize,and type if not already set. Block size first so that local sizes will be compatible. */
    100:   PetscOptionsGetInt(NULL,((PetscObject)vec)->prefix, "-vecload_block_size", &bs, &flag);
    101:   if (flag) {
    102:     VecSetBlockSize(vec, bs);
    103:   }
    104:   if (vec->map->n < 0 && vec->map->N < 0) {
    105:     VecSetSizes(vec,PETSC_DECIDE,rows);
    106:   }

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

    112: #if defined(PETSC_HAVE_MPIIO)
    113:   PetscViewerBinaryGetUseMPIIO(viewer,&useMPIIO);
    114:   if (useMPIIO) {
    115:     VecLoad_Binary_MPIIO(vec, viewer);
    116:     return(0);
    117:   }
    118: #endif

    120:   VecGetLocalSize(vec,&n);
    121:   PetscObjectGetNewTag((PetscObject)viewer,&tag);
    122:   VecGetArray(vec,&avec);
    123:   if (!rank) {
    124:     PetscBinaryRead(fd,avec,n,PETSC_SCALAR);

    126:     if (size > 1) {
    127:       /* read in other chuncks and send to other processors */
    128:       /* determine maximum chunck owned by other */
    129:       range = vec->map->range;
    130:       n = 1;
    131:       for (i=1; i<size; i++) n = PetscMax(n,range[i+1] - range[i]);

    133:       PetscMalloc1(n,&avecwork);
    134:       for (i=1; i<size; i++) {
    135:         n    = range[i+1] - range[i];
    136:         PetscBinaryRead(fd,avecwork,n,PETSC_SCALAR);
    137:         MPI_Isend(avecwork,n,MPIU_SCALAR,i,tag,comm,&request);
    138:         MPI_Wait(&request,&status);
    139:       }
    140:       PetscFree(avecwork);
    141:     }
    142:   } else {
    143:     MPI_Recv(avec,n,MPIU_SCALAR,0,tag,comm,&status);
    144:   }

    146:   VecRestoreArray(vec,&avec);
    147:   VecAssemblyBegin(vec);
    148:   VecAssemblyEnd(vec);
    149:   return(0);
    150: }

    152: #if defined(PETSC_HAVE_HDF5)
    155: PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId)
    156: {
    157:   hid_t          file_id, group;
    158:   htri_t         found;
    159:   const char     *groupName = NULL;

    163:   PetscViewerHDF5GetFileId(viewer, &file_id);
    164:   PetscViewerHDF5GetGroup(viewer, &groupName);
    165:   /* Open group */
    166:   if (groupName) {
    167:     PetscBool root;

    169:     PetscStrcmp(groupName, "/", &root);
    170:     PetscStackCall("H5Lexists",found = H5Lexists(file_id, groupName, H5P_DEFAULT));
    171:     if (!root && (found <= 0)) {
    172: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
    173:       PetscStackCallHDF5Return(group,H5Gcreate2,(file_id, groupName, 0, H5P_DEFAULT, H5P_DEFAULT));
    174: #else /* deprecated HDF5 1.6 API */
    175:       PetscStackCallHDF5Return(group,H5Gcreate,(file_id, groupName, 0));
    176: #endif
    177:       PetscStackCallHDF5(H5Gclose,(group));
    178:     }
    179: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
    180:     PetscStackCallHDF5Return(group,H5Gopen2,(file_id, groupName, H5P_DEFAULT));
    181: #else
    182:     PetscStackCallHDF5Return(group,H5Gopen,file_id, groupName));
    183: #endif
    184:   } else group = file_id;

    186:   *fileId  = file_id;
    187:   *groupId = group;
    188:   return(0);
    189: }

    193: PetscErrorCode PetscViewerHDF5ReadSizes(PetscViewer viewer, const char name[], PetscInt *bs, PetscInt *N)
    194: {
    195:   hid_t          file_id, group, dset_id, filespace;
    196:   int            rdim, dim;
    197:   hsize_t        dims[4];
    198:   PetscInt       bsInd, lenInd, timestep;

    202:   PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
    203:   PetscViewerHDF5GetTimestep(viewer, &timestep);
    204: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
    205:   PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, name, H5P_DEFAULT));
    206: #else
    207:   PetscStackCallHDF5Return(dset_id,H5Dopen,(group, name));
    208: #endif
    209:   PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id));
    210:   dim = 0;
    211:   if (timestep >= 0) ++dim;
    212:   ++dim; /* length in blocks */
    213:   ++dim; /* block size */
    214: #if defined(PETSC_USE_COMPLEX)
    215:   ++dim;
    216: #endif
    217:   PetscStackCallHDF5Return(rdim,H5Sget_simple_extent_dims,(filespace, dims, NULL));
    218: #if defined(PETSC_USE_COMPLEX)
    219:   bsInd = rdim-2;
    220: #else
    221:   bsInd = rdim-1;
    222: #endif
    223:   lenInd = timestep >= 0 ? 1 : 0;
    224:   if (rdim != dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file %d not %d as expected", rdim, dim);
    225:   /* Close/release resources */
    226:   PetscStackCallHDF5(H5Sclose,(filespace));
    227:   PetscStackCallHDF5(H5Dclose,(dset_id));
    228:   if (group != file_id) PetscStackCallHDF5(H5Gclose,(group));
    229:   if (bs) *bs = (PetscInt) dims[bsInd];
    230:   if (N)  *N  = (PetscInt) dims[lenInd]*dims[bsInd];
    231:   return(0);
    232: }

    236: /*
    237:      This should handle properly the cases where PetscInt is 32 or 64 and hsize_t is 32 or 64. These means properly casting with
    238:    checks back and forth between the two types of variables.
    239: */
    240: PetscErrorCode VecLoad_HDF5(Vec xin, PetscViewer viewer)
    241: {
    242:   hid_t          file_id, group, dset_id, filespace, memspace, plist_id;
    243:   int            rdim, dim;
    244:   hsize_t        dims[4], count[4], offset[4];
    245:   PetscInt       n, N, bs = 1, bsInd, lenInd, low, timestep;
    246:   PetscScalar    *x;
    247:   hid_t          scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
    248:   const char     *vecname;
    250:   PetscBool      dim2 = PETSC_FALSE;

    253: #if defined(PETSC_USE_REAL_SINGLE)
    254:   scalartype = H5T_NATIVE_FLOAT;
    255: #elif defined(PETSC_USE_REAL___FLOAT128)
    256: #error "HDF5 output with 128 bit floats not supported."
    257: #else
    258:   scalartype = H5T_NATIVE_DOUBLE;
    259: #endif

    261:   PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
    262:   PetscViewerHDF5GetTimestep(viewer, &timestep);
    263:   VecGetBlockSize(xin,&bs);
    264:   /* Create the dataset with default properties and close filespace */
    265:   PetscObjectGetName((PetscObject)xin,&vecname);
    266: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
    267:   PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT));
    268: #else
    269:   PetscStackCallHDF5Return(dset_id,H5Dopen,(group, vecname));
    270: #endif
    271:   /* Retrieve the dataspace for the dataset */
    272:   PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id));
    273:   dim = 0;
    274:   if (timestep >= 0) ++dim;
    275:   ++dim;
    276:   if (bs > 1) ++dim;
    277: #if defined(PETSC_USE_COMPLEX)
    278:   ++dim;
    279: #endif
    280:   PetscStackCallHDF5Return(rdim,H5Sget_simple_extent_dims,(filespace, dims, NULL));
    281: #if defined(PETSC_USE_COMPLEX)
    282:   bsInd = rdim-2;
    283: #else
    284:   bsInd = rdim-1;
    285: #endif
    286:   lenInd = timestep >= 0 ? 1 : 0;
    287:
    288:   if (rdim != dim) {
    289:     /* In this case the input dataset have one extra, unexpected dimension. */
    290:     if (rdim == dim+1)
    291:     {
    292:       /* In this case the block size is unset */
    293:       if (bs == -1)
    294:       {
    295:         VecSetBlockSize(xin, dims[bsInd]);
    296:         bs = dims[bsInd];
    297:       }
    298:
    299:       /* In this case the block size unity */
    300:       else if (bs == 1 && dims[bsInd] == 1) dim2 = PETSC_TRUE;
    301:
    302:       /* Special error message for the case where bs does not match the input file */
    303:       else if (bs != (PetscInt) dims[bsInd]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Block size of array in file is %D, not %D as expected",(PetscInt)dims[bsInd],bs);
    304:
    305:       /* All other cases is errors */
    306:       else SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file is %d, not %d as expected with bs = %D",rdim,dim,bs);
    307:     }
    308:     else SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file is %d, not %d as expected",rdim,dim);
    309:   } else if (bs > 1 && bs != (PetscInt) dims[bsInd]) {
    310:     VecSetBlockSize(xin, dims[bsInd]);
    311:     bs = dims[bsInd];
    312:   }
    313:
    314:   /* Set Vec sizes,blocksize,and type if not already set */
    315:   if ((xin)->map->n < 0 && (xin)->map->N < 0) {
    316:     VecSetSizes(xin, PETSC_DECIDE, dims[lenInd]*bs);
    317:   }
    318:   /* If sizes and type already set,check if the vector global size is correct */
    319:   VecGetSize(xin, &N);
    320:   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);

    322:   /* Each process defines a dataset and reads it from the hyperslab in the file */
    323:   VecGetLocalSize(xin, &n);
    324:   dim  = 0;
    325:   if (timestep >= 0) {
    326:     count[dim] = 1;
    327:     ++dim;
    328:   }
    329:   PetscHDF5IntCast(n/bs,count + dim);
    330:   ++dim;
    331:   if (bs > 1 || dim2) {
    332:     count[dim] = bs;
    333:     ++dim;
    334:   }
    335: #if defined(PETSC_USE_COMPLEX)
    336:   count[dim] = 2;
    337:   ++dim;
    338: #endif
    339:   PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL));

    341:   /* Select hyperslab in the file */
    342:   VecGetOwnershipRange(xin, &low, NULL);
    343:   dim  = 0;
    344:   if (timestep >= 0) {
    345:     offset[dim] = timestep;
    346:     ++dim;
    347:   }
    348:   PetscHDF5IntCast(low/bs,offset + dim);
    349:   ++dim;
    350:   if (bs > 1 || dim2) {
    351:     offset[dim] = 0;
    352:     ++dim;
    353:   }
    354: #if defined(PETSC_USE_COMPLEX)
    355:   offset[dim] = 0;
    356:   ++dim;
    357: #endif
    358:   PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL));

    360:   /* Create property list for collective dataset read */
    361:   PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER));
    362: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
    363:   PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE));
    364: #endif
    365:   /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */

    367:   VecGetArray(xin, &x);
    368:   PetscStackCallHDF5(H5Dread,(dset_id, scalartype, memspace, filespace, plist_id, x));
    369:   VecRestoreArray(xin, &x);

    371:   /* Close/release resources */
    372:   if (group != file_id) {
    373:     PetscStackCallHDF5(H5Gclose,(group));
    374:   }
    375:   PetscStackCallHDF5(H5Pclose,(plist_id));
    376:   PetscStackCallHDF5(H5Sclose,(filespace));
    377:   PetscStackCallHDF5(H5Sclose,(memspace));
    378:   PetscStackCallHDF5(H5Dclose,(dset_id));

    380:   VecAssemblyBegin(xin);
    381:   VecAssemblyEnd(xin);
    382:   return(0);
    383: }
    384: #endif

    389: PetscErrorCode  VecLoad_Default(Vec newvec, PetscViewer viewer)
    390: {
    392:   PetscBool      isbinary;
    393: #if defined(PETSC_HAVE_HDF5)
    394:   PetscBool      ishdf5;
    395: #endif

    398:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
    399: #if defined(PETSC_HAVE_HDF5)
    400:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
    401: #endif

    403: #if defined(PETSC_HAVE_HDF5)
    404:   if (ishdf5) {
    405:     if (!((PetscObject)newvec)->name) {
    406:       PetscLogEventEnd(VEC_Load,viewer,0,0,0);
    407:       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()");
    408:     }
    409:     VecLoad_HDF5(newvec, viewer);
    410:   } else
    411: #endif
    412:   {
    413:     VecLoad_Binary(newvec, viewer);
    414:   }
    415:   return(0);
    416: }

    420: /*@
    421:   VecChop - Set all values in the vector with an absolute value less than the tolerance to zero

    423:   Input Parameters:
    424: + v   - The vector
    425: - tol - The zero tolerance

    427:   Output Parameters:
    428: . v - The chopped vector

    430:   Level: intermediate

    432: .seealso: VecCreate(), VecSet()
    433: @*/
    434: PetscErrorCode VecChop(Vec v, PetscReal tol)
    435: {
    436:   PetscScalar    *a;
    437:   PetscInt       n, i;

    441:   VecGetLocalSize(v, &n);
    442:   VecGetArray(v, &a);
    443:   for (i = 0; i < n; ++i) {
    444:     if (PetscAbsScalar(a[i]) < tol) a[i] = 0.0;
    445:   }
    446:   VecRestoreArray(v, &a);
    447:   return(0);
    448: }