Exemplo n.º 1
0
PetscErrorCode ISView_General_HDF5(IS is, PetscViewer viewer)
{
  hid_t           filespace;  /* file dataspace identifier */
  hid_t           chunkspace; /* chunk dataset property identifier */
  hid_t           plist_id;   /* property list identifier */
  hid_t           dset_id;    /* dataset identifier */
  hid_t           memspace;   /* memory dataspace identifier */
  hid_t           inttype;    /* int type (H5T_NATIVE_INT or H5T_NATIVE_LLONG) */
  hid_t           file_id, group;
  herr_t          status;
  hsize_t         dim, maxDims[3], dims[3], chunkDims[3], count[3],offset[3];
  PetscInt        bs, N, n, timestep, low;
  const PetscInt *ind;
  const char     *isname;
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  ierr = ISGetBlockSize(is,&bs);CHKERRQ(ierr);
  ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetTimestep(viewer, &timestep);CHKERRQ(ierr);

  /* Create the dataspace for the dataset.
   *
   * dims - holds the current dimensions of the dataset
   *
   * maxDims - holds the maximum dimensions of the dataset (unlimited
   * for the number of time steps with the current dimensions for the
   * other dimensions; so only additional time steps can be added).
   *
   * chunkDims - holds the size of a single time step (required to
   * permit extending dataset).
   */
  dim = 0;
  if (timestep >= 0) {
    dims[dim]      = timestep+1;
    maxDims[dim]   = H5S_UNLIMITED;
    chunkDims[dim] = 1;
    ++dim;
  }
  ierr = ISGetSize(is, &N);CHKERRQ(ierr);
  ierr = ISGetLocalSize(is, &n);CHKERRQ(ierr);
  ierr = PetscHDF5IntCast(N/bs,dims + dim);CHKERRQ(ierr);

  maxDims[dim]   = dims[dim];
  chunkDims[dim] = dims[dim];
  ++dim;
  if (bs >= 1) {
    dims[dim]      = bs;
    maxDims[dim]   = dims[dim];
    chunkDims[dim] = dims[dim];
    ++dim;
  }
  filespace = H5Screate_simple(dim, dims, maxDims);
  if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");

#if defined(PETSC_USE_64BIT_INDICES)
  inttype = H5T_NATIVE_LLONG;
#else
  inttype = H5T_NATIVE_INT;
#endif

  /* Create the dataset with default properties and close filespace */
  ierr = PetscObjectGetName((PetscObject) is, &isname);CHKERRQ(ierr);
  if (!H5Lexists(group, isname, H5P_DEFAULT)) {
    /* Create chunk */
    chunkspace = H5Pcreate(H5P_DATASET_CREATE);
    if (chunkspace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Pcreate()");
    status = H5Pset_chunk(chunkspace, dim, chunkDims);CHKERRQ(status);

#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
    dset_id = H5Dcreate2(group, isname, inttype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT);
#else
    dset_id = H5Dcreate(group, isname, inttype, filespace, H5P_DEFAULT);
#endif
    if (dset_id == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Dcreate2()");
    status = H5Pclose(chunkspace);CHKERRQ(status);
  } else {
    dset_id = H5Dopen2(group, isname, H5P_DEFAULT);
    status  = H5Dset_extent(dset_id, dims);CHKERRQ(status);
  }
  status = H5Sclose(filespace);CHKERRQ(status);

  /* Each process defines a dataset and writes it to the hyperslab in the file */
  dim = 0;
  if (timestep >= 0) {
    count[dim] = 1;
    ++dim;
  }
  ierr = PetscHDF5IntCast(n/bs,count + dim);CHKERRQ(ierr);
  ++dim;
  if (bs >= 1) {
    count[dim] = bs;
    ++dim;
  }
  if (n > 0) {
    memspace = H5Screate_simple(dim, count, NULL);
    if (memspace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Screate_simple()");
  } else {
    /* Can't create dataspace with zero for any dimension, so create null dataspace. */
    memspace = H5Screate(H5S_NULL);
    if (memspace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Screate()");
  }

  /* Select hyperslab in the file */
  ierr = PetscLayoutGetRange(is->map, &low, NULL);CHKERRQ(ierr);
  dim  = 0;
  if (timestep >= 0) {
    offset[dim] = timestep;
    ++dim;
  }
  ierr = PetscHDF5IntCast(low/bs,offset + dim);CHKERRQ(ierr);
  ++dim;
  if (bs >= 1) {
    offset[dim] = 0;
    ++dim;
  }
  if (n > 0) {
    filespace = H5Dget_space(dset_id);
    if (filespace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Dget_space()");
    status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);
  } else {
    /* Create null filespace to match null memspace. */
    filespace = H5Screate(H5S_NULL);
    if (filespace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Screate(H5S_NULL)");
  }

  /* Create property list for collective dataset write */
  plist_id = H5Pcreate(H5P_DATASET_XFER);
  if (plist_id == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Pcreate()");
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
  status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
#endif
  /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */

  ierr   = ISGetIndices(is, &ind);CHKERRQ(ierr);
  status = H5Dwrite(dset_id, inttype, memspace, filespace, plist_id, ind);CHKERRQ(status);
  status = H5Fflush(file_id, H5F_SCOPE_GLOBAL);CHKERRQ(status);
  ierr   = ISGetIndices(is, &ind);CHKERRQ(ierr);

  /* Close/release resources */
  if (group != file_id) {status = H5Gclose(group);CHKERRQ(status);}
  status = H5Pclose(plist_id);CHKERRQ(status);
  status = H5Sclose(filespace);CHKERRQ(status);
  status = H5Sclose(memspace);CHKERRQ(status);
  status = H5Dclose(dset_id);CHKERRQ(status);
  ierr = PetscInfo1(is, "Wrote IS object with name %s\n", isname);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Exemplo n.º 2
0
/*
     This should handle properly the cases where PetscInt is 32 or 64 and hsize_t is 32 or 64. These means properly casting with
   checks back and forth between the two types of variables.
*/
PetscErrorCode VecLoad_HDF5(Vec xin, PetscViewer viewer)
{
  hid_t          file_id, group, dset_id, filespace, memspace, plist_id;
  hsize_t        rdim, dim;
  hsize_t        dims[4], count[4], offset[4];
  herr_t         status;
  PetscInt       n, N, bs = 1, bsInd, lenInd, low, timestep;
  PetscScalar    *x;
  const char     *vecname;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetTimestep(viewer, &timestep);CHKERRQ(ierr);
  ierr = VecGetBlockSize(xin,&bs);CHKERRQ(ierr);
  /* Create the dataset with default properties and close filespace */
  ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr);
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
  dset_id = H5Dopen2(group, vecname, H5P_DEFAULT);
#else
  dset_id = H5Dopen(group, vecname);
#endif
  if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Dopen() with Vec named %s",vecname);
  /* Retrieve the dataspace for the dataset */
  filespace = H5Dget_space(dset_id);
  if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Dget_space()");
  dim = 0;
  if (timestep >= 0) ++dim;
  ++dim;
  if (bs >= 1) ++dim;
#if defined(PETSC_USE_COMPLEX)
  ++dim;
#endif
  rdim = H5Sget_simple_extent_dims(filespace, dims, NULL);
#if defined(PETSC_USE_COMPLEX)
  bsInd = rdim-2;
#else
  bsInd = rdim-1;
#endif
  lenInd = timestep >= 0 ? 1 : 0;
  if (rdim != dim) {
    if (rdim == dim+1 && bs == -1) bs = dims[bsInd];
    else SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file %d not %d as expected",rdim,dim);
  } else if (bs >= 1 && bs != (PetscInt) dims[bsInd]) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Block size %d specified for vector does not match blocksize in file %d",bs,dims[bsInd]);

  /* Set Vec sizes,blocksize,and type if not already set */
  if ((xin)->map->n < 0 && (xin)->map->N < 0) {
    ierr = VecSetSizes(xin, PETSC_DECIDE, dims[lenInd]*bs);CHKERRQ(ierr);
  }
  /* If sizes and type already set,check if the vector global size is correct */
  ierr = VecGetSize(xin, &N);CHKERRQ(ierr);
  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);

  /* Each process defines a dataset and reads it from the hyperslab in the file */
  ierr = VecGetLocalSize(xin, &n);CHKERRQ(ierr);
  dim  = 0;
  if (timestep >= 0) {
    count[dim] = 1;
    ++dim;
  }
  ierr = PetscHDF5IntCast(n/bs,count + dim);CHKERRQ(ierr);
  ++dim;
  if (bs >= 1) {
    count[dim] = bs;
    ++dim;
  }
#if defined(PETSC_USE_COMPLEX)
  count[dim] = 2;
  ++dim;
#endif
  memspace = H5Screate_simple(dim, count, NULL);
  if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Screate_simple()");

  /* Select hyperslab in the file */
  ierr = VecGetOwnershipRange(xin, &low, NULL);CHKERRQ(ierr);
  dim  = 0;
  if (timestep >= 0) {
    offset[dim] = timestep;
    ++dim;
  }
  ierr = PetscHDF5IntCast(low/bs,offset + dim);CHKERRQ(ierr);
  ++dim;
  if (bs >= 1) {
    offset[dim] = 0;
    ++dim;
  }
#if defined(PETSC_USE_COMPLEX)
  offset[dim] = 0;
  ++dim;
#endif
  status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);

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

  ierr   = VecGetArray(xin, &x);CHKERRQ(ierr);
  status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, plist_id, x);CHKERRQ(status);
  ierr   = VecRestoreArray(xin, &x);CHKERRQ(ierr);

  /* Close/release resources */
  if (group != file_id) {
    status = H5Gclose(group);CHKERRQ(status);
  }
  status = H5Pclose(plist_id);CHKERRQ(status);
  status = H5Sclose(filespace);CHKERRQ(status);
  status = H5Sclose(memspace);CHKERRQ(status);
  status = H5Dclose(dset_id);CHKERRQ(status);

  ierr = VecAssemblyBegin(xin);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(xin);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}