PetscErrorCode PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
{
PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
MPI_Info info = MPI_INFO_NULL;
#endif
hid_t plist_id;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscStrallocpy(name, &hdf5->filename);CHKERRQ(ierr);
/* Set up file access property list with parallel I/O access */
PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_FILE_ACCESS));
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
PetscStackCallHDF5(H5Pset_fapl_mpio,(plist_id, PetscObjectComm((PetscObject)viewer), info));
#endif
/* Create or open the file collectively */
switch (hdf5->btype) {
case FILE_MODE_READ:
PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDONLY, plist_id));
break;
case FILE_MODE_APPEND:
PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id));
break;
case FILE_MODE_WRITE:
PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));
break;
default:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
}
if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
PetscStackCallHDF5(H5Pclose,(plist_id));
PetscFunctionReturn(0);
}
static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer)
{
PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)viewer->data;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscFree(hdf5->filename);CHKERRQ(ierr);
if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
PetscFunctionReturn(0);
}
static 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;
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, ×tep);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;
}
PetscStackCallHDF5Return(filespace,H5Screate_simple,(dim, dims, maxDims));
#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 */
PetscStackCallHDF5Return(chunkspace,H5Pcreate,(H5P_DATASET_CREATE));
PetscStackCallHDF5(H5Pset_chunk,(chunkspace, dim, chunkDims));
PetscStackCallHDF5Return(dset_id,H5Dcreate2,(group, isname, inttype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT));
PetscStackCallHDF5(H5Pclose,(chunkspace));
} else {
PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, isname, H5P_DEFAULT));
PetscStackCallHDF5(H5Dset_extent,(dset_id, dims));
}
PetscStackCallHDF5(H5Sclose,(filespace));
/* 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) {
PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL));
} else {
/* Can't create dataspace with zero for any dimension, so create null dataspace. */
PetscStackCallHDF5Return(memspace,H5Screate,(H5S_NULL));
}
/* 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) {
PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id));
PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL));
} else {
/* Create null filespace to match null memspace. */
PetscStackCallHDF5Return(filespace,H5Screate,(H5S_NULL));
}
/* Create property list for collective dataset write */
PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER));
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE));
#endif
/* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
ierr = ISGetIndices(is, &ind);CHKERRQ(ierr);
PetscStackCallHDF5(H5Dwrite,(dset_id, inttype, memspace, filespace, plist_id, ind));
PetscStackCallHDF5(H5Fflush,(file_id, H5F_SCOPE_GLOBAL));
ierr = ISRestoreIndices(is, &ind);CHKERRQ(ierr);
/* Close/release resources */
PetscStackCallHDF5(H5Gclose,(group));
PetscStackCallHDF5(H5Pclose,(plist_id));
PetscStackCallHDF5(H5Sclose,(filespace));
PetscStackCallHDF5(H5Sclose,(memspace));
PetscStackCallHDF5(H5Dclose,(dset_id));
ierr = PetscInfo1(is, "Wrote IS object with name %s\n", isname);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
