void BigArray<T>::loadNC(const std::string &fileName)
{
dataFileName = fileName;
connection.disconnect();
connection = releaseSignal().connect(boost::bind(&gurls::BigArray<T>::close, this));
std::string errorString = "Error opening file " + fileName + ":";
// Set up file access property list with parallel I/O access
plist_id = H5Pcreate(H5P_FILE_ACCESS);
if(plist_id == -1)
throw gException(errorString);
herr_t status;
#ifdef USE_MPIIO
status = H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);
#else
status = H5Pset_fapl_mpiposix(plist_id, MPI_COMM_WORLD, false);
#endif
CHECK_HDF5_ERR(status, errorString)
// Create a new file collectively and release property list identifier.
file_id = H5Fopen(fileName.c_str(), H5F_ACC_RDWR, plist_id);
CHECK_HDF5_ERR(file_id, errorString)
status = H5Pclose(plist_id);
CHECK_HDF5_ERR(status, errorString)
dset_id = H5Dopen(file_id, "mat", H5P_DEFAULT);
CHECK_HDF5_ERR(dset_id, errorString)
hid_t filespace = H5Dget_space( dset_id );
CHECK_HDF5_ERR(filespace, errorString)
hsize_t dims[2], maxDims[2];
status = H5Sget_simple_extent_dims(filespace, dims, maxDims);
CHECK_HDF5_ERR(status, errorString)
status = H5Sclose(filespace);
CHECK_HDF5_ERR(status, errorString)
this->numrows = static_cast<unsigned long>(dims[1]);
this->numcols = static_cast<unsigned long>(dims[0]);
// Create property list for collective dataset write.
plist_id = H5Pcreate(H5P_DATASET_XFER);
if(plist_id == -1)
throw gException(errorString);
status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
CHECK_HDF5_ERR(status, errorString)
}
/*
* Create the appropriate File access property list
*/
hid_t
create_faccess_plist(MPI_Comm comm, MPI_Info info, int l_facc_type,
hbool_t use_gpfs)
{
hid_t ret_pl = -1;
herr_t ret; /* generic return value */
int mpi_rank; /* mpi variables */
/* need the rank for error checking macros */
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
ret_pl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((ret_pl >= 0), "H5P_FILE_ACCESS");
if (l_facc_type == FACC_DEFAULT)
return (ret_pl);
if (l_facc_type == FACC_MPIO) {
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(ret_pl, comm, info);
VRFY((ret >= 0), "");
return(ret_pl);
}
if (l_facc_type == (FACC_MPIO | FACC_SPLIT)) {
hid_t mpio_pl;
mpio_pl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((mpio_pl >= 0), "");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(mpio_pl, comm, info);
VRFY((ret >= 0), "");
/* setup file access template */
ret_pl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((ret_pl >= 0), "");
/* set Parallel access with communicator */
ret = H5Pset_fapl_split(ret_pl, ".meta", mpio_pl, ".raw", mpio_pl);
VRFY((ret >= 0), "H5Pset_fapl_split succeeded");
H5Pclose(mpio_pl);
return(ret_pl);
}
if (l_facc_type == FACC_MPIPOSIX) {
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpiposix(ret_pl, comm, use_gpfs);
VRFY((ret >= 0), "H5Pset_fapl_mpiposix succeeded");
return(ret_pl);
}
/* unknown file access types */
return (ret_pl);
}
/*----------------------------------------------------------------------------
* Name: h5pset_fapl_mpiposix_c
* Purpose: Call H5Pset_fapl_mpiposix to set mode for parallel I/O and the user
* supplied communicator
* Inputs: prp_id - property list identifier
* comm - MPI communicator
* flag - flag to use GPFS hints
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Tuesday, May 6, 2003
* Modifications:
*---------------------------------------------------------------------------*/
int_f
nh5pset_fapl_mpiposix_c(hid_t_f *prp_id, int_f* comm, int_f* flag)
{
int ret_value = -1;
hid_t c_prp_id;
herr_t ret;
hbool_t c_flag;
MPI_Comm c_comm;
c_comm = MPI_Comm_f2c(*comm);
c_flag = (hbool_t)*flag;
/*
* Call H5Pset_fapl_mpiposix function.
*/
c_prp_id = (hid_t) *prp_id;
ret = H5Pset_fapl_mpiposix(c_prp_id, c_comm, c_flag);
if (ret < 0) return ret_value;
ret_value = 0;
return ret_value;
}
void BigArray<T>::init(std::string& fileName, unsigned long r, unsigned long c)
{
dataFileName = fileName;
connection.disconnect();
connection = releaseSignal().connect(boost::bind(&gurls::BigArray<T>::close, this));
std::string errorString = "Error creating file " + fileName + ":";
// Set up file access property list with parallel I/O access
plist_id = H5Pcreate(H5P_FILE_ACCESS);
if(plist_id == -1)
throw gException(errorString);
herr_t status;
#ifdef USE_MPIIO
status = H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);
#else
status = H5Pset_fapl_mpiposix(plist_id, MPI_COMM_WORLD, false);
#endif
CHECK_HDF5_ERR(status, errorString)
// Create a new file collectively and release property list identifier.
file_id = H5Fcreate(fileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
CHECK_HDF5_ERR(file_id, errorString)
status = H5Pclose(plist_id);
CHECK_HDF5_ERR(status, errorString)
// Create the dataspace for the dataset.
hsize_t dims[2];
dims[0] = static_cast<hsize_t>(c);
dims[1] = static_cast<hsize_t>(r);
hid_t filespace = H5Screate_simple(2, dims, NULL);
CHECK_HDF5_ERR(filespace, errorString)
hid_t plist_dset_id = H5Pcreate(H5P_DATASET_CREATE);
if(plist_dset_id == -1)
throw gException(errorString);
dset_id = H5Dcreate(file_id, "mat", getHdfType<T>(), filespace, H5P_DEFAULT, plist_dset_id, H5P_DEFAULT);
CHECK_HDF5_ERR(dset_id, errorString)
status = H5Pclose(plist_dset_id);
CHECK_HDF5_ERR(status, errorString)
status = H5Sclose(filespace);
CHECK_HDF5_ERR(status, errorString)
this->numrows = r;
this->numcols = c;
// Create property list for collective dataset write.
plist_id = H5Pcreate(H5P_DATASET_XFER);
if(plist_id == -1)
throw gException(errorString);
status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
CHECK_HDF5_ERR(status, errorString)
flush();
}
