void Simulation3D::dumpCenterFields(double* eFields, hsize_t nSteps) {
std::ostringstream filename(std::ios::out);
filename << dumpDir << "/center_fields_dx" << dx << "_dt" << dt << ".h5";
hid_t file_id=H5Fcreate(filename.str().c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
hid_t fieldspace=H5Screate_simple(1, & nSteps, NULL);
hid_t dx_space = H5Screate(H5S_SCALAR);
hid_t dt_space = H5Screate(H5S_SCALAR);
hid_t field_dset_id = H5Dcreate(file_id, "timings", H5T_NATIVE_DOUBLE, fieldspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t dx_attr_id = H5Acreate(field_dset_id, "dx", H5T_NATIVE_DOUBLE, dx_space,
H5P_DEFAULT, H5P_DEFAULT);
hid_t dt_attr_id = H5Acreate(field_dset_id, "dt", H5T_NATIVE_DOUBLE, dt_space,
H5P_DEFAULT, H5P_DEFAULT);
herr_t status = H5Dwrite(field_dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, eFields);
status = H5Awrite(dx_attr_id, H5T_NATIVE_DOUBLE, & dx);
status = H5Awrite(dt_attr_id, H5T_NATIVE_DOUBLE, & dt);
H5Sclose(fieldspace); H5Sclose(dx_space); H5Sclose(dt_space);
H5Aclose(dx_attr_id); H5Aclose(dt_attr_id);
H5Dclose(field_dset_id);
H5Fclose(file_id);
}
/* Create and write attribute for a group or a dataset. For groups, attribute
* is a scalar datum; for dataset, it is a one-dimensional array.
*/
void write_attribute(hid_t obj_id, int this_type, int num)
{
hid_t sid, aid;
hsize_t dspace_dims[1]={8};
int i, mpi_rank, attr_data[8], dspace_rank=1;
char attr_name[32];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
if(this_type == is_group) {
sprintf(attr_name, "Group Attribute %d", num);
sid = H5Screate(H5S_SCALAR);
aid = H5Acreate(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT);
H5Awrite(aid, H5T_NATIVE_INT, &num);
H5Aclose(aid);
H5Sclose(sid);
}
else if(this_type == is_dset) {
sprintf(attr_name, "Dataset Attribute %d", num);
for(i=0; i<8; i++)
attr_data[i] = i;
sid = H5Screate_simple(dspace_rank, dspace_dims, NULL);
aid = H5Acreate(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT);
H5Awrite(aid, H5T_NATIVE_INT, attr_data);
H5Aclose(aid);
H5Sclose(sid);
}
}
void Simulation3D::dumpTimings(unsigned long* timings, hsize_t total_timings,
unsigned int steps_per_timing) {
std::ostringstream filename(std::ios::out);
filename << dumpDir << "/timing_s" << blockSize << "_p" << world.size() << ".h5";
hid_t file_id=H5Fcreate(filename.str().c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
hid_t timingspace=H5Screate_simple(1, & total_timings, NULL);
hid_t dx_space = H5Screate(H5S_SCALAR);
hid_t dt_space = H5Screate(H5S_SCALAR);
hid_t bs_space = H5Screate(H5S_SCALAR);
hid_t ns_space = H5Screate(H5S_SCALAR);
hid_t alg_name_space = H5Screate(H5S_SCALAR);
hid_t atype = H5Tcopy(H5T_C_S1);
#ifndef YEE
H5Tset_size(atype, xUpdateRHSs->getAlgName().length());
#else
H5Tset_size(atype, std::string("Yee").length());
#endif
H5Tset_strpad(atype, H5T_STR_NULLTERM);
hid_t timing_dset_id = H5Dcreate(file_id, "timings", H5T_NATIVE_LONG, timingspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t dx_attr_id = H5Acreate(timing_dset_id, "dx", H5T_NATIVE_DOUBLE, dx_space,
H5P_DEFAULT, H5P_DEFAULT);
hid_t dt_attr_id = H5Acreate(timing_dset_id, "dt", H5T_NATIVE_DOUBLE, dt_space,
H5P_DEFAULT, H5P_DEFAULT);
hid_t bs_attr_id = H5Acreate(timing_dset_id, "blockSize", H5T_NATIVE_UINT, bs_space,
H5P_DEFAULT, H5P_DEFAULT);
hid_t ns_attr_id = H5Acreate(timing_dset_id, "stepsPerTiming", H5T_NATIVE_UINT, ns_space,
H5P_DEFAULT, H5P_DEFAULT);
hid_t alg_attr_id = H5Acreate(timing_dset_id,"communicationStrategy", atype, alg_name_space,
H5P_DEFAULT, H5P_DEFAULT);
herr_t status = H5Dwrite(timing_dset_id, H5T_NATIVE_LONG, H5S_ALL, H5S_ALL,
H5P_DEFAULT, timings);
status = H5Awrite(dx_attr_id, H5T_NATIVE_DOUBLE, & dx);
status = H5Awrite(dt_attr_id, H5T_NATIVE_DOUBLE, & dt);
status = H5Awrite(bs_attr_id, H5T_NATIVE_UINT, & blockSize);
status = H5Awrite(ns_attr_id, H5T_NATIVE_UINT, & steps_per_timing);
#ifndef YEE
status = H5Awrite(alg_attr_id, atype, xUpdateRHSs->getAlgName().c_str());
#else
status = H5Awrite(alg_attr_id, atype, "Yee");
#endif
H5Sclose(timingspace); H5Sclose(dx_space); H5Sclose(dt_space);
H5Sclose(alg_name_space); H5Sclose(bs_space); H5Sclose(ns_space);
H5Tclose(atype);
H5Aclose(dx_attr_id); H5Aclose(dt_attr_id); H5Aclose(bs_attr_id);
H5Aclose(alg_attr_id); H5Aclose(ns_attr_id);
H5Dclose(timing_dset_id);
H5Fclose(file_id);
}
char AH5_write_str_root_attr(hid_t loc_id, const char *attr_name, const char *wdata)
{
char success = AH5_FALSE;
hid_t aid = H5Screate(H5S_SCALAR);
hid_t atype = H5Tcopy(H5T_C_S1);
htri_t attr_exists = H5Aexists(loc_id, attr_name);
hid_t attr = -1;
H5Tset_size(atype, strlen(wdata));
if (atype >= 0) {
if (attr_exists == 0) {
attr = H5Acreate(loc_id, attr_name, atype, aid, H5P_DEFAULT, H5P_DEFAULT);
} else if (attr_exists > 0) {
attr = H5Aopen(loc_id, attr_name, H5P_DEFAULT);
}
if (attr && H5Awrite(attr, atype, wdata) >= 0 && H5Aclose(attr) >= 0)
success = AH5_TRUE;
}
success &= (H5Tclose(atype) >= 0);
success &= (H5Sclose(aid) >= 0);
return success;
}
estatus_t
e5_write_attr_list(
hid_t e5_group_id, e5_attr* e5_attr_list)
{
int i;
eid_t status = E5_SUCCESS;
hid_t e5_attribute_id;
hid_t e5_dataspace_id = H5Screate(H5S_SCALAR);
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
if(e5_is_valid_type(e5_attr_list[i].type) != E5_TRUE)
{
status = E5_INVALID_TYPE;
e5_error(e5_group_id, status, "Invalid type requested for attribute [type='%d', name='%s', value='%p']\n", attr->type, attr->name, attr->value);
continue;
}
hid_t hdf_type = e5_convert_type_to_hdf(e5_attr_list[i].type);
hid_t hdf_format = e5_convert_format_to_hdf(e5_attr_list[i].type);
if(H5Aexists(e5_group_id, attr->name) <= 0)
e5_attribute_id = H5Acreate(e5_group_id, attr->name, hdf_type, e5_dataspace_id, H5P_DEFAULT);
e5_info(e5_group_id, "Adding attribute [type='integer', name='%s', value='%d']\n", attr->name, attr->value);
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
H5Awrite(e5_attribute_id, hdf_format, &(attr->value));
H5Aclose(e5_attribute_id);
}
H5Sclose(e5_dataspace_id);
return E5_SUCCESS;
}
bool save_bc(hid_t parent_group_id, Mesh *mesh) {
herr_t status;
// create main group
hid_t group_id = H5Gcreate(parent_group_id, "bc", 0);
// count
hid_t dataspace_id = H5Screate(H5S_SCALAR);
hid_t attr_count = H5Acreate(group_id, "count", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
uint count = mesh->boundaries.count();
status = H5Awrite(attr_count, H5T_NATIVE_UINT32, &count);
H5Aclose(attr_count);
H5Sclose(dataspace_id);
///
///
JudyArray<Boundary *> tri, quad;
for (int i = 0; i < count; i++) {
Boundary *bnd = mesh->boundaries[i];
switch (bnd->get_mode()) {
case HERMES_MODE_TRIANGLE: tri.add(bnd); break;
case HERMES_MODE_QUAD: quad.add(bnd); break;
}
}
save_tri_bc(group_id, tri);
save_quad_bc(group_id, quad);
status = H5Gclose(group_id); // close the group
}
bool save_hex(hid_t parent_group_id, JudyArray<Element *> &elems) {
herr_t status;
// create main group
hid_t group_id = H5Gcreate(parent_group_id, "hex", 0);
// count
hid_t dataspace_id = H5Screate(H5S_SCALAR);
hid_t attr_count = H5Acreate(group_id, "count", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
uint count = elems.count();
status = H5Awrite(attr_count, H5T_NATIVE_UINT32, &count);
H5Aclose(attr_count);
H5Sclose(dataspace_id);
///
hsize_t dims = Hex::NUM_VERTICES;
hid_t elem_dataspace_id = H5Screate_simple(1, &dims, NULL);
// dump vertices
for (int i = 0; i < count; i++) {
char name[256];
sprintf(name, "%d", i);
// the dataset
hid_t dataset_id = H5Dcreate(group_id, name, H5T_NATIVE_UINT32, elem_dataspace_id, H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_NATIVE_UINT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, elems[i]->get_vertices());
status = H5Dclose(dataset_id);
}
H5Sclose(elem_dataspace_id);
status = H5Gclose(group_id); // close the group
}
bool save_elements(hid_t parent_group_id, Mesh *mesh) {
herr_t status;
// create main group
hid_t group_id = H5Gcreate(parent_group_id, "elements", 0);
// count
hid_t dataspace_id = H5Screate(H5S_SCALAR);
hid_t attr_count = H5Acreate(group_id, "count", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
uint count = mesh->elements.count();
status = H5Awrite(attr_count, H5T_NATIVE_UINT32, &count);
H5Aclose(attr_count);
H5Sclose(dataspace_id);
///
JudyArray<Element *> tet, hex, pri;
for (int i = 0; i < count; i++) {
Element *elem = mesh->elements[i];
switch (elem->get_mode()) {
case HERMES_MODE_TET: tet.add(elem); break;
case HERMES_MODE_HEX: hex.add(elem); break;
case HERMES_MODE_PRISM: pri.add(elem); break;
}
}
save_tetra(group_id, tet);
save_hex(group_id, hex);
save_prism(group_id, pri);
status = H5Gclose(group_id); // close the group
}
void DCAttribute::writeAttribute(const char* name, const hid_t type, hid_t parent,
uint32_t ndims, const Dimensions dims, const void* src)
throw (DCException)
{
hid_t attr = -1;
if (H5Aexists(parent, name))
attr = H5Aopen(parent, name, H5P_DEFAULT);
else
{
hid_t dsp;
if( ndims == 1 && dims.getScalarSize() == 1 )
dsp = H5Screate(H5S_SCALAR);
else
dsp = H5Screate_simple( ndims, dims.getPointer(), dims.getPointer() );
attr = H5Acreate(parent, name, type, dsp, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(dsp);
}
if (attr < 0)
throw DCException(getExceptionString(name, "Attribute could not be opened or created"));
if (H5Awrite(attr, type, src) < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Attribute could not be written"));
}
H5Aclose(attr);
}
escdf_errno_t utils_hdf5_create_attr(hid_t loc_id, const char *name,
hid_t type_id, hsize_t *dims,
unsigned int ndims, hid_t *attr_pt)
{
hid_t attr_id, dtspace_id;
/* Create space dimensions. */
if ((dtspace_id = H5Screate_simple(ndims, dims, NULL)) < 0) {
RETURN_WITH_ERROR(dtspace_id);
}
if ((attr_id = H5Acreate(loc_id, name, type_id, dtspace_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
DEFER_FUNC_ERROR(attr_id);
goto cleanup_dtspace;
}
H5Sclose(dtspace_id);
if (attr_pt)
*attr_pt = attr_id;
else
H5Aclose(attr_id);
return ESCDF_SUCCESS;
cleanup_dtspace:
H5Sclose(attr_id);
return ESCDF_ERROR;
}
int
e5_write_attr_list_double(
hid_t e5_group_id, e5_attr_double* e5_attr_list)
{
int i;
hid_t e5_attribute_id;
hid_t e5_dataspace_id = H5Screate(H5S_SCALAR);
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr_double *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
if(H5Aexists(e5_group_id, attr->name) <= 0)
e5_attribute_id = H5Acreate(e5_group_id, attr->name, H5T_IEEE_F64LE, e5_dataspace_id, H5P_DEFAULT);
else
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
e5_info(e5_group_id, "Adding attribute [type='double', name='%s', value='%f']\n", attr->name, attr->value);
H5Awrite(e5_attribute_id, H5T_NATIVE_DOUBLE, &(attr->value));
H5Aclose(e5_attribute_id);
}
H5Sclose(e5_dataspace_id);
return E5_SUCCESS;
}
void write_internal(hdf5dataset& hdataset, const std::string& name, hid_t type_id, const void* buffer, bool overwrite)
{
bool exists = H5Aexists(hdataset.handle(), name.c_str());
hid_t attribute_id = -1;
if(exists && overwrite)
{
attribute_id = H5Aopen(hdataset.handle(), name.c_str(), H5P_DEFAULT);
//H5Ldelete(_hfile.handle(), name.c_str(), H5P_DEFAULT);
}
else if(exists && !overwrite)
throw std::runtime_error("Attribute already exists: (" + name + ")");
else
{
hsize_t dims = 1;
hid_t space_id = H5Screate_simple(1, &dims, NULL);
attribute_id = H5Acreate(hdataset.handle(), name.c_str(), type_id, space_id, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(space_id);
}
if(attribute_id < 0)
throw std::runtime_error("Error creating or opening attribute () in file (" + name + ")");
H5Awrite(attribute_id, type_id, buffer);
H5Tclose(type_id);
H5Aclose(attribute_id);
}
estatus_t
e5_write_attr_list_str(
hid_t e5_group_id, e5_attr_str* e5_attr_list)
{
int i;
hid_t e5_attribute_id;
hid_t e5_dataspace_id = H5Screate(H5S_SCALAR);
hid_t e5_string_type = H5Tcopy(H5T_C_S1);
H5Tset_size(e5_string_type, E5_MAX_ATTR_STRING_LENGTH);
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr_str *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
if(attr->value == 0 || strlen(attr->value) < 1)
continue;
if(H5Aexists(e5_group_id, attr->name) <= 0)
e5_attribute_id = H5Acreate(e5_group_id, attr->name, e5_string_type, e5_dataspace_id, H5P_DEFAULT);
else
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
e5_info(e5_group_id, "Adding attribute [type='string', name='%s', value='%s']\n", attr->name, attr->value);
H5Awrite(e5_attribute_id, e5_string_type, &(attr->value));
H5Aclose(e5_attribute_id);
}
H5Sclose(e5_dataspace_id);
return E5_SUCCESS;
}
// Write complex attribute <attr_name> given by address <path>
char AH5_write_cpx_attr(hid_t loc_id, const char* path, char* attr_name, const AH5_complex_t wdata)
{
char success = AH5_FALSE;
hid_t attr_id = 0, cpx_filetype, cpx_memtype, object_id, space;
hsize_t dims[1] = {1};
cpx_filetype = AH5_H5Tcreate_cpx_filetype();
cpx_memtype = AH5_H5Tcreate_cpx_memtype();
space = H5Screate_simple (1, dims, NULL);
if (AH5_path_valid(loc_id, path))
{
if ((object_id = H5Oopen(loc_id, path, H5P_DEFAULT)) >= 0)
{
if ((attr_id = H5Acreate(object_id, attr_name, cpx_filetype, space, H5P_DEFAULT, H5P_DEFAULT)) >= 0)
{
if (H5Awrite(attr_id, cpx_memtype, &wdata) >= 0)
{
success = AH5_TRUE;
}
H5Aclose(attr_id);
}
H5Oclose(object_id);
}
}
H5Sclose(space);
H5Tclose(cpx_memtype);
H5Tclose(cpx_filetype);
return success;
}
bool save_vertices(hid_t parent_group_id, Mesh *mesh) {
herr_t status;
// create main group
hid_t group_id = H5Gcreate(parent_group_id, "vertices", 0);
// count
hid_t dataspace_id = H5Screate(H5S_SCALAR);
hid_t attr_count = H5Acreate(group_id, "count", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
uint count = mesh->vertices.count();
status = H5Awrite(attr_count, H5T_NATIVE_UINT32, &count);
H5Aclose(attr_count);
H5Sclose(dataspace_id);
hsize_t dims = 3;
hid_t vertex_dataspace_id = H5Screate_simple(1, &dims, NULL);
// dump vertices
for (int i = 0; i < count; i++) {
char name[256];
sprintf(name, "%d", i);
// Create the dataset
hid_t dataset_id = H5Dcreate(group_id, name, H5T_NATIVE_DOUBLE, vertex_dataspace_id, H5P_DEFAULT);
double pt[] = { mesh->vertices[i]->x, mesh->vertices[i]->y, mesh->vertices[i]->z };
status = H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, pt);
status = H5Dclose(dataset_id);
}
H5Sclose(vertex_dataspace_id);
status = H5Gclose(group_id); // close the group
}
extern void put_int_attribute(hid_t parent, char *name, int value)
{
hid_t attr, space_attr;
hsize_t dim_attr[1] = {1}; // Single dimension array of values
space_attr = H5Screate_simple(1, dim_attr, NULL);
if (space_attr < 0) {
debug3("PROFILE: failed to create space for attribute %s",
name);
return;
}
attr = H5Acreate(parent, name, H5T_NATIVE_INT, space_attr,
H5P_DEFAULT, H5P_DEFAULT);
if (attr < 0) {
H5Sclose(space_attr);
debug3("PROFILE: failed to create attribute %s", name);
return;
}
if (H5Awrite(attr, H5T_NATIVE_INT, &value) < 0) {
debug3("PROFILE: failed to write attribute %s", name);
// Fall through to release resources
}
H5Sclose(space_attr);
H5Aclose(attr);
return;
}
hid_t seissol::checkpoint::h5::Fault::initFile(int odd, const char* filename)
{
hid_t h5file;
if (loaded()) {
// Open the file
h5file = open(filename, false);
checkH5Err(h5file);
// Fault writer
m_h5timestepFault[odd] = H5Aopen(h5file, "timestep_fault", H5P_DEFAULT);
checkH5Err(m_h5timestepFault[odd]);
// Data
for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
m_h5data[odd][i] = H5Dopen(h5file, VAR_NAMES[i], H5P_DEFAULT);
checkH5Err(m_h5data[odd][i]);
}
} else {
// Create the file
hid_t h5plist = H5Pcreate(H5P_FILE_ACCESS);
checkH5Err(h5plist);
checkH5Err(H5Pset_libver_bounds(h5plist, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST));
#ifdef USE_MPI
checkH5Err(H5Pset_fapl_mpio(h5plist, comm(), MPI_INFO_NULL));
#endif // USE_MPI
h5file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, h5plist);
checkH5Err(h5file);
checkH5Err(H5Pclose(h5plist));
// Create scalar dataspace for attributes
hid_t h5spaceScalar = H5Screate(H5S_SCALAR);
checkH5Err(h5spaceScalar);
// Fault writer
m_h5timestepFault[odd] = H5Acreate(h5file, "timestep_fault",
H5T_STD_I32LE, h5spaceScalar, H5P_DEFAULT, H5P_DEFAULT);
checkH5Err(m_h5timestepFault[odd]);
int t = 0;
checkH5Err(H5Awrite(m_h5timestepFault[odd], H5T_NATIVE_INT, &t));
checkH5Err(H5Sclose(h5spaceScalar));
// Variables
for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
h5plist = H5Pcreate(H5P_DATASET_CREATE);
checkH5Err(h5plist);
checkH5Err(H5Pset_layout(h5plist, H5D_CONTIGUOUS));
checkH5Err(H5Pset_alloc_time(h5plist, H5D_ALLOC_TIME_EARLY));
m_h5data[odd][i] = H5Dcreate(h5file, VAR_NAMES[i], H5T_IEEE_F64LE, m_h5fSpaceData,
H5P_DEFAULT, h5plist, H5P_DEFAULT);
checkH5Err(m_h5data[odd][i]);
checkH5Err(H5Pclose(h5plist));
}
}
return h5file;
}
void
HDF5Attribute::create(const HDF5Id location_id, const String &name,
const HDF5Id type_id, const HDF5Id space_id)
{
// create the attribute in memory
m_id = H5Acreate(location_id, name.c_str(), type_id, space_id,
H5P_DEFAULT, H5P_DEFAULT);
}
static attribute create(handle const& loc, const char* name,
datatype const& type, dataspace const& space)
{
hid_t id = H5Acreate(loc.getId(), name, type, space,
H5P_DEFAULT, H5P_DEFAULT);
assert(id >= 0);
return attribute(std::move(id));
}
bool dump_hdf5(const char *file_name, Mesh *mesh) {
herr_t status;
// init HDF5
H5open();
// create a file
hid_t file_id = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// create main group
hid_t mesh_group_id = H5Gcreate(file_id, "/mesh3d", 0);
// version
hsize_t dims = 2;
hid_t dataspace_id = H5Screate_simple(1, &dims, NULL);
hid_t attr_ver = H5Acreate(mesh_group_id, "version", H5T_STD_I8BE, dataspace_id, H5P_DEFAULT);
char attr_data[2] = { 1, 0 };
status = H5Awrite(attr_ver, H5T_NATIVE_CHAR, attr_data);
H5Aclose(attr_ver);
H5Sclose(dataspace_id);
// description
hid_t type = H5Tcopy(H5T_C_S1);
status = H5Tset_size(type, H5T_VARIABLE);
const char *descr = "Test mesh";
hid_t dataspace_id2 = H5Screate(H5S_SCALAR);
hid_t attr_descr = H5Acreate(mesh_group_id, "description", type, dataspace_id2, H5P_DEFAULT);
status = H5Awrite(attr_descr, type, &descr);
H5Aclose(attr_descr);
H5Tclose(type);
H5Sclose(dataspace_id2);
save_vertices(mesh_group_id, mesh);
save_elements(mesh_group_id, mesh);
save_bc(mesh_group_id, mesh);
status = H5Gclose(mesh_group_id); // close the group
status = H5Fclose(file_id); // close the file
// deinit HDF5
H5close();
return 0;
}
herr_t writeAttribute_int(hid_t file_id, const char *dsName, const char *attrName,void *val) {
hid_t dataset = H5Dopen(file_id,dsName,H5P_DEFAULT);
hid_t aid = H5Screate(H5S_SCALAR);
hid_t attr = H5Acreate(dataset,attrName, H5T_NATIVE_INT, aid, H5P_DEFAULT,H5P_DEFAULT);
herr_t ret = H5Awrite(attr,H5T_NATIVE_INT,val);
ret = H5Sclose(aid);
ret = H5Aclose(attr);
return ret;
}
int fclib_create_int_attributes_in_info(const char *path, const char * attr_name,
int attr_value)
{
hid_t file_id, id, dataspace_id, attr_id;
hsize_t dim = 1;
hsize_t dims[1];
FILE *f;
if ((f = fopen (path, "r"))) /* HDF5 outputs lots of warnings when file does not exist */
{
fclose (f);
if ((file_id = H5Fopen (path, H5F_ACC_RDWR, H5P_DEFAULT)) < 0)
{
fprintf (stderr, "ERROR: opening file failed\n");
return 0;
}
}
if (H5Lexists (file_id, "/fclib_local/info", H5P_DEFAULT))
{
IO (id = H5Gopen (file_id, "/fclib_local/info", H5P_DEFAULT));
dims[0]=1;
dataspace_id = H5Screate_simple(1, dims, NULL);
attr_id = H5Acreate (id, attr_name, H5T_NATIVE_INT, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT);
IO(H5Awrite(attr_id, H5T_NATIVE_INT , &attr_value ));
IO(H5Aclose (attr_id));
IO (H5Gclose (id));
}
else
{
IO (id = H5Gmake (file_id, "/fclib_local/info"));
dims[0]=1;
dataspace_id = H5Screate_simple(1, dims, NULL);
attr_id = H5Acreate (id, attr_name, H5T_NATIVE_INT, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT);
IO(H5Awrite(attr_id, H5T_NATIVE_INT , &attr_value ));
IO(H5Aclose (attr_id));
IO (H5Gclose (id));
}
IO (H5Fclose (file_id));
return 1;
}
bool save_quad_bc(hid_t parent_group_id, JudyArray<Boundary *> &bcs) {
herr_t status;
// create main group
hid_t group_id = H5Gcreate(parent_group_id, "quad", 0);
// count
hid_t dataspace_id = H5Screate(H5S_SCALAR);
hid_t attr_count = H5Acreate(group_id, "count", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
uint count = bcs.count();
status = H5Awrite(attr_count, H5T_NATIVE_UINT32, &count);
H5Aclose(attr_count);
///
hsize_t dims = Quad::NUM_VERTICES;
hid_t elem_dataspace_id = H5Screate_simple(1, &dims, NULL);
hid_t merker_dataspace_id = H5Screate(H5S_SCALAR);
// dump vertices
for (int i = 0; i < count; i++) {
char name[256];
sprintf(name, "%d", i);
// the dataset
hid_t dataset_id = H5Dcreate(group_id, name, H5T_NATIVE_UINT32, elem_dataspace_id, H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_NATIVE_UINT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, bcs[i]->get_vertices());
// marker
hid_t attr_marker = H5Acreate(dataset_id, "marker", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
uint marker = bcs[i]->get_marker();
status = H5Awrite(attr_marker, H5T_NATIVE_UINT32, &marker);
H5Aclose(attr_marker);
status = H5Dclose(dataset_id);
}
H5Sclose(elem_dataspace_id);
H5Sclose(dataspace_id);
status = H5Gclose(group_id); // close the group
}
herr_t attribute_read(char *attribute_name, enum my_hdf5_types hdf5_type,
hid_t hdf5_file_handle, void *buf)
{
hid_t hdf5_attribute_id, hdf5_dataspace, hdf5_datatype;
herr_t hdf5_status = 0;
//here we get an identifier for a datatype
switch (hdf5_type)
{
case my_hdf5_int:
hdf5_datatype = H5Tcopy(H5T_NATIVE_INT);
break;
case my_hdf5_long:
hdf5_datatype = H5Tcopy(H5T_NATIVE_LONG);
break;
case my_hdf5_float:
hdf5_datatype = H5Tcopy(H5T_NATIVE_FLOAT);
break;
case my_hdf5_double:
hdf5_datatype = H5Tcopy(H5T_NATIVE_DOUBLE);
break;
default:
exit(-1);
break;
}
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute_id =
H5Acreate(hdf5_file_handle, attribute_name, hdf5_datatype, hdf5_dataspace, H5P_DEFAULT); //here we 'create' an attribute
switch (hdf5_type)
{
case my_hdf5_int:
hdf5_status = H5Aread(hdf5_attribute_id, hdf5_datatype, (int *) buf);
break;
case my_hdf5_long:
hdf5_status = H5Aread(hdf5_attribute_id, hdf5_datatype, (long *) buf);
break;
case my_hdf5_float:
hdf5_status = H5Aread(hdf5_attribute_id, hdf5_datatype, (float *) buf);
break;
case my_hdf5_double:
hdf5_status = H5Aread(hdf5_attribute_id, hdf5_datatype, (double *) buf);
break;
default:
exit(-1);
break;
}
H5Tclose(hdf5_datatype);
H5Aclose(hdf5_attribute_id);
H5Sclose(hdf5_dataspace);
return hdf5_status;
}
/* add a single attribute */
int add_attr(hid_t oid, const char *name, hid_t tid, hid_t sid, void *buf)
{
hid_t aid;
aid = H5Acreate (oid, name, tid, sid, H5P_DEFAULT, H5P_DEFAULT);
if (aid <0)
return 0;
H5Awrite(aid, tid, buf);
H5Aclose(aid);
return 1;
}
herr_t ASDF_write_double_attribute(hid_t dataset_id,
const char *attr_name,
double attr_value) {
hid_t space_id, attr_id;
CHK_H5(space_id = H5Screate(H5S_SCALAR));
CHK_H5(attr_id = H5Acreate(dataset_id, attr_name, H5T_IEEE_F64LE, space_id, H5P_DEFAULT, H5P_DEFAULT));
CHK_H5(H5Awrite(attr_id, H5T_IEEE_F64LE, &attr_value));
CHK_H5(H5Aclose(attr_id));
CHK_H5(H5Sclose(space_id));
return 0; // Success
}
herr_t ASDF_write_integer_attribute(hid_t dataset_id,
const char *attr_name,
long long int attr_value) {
hid_t space_id, attr_id;
CHK_H5(space_id = H5Screate(H5S_SCALAR));
CHK_H5(attr_id = H5Acreate(dataset_id, attr_name, H5T_STD_I64LE, space_id, H5P_DEFAULT, H5P_DEFAULT));
CHK_H5(H5Awrite(attr_id, H5T_STD_I64LE, &attr_value));
CHK_H5(H5Aclose(attr_id));
CHK_H5(H5Sclose(space_id));
return 0; // Success
}
hid_t _write_grid(hid_t loc_id, std::string attr_name, double *attr_array, const hsize_t size)
{
herr_t status;
hid_t attr_id;
DataspaceCreate x_grid_space(H5S_SCALAR);
status = H5Sset_extent_simple(x_grid_space.dataspace_id, 1, &size, NULL);
attr_id = H5Acreate(loc_id, attr_name.c_str(), H5T_NATIVE_DOUBLE, x_grid_space.dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
status = H5Awrite(attr_id, H5T_NATIVE_DOUBLE, attr_array);
H5Aclose(attr_id);
return status;
}
int
NC4_put_propattr(NC_HDF5_FILE_INFO_T* h5)
{
int ncstat = NC_NOERR;
H5T_class_t t_class;
size_t size;
hid_t grp = -1;
hid_t exists = -1;
hid_t attid = -1;
hid_t aspace = -1;
hid_t atype = -1;
herr_t herr = 0;
char* text = NULL;
/* Get root group */
grp = h5->root_grp->hdf_grpid; /* get root group */
/* See if the NCPROPS attribute exists */
if(H5Aexists(grp,NCPROPS) == 0) { /* Does not exist */
ncstat = NC4_buildpropinfo(&h5->fileinfo->propattr,&text);
if(text == NULL || ncstat != NC_NOERR) {
goto done;
}
herr = -1;
/* Create a datatype to refer to. */
HCHECK((atype = H5Tcopy(H5T_C_S1)));
HCHECK((H5Tset_cset(atype, H5T_CSET_ASCII)));
HCHECK((H5Tset_size(atype, strlen(text)+1))); /*keep nul term */
HCHECK((aspace = H5Screate(H5S_SCALAR)));
HCHECK((attid = H5Acreate(grp, NCPROPS, atype, aspace, H5P_DEFAULT)));
HCHECK((H5Awrite(attid, atype, text)));
herr = 0;
}
done:
if(ncstat != NC_NOERR) {
if(text != NULL) {
free(text);
text = NULL;
}
}
if(attid >= 0) HCHECK((H5Aclose(attid)));
if(aspace >= 0) HCHECK((H5Sclose(aspace)));
if(atype >= 0) HCHECK((H5Tclose(atype)));
return ncstat;
}
herr_t ASDF_write_string_attribute(hid_t dataset_id,
const char *attr_name,
const char *attr_value) {
hid_t space_id, type_id, attr_id;
CHK_H5(space_id = H5Screate(H5S_SCALAR));
CHK_H5(type_id = H5Tcopy(H5T_C_S1));
CHK_H5(H5Tset_size(type_id, strlen(attr_value)));
CHK_H5(H5Tset_strpad(type_id,H5T_STR_NULLPAD));
CHK_H5(attr_id = H5Acreate(dataset_id, attr_name, type_id, space_id,
H5P_DEFAULT, H5P_DEFAULT));
CHK_H5(H5Awrite(attr_id, type_id, attr_value));
CHK_H5(H5Aclose(attr_id));
CHK_H5(H5Tclose(type_id));
CHK_H5(H5Sclose(space_id));
return 0; // Success
}
