void Grid::initData(FileIO *fileIO)
{
hid_t gridGroup = fileIO->newGroup("/Grid");
// set lengths
check(H5LTset_attribute_double(gridGroup, ".", "Lx", &Lx, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Ly", &Ly, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Lz", &Lz, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Lv", &Lv, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Lm", &Lm, 1), DMESG("HDF-5 Error"));
// set grid point number
check(H5LTset_attribute_int(gridGroup, ".", "Nx", &Nx , 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Nky",&Nky, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Nz", &Nz , 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Nv", &Nv , 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Nm", &Nm , 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Ns", &Ns , 1), DMESG("HDF-5 Error"));
// set grids
check(H5LTset_attribute_double(gridGroup, ".", "X", &X[NxGlD], Nx), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Z", &Z[NzGlD], Nz), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "V", &V[NvGlD], Nv), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "M", &M[NmGlD], Nm), DMESG("HDF-5 Error"));
check(H5LTset_attribute_string(gridGroup, ".", "MuIntegrationType", muIntegrationType.c_str()), DMESG("HDF-5 Error"));
H5Gclose(gridGroup);
}
int GWriteHDFFile::WriteHeader(gadget_header& header)
{
herr_t herr;
for(int i=0; i<N_TYPE; i++){
header.npart[i]=npart[i];
}
hid_t handle = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
if (handle < 0)
return -1*handle;
// Lite interface for making simple attributes
// H5LTset_attribute_int (file_id, dset_name, attr_name, data, size);
// herr_t H5LTset_attribute_int( hid_t loc_id, const char *obj_name, const char *attr_name, int *buffer, size_t size)
hid_t hdgrp = H5Gcreate2(handle, "Header", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
herr = H5LTset_attribute_uint(handle, "Header", "NumPart_ThisFile", header.npart, N_TYPE);
if (herr < 0) {
WARN("Could not write to header");
return -1*herr;
}
herr = H5LTset_attribute_uint(handle, "Header", "NumPart_Total", header.npartTotal, N_TYPE);
herr = H5LTset_attribute_uint(handle, "Header", "NumPart_Total_HighWord", header.NallHW, N_TYPE);
herr = H5LTset_attribute_double(handle, "Header", "MassTable", header.mass, N_TYPE);
if (herr < 0) {
WARN("Could not write particle numbers");
return -1*herr;
}
herr = H5LTset_attribute_double(handle, "Header", "Time", &header.time, 1);
herr = H5LTset_attribute_double(handle, "Header", "Redshift", &header.redshift, 1);
herr = H5LTset_attribute_double(handle, "Header", "BoxSize", &header.BoxSize, 1);
herr = H5LTset_attribute_int(handle, "Header", "NumFilesPerSnapshot", &header.num_files, 1);
herr = H5LTset_attribute_double(handle, "Header", "Omega0", &header.Omega0, 1);
herr = H5LTset_attribute_double(handle, "Header", "OmegaLambda", &header.OmegaLambda, 1);
herr = H5LTset_attribute_double(handle, "Header", "HubbleParam", &header.HubbleParam, 1);
herr = H5LTset_attribute_int(handle, "Header", "Flag_Sfr", &header.flag_sfr, 1);
herr = H5LTset_attribute_int(handle, "Header", "Flag_Cooling", &header.flag_cooling, 1);
herr = H5LTset_attribute_int(handle, "Header", "Flag_StellarAge", &header.flag_stellarage, 1);
herr = H5LTset_attribute_int(handle, "Header", "Flag_Metals", &header.flag_metals, 1);
herr = H5LTset_attribute_int(handle, "Header", "Flag_Feedback", &header.flag_feedback, 1);
herr = H5LTset_attribute_int(handle, "Header", "Flag_DoublePrecision", &header.flag_doubleprecision, 1);
herr = H5LTset_attribute_int(handle, "Header", "Flag_IC_Info", &header.flag_ic_info, 1);
herr = H5LTset_attribute_double(handle, "Header", "UnitLength_in_cm", &header.UnitLength_in_cm, 1);
herr = H5LTset_attribute_double(handle, "Header", "UnitMass_in_g", &header.UnitMass_in_g, 1);
herr = H5LTset_attribute_double(handle, "Header", "UnitVelocity_in_cm_per_s", &header.UnitVelocity_in_cm_per_s, 1);
if (herr < 0) {
WARN("Could not write final header flags");
return -1*herr;
}
H5Gclose(hdgrp);
H5Fclose(handle);
return 0;
}
/*writes properties of the current run related to implementation and command line choices*/
herr_t /*hdf5 error*/
append_meta_properties(hdf5block_t *h5block,/*hdf5 file ids*/
double *seed,/*random number seed*/
size_t *BurnInSampleSize, /*tuning iterations*/
char *h5file, /*name of hdf5 file containing the experimental data and prior set-up*/
char *lib_base)/*basename of the library file @code .so@ file*/{
herr_t status;
int omp_n,omp_np,i;
status&=H5LTset_attribute_double(h5block->file_id, "LogParameters", "seed", seed, 1);
status&=H5LTset_attribute_ulong(h5block->file_id, "LogParameters", "BurnIn", BurnInSampleSize, 1);
status&=H5LTset_attribute_string(h5block->file_id, "LogParameters", "DataFrom", h5file);
status&=H5LTmake_dataset_string(h5block->file_id,"Model",lib_base);
// here we make a short test to see what the automatic choice of the
// number of threads turns out to be.
#pragma omp parallel private(omp_n,omp_np) reduction(+:i)
{
i=1;
omp_n=omp_get_num_threads();
omp_np=omp_get_num_procs();
}
if (i!=omp_n){
fprintf(stderr,"[append_meta_properties] warning: finding out number of threads possibly failed reduction of (n×1: %i) != get_num_threads():%i.\n",i,omp_n);
} else {
h5block->size[0]=1;
h5block->size[1]=1;
status&=H5LTmake_dataset_int(h5block->file_id,"OMP_NUM_THREADS",1,h5block->size,&omp_n);
status&=H5LTmake_dataset_int(h5block->file_id,"OMP_NUM_PROCS",1,h5block->size,&omp_np);
}
return status;
}
int_f
nh5ltset_attribute_double_c(hid_t_f *loc_id,
int_f *namelen,
_fcd dsetname,
int_f *attrnamelen,
_fcd attrname,
size_t_f *size,
void *buf)
{
int ret_value = -1;
herr_t ret;
hid_t c_loc_id;
char *c_name = NULL;
char *c_attrname = NULL;
int c_namelen;
int c_attrnamelen;
size_t c_size;
/*
* Convert FORTRAN name to C name
*/
c_namelen = *namelen;
c_name = (char *)HD5f2cstring(dsetname, c_namelen);
if (c_name == NULL)
goto done;
c_attrnamelen = *attrnamelen;
c_attrname = (char *)HD5f2cstring(attrname, c_attrnamelen);
if (c_attrname == NULL)
goto done;
/*
* Call H5LTset_attribute_double function.
*/
c_loc_id = (hid_t)*loc_id;
c_size = (size_t)*size;
ret = H5LTset_attribute_double(c_loc_id,c_name,c_attrname,buf,c_size);
if (ret < 0)
goto done;
ret_value = 0;
done:
if(c_name!=NULL)
free(c_name);
if(c_attrname!=NULL)
free(c_attrname);
return ret_value;
}
void Particle_source_box::write_hdf5_source_parameters( hid_t current_source_group_id )
{
Particle_source::write_hdf5_source_parameters( current_source_group_id );
herr_t status;
int single_element = 1;
std::string current_group = "./";
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"box_x_left", &xleft, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"box_x_right", &xright, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"box_y_top", &ytop, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"box_y_bottom", &ybottom, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"box_z_far", &zfar, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"box_z_near", &znear, single_element );
hdf5_status_check( status );
}
void Particle_source::write_hdf5_source_parameters( hid_t current_source_group_id )
{
herr_t status;
int single_element = 1;
std::string current_group = "./";
double mean_mom_x = vec3d_x( mean_momentum );
double mean_mom_y = vec3d_y( mean_momentum );
double mean_mom_z = vec3d_z( mean_momentum );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"temperature", &temperature, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"mean_momentum_x", &mean_mom_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"mean_momentum_y", &mean_mom_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"mean_momentum_z", &mean_mom_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"charge", &charge, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"mass", &mass, single_element );
hdf5_status_check( status );
}
int pioAddAttributeDouble(PIOObject pioObject,
const char* attr_name, double attr_value)
{
if (pioAttributeIsProtected(attr_name))
{
fprintf(stdout,
"WARNING: Attribute name %s is a reserved for pinocchIO internal use.\n",
attr_name);
return -1;
}
return H5LTset_attribute_double(pioObject.identifier, ".",
attr_name, &attr_value, 1);
}
//-*****************************************************************************
void WriteTimeSampling( hid_t iGroup,
const std::string &iName,
const AbcA::TimeSampling &iTsmp )
{
AbcA::TimeSamplingType tst = iTsmp.getTimeSamplingType();
WriteTimeSamplingType( iGroup, iName, tst );
//-*************************************************************************
// WRITE TIMES.
//-*************************************************************************
std::string timeSampsName = iName + ".time";
const std::vector < chrono_t > & samps = iTsmp.getStoredTimes();
ABCA_ASSERT( samps.size() > 0, "No TimeSamples to write!");
H5LTset_attribute_double ( iGroup, ".", timeSampsName.c_str(),
&samps.front(), samps.size() );
}
void Particle_source_cylinder::write_hdf5_source_parameters( hid_t current_source_group_id )
{
Particle_source::write_hdf5_source_parameters( current_source_group_id );
herr_t status;
int single_element = 1;
std::string current_group = "./";
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"cylinder_axis_start_x", &axis_start_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"cylinder_axis_start_y", &axis_start_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"cylinder_axis_start_z", &axis_start_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"cylinder_axis_end_x", &axis_end_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"cylinder_axis_end_y", &axis_end_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"cylinder_axis_end_z", &axis_end_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_source_group_id,
current_group.c_str(),
"cylinder_radius", &radius, single_element );
hdf5_status_check( status );
}
/* ------- begin -------------------------- init_hdf5_indata.c --- */
void init_hdf5_indata_new(void)
/* Creates the netCDF file for the input data */
{
const char routineName[] = "init_hdf5_indata_new";
int i, PRD_angle_dep;
double *eweight, *eabund, *x, *y;
/* This value is harcoded for efficiency.
Maximum number of iterations ever needed */
int NMaxIter = 1500;
hid_t plist, ncid, file_dspace, ncid_input, ncid_atmos, ncid_mpi;
hsize_t dims[4];
bool_t XRD;
char startJ[MAX_LINE_SIZE], StokesMode[MAX_LINE_SIZE], angleSet[MAX_LINE_SIZE];
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(INPUTDATA_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Create groups */
if (( ncid_input = H5Gcreate(ncid, "/input", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_atmos = H5Gcreate(ncid, "/atmos", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_mpi = H5Gcreate(ncid, "/mpi", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* --- Definitions for the INPUT group --- */
/* attributes */
if ( atmos.NPRDactive > 0)
PRD_angle_dep = input.PRD_angle_dep;
else
PRD_angle_dep=0;
XRD = (input.XRD && atmos.NPRDactive > 0);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Magneto_optical",
(unsigned char *) &input.magneto_optical, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "PRD_angle_dep",
(unsigned char *) &PRD_angle_dep, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "XRD",
(unsigned char *) &XRD, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Background_polarization",
(unsigned char *) &input.backgr_pol, 1)) < 0) HERR(routineName);
switch (input.startJ) {
case UNKNOWN:
strcpy(startJ, "Unknown");
break;
case LTE_POPULATIONS:
strcpy(startJ, "LTE_POPULATIONS");
break;
case ZERO_RADIATION:
strcpy(startJ, "ZERO_RADIATION");
break;
case OLD_POPULATIONS:
strcpy(startJ, "OLD_POPULATIONS");
break;
case ESCAPE_PROBABILITY:
strcpy(startJ, "ESCAPE_PROBABILITY");
break;
case NEW_J:
strcpy(startJ, "NEW_J");
break;
case OLD_J:
strcpy(startJ, "OLD_J");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Start_J", startJ)) < 0)
HERR(routineName);
switch (input.StokesMode) {
case NO_STOKES:
strcpy(StokesMode, "NO_STOKES");
break;
case FIELD_FREE:
strcpy(StokesMode, "FIELD_FREE");
break;
case POLARIZATION_FREE:
strcpy(StokesMode, "POLARIZATION_FREE");
break;
case FULL_STOKES:
strcpy(StokesMode, "FULL_STOKES");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Stokes_mode",
StokesMode) ) < 0) HERR(routineName);
switch (atmos.angleSet.set) {
case SET_VERTICAL:
strcpy(angleSet, "SET_VERTICAL");
break;
case SET_GL:
strcpy(angleSet, "SET_GL");
break;
case SET_A2:
strcpy(angleSet, "SET_A2");
break;
case SET_A4:
strcpy(angleSet, "SET_A4");
break;
case SET_A6:
strcpy(angleSet, "SET_A6");
break;
case SET_A8:
strcpy(angleSet, "SET_A8");
break;
case SET_B4:
strcpy(angleSet, "SET_B4");
break;
case SET_B6:
strcpy(angleSet, "SET_B6");
break;
case SET_B8:
strcpy(angleSet, "SET_B8");
break;
case NO_SET:
strcpy(angleSet, "NO_SET");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Angle_set",
angleSet) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Atmos_file",
input.atmos_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Abundances_file",
input.abund_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Kurucz_PF_data",
input.pfData) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Iteration_limit",
&input.iterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "PRD_Iteration_limit",
&input.PRDiterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "N_max_iter",
&input.NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_delay",
&input.Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_order",
&input.Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_period",
&input.Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_N_max_iter",
&input.PRD_NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_delay",
&input.PRD_Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_order",
&input.PRD_Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_period",
&input.PRD_Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Metallicity",
&input.metallicity, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Lambda_reference",
&atmos.lambda_ref, 1) ) < 0) HERR(routineName);
/* --- Definitions for the ATMOS group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_atmos, ".", "nhydr",
&atmos.H->Nlevel, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nelements",
&atmos.Nelem, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nrays",
&geometry.Nrays, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = infile.nz;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_atmos_T = H5Dcreate(ncid_atmos, "temperature", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_vz = H5Dcreate(ncid_atmos, "velocity_z", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_z = H5Dcreate(ncid_atmos, "height", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* --- Write some data that does not depend on xi, yi, ATMOS group --- */
/* arrays of number of elements */
eweight = (double *) malloc(atmos.Nelem * sizeof(double));
eabund = (double *) malloc(atmos.Nelem * sizeof(double));
for (i=0; i < atmos.Nelem; i++) {
eweight[i] = atmos.elements[i].weight;
eabund[i] = atmos.elements[i].abund;
}
dims[0] = atmos.Nelem;
if (( H5LTmake_dataset(ncid_atmos, "element_weight", 1, dims,
H5T_NATIVE_DOUBLE, eweight) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "element_abundance", 1, dims,
H5T_NATIVE_DOUBLE, eabund) ) < 0) HERR(routineName);
/* Not writing element_id for now
dims[1] = strlen;
if (( H5LTmake_dataset(ncid_atmos, "element_id", 2, dims,
H5T_C_S1, eID) ) < 0) HERR(routineName);
*/
free(eweight);
free(eabund);
dims[0] = geometry.Nrays;
if (( H5LTmake_dataset(ncid_atmos, "muz", 1, dims,
H5T_NATIVE_DOUBLE, geometry.muz) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "wmu", 1, dims,
H5T_NATIVE_DOUBLE, geometry.wmu) ) < 0) HERR(routineName);
x = (double *) malloc(mpi.nx * sizeof(double));
y = (double *) malloc(mpi.ny * sizeof(double));
for (i=0; i < mpi.nx; i++) x[i] = infile.x[mpi.xnum[i]];
for (i=0; i < mpi.ny; i++) y[i] = infile.y[mpi.ynum[i]];
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atmos, "x", 1, dims,
H5T_NATIVE_DOUBLE, x) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atmos, "y", 1, dims,
H5T_NATIVE_DOUBLE, y) ) < 0) HERR(routineName);
free(x);
free(y);
/* attributes */
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "moving",
(unsigned char *) &atmos.moving, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "stokes",
(unsigned char *) &atmos.Stokes, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "temperature", "units",
"K") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "velocity_z", "units",
"m s^-1") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "height", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "element_weight", "units",
"atomic_mass_units") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "x", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "y", "units",
"m") ) < 0) HERR(routineName);
/* --- Definitions for the MPI group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_mpi, ".", "nprocesses",
&mpi.size, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "niterations",
&NMaxIter, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mpi, XNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.xnum) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mpi, YNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.ynum) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
if (( file_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_tm = H5Dcreate(ncid_mpi, TASK_MAP, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_tn = H5Dcreate(ncid_mpi, TASK_NUMBER, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_it = H5Dcreate(ncid_mpi, ITER_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_conv = H5Dcreate(ncid_mpi, CONV_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_dm = H5Dcreate(ncid_mpi, DM_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_zc = H5Dcreate(ncid_mpi, ZC_NAME, H5T_NATIVE_INT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = NMaxIter;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_dmh = H5Dcreate(ncid_mpi, DMH_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* attributes */
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_start",
&input.p15d_x0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_end",
&input.p15d_x1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_step",
&input.p15d_xst, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_start",
&input.p15d_y0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_end",
&input.p15d_y1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_step",
&input.p15d_yst, 1) ) < 0) HERR(routineName);
/* Tiago: most of the arrays involving Ntasks or rank as index are not
currently being written. They should eventually be migrated into
arrays of [ix, iy] and be written for each task. This is to
avoid causing problems with pool mode, where these quantities are
not known from the start.
*/
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
/* --- Copy stuff to the IO data struct --- */
io.in_ncid = ncid;
io.in_input_ncid = ncid_input;
io.in_atmos_ncid = ncid_atmos;
io.in_mpi_ncid = ncid_mpi;
return;
}
static herr_t make_attributes( hid_t loc_id, const char* obj_name )
{
int rank_out;
hsize_t *dims_out = 0;
H5T_class_t type_class;
size_t type_size;
int i;
char attr_str_in[] = {"My attribute"};
char attr_str_out[20];
char attr_char_in[5] = {1,2,3,4,5};
char attr_char_out[5];
short attr_short_in[5] = {1,2,3,4,5};
short attr_short_out[5];
int attr_int_in[5] = {1,2,3,4,5};
int attr_int_out[5];
long attr_long_in[5] = {1,2,3,4,5};
long attr_long_out[5];
float attr_float_in[5] = {1,2,3,4,5};
float attr_float_out[5];
double attr_double_in[5] = {1,2,3,4,5};
double attr_double_out[5];
unsigned char attr_uchar_in[5] = {1,2,3,4,5};
unsigned char attr_uchar_out[5];
unsigned short attr_ushort_in[5] = {1,2,3,4,5};
unsigned short attr_ushort_out[5];
unsigned int attr_uint_in[5] = {1,2,3,4,5};
unsigned int attr_uint_out[5];
unsigned long attr_ulong_in[5] = {1,2,3,4,5};
unsigned long attr_ulong_out[5];
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_string");
/* Set the attribute */
if ( H5LTset_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_in ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_string");
/* Get the attribute */
if ( H5LTget_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_out ) < 0 )
return -1;
if ( strcmp( attr_str_in, attr_str_out ) != 0 )
{
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_char");
/* Set the attribute */
if ( H5LTset_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_char");
/* Get the attribute */
if ( H5LTget_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR2_NAME, H5T_NATIVE_CHAR, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_short");
/* Set the attribute */
if ( H5LTset_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_short");
/* Get the attribute */
if ( H5LTget_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR3_NAME, H5T_NATIVE_SHORT, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_int");
/* Set the attribute */
if ( H5LTset_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_int");
/* Get the attribute */
if ( H5LTget_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR4_NAME, H5T_NATIVE_INT, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_long");
/* Set the attribute */
if ( H5LTset_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_long");
/* Get the attribute */
if ( H5LTget_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR5_NAME, H5T_NATIVE_LONG, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uchar");
/* Set the attribute */
if ( H5LTset_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uchar");
/* Get the attribute */
if ( H5LTget_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR6_NAME, H5T_NATIVE_UCHAR, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ushort");
/* Set the attribute */
if ( H5LTset_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ushort");
/* Get the attribute */
if ( H5LTget_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR7_NAME, H5T_NATIVE_USHORT, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uint");
/* Set the attribute */
if ( H5LTset_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uint");
/* Get the attribute */
if ( H5LTget_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR8_NAME, H5T_NATIVE_UINT, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ulong test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ulong");
/* Set the attribute */
if ( H5LTset_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ulong");
/* Get the attribute */
if ( H5LTget_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR9_NAME, H5T_NATIVE_ULONG, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_float");
/* Set the attribute */
if ( H5LTset_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_float");
/* Get the attribute */
if ( H5LTget_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR10_NAME, H5T_NATIVE_FLOAT, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_double");
/* Set the attribute */
if ( H5LTset_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_double");
/* Get the attribute */
if ( H5LTget_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR11_NAME, H5T_NATIVE_DOUBLE, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ndims test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ndims");
if ( H5LTget_attribute_ndims( loc_id, obj_name, ATTR2_NAME, &rank_out ) < 0 )
return -1;
if ( rank_out != 1 ) {
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_info test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_info");
dims_out = (hsize_t*) malloc( sizeof(hsize_t) * rank_out );
if ( H5LTget_attribute_info( loc_id, obj_name, ATTR2_NAME, dims_out, &type_class,
&type_size) < 0 )
return -1;
for (i = 0; i < rank_out; i++)
{
if ( dims_out[i] != 5 ) {
return -1;
}
}
if ( type_class != H5T_INTEGER ) {
return -1;
}
if ( dims_out )
free( dims_out );
PASSED();
return 0;
}
/*main mcmc loop, records sampled values, performs no tuning of the step size.*/
int /*always returns success*/
mcmc_foreach(int rank, /*MPI rank*/
int R, /*MPI Comm size*/
size_t SampleSize, /*number of iterations of MCMC*/
ode_model_parameters *omp, /*ODE problem cpecification and pre-allocated space*/
mcmc_kernel *kernel, /* MCMC kernel sturct, holds MCMC-algorithm's parameters*/
hdf5block_t *h5block, /*defines the hdf5 file to write into, holds ids and sizes*/
void *buffer, /* for MPI communication, similar to kernel*/
main_options *option)/*options from defaults, files and command line*/{
clock_t ct=clock();
gsl_matrix *log_para_chunk;
gsl_vector *log_post_chunk;
int D=get_number_of_MCMC_variables(omp);
log_para_chunk=gsl_matrix_alloc(CHUNK,D);
log_post_chunk=gsl_vector_alloc(CHUNK);
gsl_vector_view current;
gsl_vector_view x_state;
int swaps = 0; // swap success counter
int acc=no; // acceptance flag
int acc_c=0; // acceptance counter
double acc_rate=0.0;
size_t it;
int master=no;
int DEST;
double beta=mcmc_get_beta(kernel);
herr_t status;
int resume_EC;
int last_chunk=no, not_written_yet=yes;
for (it = 0; it < SampleSize; it++) {
mcmc_sample(kernel, &acc);
last_chunk=SampleSize-it<CHUNK;
if (acc && last_chunk && not_written_yet){
resume_EC=write_resume_state(option->resume_file, rank, R, kernel);
if (resume_EC==EXIT_SUCCESS){
not_written_yet=no;
}
}
acc_c += acc;
master=(it%2==rank%2);
if (master){
DEST=(rank+1)%R; // this process is the master process for swap decisions
} else {
DEST=(R+rank-1)%R; // this process has to accept swap decisions from DEST
}
//their_beta=BETA(DEST,R); // the other proc's
if (R>1){
mcmc_exchange_information(kernel,DEST,buffer);
swaps+=mcmc_swap_chains(kernel,master,rank,DEST,buffer);
}
/* save sampled point for writing */
current=gsl_matrix_row(log_para_chunk,it%CHUNK);
x_state=gsl_vector_view_array(kernel->x,D);
gsl_vector_memcpy(&(current.vector),&(x_state.vector));
gsl_vector_set(log_post_chunk,it%CHUNK,kernel->fx[0]);
/* print sample log and statistics every 100 samples */
if ( ((it + 1) % CHUNK) == 0 ) {
acc_rate = ((double) acc_c) / ((double) CHUNK);
fprintf(stdout, "# [rank % 2i/% 2i; β=%5f; %3li%% done] (it %5li)\tacc. rate: %3.2f;\t%3i %% swap success\t",rank,R,beta,(100*it)/SampleSize,it,acc_rate,swaps);
mcmc_print_stats(kernel, stdout);
acc_c = 0;
// print chunk to hdf5 file
status=h5write_current_chunk(h5block,log_para_chunk,log_post_chunk);
h5block->offset[0]=it+1;
swaps=0;
}
}
assert(status==0);
// write remaining data to the output hdf5 file
int Rest=SampleSize % CHUNK;
printf("[main] last iteration done %i points remain to write.\n",Rest);
if (Rest > 0){
h5block->chunk_size[0]=Rest;
h5block->chunk_size[1]=D;
h5block->para_chunk_id=H5Screate_simple(2, h5block->chunk_size, NULL);
h5block->chunk_size[0]=Rest;
h5block->chunk_size[1]=1;
h5block->post_chunk_id=H5Screate_simple(2, h5block->chunk_size, NULL);
printf("[main] writing the remaining %i sampled parametrisations to file.\n",Rest);
h5block->block[0]=Rest;
h5block->block[1]=D;
display_chunk_properties(h5block);
status = H5Sselect_hyperslab(h5block->para_dataspace_id, H5S_SELECT_SET, h5block->offset, h5block->stride, h5block->count, h5block->block);
H5Dwrite(h5block->parameter_set_id, H5T_NATIVE_DOUBLE, h5block->para_chunk_id, h5block->para_dataspace_id, H5P_DEFAULT, log_para_chunk->data);
h5block->block[1]=1;
printf("[main] writing their %i log-posterior values to file.\n",Rest);
display_chunk_properties(h5block);
status &= H5Sselect_hyperslab(h5block->post_dataspace_id, H5S_SELECT_SET, h5block->offset, h5block->stride, h5block->count, h5block->block);
H5Dwrite(h5block->posterior_set_id, H5T_NATIVE_DOUBLE, h5block->post_chunk_id, h5block->post_dataspace_id, H5P_DEFAULT, log_post_chunk->data);
assert(status>=0);
}
// annotate written sample with all necessary information
//printf("[main] writing some annotation about the sampled points as hdf5 attributes.\n");
status&=H5LTset_attribute_int(h5block->file_id, "LogParameters", "MPI_RANK", &rank, 1);
status&=H5LTset_attribute_ulong(h5block->file_id, "LogParameters", "SampleSize", &SampleSize, 1);
status&=H5LTset_attribute_double(h5block->file_id, "LogParameters", "InverseTemperature_Beta", &beta, 1);
ct=clock()-ct;
double sampling_time=((double) ct)/((double) CLOCKS_PER_SEC);
int ts=round(sampling_time);
int hms[3]; // hours, minutes, seconds
hms[0]=ts/3600;
hms[1]=(ts%3600)/60;
hms[2]=(ts%60);
printf("# computation time spend sampling: %i:%i:%i\n",hms[0],hms[1],hms[2]);
h5block->size[0]=1;
status&=H5LTmake_dataset_double (h5block->file_id, "SamplingTime_s", 1, h5block->size, &sampling_time);
h5block->size[0]=3;
status&=H5LTmake_dataset_int(h5block->file_id, "SamplingTime_hms", 1, h5block->size, hms);
if(status){
printf("[rank %i] statistics written to file.\n",rank);
}
return EXIT_SUCCESS;
}
int FileIO::create(Setup *setup) {
hid_t file_plist = H5Pcreate(H5P_FILE_ACCESS);
#ifdef GKC_PARALLEL_MPI
// pass some information onto the underlying MPI_File_open call
MPI_Info file_info;
check(MPI_Info_create(&file_info), DMESG("File info"));
/*
H5Pset_sieve_buf_size(file_plist, 262144);
H5Pset_alignment(file_plist, 524288, 262144);
MPI_Info_set(file_info, (char *) "access_style" , (char *) "write_once");
MPI_Info_set(file_info, (char *) "collective_buffering", (char *) "true");
MPI_Info_set(file_info, (char *) "cb_block_size" , (char *) "1048576");
MPI_Info_set(file_info, (char *) "cb_buffer_size" , (char *) "4194304");
* */
check( H5Pset_fapl_mpio(file_plist, parallel->Comm[DIR_ALL], file_info), DMESG("Set MPI Property"));
#endif
file = check(H5Fcreate(outputFileName.c_str(), (overwriteFile ? H5F_ACC_TRUNC : H5F_ACC_EXCL),
H5P_DEFAULT, file_plist ), DMESG("H5FCreate : HDF5 File (File already exists ? use -f to overwrite) : " + outputFileName));
check( H5Pclose(file_plist), DMESG("H5Pclose"));
#ifdef GKC_PARALLEL_MPI
MPI_Info_free(&file_info);
#endif
//////////////////////////////////////////////////////////////// Info Group ////////////////////////////////////////////////////////
hid_t infoGroup = check(H5Gcreate(file, "/Info",H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT), DMESG("Error creating group file for Phasespace : H5Gcreate"));
check(H5LTset_attribute_string(infoGroup, ".", "Output", outputFileName.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Input", inputFileName.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Version", PACKAGE_VERSION), DMESG("H5LTset_attribute"));
// Some Simulation specific stuff
//check(H5LTset_attribute_string(infoGroup, ".", "Solver", ((setup->Solver & VL_LIN) ? "Linear" : "Non-Linear")), DMESG("H5LTset_attribute"));
//heck(H5LTset_attribute_string(infoGroup, ".", "Type", ((setup->VlasovType & VLASOV_LOCAL ) ? "Local" : "Global" )), DMESG("H5LTset_attribute"));
//heck(H5LTset_attribute_string(infoGroup, ".", "FFTSolverS", ((setup->VlasovType & VLASOV_LOCAL ) ? "Local" : "Global" )), DMESG("H5LTset_attribute"));
//check(H5LTset_attribute_string(infoGroup, ".", "Initial Condition", setup->PerturbationMethod.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Info", info.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Config", setup->configFileString.c_str()), DMESG("H5LTset_attribute"));
H5Gclose(infoGroup);
/// Wrote setup constants, ugly here ////
hid_t constantsGroup = check(H5Gcreate(file, "/Constants",H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT), DMESG("Error creating group file for Phasespace : H5Gcreate"));
//
if (!setup->parser_constants.empty()) {
std::vector<std::string> const_vec = Setup::split(setup->parser_constants, ",");
for(int s = 0; s < const_vec.size(); s++) {
std::vector<std::string> key_value = Setup::split(const_vec[s],"=");
double value = Setup::string_to_double(key_value[1]);
int dim[] = { 1 };
// check(H5LTmake_dataset_double(constantsGroup, Setup::trimLower(key_value[0], false).c_str(), 1, dim, &value ), DMESG("Write Constants Attributes"));
check(H5LTset_attribute_double(constantsGroup, ".", Setup::trimLower(key_value[0], false).c_str(), &value, 1), DMESG("H5LTset_attribute"));
//check(H5LTset_attribute_double(constantsGroup, ".", Setup::trimLower(key_value[0], false).c_str(), &(Setup::string_to_double(key_value[1])), 1), DMESG("H5LTset_attribute"));
};
}
H5Gclose(constantsGroup);
// ********************* setup Table for CFL *****************88
cfl_table = new CFLTable();
cfl_offset[0] = HOFFSET( CFLTable, timeStep );
cfl_offset[1] = HOFFSET( CFLTable, time );
cfl_offset[2] = HOFFSET( CFLTable, Fx );
cfl_offset[3] = HOFFSET( CFLTable, Fy );
cfl_offset[4] = HOFFSET( CFLTable, Fz );
cfl_offset[5] = HOFFSET( CFLTable, Fv );
cfl_offset[6] = HOFFSET( CFLTable, total );
for(int i = 1; i < 7; i++) cfl_sizes[i] = sizeof(double); cfl_sizes[0] = sizeof(int);
hid_t cfl_type[7]; for(int i = 1; i < 7; i++) cfl_type [i] = H5T_NATIVE_DOUBLE; cfl_type[0] = H5T_NATIVE_INT;
const char *cfl_names[7];
cfl_names[0] = "timeStep";
cfl_names[1] = "time";
cfl_names[2] = "Fx"; cfl_names[3] = "Fy"; cfl_names[4] = "Fz"; cfl_names[5] = "Fv"; cfl_names[6] = "Total";
check(H5TBmake_table("cflTable", file, "cfl", (hsize_t) 7, (hsize_t) 0, sizeof(CFLTable), (const char**) cfl_names,
cfl_offset, cfl_type, 32, NULL, 0, cfl_table ), DMESG("H5Tmake_table : cfl"));
return HELIOS_SUCCESS;
}
int SpIO_FwriteModel(SpFile *sfp, SpModel model)
{
int status = 0;
herr_t hstatus;
/* Write the version of format */
if(!status) {
hstatus = H5LTset_attribute_string(sfp->h5f_id, "/", "format", "SPARX format v3");
if(hstatus < 0)
status = 1;
}
/* Write the type of coordinat system */
if(!status) {
DatINode *geom = Dat_IList_IdxLookup(GEOM_TYPES, model.parms.geom);
Deb_ASSERT(geom != NULL);
hstatus = H5LTset_attribute_string(sfp->h5f_id, "/", "geom", geom->name);
if(hstatus < 0)
status = 1;
}
/* Write T_cmb */
if(!status) {
hstatus = H5LTset_attribute_double(sfp->h5f_id, "/", "T_cmb", &model.parms.T_cmb, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write T_in */
if(!status) {
hstatus = H5LTset_attribute_double(sfp->h5f_id, "/", "T_in", &model.parms.T_in, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write molecule name */
if(!status) {
Molec *mol = model.parms.mol;
hstatus = H5LTset_attribute_string(sfp->h5f_id, "/", "molec", mol ? mol->name : "");
if(hstatus < 0)
status = 1;
}
/* Write pops-switch */
if(!status) {
hstatus = H5LTset_attribute_int(sfp->h5f_id, "/", "pops", &model.parms.pops, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write dust-switch */
if(!status) {
hstatus = H5LTset_attribute_int(sfp->h5f_id, "/", "dust", &model.parms.dust, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write polariz-switch */
if(!status) {
hstatus = H5LTset_attribute_int(sfp->h5f_id, "/", "polariz", &model.parms.polariz, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write polariz-switch */
if(!status) {
hstatus = H5LTset_attribute_double(sfp->h5f_id, "/", "z", &model.parms.z, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write grid */
if(!status)
status = SpIO_H5WriteGrid(sfp->h5f_id, model.grid, &model.parms);
if(status)
status = Err_SETSTRING("Error writing model to file `%s'", sfp->name);
return status;
}