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#include <cassert>
#include <cstdio>
#include <cstring>
#include <iostream>
#include <list>
#include <string>
#include <vector>
#include <cctk_Config.h>
#include <hdf5.h>
using namespace std;
// Global constants
int const dim = 3;
// Files and datasets
int const num_input_files = 0;
char const *const input_file_pattern = "interptoarray::parrays3d.file_%d.h5";
int const iteration_divisor = 1024;
char const *const output_file_name = "parrays3d-float.h5";
char const *const output_dataset_name = "phi";
hsize_t const output_dims[] = { 0, 1024, 1024, 1024 }; // [t,z,y,x]
hsize_t const output_maxdims[] = { H5S_UNLIMITED, 1024, 1024, 1024 };
typedef float output_t;
hid_t const output_type = H5T_NATIVE_FLOAT;
// Technical details
hsize_t const chunk_size[] = { 1, 128, 128, 128 }; // 8 MB for float
int const compression_level = 1;
bool const write_checksum = true;
// Check a return value
#define check(_expr) do { bool const _val = (_expr); assert(_val); } while(0)
static herr_t add_name (hid_t group, const char *name,
H5L_info_t const *info, void *op_data);
int main (int argc, char **argv)
{
cout << "hdf5_recombiner" << endl
<< "Copyright 2009 Erik Schnetter <schnetter@cct.lsu.edu>" << endl
<< endl;
cout << "Opening output file \"" << output_file_name << "\"" << endl;
htri_t is_hdf5;
H5E_BEGIN_TRY {
is_hdf5 = H5Fis_hdf5 (output_file_name);
} H5E_END_TRY;
bool const file_exists = is_hdf5 > 0;
hid_t const output_file =
file_exists ?
H5Fopen (output_file_name, H5F_ACC_RDWR, H5P_DEFAULT) :
H5Fcreate (output_file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
cout << "Opening output dataset \"" << output_dataset_name << "\""<< endl;
hid_t const output_datatype = output_type;
hid_t const output_dataspace =
H5Screate_simple (dim+1, output_dims, output_maxdims);
assert (output_dataspace >= 0);
hid_t const output_properties = H5Pcreate (H5P_DATASET_CREATE);
assert (output_properties >= 0);
check (not H5Pset_chunk (output_properties, dim+1, chunk_size));
if (compression_level > 0) {
check (not H5Pset_deflate (output_properties, compression_level));
}
if (write_checksum) {
check (not H5Pset_fletcher32 (output_properties));
}
hid_t const output_dataset =
file_exists ?
H5Dopen (output_file, output_dataset_name, H5P_DEFAULT) :
H5Dcreate (output_file, output_dataset_name,
output_datatype, output_dataspace,
H5P_DEFAULT, output_properties, H5P_DEFAULT);
assert (output_dataset >= 0);
list<string> input_file_names;
for (int input_file_num=0; input_file_num<num_input_files; ++input_file_num) {
char input_file_name[10000];
snprintf (input_file_name, sizeof input_file_name,
input_file_pattern, input_file_num);
input_file_names.push_back (input_file_name);
}
for (int n=1; n<argc; ++n) {
input_file_names.push_back (argv[n]);
}
for (list<string>::const_iterator iinput_file_name = input_file_names.begin();
iinput_file_name != input_file_names.end();
++ iinput_file_name)
{
string const& input_file_name = *iinput_file_name;
cout << "Opening input file \"" << input_file_name << "\"" << endl;
hid_t const input_file =
H5Fopen (input_file_name.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
assert (input_file >= 0);
typedef list<string> names_t;
names_t names;
hsize_t idx = 0;
check (not H5Literate (input_file,
H5_INDEX_NAME, H5_ITER_NATIVE,
&idx, add_name, &names));
for (names_t::const_iterator iname =
names.begin(); iname!=names.end(); ++iname)
{
char const *const input_dataset_name = iname->c_str();
cout << "Reading input dataset \"" << input_dataset_name << "\"" << endl;
char varname[10000];
int it, tl, c;
int const icnt = sscanf (input_dataset_name,
"%s it=%d tl=%d c=%d", varname, &it, &tl, &c);
assert (icnt == 4);
assert (it % iteration_divisor == 0);
int const iteration = it / iteration_divisor;
hid_t const input_dataset =
H5Dopen (input_file, input_dataset_name, H5P_DEFAULT);
assert (input_dataset >= 0);
int iorigin[dim];
hid_t const iorigin_attr =
H5Aopen (input_dataset, "iorigin", H5P_DEFAULT);
assert (iorigin_attr >= 0);
check (not H5Aread (iorigin_attr, H5T_NATIVE_INT, iorigin));
check (not H5Aclose (iorigin_attr));
hid_t const input_dataspace = H5Dget_space (input_dataset);
assert (input_dataspace >= 0);
assert (H5Sis_simple (input_dataspace) > 0);
assert (H5Sget_simple_extent_ndims (input_dataspace) == dim);
hsize_t input_dims[dim];
check (H5Sget_simple_extent_dims (input_dataspace, input_dims, NULL) ==
dim);
hid_t const input_memory_dataspace =
H5Screate_simple (dim, input_dims, NULL);
assert (input_memory_dataspace);
hssize_t const input_memory_npoints =
H5Sget_simple_extent_npoints (input_memory_dataspace);
vector<output_t> data (input_memory_npoints);
check (not H5Dread (input_dataset,
output_type, input_memory_dataspace,
input_dataspace,
H5P_DEFAULT, &data.front()));
check (not H5Sclose (input_memory_dataspace));
check (not H5Sclose (input_dataspace));
check (not H5Dclose (input_dataset));
cout << "Writing output dataset" << endl;
hsize_t output_extent[dim+1];
output_extent[0] = iteration + 1;
for (int d=0; d<dim; ++d) {
output_extent[d+1] = output_dims[d+1];
}
check (not H5Dextend (output_dataset, output_extent));
hid_t const output_dataspace =
H5Screate_simple (dim+1, output_extent, output_maxdims);
assert (output_dataspace >= 0);
hsize_t output_offset[dim+1];
hsize_t output_dims[dim+1];
output_offset[0] = iteration;
output_dims [0] = 1;
for (int d=0; d<dim; ++d) {
output_offset[d+1] = iorigin[dim-1-d];
output_dims [d+1] = input_dims[d];
}
check (not H5Sselect_hyperslab (output_dataspace, H5S_SELECT_SET,
output_offset, NULL, output_dims, NULL));
cout << " extent ["
<< output_offset[3] << ","
<< output_offset[2] << ","
<< output_offset[1] << ","
<< output_offset[0] << "] - ["
<< output_offset[3] + output_dims[3] << ","
<< output_offset[2] + output_dims[2] << ","
<< output_offset[1] + output_dims[1] << ","
<< output_offset[0] + output_dims[0] << "] "
<< "(" << data.size() << " points)" << endl;
hid_t const output_memory_dataspace =
H5Screate_simple (dim+1, output_dims, NULL);
assert (output_memory_dataspace);
hssize_t const output_memory_npoints =
H5Sget_simple_extent_npoints (output_memory_dataspace);
assert (output_memory_npoints == input_memory_npoints);
check (not H5Dwrite (output_dataset,
output_type, output_memory_dataspace,
output_dataspace,
H5P_DEFAULT, &data.front()));
H5Sclose (output_memory_dataspace);
H5Sclose (output_dataspace);
} // for names
check (not H5Fclose (input_file));
} // for input_file_num
check (not H5Dclose (output_dataset));
check (not H5Pclose (output_properties));
check (not H5Sclose (output_dataspace));
check (not H5Fclose (output_file));
cout << "Done." << endl;
return 0;
}
static herr_t add_name (hid_t const group, const char *const name,
H5L_info_t const *const info, void *const op_data)
{
typedef list<string> names_t;
names_t& names = * static_cast<names_t*> (op_data);
if (strcmp (name, "Parameters and Global Attributes") != 0) {
names.push_back (name);
}
return 0;
}
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