diff options
Diffstat (limited to 'Carpet/CarpetIOHDF5/src/util/hdf5_recombiner.cc')
| -rw-r--r-- | Carpet/CarpetIOHDF5/src/util/hdf5_recombiner.cc | 253 |
1 files changed, 253 insertions, 0 deletions
diff --git a/Carpet/CarpetIOHDF5/src/util/hdf5_recombiner.cc b/Carpet/CarpetIOHDF5/src/util/hdf5_recombiner.cc new file mode 100644 index 000000000..ecee483d3 --- /dev/null +++ b/Carpet/CarpetIOHDF5/src/util/hdf5_recombiner.cc @@ -0,0 +1,253 @@ +#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; +} |