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h5 serialization
- add an h5 serialization using hdf5 >= 1.8.9 and a file in memory. - following doc.
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test/triqs/utility/h5_seria.cpp
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57
test/triqs/utility/h5_seria.cpp
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/*******************************************************************************
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*
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* TRIQS: a Toolbox for Research in Interacting Quantum Systems
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*
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* Copyright (C) 2014 by O. Parcollet
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*
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* TRIQS is free software: you can redistribute it and/or modify it under the
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* terms of the GNU General Public License as published by the Free Software
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* Foundation, either version 3 of the License, or (at your option) any later
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* version.
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*
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* TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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* FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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* details.
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*
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* You should have received a copy of the GNU General Public License along with
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* TRIQS. If not, see <http://www.gnu.org/licenses/>.
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*
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******************************************************************************/
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#include <triqs/arrays.hpp>
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#include <triqs/h5/serialization.hpp>
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#include <iostream>
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#if H5_VERSION_GE(1, 8, 9)
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using triqs::h5::serialize;
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using triqs::h5::deserialize;
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int main() {
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using triqs::arrays::array;
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auto a = array<double, 1>{1, 2, 3, 4, 5};
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{
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auto a2 = array<double, 1>(10000);
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a2() = 8.3;
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auto s2 = serialize(a2);
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std::cout << "len " << s2.size() << std::endl;
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}
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{
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auto a2 = array<double, 1>(20000);
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a2() = 8.3;
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auto s2 = serialize(a2);
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std::cout << "len " << s2.size() << std::endl;
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}
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auto s1 = serialize(a);
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auto b = deserialize<array<double, 1>>(s1);
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std::cout << "a = " << a << " == " << b << std::endl;
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#endif
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}
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triqs/h5/serialization.hpp
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triqs/h5/serialization.hpp
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/*******************************************************************************
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*
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* TRIQS: a Toolbox for Research in Interacting Quantum Systems
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*
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* Copyright (C) 2012 by M. Ferrero, O. Parcollet
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*
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* TRIQS is free software: you can redistribute it and/or modify it under the
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* terms of the GNU General Public License as published by the Free Software
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* Foundation, either version 3 of the License, or (at your option) any later
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* version.
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*
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* TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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* FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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* details.
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*
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* You should have received a copy of the GNU General Public License along with
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* TRIQS. If not, see <http://www.gnu.org/licenses/>.
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*
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******************************************************************************/
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#pragma once
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//#include <hdf5.h>
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#include <triqs/h5.hpp>
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#include <triqs/utility/view_tools.hpp>
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//#define CHECK_OR_THROW(Cond, Mess)
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#define CHECK_OR_THROW(Cond, Mess) \
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if (!Cond) TRIQS_RUNTIME_ERROR << "Error in h5 (de)serialization " << Mess;
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namespace triqs {
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namespace h5 {
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template <typename T> std::string serialize(T const &x) {
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hid_t fapl_id = H5Pcreate(H5P_FILE_ACCESS);
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CHECK_OR_THROW((fapl_id >= 0), "creating fapl");
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auto err = H5Pset_fapl_core(fapl_id, (size_t)(64 * 1024), false);
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CHECK_OR_THROW((err >= 0), "setting core file driver in fapl.");
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hid_t file_id = H5Fcreate("serialization", 0, H5P_DEFAULT, fapl_id);
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CHECK_OR_THROW((file_id >= 0), "created core file");
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auto gr = triqs::h5::group(file_id, false);
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h5_write(gr, "object", x);
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err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
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CHECK_OR_THROW((err >= 0), "flushed core file.");
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ssize_t image_len = H5Fget_file_image(file_id, NULL, (size_t)0);
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CHECK_OR_THROW((image_len > 0), "got image file size");
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std::string buf(image_len, 0);
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ssize_t bytes_read = H5Fget_file_image(file_id, (void *)&buf[0], (size_t)image_len);
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CHECK_OR_THROW(bytes_read == image_len, "wrote file into image buffer");
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err = H5Fclose(file_id);
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CHECK_OR_THROW((err >= 0), "closed core file(1).");
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err = H5Pclose(fapl_id);
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CHECK_OR_THROW((err >= 0), "closed fapl(1).");
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return buf;
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}
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template <typename T> T deserialize(std::string const &buf) {
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T res;
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hid_t fapl_id = H5Pcreate(H5P_FILE_ACCESS);
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CHECK_OR_THROW((fapl_id >= 0), "creating fapl");
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auto err = H5Pset_fapl_core(fapl_id, (size_t)(64 * 1024), false);
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CHECK_OR_THROW((err >= 0), "setting core file driver in fapl.");
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err = H5Pset_file_image(fapl_id, (void *)&buf[0], buf.size());
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CHECK_OR_THROW((err >= 0), "set file image in fapl.");
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hid_t file_id = H5Fopen("serialization", H5F_ACC_RDONLY, fapl_id);
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CHECK_OR_THROW((file_id >= 0), "opened received file image file");
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auto gr = triqs::h5::group(file_id, false);
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h5_read(gr, "object", res);
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err = H5Fclose(file_id);
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CHECK_OR_THROW((err >= 0), "closed core file(1).");
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err = H5Pclose(fapl_id);
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CHECK_OR_THROW((err >= 0), "closed fapl(1).");
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return res;
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}
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}
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#undef CHECK_OR_THROW
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}
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