h5 serialization

- add an h5 serialization using hdf5 >= 1.8.9
  and a file in memory.
- following doc.

test/triqs/utility/h5_seria.cpp

@@ -0,0 +1,57 @@
+/*******************************************************************************
+ *
+ * TRIQS: a Toolbox for Research in Interacting Quantum Systems
+ *
+ * Copyright (C) 2014 by O. Parcollet
+ *
+ * TRIQS is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU General Public License as published by the Free Software
+ * Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ *
+ * TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * TRIQS. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#include <triqs/arrays.hpp>
+#include <triqs/h5/serialization.hpp>
+#include <iostream>
+
+#if H5_VERSION_GE(1, 8, 9)
+
+using triqs::h5::serialize;
+using triqs::h5::deserialize;
+
+int main() {
+
+ using triqs::arrays::array;
+
+ auto a = array<double, 1>{1, 2, 3, 4, 5};
+
+ {
+  auto a2 = array<double, 1>(10000);
+  a2() = 8.3;
+  auto s2 = serialize(a2);
+  std::cout << "len " << s2.size() << std::endl;
+ }
+
+ {
+  auto a2 = array<double, 1>(20000);
+  a2() = 8.3;
+  auto s2 = serialize(a2);
+  std::cout << "len " << s2.size() << std::endl;
+ }
+
+ auto s1 = serialize(a);
+ auto b = deserialize<array<double, 1>>(s1);
+
+ std::cout << "a = " << a << " == " << b << std::endl;
+
+#endif
+}
+

triqs/h5/serialization.hpp

@@ -0,0 +1,97 @@
+/*******************************************************************************
+ *
+ * TRIQS: a Toolbox for Research in Interacting Quantum Systems
+ *
+ * Copyright (C) 2012 by M. Ferrero, O. Parcollet
+ *
+ * TRIQS is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU General Public License as published by the Free Software
+ * Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ *
+ * TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * TRIQS. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#pragma once
+//#include <hdf5.h>
+#include <triqs/h5.hpp>
+#include <triqs/utility/view_tools.hpp>
+
+//#define CHECK_OR_THROW(Cond, Mess)
+#define CHECK_OR_THROW(Cond, Mess)                                                                                               \
+ if (!Cond) TRIQS_RUNTIME_ERROR << "Error in h5 (de)serialization " << Mess;
+
+namespace triqs {
+namespace h5 {
+
+ template <typename T> std::string serialize(T const &x) {
+
+  hid_t fapl_id = H5Pcreate(H5P_FILE_ACCESS);
+  CHECK_OR_THROW((fapl_id >= 0), "creating fapl");
+
+  auto err = H5Pset_fapl_core(fapl_id, (size_t)(64 * 1024), false);
+  CHECK_OR_THROW((err >= 0), "setting core file driver in fapl.");
+
+  hid_t file_id = H5Fcreate("serialization", 0, H5P_DEFAULT, fapl_id);
+  CHECK_OR_THROW((file_id >= 0), "created core file");
+
+  auto gr = triqs::h5::group(file_id, false);
+  h5_write(gr, "object", x);
+
+  err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
+  CHECK_OR_THROW((err >= 0), "flushed core file.");
+
+  ssize_t image_len = H5Fget_file_image(file_id, NULL, (size_t)0);
+  CHECK_OR_THROW((image_len > 0), "got image file size");
+
+  std::string buf(image_len, 0);
+
+  ssize_t bytes_read = H5Fget_file_image(file_id, (void *)&buf[0], (size_t)image_len);
+  CHECK_OR_THROW(bytes_read == image_len, "wrote file into image buffer");
+
+  err = H5Fclose(file_id);
+  CHECK_OR_THROW((err >= 0), "closed core file(1).");
+
+  err = H5Pclose(fapl_id);
+  CHECK_OR_THROW((err >= 0), "closed fapl(1).");
+
+  return buf;
+ }
+
+ template <typename T> T deserialize(std::string const &buf) {
+  T res;
+
+  hid_t fapl_id = H5Pcreate(H5P_FILE_ACCESS);
+  CHECK_OR_THROW((fapl_id >= 0), "creating fapl");
+
+  auto err = H5Pset_fapl_core(fapl_id, (size_t)(64 * 1024), false);
+  CHECK_OR_THROW((err >= 0), "setting core file driver in fapl.");
+
+  err = H5Pset_file_image(fapl_id, (void *)&buf[0], buf.size());
+  CHECK_OR_THROW((err >= 0), "set file image in fapl.");
+
+  hid_t file_id = H5Fopen("serialization", H5F_ACC_RDONLY, fapl_id);
+  CHECK_OR_THROW((file_id >= 0), "opened received file image file");
+
+  auto gr = triqs::h5::group(file_id, false);
+  h5_read(gr, "object", res);
+
+  err = H5Fclose(file_id);
+  CHECK_OR_THROW((err >= 0), "closed core file(1).");
+
+  err = H5Pclose(fapl_id);
+  CHECK_OR_THROW((err >= 0), "closed fapl(1).");
+
+  return res;
+ }
+}
+
+#undef CHECK_OR_THROW
+}
+