From 60f5071945ef8fa510310988c6f945474a231ecd Mon Sep 17 00:00:00 2001
From: Daniel Garcia-Sanchez <daniel.garcia-sanchez@insp.upmc.fr>
Date: Tue, 16 Oct 2018 12:16:38 +0200
Subject: [PATCH] Add test hdf5_05

The test hdf5_05 is based on the test hdf5_03
---
 tests/base/hdf5_05.cc                         | 427 ++++++++++++++++++
 ...rue.with_complex_values=on.mpirun=4.output |  27 ++
 2 files changed, 454 insertions(+)
 create mode 100644 tests/base/hdf5_05.cc
 create mode 100644 tests/base/hdf5_05.with_hdf5=true.with_complex_values=on.mpirun=4.output

diff --git a/tests/base/hdf5_05.cc b/tests/base/hdf5_05.cc
new file mode 100644
index 0000000000..f773cedec3
--- /dev/null
+++ b/tests/base/hdf5_05.cc
@@ -0,0 +1,427 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2015 - 2018 by the deal.II Authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+// Read/write tests with parallel HDF5. This tests different hyperslab shapes
+// with different ranks.
+
+#include <deal.II/base/conditional_ostream.h>
+#include <deal.II/base/hdf5.h>
+
+#include <deal.II/lac/full_matrix.h>
+#include <deal.II/lac/vector.h>
+
+#include <boost/lexical_cast.hpp>
+#include <boost/type_traits.hpp>
+
+#include <numeric>
+
+#include "../tests.h"
+
+// This function initializes a container of Number type
+template <template <class...> class Container, typename Number>
+typename std::enable_if<
+  std::is_same<Container<Number>, std::vector<Number>>::value,
+  Container<Number>>::type
+initialize_container(std::vector<hsize_t> dimensions)
+{
+  return Container<Number>(std::accumulate(
+    dimensions.begin(), dimensions.end(), 1, std::multiplies<int>()));
+}
+
+
+
+template <template <class...> class Container, typename Number>
+typename std::enable_if<std::is_same<Container<Number>, Vector<Number>>::value,
+                        Container<Number>>::type
+initialize_container(std::vector<hsize_t> dimensions)
+{
+  return Container<Number>(std::accumulate(
+    dimensions.begin(), dimensions.end(), 1, std::multiplies<int>()));
+}
+
+
+
+template <template <class...> class Container, typename Number>
+typename std::enable_if<
+  std::is_same<Container<Number>, FullMatrix<Number>>::value,
+  Container<Number>>::type
+initialize_container(std::vector<hsize_t> dimensions)
+{
+  return FullMatrix<Number>(dimensions[0], dimensions[1]);
+}
+
+
+
+// This function assignes data to the elements of the container
+template <template <class...> class Container, typename Number>
+typename std::enable_if<
+  std::is_same<Container<Number>, std::vector<Number>>::value,
+  void>::type
+assign_data(Container<Number> &data)
+{
+  for (unsigned int idx = 0; idx < data.size(); ++idx)
+    {
+      data[idx] = idx;
+    }
+}
+
+
+
+template <template <class...> class Container, typename Number>
+typename std::enable_if<std::is_same<Container<Number>, Vector<Number>>::value,
+                        void>::type
+assign_data(Container<Number> &data)
+{
+  for (unsigned int idx = 0; idx < data.size(); ++idx)
+    {
+      data[idx] = idx;
+    }
+}
+
+
+
+template <template <class...> class Container, typename Number>
+typename std::enable_if<
+  std::is_same<Container<Number>, FullMatrix<Number>>::value,
+  void>::type
+assign_data(Container<Number> &data)
+{
+  for (unsigned int row_idx = 0; row_idx < data.m(); ++row_idx)
+    {
+      for (unsigned int col_idx = 0; col_idx < data.n(); ++col_idx)
+        {
+          data[row_idx][col_idx] = (row_idx * data.n() + col_idx);
+        }
+    }
+}
+
+
+// This function converts the data to a string
+template <typename Number>
+std::string
+container_to_string(std::vector<Number> &data)
+{
+  std::string data_string;
+
+  auto append_to_data_string = [&data_string](const std::string p) {
+    if (data_string.length() > 0)
+      data_string += ", ";
+    data_string += p;
+  };
+
+  for (unsigned int idx = 0; idx < data.size(); ++idx)
+    {
+      append_to_data_string(boost::lexical_cast<std::string>(data[idx]));
+    }
+
+  return "[" + data_string + "]";
+}
+
+template <typename Number>
+std::string
+container_to_string(FullMatrix<Number> &data)
+{
+  std::string data_string;
+
+  for (unsigned int row_idx = 0; row_idx < data.m(); ++row_idx)
+    {
+      if (row_idx > 0)
+        data_string += ", ";
+      data_string += "[";
+      for (unsigned int col_idx = 0; col_idx < data.n(); ++col_idx)
+        {
+          if (col_idx > 0)
+            data_string += ", ";
+          data_string +=
+            boost::lexical_cast<std::string>(data[row_idx][col_idx]);
+        }
+      data_string += "]";
+    }
+
+  return "[" + data_string + "]";
+}
+
+// This constexpr function converts a type to a std::string
+template <typename Number>
+std::string
+type_to_string()
+{
+  std::string type_name;
+
+  if (std::is_same<Number, float>::value)
+    {
+      type_name = std::string("float");
+    }
+  else if (std::is_same<Number, double>::value)
+    {
+      type_name = std::string("double");
+    }
+  else if (std::is_same<Number, std::complex<float>>::value)
+    {
+      type_name = std::string("std::complex<float>");
+    }
+  else if (std::is_same<Number, std::complex<double>>::value)
+    {
+      type_name = std::string("std::complex<double>");
+    }
+  else if (std::is_same<Number, int>::value)
+    {
+      type_name = std::string("int");
+    }
+  else if (std::is_same<Number, unsigned int>::value)
+    {
+      type_name = std::string("unsigned int");
+    }
+
+  return type_name;
+}
+
+
+
+// This function tests parallel write and gets the group by reference
+template <typename Number>
+void
+write_test(HDF5::Group &      root_group,
+           MPI_Comm           mpi_communicator,
+           ConditionalOStream pcout)
+{
+  const std::string type_name = type_to_string<Number>();
+
+  deallog << "Write tests for " << type_name << " datasets" << std::endl;
+
+  auto group = root_group.create_group(type_name);
+
+
+  {
+    std::string dataset_name("dataset_1");
+
+    // Write matrix of 5x3
+    // Output generated by h5dump
+    //  (0,0): 0, 1, 2,
+    //  (1,0): 3, 4, 5,
+    //  (2,0): 6, 7, 8,
+    //  (3,0): 9, 10, 11,
+    //  (4,0): 12, 13, 14
+
+    const std::vector<hsize_t> dataset_dimensions = {5, 3};
+    auto                       dataset =
+      group.create_dataset<Number>(dataset_name, dataset_dimensions);
+    dataset.set_query_io_mode(true);
+    deallog << "Dimensions " << dataset_name << "<" << type_name << ">"
+            << " (Write): " << dataset.get_dimensions() << std::endl;
+    deallog << "Size " << dataset_name << "<" << type_name << ">"
+            << " (Write): " << dataset.get_size() << std::endl;
+    deallog << "Rank " << dataset_name << "<" << type_name << ">"
+            << " (Write): " << dataset.get_rank() << std::endl;
+    auto data = initialize_container<std::vector, Number>(dataset_dimensions);
+    assign_data(data);
+    if (Utilities::MPI::this_mpi_process(mpi_communicator) == 0)
+      {
+        dataset.write(data);
+      }
+    else
+      {
+        dataset.template write_none<Number>();
+      }
+    deallog << "Data " + dataset_name << "<" << type_name << ">"
+            << " (Write): " << container_to_string(data) << std::endl;
+    pcout << "IO mode " + dataset_name << "<" << type_name << ">"
+          << " (Write): " << dataset.get_io_mode() << std::endl;
+    pcout << "Local no collective cause " + dataset_name << "<" << type_name
+          << ">"
+          << " (Write): " << dataset.get_local_no_collective_cause()
+          << std::endl;
+    pcout << "Global no collective cause " + dataset_name << "<" << type_name
+          << ">"
+          << " (Write): " << dataset.get_global_no_collective_cause()
+          << std::endl;
+  }
+}
+
+
+// This function tests parallel read. Unlike write_test, this functions gets a
+// copy of the group
+template <typename Number>
+void
+read_test(HDF5::Group        root_group,
+          MPI_Comm           mpi_communicator,
+          ConditionalOStream pcout)
+{
+  const std::string type_name = type_to_string<Number>();
+
+  deallog << "Read tests for " << type_name << " datasets" << std::endl;
+
+  auto group = root_group.group(type_name);
+
+  {
+    std::string dataset_name("dataset_1");
+    auto        dataset = group.dataset(dataset_name);
+    dataset.set_query_io_mode(true);
+    deallog << "Dimensions " + dataset_name << "<" << type_name << ">"
+            << " (Read): " << dataset.get_dimensions() << std::endl;
+    deallog << "Size " + dataset_name << "<" << type_name << ">"
+            << " (Read): " << dataset.get_size() << std::endl;
+    deallog << "Rank " + dataset_name << "<" << type_name << ">"
+            << " (Read): " << dataset.get_rank() << std::endl;
+    {
+      auto data = dataset.read<FullMatrix<Number>>();
+
+      pcout << "IO mode " + dataset_name << "<" << type_name << ">"
+            << " (Read): " << dataset.get_io_mode() << std::endl;
+      pcout << "Local no collective cause " << dataset_name << "<" << type_name
+            << ">"
+            << " (Read): " << dataset.get_local_no_collective_cause()
+            << std::endl;
+      pcout << "Global no collective cause " << dataset_name << "<" << type_name
+            << ">"
+            << " (Read): " << dataset.get_global_no_collective_cause()
+            << std::endl;
+
+      deallog << "Data " + dataset_name << "<" << type_name << ">"
+              << " (Read): " << container_to_string(data) << std::endl;
+    }
+
+    {
+      // The output should be the column vector [7, 10, 13]
+      const std::vector<hsize_t> hyperslab_offset = {2, 1};
+      const std::vector<hsize_t> hyperslab_count  = {3, 1};
+      auto data = dataset.read_hyperslab<std::vector<Number>>(hyperslab_offset,
+                                                              hyperslab_count);
+
+      pcout << "Column vector" << std::endl;
+      pcout << "IO mode " + dataset_name << "<" << type_name << ">"
+            << " (Read): " << dataset.get_io_mode() << std::endl;
+      pcout << "Local no collective cause " << dataset_name << "<" << type_name
+            << ">"
+            << " (Read): " << dataset.get_local_no_collective_cause()
+            << std::endl;
+      pcout << "Global no collective cause " << dataset_name << "<" << type_name
+            << ">"
+            << " (Read): " << dataset.get_global_no_collective_cause()
+            << std::endl;
+
+      deallog << "Column vector " + dataset_name << "<" << type_name << ">"
+              << " (Read): " << container_to_string(data) << std::endl;
+    }
+
+    {
+      // The output should be the row vector [9, 10, 11]
+      const std::vector<hsize_t> hyperslab_offset = {3, 0};
+      const std::vector<hsize_t> hyperslab_count  = {1, 3};
+      auto data = dataset.read_hyperslab<std::vector<Number>>(hyperslab_offset,
+                                                              hyperslab_count);
+
+      pcout << "Row vector" << std::endl;
+      pcout << "IO mode " + dataset_name << "<" << type_name << ">"
+            << " (Read): " << dataset.get_io_mode() << std::endl;
+      pcout << "Local no collective cause " << dataset_name << "<" << type_name
+            << ">"
+            << " (Read): " << dataset.get_local_no_collective_cause()
+            << std::endl;
+      pcout << "Global no collective cause " << dataset_name << "<" << type_name
+            << ">"
+            << " (Read): " << dataset.get_global_no_collective_cause()
+            << std::endl;
+
+      deallog << "Row vector " + dataset_name << "<" << type_name << ">"
+              << " (Read): " << container_to_string(data) << std::endl;
+    }
+
+    {
+      // The output should be the matrix [[3, 4, 5], [6, 7, 8]]
+      const std::vector<hsize_t> hyperslab_offset = {1, 0};
+      const std::vector<hsize_t> hyperslab_count  = {2, 3};
+      auto data = dataset.read_hyperslab<FullMatrix<Number>>(hyperslab_offset,
+                                                             hyperslab_count);
+
+      pcout << "Sub-matrix" << std::endl;
+      pcout << "IO mode " + dataset_name << "<" << type_name << ">"
+            << " (Read): " << dataset.get_io_mode() << std::endl;
+      pcout << "Local no collective cause " << dataset_name << "<" << type_name
+            << ">"
+            << " (Read): " << dataset.get_local_no_collective_cause()
+            << std::endl;
+      pcout << "Global no collective cause " << dataset_name << "<" << type_name
+            << ">"
+            << " (Read): " << dataset.get_global_no_collective_cause()
+            << std::endl;
+
+      deallog << "Sub-matrix " + dataset_name << "<" << type_name << ">"
+              << " (Read): " << container_to_string(data) << std::endl;
+    }
+  }
+}
+
+
+int
+main(int argc, char **argv)
+{
+  initlog();
+
+  try
+    {
+      Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+      MPI_Comm mpi_communicator = MPI_COMM_WORLD;
+
+      ConditionalOStream pcout(
+        std::cout, Utilities::MPI::this_mpi_process(mpi_communicator) == 0);
+
+      std::string filename = "test.h5";
+
+      {
+        HDF5::File data_file(filename,
+                             mpi_communicator,
+                             HDF5::File::Mode::create);
+
+        write_test<double>(data_file, mpi_communicator, pcout);
+        write_test<std::complex<double>>(data_file, mpi_communicator, pcout);
+      }
+
+      {
+        HDF5::File data_file(filename,
+                             mpi_communicator,
+                             HDF5::File::Mode::open);
+        read_test<double>(data_file, mpi_communicator, pcout);
+        read_test<std::complex<double>>(data_file, mpi_communicator, pcout);
+      }
+    }
+  catch (std::exception &exc)
+    {
+      std::cerr << std::endl
+                << std::endl
+                << "----------------------------------------------------"
+                << std::endl;
+      std::cerr << "Exception on processing: " << std::endl
+                << exc.what() << std::endl
+                << "Aborting!" << std::endl
+                << "----------------------------------------------------"
+                << std::endl;
+
+      return 1;
+    }
+  catch (...)
+    {
+      std::cerr << std::endl
+                << std::endl
+                << "----------------------------------------------------"
+                << std::endl;
+      std::cerr << "Unknown exception!" << std::endl
+                << "Aborting!" << std::endl
+                << "----------------------------------------------------"
+                << std::endl;
+      return 1;
+    };
+}
diff --git a/tests/base/hdf5_05.with_hdf5=true.with_complex_values=on.mpirun=4.output b/tests/base/hdf5_05.with_hdf5=true.with_complex_values=on.mpirun=4.output
new file mode 100644
index 0000000000..85bce4bdbe
--- /dev/null
+++ b/tests/base/hdf5_05.with_hdf5=true.with_complex_values=on.mpirun=4.output
@@ -0,0 +1,27 @@
+
+DEAL::Write tests for double datasets
+DEAL::Dimensions dataset_1<double> (Write): 5 3
+DEAL::Size dataset_1<double> (Write): 15
+DEAL::Rank dataset_1<double> (Write): 2
+DEAL::Data dataset_1<double> (Write): [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]
+DEAL::Write tests for std::complex<double> datasets
+DEAL::Dimensions dataset_1<std::complex<double>> (Write): 5 3
+DEAL::Size dataset_1<std::complex<double>> (Write): 15
+DEAL::Rank dataset_1<std::complex<double>> (Write): 2
+DEAL::Data dataset_1<std::complex<double>> (Write): [(0,0), (1,0), (2,0), (3,0), (4,0), (5,0), (6,0), (7,0), (8,0), (9,0), (10,0), (11,0), (12,0), (13,0), (14,0)]
+DEAL::Read tests for double datasets
+DEAL::Dimensions dataset_1<double> (Read): 5 3
+DEAL::Size dataset_1<double> (Read): 15
+DEAL::Rank dataset_1<double> (Read): 2
+DEAL::Data dataset_1<double> (Read): [[0, 1, 2], [3, 4, 5], [6, 7, 8], [9, 10, 11], [12, 13, 14]]
+DEAL::Column vector dataset_1<double> (Read): [7, 10, 13]
+DEAL::Row vector dataset_1<double> (Read): [9, 10, 11]
+DEAL::Sub-matrix dataset_1<double> (Read): [[3, 4, 5], [6, 7, 8]]
+DEAL::Read tests for std::complex<double> datasets
+DEAL::Dimensions dataset_1<std::complex<double>> (Read): 5 3
+DEAL::Size dataset_1<std::complex<double>> (Read): 15
+DEAL::Rank dataset_1<std::complex<double>> (Read): 2
+DEAL::Data dataset_1<std::complex<double>> (Read): [[(0,0), (1,0), (2,0)], [(3,0), (4,0), (5,0)], [(6,0), (7,0), (8,0)], [(9,0), (10,0), (11,0)], [(12,0), (13,0), (14,0)]]
+DEAL::Column vector dataset_1<std::complex<double>> (Read): [(7,0), (10,0), (13,0)]
+DEAL::Row vector dataset_1<std::complex<double>> (Read): [(9,0), (10,0), (11,0)]
+DEAL::Sub-matrix dataset_1<std::complex<double>> (Read): [[(3,0), (4,0), (5,0)], [(6,0), (7,0), (8,0)]]
-- 
2.39.5