Fix serialization of variable data attachements

diff --git a/source/distributed/tria.cc b/source/distributed/tria.cc
index 99068c23dac9dbc32c0b8dc41c5277af195d3d6f..5fe3afb1c8347f6eeb5d799357f7395780272083 100644 (file)
--- a/source/distributed/tria.cc
+++ b/source/distributed/tria.cc
@@ -2751,6 +2751,7 @@ namespace parallel
 
         tria->cell_attached_data.n_attached_data_sets = 0;
         tria->cell_attached_data.pack_callbacks_fixed.clear();
+        tria->cell_attached_data.pack_callbacks_variable.clear();
       }
     }
 

diff --git a/tests/mpi/p4est_save_07.cc b/tests/mpi/p4est_save_07.cc
new file mode 100644 (file)
index 0000000..e409ce4
--- /dev/null
+++ b/tests/mpi/p4est_save_07.cc
@@ -0,0 +1,205 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2009 - 2017 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.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// save and load a triangulation with a different number of cpus
+// with variable size data attach
+// this is a variation of p4est_save_05, but it saves the triangulation
+// multiple times before loading to catch a bug that was not properly
+// clearing variables upon save (i.e. multiple saves before a load would
+// cause corrupted checkpoints for variable data size attachments).
+
+#include <deal.II/base/tensor.h>
+#include <deal.II/base/utilities.h>
+
+#include <deal.II/distributed/tria.h>
+
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/grid_out.h>
+#include <deal.II/grid/grid_tools.h>
+#include <deal.II/grid/tria.h>
+#include <deal.II/grid/tria_accessor.h>
+
+#include "../tests.h"
+
+
+
+template <int dim>
+std::vector<char>
+pack_function(
+  const typename parallel::distributed::Triangulation<dim, dim>::cell_iterator
+    &cell,
+  const typename parallel::distributed::Triangulation<dim, dim>::CellStatus
+    status)
+{
+  static unsigned int       some_number = 1;
+  std::vector<unsigned int> some_vector(some_number);
+  for (unsigned int i = 0; i < some_number; ++i)
+    some_vector[i] = i;
+
+  std::vector<char> buffer;
+  buffer.reserve(some_number * sizeof(unsigned int));
+  for (auto vector_it = some_vector.cbegin(); vector_it != some_vector.cend();
+       ++vector_it)
+    {
+      Utilities::pack(*vector_it, buffer, /*allow_compression=*/false);
+    }
+
+  deallog << "packing cell " << cell->id()
+          << " with data size=" << buffer.size() << " accumulated data="
+          << std::accumulate(some_vector.begin(), some_vector.end(), 0)
+          << std::endl;
+
+  Assert((status ==
+          parallel::distributed::Triangulation<dim, dim>::CELL_PERSIST),
+         ExcInternalError());
+
+  ++some_number;
+  return buffer;
+}
+
+
+
+template <int dim>
+void
+unpack_function(
+  const typename parallel::distributed::Triangulation<dim, dim>::cell_iterator
+    &cell,
+  const typename parallel::distributed::Triangulation<dim, dim>::CellStatus
+                                                                  status,
+  const boost::iterator_range<std::vector<char>::const_iterator> &data_range)
+{
+  const unsigned int data_in_bytes =
+    std::distance(data_range.begin(), data_range.end());
+
+  std::vector<unsigned int> intdatavector(data_in_bytes / sizeof(unsigned int));
+
+  auto vector_it = intdatavector.begin();
+  auto data_it   = data_range.begin();
+  for (; data_it != data_range.end();
+       ++vector_it, data_it += sizeof(unsigned int))
+    {
+      *vector_it =
+        Utilities::unpack<unsigned int>(data_it,
+                                        data_it + sizeof(unsigned int),
+                                        /*allow_compression=*/false);
+    }
+
+  deallog << "unpacking cell " << cell->id() << " with data size="
+          << std::distance(data_range.begin(), data_range.end())
+          << " accumulated data="
+          << std::accumulate(intdatavector.begin(), intdatavector.end(), 0)
+          << std::endl;
+
+  Assert((status ==
+          parallel::distributed::Triangulation<dim, dim>::CELL_PERSIST),
+         ExcInternalError());
+}
+
+
+
+template <int dim>
+void
+save(MPI_Comm com_small, parallel::distributed::Triangulation<dim> &tr)
+{
+  deallog << "writing with " << Utilities::MPI::n_mpi_processes(com_small)
+          << std::endl;
+
+  unsigned int handle =
+    tr.register_data_attach(pack_function<dim>,
+                            /*returns_variable_size_data=*/true);
+
+  tr.save("file");
+  deallog << "#cells = " << tr.n_global_active_cells() << std::endl;
+  deallog << "Checksum: " << tr.get_checksum() << std::endl;
+}
+
+
+
+template <int dim>
+void
+test()
+{
+  unsigned int myid    = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD);
+  MPI_Comm     com_all = MPI_COMM_WORLD;
+  MPI_Comm     com_small;
+
+  // split the communicator in proc 0,1,2 and 3,4
+  MPI_Comm_split(com_all, (myid < 3) ? 0 : 1, myid, &com_small);
+
+  // write with small com
+  if (myid < 3)
+    {
+      parallel::distributed::Triangulation<dim> tr(com_small);
+      GridGenerator::subdivided_hyper_cube(tr, 2);
+      tr.refine_global(1);
+
+      typename Triangulation<dim, dim>::active_cell_iterator cell;
+      for (cell = tr.begin_active(); cell != tr.end(); ++cell)
+        {
+          if (cell->is_locally_owned())
+            {
+              if (cell->id().to_string() == "0_1:0")
+                cell->set_refine_flag();
+              else if (cell->parent()->id().to_string() == "3_0:")
+                cell->set_coarsen_flag();
+            }
+        }
+      tr.execute_coarsening_and_refinement();
+
+      // save two times into the same file, overwrite it the second time
+      save(com_small, tr);
+      save(com_small, tr);
+    }
+
+  MPI_Barrier(MPI_COMM_WORLD);
+
+  deallog << "reading with " << Utilities::MPI::n_mpi_processes(com_all)
+          << std::endl;
+
+  {
+    parallel::distributed::Triangulation<dim> tr(com_all);
+
+    GridGenerator::subdivided_hyper_cube(tr, 2);
+    tr.load("file");
+
+    unsigned int handle =
+      tr.register_data_attach(pack_function<dim>,
+                              /*returns_variable_size_data=*/true);
+
+    tr.notify_ready_to_unpack(handle, unpack_function<dim>);
+
+    deallog << "#cells = " << tr.n_global_active_cells() << std::endl;
+    deallog << "Checksum: " << tr.get_checksum() << std::endl;
+
+    // now check if saving again succeeds. This checks for the correct number of
+    // attached data packs in tr and caught the bug.
+    save(com_all, tr);
+  }
+
+  if (Utilities::MPI::this_mpi_process(MPI_COMM_WORLD) == 0)
+    deallog << "OK" << std::endl;
+}
+
+
+int
+main(int argc, char *argv[])
+{
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+  MPILogInitAll                    log;
+
+  test<2>();
+}

diff --git a/tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output b/tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output
new file mode 100644 (file)
index 0000000..06bf11b
--- /dev/null
+++ b/tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output
@@ -0,0 +1,122 @@
+
+DEAL:0::writing with 3
+DEAL:0::packing cell 0_2:00 with data size=4 accumulated data=0
+DEAL:0::packing cell 0_2:01 with data size=8 accumulated data=1
+DEAL:0::packing cell 0_2:02 with data size=12 accumulated data=3
+DEAL:0::packing cell 0_2:03 with data size=16 accumulated data=6
+DEAL:0::packing cell 0_1:1 with data size=20 accumulated data=10
+DEAL:0::#cells = 16
+DEAL:0::Checksum: 2822439380
+DEAL:0::writing with 3
+DEAL:0::packing cell 0_2:00 with data size=24 accumulated data=15
+DEAL:0::packing cell 0_2:01 with data size=28 accumulated data=21
+DEAL:0::packing cell 0_2:02 with data size=32 accumulated data=28
+DEAL:0::packing cell 0_2:03 with data size=36 accumulated data=36
+DEAL:0::packing cell 0_1:1 with data size=40 accumulated data=45
+DEAL:0::#cells = 16
+DEAL:0::Checksum: 2822439380
+DEAL:0::reading with 5
+DEAL:0::unpacking cell 0_2:00 with data size=24 accumulated data=15
+DEAL:0::unpacking cell 0_2:01 with data size=28 accumulated data=21
+DEAL:0::unpacking cell 0_2:02 with data size=32 accumulated data=28
+DEAL:0::unpacking cell 0_2:03 with data size=36 accumulated data=36
+DEAL:0::#cells = 16
+DEAL:0::Checksum: 2822439380
+DEAL:0::writing with 5
+DEAL:0::packing cell 0_2:00 with data size=44 accumulated data=55
+DEAL:0::packing cell 0_2:01 with data size=48 accumulated data=66
+DEAL:0::packing cell 0_2:02 with data size=52 accumulated data=78
+DEAL:0::packing cell 0_2:03 with data size=56 accumulated data=91
+DEAL:0::#cells = 16
+DEAL:0::Checksum: 2822439380
+DEAL:0::OK
+
+DEAL:1::writing with 3
+DEAL:1::packing cell 0_1:2 with data size=4 accumulated data=0
+DEAL:1::packing cell 0_1:3 with data size=8 accumulated data=1
+DEAL:1::packing cell 1_1:0 with data size=12 accumulated data=3
+DEAL:1::packing cell 1_1:1 with data size=16 accumulated data=6
+DEAL:1::packing cell 1_1:2 with data size=20 accumulated data=10
+DEAL:1::packing cell 1_1:3 with data size=24 accumulated data=15
+DEAL:1::#cells = 16
+DEAL:1::Checksum: 0
+DEAL:1::writing with 3
+DEAL:1::packing cell 0_1:2 with data size=28 accumulated data=21
+DEAL:1::packing cell 0_1:3 with data size=32 accumulated data=28
+DEAL:1::packing cell 1_1:0 with data size=36 accumulated data=36
+DEAL:1::packing cell 1_1:1 with data size=40 accumulated data=45
+DEAL:1::packing cell 1_1:2 with data size=44 accumulated data=55
+DEAL:1::packing cell 1_1:3 with data size=48 accumulated data=66
+DEAL:1::#cells = 16
+DEAL:1::Checksum: 0
+DEAL:1::reading with 5
+DEAL:1::unpacking cell 0_1:1 with data size=40 accumulated data=45
+DEAL:1::unpacking cell 0_1:2 with data size=28 accumulated data=21
+DEAL:1::#cells = 16
+DEAL:1::Checksum: 0
+DEAL:1::writing with 5
+DEAL:1::packing cell 0_1:1 with data size=52 accumulated data=78
+DEAL:1::packing cell 0_1:2 with data size=56 accumulated data=91
+DEAL:1::#cells = 16
+DEAL:1::Checksum: 0
+
+
+DEAL:2::writing with 3
+DEAL:2::packing cell 2_1:0 with data size=4 accumulated data=0
+DEAL:2::packing cell 2_1:1 with data size=8 accumulated data=1
+DEAL:2::packing cell 2_1:2 with data size=12 accumulated data=3
+DEAL:2::packing cell 2_1:3 with data size=16 accumulated data=6
+DEAL:2::packing cell 3_0: with data size=20 accumulated data=10
+DEAL:2::#cells = 16
+DEAL:2::Checksum: 0
+DEAL:2::writing with 3
+DEAL:2::packing cell 2_1:0 with data size=24 accumulated data=15
+DEAL:2::packing cell 2_1:1 with data size=28 accumulated data=21
+DEAL:2::packing cell 2_1:2 with data size=32 accumulated data=28
+DEAL:2::packing cell 2_1:3 with data size=36 accumulated data=36
+DEAL:2::packing cell 3_0: with data size=40 accumulated data=45
+DEAL:2::#cells = 16
+DEAL:2::Checksum: 0
+DEAL:2::reading with 5
+DEAL:2::unpacking cell 0_1:3 with data size=32 accumulated data=28
+DEAL:2::unpacking cell 1_1:0 with data size=36 accumulated data=36
+DEAL:2::unpacking cell 1_1:1 with data size=40 accumulated data=45
+DEAL:2::unpacking cell 1_1:2 with data size=44 accumulated data=55
+DEAL:2::unpacking cell 1_1:3 with data size=48 accumulated data=66
+DEAL:2::#cells = 16
+DEAL:2::Checksum: 0
+DEAL:2::writing with 5
+DEAL:2::packing cell 0_1:3 with data size=44 accumulated data=55
+DEAL:2::packing cell 1_1:0 with data size=48 accumulated data=66
+DEAL:2::packing cell 1_1:1 with data size=52 accumulated data=78
+DEAL:2::packing cell 1_1:2 with data size=56 accumulated data=91
+DEAL:2::packing cell 1_1:3 with data size=60 accumulated data=105
+DEAL:2::#cells = 16
+DEAL:2::Checksum: 0
+
+
+DEAL:3::reading with 5
+DEAL:3::#cells = 16
+DEAL:3::Checksum: 0
+DEAL:3::writing with 5
+DEAL:3::#cells = 16
+DEAL:3::Checksum: 0
+
+
+DEAL:4::reading with 5
+DEAL:4::unpacking cell 2_1:0 with data size=24 accumulated data=15
+DEAL:4::unpacking cell 2_1:1 with data size=28 accumulated data=21
+DEAL:4::unpacking cell 2_1:2 with data size=32 accumulated data=28
+DEAL:4::unpacking cell 2_1:3 with data size=36 accumulated data=36
+DEAL:4::unpacking cell 3_0: with data size=40 accumulated data=45
+DEAL:4::#cells = 16
+DEAL:4::Checksum: 0
+DEAL:4::writing with 5
+DEAL:4::packing cell 2_1:0 with data size=4 accumulated data=0
+DEAL:4::packing cell 2_1:1 with data size=8 accumulated data=1
+DEAL:4::packing cell 2_1:2 with data size=12 accumulated data=3
+DEAL:4::packing cell 2_1:3 with data size=16 accumulated data=6
+DEAL:4::packing cell 3_0: with data size=20 accumulated data=10
+DEAL:4::#cells = 16
+DEAL:4::Checksum: 0
+

diff --git a/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output b/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output
new file mode 100644 (file)
index 0000000..bf97dfd
--- /dev/null
+++ b/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output
@@ -0,0 +1,10 @@
+
+DEAL:0:2d::hyper_cube
+DEAL:0:2d::#cells = 19
+DEAL:0:2d::cells(0) = 10
+DEAL:0:2d::Checksum: 136119115
+DEAL:0:2d::#cells = 19
+DEAL:0:2d::cells(0) = 10
+DEAL:0:2d::Checksum: 136119115
+DEAL:0:2d::sum: 435.000 870.000
+DEAL:0:2d::OK