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Message #26246
Re: [Branch ~dolfin-core/dolfin/trunk] Rev 7202: merge phdf5 branch
Was the changes to CMakeLists.txt in this merge made on purpose?
Johannes
On Fri, Dec 7, 2012 at 4:59 PM, <noreply@xxxxxxxxxxxxx> wrote:
> Merge authors:
> Chris Richardson (chris-bpi)
> Garth Wells (garth-wells)
> ------------------------------------------------------------
> revno: 7202 [merge]
> committer: Garth N. Wells <gnw20@xxxxxxxxx>
> branch nick: clean_test
> timestamp: Fri 2012-12-07 15:57:55 +0000
> message:
> merge phdf5 branch
> modified:
> CMakeLists.txt
> dolfin/graph/GraphBuilder.cpp
> dolfin/io/HDF5File.cpp
> dolfin/io/HDF5File.h
> dolfin/io/HDF5Interface.cpp
> dolfin/io/HDF5Interface.h
> dolfin/io/XDMFFile.cpp
> test/unit/io/python/HDF5.py
>
>
> --
> lp:dolfin
> https://code.launchpad.net/~dolfin-core/dolfin/trunk
>
> Your team DOLFIN Core Team is subscribed to branch lp:dolfin.
> To unsubscribe from this branch go to https://code.launchpad.net/~dolfin-core/dolfin/trunk/+edit-subscription
>
> === modified file 'CMakeLists.txt'
> --- CMakeLists.txt 2012-12-05 10:44:03 +0000
> +++ CMakeLists.txt 2012-12-07 15:09:46 +0000
> @@ -215,18 +215,16 @@
> set(Boost_USE_MULTITHREADED $ENV{BOOST_USE_MULTITHREADED})
> set(Boost_ADDITIONAL_VERSIONS 1.43 1.43.0 1.44 1.44.0 1.45 1.45.0 1.46 1.46.0 1.46.1 1.47 1.47.0 1.48 1.48.0 1.49 1.49.0 1.50 1.50.0)
>
> -find_package(Boost 1.36 QUIET REQUIRED)
> -
> -set(DOLFIN_BOOST_COMPONENTS filesystem program_options system thread iostreams math_tr1)
> if (DOLFIN_ENABLE_MPI AND MPI_CXX_FOUND)
> - list(APPEND DOLFIN_BOOST_COMPONENTS mpi serialization)
> + find_package(Boost 1.36 COMPONENTS filesystem program_options system thread iostreams math_tr1 mpi serialization REQUIRED)
> +else()
> + find_package(Boost 1.36 COMPONENTS filesystem program_options system thread iostreams math_tr1 REQUIRED)
> endif()
>
> # Boost timer was not a separate Boost component until version 1.48
> -if ("${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}" VERSION_GREATER "1.47")
> - list(APPEND DOLFIN_BOOST_COMPONENTS timer)
> -endif()
> -find_package(Boost COMPONENTS ${DOLFIN_BOOST_COMPONENTS} REQUIRED)
> +# if ("${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}" VERSION_GREATER "1.47")
> +# find_package(Boost COMPONENTS timer REQUIRED)
> +# endif()
>
> # Check for required package UFC
> find_package(UFC 2.0.2 QUIET HINTS ${UFC_DIR})
>
> === modified file 'dolfin/graph/GraphBuilder.cpp'
> --- dolfin/graph/GraphBuilder.cpp 2012-12-06 21:40:39 +0000
> +++ dolfin/graph/GraphBuilder.cpp 2012-12-07 15:09:46 +0000
> @@ -18,7 +18,7 @@
> // Modified by Chris Richardson, 2012
> //
> // First added: 2010-02-19
> -// Last changed: 2012-11-24
> +// Last changed: 2012-12-07
>
> #include <algorithm>
> #include <numeric>
> @@ -372,8 +372,6 @@
> double tt = time();
>
> // Create mapping from facets (vector) to cells
> - // FIXME: potential speedup by using a hash directly for the map key
> - // instead of a vector
> typedef boost::unordered_map<std::vector<std::size_t>, std::size_t> vectormap;
> vectormap facet_cell;
>
> @@ -451,7 +449,8 @@
> }
>
> // Go through local facets, looking for a matching facet in othermap
> - for(vectormap::iterator fcell = facet_cell.begin(); fcell != facet_cell.end(); ++fcell)
> + vectormap::iterator fcell = facet_cell.begin();
> + while(fcell != facet_cell.end())
> {
> vectormap::iterator join_cell = othermap.find(fcell->first);
> if (join_cell != othermap.end())
> @@ -460,10 +459,13 @@
> // from both maps
> local_graph[fcell->second].insert(join_cell->second);
> ghost_vertices.insert(join_cell->second);
> - facet_cell.erase(fcell);
> + facet_cell.erase(fcell++);
> othermap.erase(join_cell);
> }
> + else
> + ++fcell;
> }
> +
> }
>
> // remaining facets are exterior boundary - could be useful
>
> === modified file 'dolfin/io/HDF5File.cpp'
> --- dolfin/io/HDF5File.cpp 2012-12-04 11:29:59 +0000
> +++ dolfin/io/HDF5File.cpp 2012-12-04 22:20:41 +0000
> @@ -18,7 +18,7 @@
> // Modified by Garth N. Wells, 2012
> //
> // First added: 2012-06-01
> -// Last changed: 2012-11-27
> +// Last changed: 2012-12-04
>
> #ifdef HAS_HDF5
>
> @@ -54,7 +54,7 @@
> using namespace dolfin;
>
> //-----------------------------------------------------------------------------
> -HDF5File::HDF5File(const std::string filename, bool truncate, bool use_mpiio)
> +HDF5File::HDF5File(const std::string filename, const std::string file_mode, bool use_mpiio)
> : hdf5_file_open(false), hdf5_file_id(0),
> mpi_io(MPI::num_processes() > 1 && use_mpiio ? true : false)
> {
> @@ -62,7 +62,7 @@
> parameters.add("chunking", false);
>
> // OPen HDF5 file
> - hdf5_file_id = HDF5Interface::open_file(filename, truncate, mpi_io);
> + hdf5_file_id = HDF5Interface::open_file(filename, file_mode, mpi_io);
> hdf5_file_open = true;
> }
> //-----------------------------------------------------------------------------
> @@ -121,7 +121,7 @@
> //-----------------------------------------------------------------------------
> void HDF5File::write(const Mesh& mesh, std::size_t cell_dim, const std::string name)
> {
> - warning("Writing mesh with global index - not suitable for visualisation");
> + warning("Writing globally indexed mesh - not suitable for visualisation");
>
> dolfin_assert(hdf5_file_open);
>
> @@ -357,7 +357,6 @@
> void HDF5File::read(Mesh& input_mesh, const std::string name)
> {
> warning("HDF5 Mesh input is still experimental");
> - warning("HDF5 Mesh input will always repartition the mesh");
>
> dolfin_assert(hdf5_file_open);
>
> @@ -391,8 +390,6 @@
> const std::string coordinates_name,
> const std::string topology_name)
> {
> - // FIXME: should not call repartition if running serial
> - warning("HDF5 Mesh read will repartition this mesh");
> Timer t("HDF5: ReadMesh");
>
> // Structure to store local mesh
>
> === modified file 'dolfin/io/HDF5File.h'
> --- dolfin/io/HDF5File.h 2012-12-04 11:29:59 +0000
> +++ dolfin/io/HDF5File.h 2012-12-04 22:20:41 +0000
> @@ -18,7 +18,7 @@
> // Modified by Garth N. Wells, 2012
> //
> // First added: 2012-05-22
> -// Last changed: 2012-11-27
> +// Last changed: 2012-12-04
>
> #ifndef __DOLFIN_HDF5FILE_H
> #define __DOLFIN_HDF5FILE_H
> @@ -47,7 +47,7 @@
> public:
>
> /// Constructor
> - HDF5File(const std::string filename, bool truncate, bool use_mpiio=true);
> + HDF5File(const std::string filename, const std::string file_mode, bool use_mpiio=true);
>
> /// Destructor
> ~HDF5File();
>
> === modified file 'dolfin/io/HDF5Interface.cpp'
> --- dolfin/io/HDF5Interface.cpp 2012-12-04 11:29:59 +0000
> +++ dolfin/io/HDF5Interface.cpp 2012-12-04 22:20:41 +0000
> @@ -18,7 +18,7 @@
> // Modified by Johannes Ring, 2012
> //
> // First Added: 2012-09-21
> -// Last Changed: 2012-10-12
> +// Last Changed: 2012-12-04
>
> #include <boost/filesystem.hpp>
>
> @@ -36,7 +36,7 @@
> using namespace dolfin;
>
> //-----------------------------------------------------------------------------
> -hid_t HDF5Interface::open_file(const std::string filename, const bool truncate,
> +hid_t HDF5Interface::open_file(const std::string filename, const std::string mode,
> const bool use_mpi_io)
> {
> // Set parallel access with communicator
> @@ -55,10 +55,10 @@
> #endif
> }
>
> - hid_t file_id;
> - if (truncate)
> + hid_t file_id = HDF5_FAIL;
> + if (mode=="w")
> {
> - // Create file, (overwriting existing file, if present)
> + // Create file for write, (overwriting existing file, if present)
> file_id = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT,
> plist_id);
> }
> @@ -72,8 +72,22 @@
> "File does not exist");
> }
>
> - // Open file existing file
> - file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, plist_id);
> + if(mode=="a")
> + {
> + // Open file existing file for append
> + file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, plist_id);
> + }
> + else if(mode=="r")
> + {
> + file_id = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, plist_id);
> + }
> + else
> + {
> + dolfin_error("HDF5Interface.cpp",
> + "open HDF5 file",
> + "Unknown file mode \"%s\"", mode.c_str());
> + }
> +
> }
> dolfin_assert(file_id != HDF5_FAIL);
>
>
> === modified file 'dolfin/io/HDF5Interface.h'
> --- dolfin/io/HDF5Interface.h 2012-12-04 11:29:59 +0000
> +++ dolfin/io/HDF5Interface.h 2012-12-04 22:20:41 +0000
> @@ -44,7 +44,7 @@
> public:
>
> /// Open HDF5 and return file descriptor
> - static hid_t open_file(const std::string filename, const bool truncate,
> + static hid_t open_file(const std::string filename, const std::string mode,
> const bool use_mpi_io);
>
>
>
> === modified file 'dolfin/io/XDMFFile.cpp'
> --- dolfin/io/XDMFFile.cpp 2012-12-04 20:34:24 +0000
> +++ dolfin/io/XDMFFile.cpp 2012-12-04 22:20:41 +0000
> @@ -18,7 +18,7 @@
> // Modified by Garth N. Wells, 2012
> //
> // First added: 2012-05-28
> -// Last changed: 2012-11-26
> +// Last changed: 2012-12-04
>
> #ifdef HAS_HDF5
>
> @@ -55,7 +55,7 @@
> hdf5_filename = p.string();
>
> // Create HDF5 file (truncate)
> - hdf5_file.reset(new HDF5File(hdf5_filename, true));
> + hdf5_file.reset(new HDF5File(hdf5_filename, "w"));
>
> // Re-write mesh (true, false or auto, with auto based on detecting
> // changes in a hash key)
>
> === modified file 'test/unit/io/python/HDF5.py'
> --- test/unit/io/python/HDF5.py 2012-12-03 21:36:45 +0000
> +++ test/unit/io/python/HDF5.py 2012-12-04 14:28:03 +0000
> @@ -30,20 +30,20 @@
> def test_save_vector(self):
> x = Vector(305)
> x[:] = 1.0
> - vector_file = HDF5File("x.h5", True)
> + vector_file = HDF5File("x.h5", "w")
> vector_file.write(x, "my_vector")
>
> def test_save_and_read_vector(self):
> # Write to file
> x = Vector(305)
> x[:] = 1.2
> - vector_file = HDF5File("vector.h5", True)
> + vector_file = HDF5File("vector.h5", "w")
> vector_file.write(x, "my_vector")
> del vector_file
>
> # Read from file
> y = Vector()
> - vector_file = HDF5File("vector.h5", False)
> + vector_file = HDF5File("vector.h5", "r")
> vector_file.read(y, "my_vector")
> self.assertEqual(y.size(), x.size())
> self.assertEqual((x - y).norm("l1"), 0.0)
>
>
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