CardiacSimulationArchiver.cpp

/*

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 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
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 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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*/

#include <fstream>

// Must be included before any other serialization headers
#include "CheckpointArchiveTypes.hpp"
#include "CardiacSimulationArchiver.hpp"

#include "Exception.hpp"
#include "ArchiveOpener.hpp"
#include "OutputFileHandler.hpp"
#include "ArchiveLocationInfo.hpp"
#include "DistributedVectorFactory.hpp"
#include "PetscTools.hpp"
#include "FileFinder.hpp"

/*
 * Archiving extravaganza:
 *
 * Various objects are archived through a pointer to an abstract class.  All the potential
 * concrete classes need to be included here, so they are registered with Boost.  If not,
 * Boost (<1.37) won't be able to find the archiving methods of the concrete class and will
 * throw the following exception:
 *
 *       terminate called after throwing an instance of 'boost::archive::archive_exception
 *       what():  unregistered class
 *
 * No member variable is defined to be of any of these clases, so removing them won't
 * produce any compiler error.  The exception above will occur at runtime.
 *
 * This might not be even necessary in certain cases, if the file is included implicitly by
 * another header file or by the test itself.  It's safer though.
 */
#include "MonodomainProblem.hpp"
#include "BidomainProblem.hpp"
#include "BidomainWithBathProblem.hpp"
#include "HeartConfigRelatedCellFactory.hpp"


template<class PROBLEM_CLASS>
void CardiacSimulationArchiver<PROBLEM_CLASS>::Save(PROBLEM_CLASS& rSimulationToArchive,
                                                    const std::string& rDirectory,
                                                    bool clearDirectory)
{
    // Clear directory if requested (and make sure it exists)
    OutputFileHandler handler(rDirectory, clearDirectory);

    // Nest the archive writing, so the ArchiveOpener goes out of scope before
    // the method ends.
    {
        // Open the archive files
        FileFinder dir(rDirectory, RelativeTo::ChasteTestOutput);
        ArchiveOpener<boost::archive::text_oarchive, std::ofstream> archive_opener(dir, "archive.arch");
        boost::archive::text_oarchive* p_main_archive = archive_opener.GetCommonArchive();

        // And save
        PROBLEM_CLASS* const p_simulation_to_archive = &rSimulationToArchive;
        (*p_main_archive) & p_simulation_to_archive;
    }

    // Write the info file
    if (PetscTools::AmMaster())
    {
        std::string info_path = handler.GetOutputDirectoryFullPath() + "archive.info";
        std::ofstream info_file(info_path.c_str());
        if (!info_file.is_open())
        {
            // Avoid deadlock...
            PetscTools::ReplicateBool(true);
            EXCEPTION("Unable to open archive information file: " + info_path);
        }
        PetscTools::ReplicateBool(false);
        unsigned archive_version = 0; 
        info_file << PetscTools::GetNumProcs() << " " << archive_version;
    }
    else
    {
        bool master_threw = PetscTools::ReplicateBool(false);
        if (master_threw)
        {
            EXCEPTION("Unable to open archive information file");
        }
    }
    // Make sure everything is written before any process continues.
    PetscTools::Barrier("CardiacSimulationArchiver::Save");
}

template<class PROBLEM_CLASS>
PROBLEM_CLASS* CardiacSimulationArchiver<PROBLEM_CLASS>::Load(const std::string& rDirectory)
{
    FileFinder directory(rDirectory, RelativeTo::ChasteTestOutput);
    return CardiacSimulationArchiver<PROBLEM_CLASS>::Migrate(directory);
}

template<class PROBLEM_CLASS>
PROBLEM_CLASS* CardiacSimulationArchiver<PROBLEM_CLASS>::Load(const FileFinder& rDirectory)
{
    return CardiacSimulationArchiver<PROBLEM_CLASS>::Migrate(rDirectory);
}


template<class PROBLEM_CLASS>
PROBLEM_CLASS* CardiacSimulationArchiver<PROBLEM_CLASS>::Migrate(const FileFinder& rDirectory)
{
    // Check the directory exists
    std::string dir_path = rDirectory.GetAbsolutePath();
    if (!rDirectory.IsDir() || !rDirectory.Exists())
    {
        EXCEPTION("Checkpoint directory does not exist: " + dir_path);
    }
    assert(*(dir_path.end()-1) == '/'); // Paranoia
    // Load the info file
    std::string info_path = dir_path + "archive.info";
    std::ifstream info_file(info_path.c_str());
    if (!info_file.is_open())
    {
        EXCEPTION("Unable to open archive information file: " + info_path);
    }
    unsigned num_procs, archive_version;
    info_file >> num_procs >> archive_version;

    PROBLEM_CLASS *p_unarchived_simulation;

    // Avoid the DistributedVectorFactory throwing a 'wrong number of processes' exception when loading,
    // and make it get the original DistributedVectorFactory from the archive so we can compare against
    // num_procs.
    DistributedVectorFactory::SetCheckNumberOfProcessesOnLoad(false);
    // Put what follows in a try-catch to make sure we reset this
    try
    {
        // Figure out which process-specific archive to load first.  If we're loading on the same number of
        // processes, we must load our own one, or the mesh gets confused.  Otherwise, start with 0 to make
        // sure it exists.
        unsigned initial_archive = num_procs == PetscTools::GetNumProcs() ? PetscTools::GetMyRank() : 0u;

        // Load the master and initial process-specific archive files.
        // This will also set up ArchiveLocationInfo for us.
        ArchiveOpener<boost::archive::text_iarchive, std::ifstream> archive_opener(rDirectory, "archive.arch", initial_archive);
        boost::archive::text_iarchive* p_main_archive = archive_opener.GetCommonArchive();
        (*p_main_archive) >> p_unarchived_simulation;

        // Work out how many more process-specific files to load
        DistributedVectorFactory* p_factory = p_unarchived_simulation->rGetMesh().GetDistributedVectorFactory();
        assert(p_factory != NULL);
        unsigned original_num_procs = p_factory->GetOriginalFactory()->GetNumProcs();
        assert(original_num_procs == num_procs); // Paranoia

        // Merge in the extra data
        for (unsigned archive_num=0; archive_num<original_num_procs; archive_num++)
        {
            if (archive_num != initial_archive)
            {
                std::string archive_path = ArchiveLocationInfo::GetProcessUniqueFilePath("archive.arch", archive_num);
                std::ifstream ifs(archive_path.c_str());
                boost::archive::text_iarchive archive(ifs);
                p_unarchived_simulation->LoadExtraArchive(archive, archive_version);
            }
        }
    }
    catch (Exception &e)
    {
        DistributedVectorFactory::SetCheckNumberOfProcessesOnLoad(true);
        throw e;
    }

    // Done.
    DistributedVectorFactory::SetCheckNumberOfProcessesOnLoad(true);
    return p_unarchived_simulation;
}

//
// Explicit instantiation
//

template class CardiacSimulationArchiver<MonodomainProblem<1> >;
template class CardiacSimulationArchiver<MonodomainProblem<2> >;
template class CardiacSimulationArchiver<MonodomainProblem<3> >;

template class CardiacSimulationArchiver<BidomainProblem<1> >;
template class CardiacSimulationArchiver<BidomainProblem<2> >;
template class CardiacSimulationArchiver<BidomainProblem<3> >;

template class CardiacSimulationArchiver<BidomainWithBathProblem<1> >;
template class CardiacSimulationArchiver<BidomainWithBathProblem<2> >;
template class CardiacSimulationArchiver<BidomainWithBathProblem<3> >;