CardiacSimulationArchiver.cpp

/*

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 * Redistributions in binary form must reproduce the above copyright notice,
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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 classes, 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; // Note that Boost version numbers are per-class; this only needs to change if we change the Load/Save methods here
        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> >;