checkpoint.cc

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#include "../../include/matrixFreePDE.h"
#include <boost/archive/binary_iarchive.hpp>
#include <boost/archive/binary_oarchive.hpp>

#ifdef DEAL_II_WITH_ZLIB
#  include <zlib.h>
#endif

// Save a checkpoint
template <int dim, int degree>
void MatrixFreePDE<dim,degree>::save_checkpoint(){
    computing_timer.enter_section("matrixFreePDE: save_checkpoint");
    unsigned int my_id = Utilities::MPI::this_mpi_process (MPI_COMM_WORLD);

    if (my_id == 0)
    {
        // if we have previously written a snapshot, then keep the last
        // snapshot in case this one fails to save. Note: static variables
        // will only be initialized once per model run.
        static bool previous_snapshot_exists = (userInputs.resume_from_checkpoint == true);

        if (previous_snapshot_exists == true)
        {
            move_file ("restart.mesh","restart.mesh.old");
            move_file ("restart.mesh.info","restart.mesh.info.old");
            move_file ("restart.time.info","restart.time.info.old");
        }
        // from now on, we know that if we get into this
        // function again that a snapshot has previously
        // been written
        previous_snapshot_exists = true;
    }

    // save Triangulation and Solution vectors:
    {
        // Serializing all of the scalars together and all of the vectors together

        // First, get lists of scalar and vector fields
        std::vector<unsigned int> scalar_var_indices, vector_var_indices;
        for (unsigned int var=0; var < userInputs.number_of_variables; var++){
            if (userInputs.var_type[var] == SCALAR){
                scalar_var_indices.push_back(var);
            }
            else {
                vector_var_indices.push_back(var);
            }
        }

        // Second, build one solution set list for scalars and one for vectors
        std::vector<const vectorType *> solSet_transfer_scalars;
        std::vector<const vectorType *> solSet_transfer_vectors;
        for(unsigned int var = 0; var < userInputs.number_of_variables; ++var){
            if (userInputs.var_type[var] == SCALAR){
                solSet_transfer_scalars.push_back(solutionSet[var]);
            }
            else {
                solSet_transfer_vectors.push_back(solutionSet[var]);
            }
        }

        // Finally, save the triangulation and the solutionTransfer objects
        if (scalar_var_indices.size() > 0 && vector_var_indices.size() == 0){
            parallel::distributed::SolutionTransfer<dim, vectorType> system_trans_scalars (*dofHandlersSet[scalar_var_indices[0]]);
            system_trans_scalars.prepare_serialization(solSet_transfer_scalars);

            triangulation.save ("restart.mesh");
        }
        else if (scalar_var_indices.size() == 0 && vector_var_indices.size() > 0){
            parallel::distributed::SolutionTransfer<dim, vectorType> system_trans_vectors (*dofHandlersSet[vector_var_indices[0]]);
            system_trans_vectors.prepare_serialization(solSet_transfer_vectors);

            triangulation.save ("restart.mesh");
        }
        else {
            parallel::distributed::SolutionTransfer<dim, vectorType> system_trans_scalars (*dofHandlersSet[scalar_var_indices[0]]);
            system_trans_scalars.prepare_serialization(solSet_transfer_scalars);

            parallel::distributed::SolutionTransfer<dim, vectorType> system_trans_vectors (*dofHandlersSet[vector_var_indices[0]]);
            system_trans_vectors.prepare_serialization(solSet_transfer_vectors);

            triangulation.save ("restart.mesh");
        }

    }

    // Save information about the current increment and current time
    if (my_id == 0){
        std::ofstream time_info_file;
        time_info_file.open("restart.time.info");
        time_info_file << currentIncrement << " (currentIncrement)\n";
        time_info_file << currentTime << " (currentTime)\n";
        time_info_file.close();
    }

    pcout << "*** Checkpoint created! ***" << std::endl << std::endl;
    computing_timer.exit_section("matrixFreePDE: save_checkpoint");

}


// Load from a previously created checkpoint
template <int dim, int degree>
void MatrixFreePDE<dim,degree>::load_checkpoint_triangulation(){

    // First check existence of the two restart files for the mesh and field variables
    verify_checkpoint_file_exists("restart.mesh");
    verify_checkpoint_file_exists("restart.mesh.info");

    pcout << std::endl << "*** Resuming from a checkpoint! ***" << std::endl << std::endl;

    try
    {
        triangulation.load ("restart.mesh");
    }
    catch (...)
    {
        AssertThrow(false, ExcMessage("PRISMS-PF Error: Cannot open snapshot mesh file or read the triangulation stored there."));
    }

}

// Load from a previously saved checkpoint
template <int dim, int degree>
void MatrixFreePDE<dim,degree>::load_checkpoint_fields(){

    // Serializing all of the scalars together and all of the vectors together

    // First, get lists of scalar and vector fields
    std::vector<unsigned int> scalar_var_indices, vector_var_indices;
    for (unsigned int var=0; var < userInputs.number_of_variables; var++){
        if (userInputs.var_type[var] == SCALAR){
            scalar_var_indices.push_back(var);
        }
        else {
            vector_var_indices.push_back(var);
        }
    }

    // Second, build one solution set list for scalars and one for vectors
    std::vector<vectorType *> solSet_transfer_scalars;
    std::vector<vectorType *> solSet_transfer_vectors;
    for(unsigned int var = 0; var < userInputs.number_of_variables; ++var){
        if (userInputs.var_type[var] == SCALAR){
            solSet_transfer_scalars.push_back(solutionSet[var]);
        }
        else {
            solSet_transfer_vectors.push_back(solutionSet[var]);
        }
    }

    // Finally, deserialize the fields to the solSet_transfer objects, which contain pointers to solutionSet
    if (scalar_var_indices.size() > 0){
        parallel::distributed::SolutionTransfer<dim, vectorType> system_trans_scalars (*dofHandlersSet[scalar_var_indices[0]]);
        system_trans_scalars.deserialize(solSet_transfer_scalars);
    }
    if (vector_var_indices.size() > 0){
        parallel::distributed::SolutionTransfer<dim, vectorType> system_trans_vectors (*dofHandlersSet[vector_var_indices[0]]);
        system_trans_vectors.deserialize(solSet_transfer_vectors);
    }

}

// Load from a previously saved checkpoint
template <int dim, int degree>
void MatrixFreePDE<dim,degree>::load_checkpoint_time_info(){

    // Make sure that restart.time.info exists
    verify_checkpoint_file_exists("restart.time.info");

    std::ifstream time_info_file;
    time_info_file.open("restart.time.info");
    std::string line;
    std::getline(time_info_file, line);
    line.erase(line.end()-19,line.end());
    currentIncrement = dealii::Utilities::string_to_int(line);

    std::getline(time_info_file, line);
    line.erase(line.end()-14,line.end());
    currentTime = dealii::Utilities::string_to_double(line);
    time_info_file.close();

}


// Move/rename a checkpoint file
template <int dim, int degree>
void MatrixFreePDE<dim,degree>::move_file (const std::string &old_name, const std::string &new_name){

    int error = system (("mv " + old_name + " " + new_name).c_str());

    // If the above call failed, e.g. because there is no command-line
    // available, try with internal functions.
    if (error != 0)
    {
        std::ifstream ifile(new_name);
        if (static_cast<bool>(ifile))
        {
            error = remove(new_name.c_str());
            AssertThrow (error == 0, ExcMessage(std::string ("Unable to remove file: "
            + new_name
            + ", although it seems to exist. "
            + "The error code is "
            + dealii::Utilities::to_string(error) + ".")));
        }

        error = rename(old_name.c_str(),new_name.c_str());
        AssertThrow (error == 0, ExcMessage(std::string ("Unable to rename files: ")
        +
        old_name + " -> " + new_name
        + ". The error code is "
        + dealii::Utilities::to_string(error) + "."));
    }
}

template <int dim, int degree>
void MatrixFreePDE<dim,degree>::verify_checkpoint_file_exists(const std::string filename){
    std::ifstream in (filename);
    if (!in){
        AssertThrow (false,
            ExcMessage (std::string("PRISMS-PF Error: You are trying to restart a previous computation, "
            "but the restart file <")
            +
            filename
            +
            "> does not appear to exist!"));
        }
}

#include "../../include/matrixFreePDE_template_instantiations.h"