// Run the analysis, blob identification, and write restart files
#include "analysis/runAnalysis.h"
#include "analysis/analysis.h"
#include "common/Array.h"
#include "common/Communication.h"
#include "common/MPI.h"
#include "common/ScaLBL.h"
#include "models/ColorModel.h"

#include "IO/MeshDatabase.h"
#include "threadpool/thread_pool.h"

#include "ProfilerApp.h"


AnalysisType &operator|=( AnalysisType &lhs, AnalysisType rhs )
{
    lhs = static_cast<AnalysisType>( static_cast<std::underlying_type<AnalysisType>::type>( lhs ) |
                                     static_cast<std::underlying_type<AnalysisType>::type>( rhs ) );
    return lhs;
}
bool matches( AnalysisType x, AnalysisType y )
{
    return ( static_cast<std::underlying_type<AnalysisType>::type>( x ) &
               static_cast<std::underlying_type<AnalysisType>::type>( y ) ) != 0;
}


// Create a shared_ptr to an array of values
template<class TYPE>
static inline std::shared_ptr<TYPE> make_shared_array( size_t N )
{
    return std::shared_ptr<TYPE>( new TYPE[N], []( const TYPE *p ) { delete[] p; } );
}


// Helper class to write the restart file from a seperate thread
class WriteRestartWorkItem : public ThreadPool::WorkItemRet<void>
{
public:
    WriteRestartWorkItem( const std::string &filename_, std::shared_ptr<double> cDen_,
        std::shared_ptr<double> cfq_, int N_ )
        : filename( filename_ ), cfq( cfq_ ), cDen( cDen_ ), N( N_ )
    {
    }
    virtual void run()
    {
        PROFILE_START( "Save Checkpoint", 1 );
        double value;
        ofstream File( filename, ios::binary );
        for ( int n = 0; n < N; n++ ) {
            // Write the two density values
            value = cDen.get()[n];
            File.write( (char *) &value, sizeof( value ) );
            value = cDen.get()[N + n];
            File.write( (char *) &value, sizeof( value ) );
        }
        for ( int n = 0; n < N; n++ ) {
            // Write the distributions
            for ( int q = 0; q < 19; q++ ) {
                value = cfq.get()[q * N + n];
                File.write( (char *) &value, sizeof( value ) );
            }
        }
        File.close();
        PROFILE_STOP( "Save Checkpoint", 1 );
    };

private:
    WriteRestartWorkItem();
    const std::string filename;
    std::shared_ptr<double> cfq, cDen;
    const int N;
};


// Helper class to compute the blob ids
typedef std::shared_ptr<std::pair<int, IntArray>> BlobIDstruct;
typedef std::shared_ptr<std::vector<BlobIDType>> BlobIDList;
static const std::string id_map_filename = "lbpm_id_map.txt";
class BlobIdentificationWorkItem1 : public ThreadPool::WorkItemRet<void>
{
public:
    BlobIdentificationWorkItem1( int timestep_, int Nx_, int Ny_, int Nz_,
        const RankInfoStruct &rank_info_, std::shared_ptr<const DoubleArray> phase_,
        const DoubleArray &dist_, BlobIDstruct last_id_, BlobIDstruct new_index_,
        BlobIDstruct new_id_, BlobIDList new_list_, runAnalysis::commWrapper &&comm_ )
        : timestep( timestep_ ),
          Nx( Nx_ ),
          Ny( Ny_ ),
          Nz( Nz_ ),
          rank_info( rank_info_ ),
          phase( phase_ ),
          dist( dist_ ),
          last_id( last_id_ ),
          new_index( new_index_ ),
          new_id( new_id_ ),
          new_list( new_list_ ),
          comm( std::move( comm_ ) )
    {
    }
    ~BlobIdentificationWorkItem1() {}
    virtual void run()
    {
        // Compute the global blob id and compare to the previous version
        PROFILE_START( "Identify blobs", 1 );
        double vF        = 0.0;
        double vS        = -1.0; // one voxel buffer region around solid
        IntArray &ids    = new_index->second;
        new_index->first = ComputeGlobalBlobIDs(
            Nx - 2, Ny - 2, Nz - 2, rank_info, *phase, dist, vF, vS, ids, comm.comm );
        PROFILE_STOP( "Identify blobs", 1 );
    }

private:
    BlobIdentificationWorkItem1();
    int timestep;
    int Nx, Ny, Nz;
    const RankInfoStruct rank_info;
    std::shared_ptr<const DoubleArray> phase;
    const DoubleArray &dist;
    BlobIDstruct last_id, new_index, new_id;
    BlobIDList new_list;
    runAnalysis::commWrapper comm;
};
class BlobIdentificationWorkItem2 : public ThreadPool::WorkItemRet<void>
{
public:
    BlobIdentificationWorkItem2( int timestep_, int Nx_, int Ny_, int Nz_,
        const RankInfoStruct &rank_info_, std::shared_ptr<const DoubleArray> phase_,
        const DoubleArray &dist_, BlobIDstruct last_id_, BlobIDstruct new_index_,
        BlobIDstruct new_id_, BlobIDList new_list_, runAnalysis::commWrapper &&comm_ )
        : timestep( timestep_ ),
          Nx( Nx_ ),
          Ny( Ny_ ),
          Nz( Nz_ ),
          rank_info( rank_info_ ),
          phase( phase_ ),
          dist( dist_ ),
          last_id( last_id_ ),
          new_index( new_index_ ),
          new_id( new_id_ ),
          new_list( new_list_ ),
          comm( std::move( comm_ ) )
    {
    }
    ~BlobIdentificationWorkItem2() {}
    virtual void run()
    {
        // Compute the global blob id and compare to the previous version
        PROFILE_START( "Identify blobs maps", 1 );
        const IntArray &ids = new_index->second;
        static int max_id   = -1;
        new_id->first       = new_index->first;
        new_id->second      = new_index->second;
        if ( last_id.get() != NULL ) {
            // Compute the timestep-timestep map
            const IntArray &old_ids = last_id->second;
            ID_map_struct map       = computeIDMap( Nx, Ny, Nz, old_ids, ids, comm.comm );
            // Renumber the current timestep's ids
            getNewIDs( map, max_id, *new_list );
            renumberIDs( *new_list, new_id->second );
            writeIDMap( map, timestep, id_map_filename );
        } else {
            max_id = -1;
            ID_map_struct map( new_id->first );
            getNewIDs( map, max_id, *new_list );
            writeIDMap( map, timestep, id_map_filename );
        }
        PROFILE_STOP( "Identify blobs maps", 1 );
    }

private:
    BlobIdentificationWorkItem2();
    int timestep;
    int Nx, Ny, Nz;
    const RankInfoStruct rank_info;
    std::shared_ptr<const DoubleArray> phase;
    const DoubleArray &dist;
    BlobIDstruct last_id, new_index, new_id;
    BlobIDList new_list;
    runAnalysis::commWrapper comm;
};


// Helper class to write the vis file from a thread
class WriteVisWorkItem : public ThreadPool::WorkItemRet<void>
{
public:
    WriteVisWorkItem( int timestep_, std::vector<IO::MeshDataStruct> &visData_,
        TwoPhase &Avgerages_, std::array<int, 3> n_, RankInfoStruct rank_info_,
        runAnalysis::commWrapper &&comm_ )
        : timestep( timestep_ ),
          visData( visData_ ),
          Averages( Avgerages_ ),
          n( std::move( n_ ) ),
          rank_info( std::move( rank_info_ ) ),
          comm( std::move( comm_ ) )
    {
    }
    ~WriteVisWorkItem() {}
    virtual void run()
    {
        PROFILE_START( "Save Vis", 1 );

        fillHalo<double> fillData( comm.comm, rank_info, n, { 1, 1, 1 }, 0, 1 );

        ASSERT( visData[0].vars[0]->name == "phase" );
        Array<double> &PhaseData = visData[0].vars[0]->data;
        fillData.copy( Averages.SDn, PhaseData );

        ASSERT( visData[0].vars[5]->name == "SignDist" );
        Array<double> &SignData = visData[0].vars[5]->data;
        fillData.copy( Averages.SDs, SignData );

        ASSERT( visData[0].vars[1]->name == "Pressure" );
        Array<double> &PressData = visData[0].vars[1]->data;
        fillData.copy( Averages.Press, PressData );

        ASSERT( visData[0].vars[2]->name == "Velocity_x" );
        ASSERT( visData[0].vars[3]->name == "Velocity_y" );
        ASSERT( visData[0].vars[4]->name == "Velocity_z" );
        Array<double> &VelxData = visData[0].vars[2]->data;
        Array<double> &VelyData = visData[0].vars[3]->data;
        Array<double> &VelzData = visData[0].vars[4]->data;
        fillData.copy( Averages.Vel_x, VelxData );
        fillData.copy( Averages.Vel_y, VelyData );
        fillData.copy( Averages.Vel_z, VelzData );

        ASSERT( visData[0].vars[6]->name == "BlobID" );
        Array<double> &BlobData = visData[0].vars[6]->data;
        fillData.copy( Averages.Label_NWP, BlobData );
        IO::writeData( timestep, visData, comm.comm );

        PROFILE_STOP( "Save Vis", 1 );
    };

private:
    WriteVisWorkItem();
    int timestep;
    std::array<int, 3> n;
    RankInfoStruct rank_info;
    std::vector<IO::MeshDataStruct> &visData;
    TwoPhase &Averages;
    runAnalysis::commWrapper comm;
};

// Helper class to write the vis file from a thread
class IOWorkItem : public ThreadPool::WorkItemRet<void>
{
public:
    IOWorkItem( int timestep_, std::shared_ptr<Database> input_db_,
        std::vector<IO::MeshDataStruct> &visData_, SubPhase &Averages_, std::array<int, 3> n_,
        RankInfoStruct rank_info_, runAnalysis::commWrapper &&comm_ )
        : timestep( timestep_ ),
          input_db( input_db_ ),
          visData( visData_ ),
          Averages( Averages_ ),
          n( std::move( n_ ) ),
          rank_info( std::move( rank_info_ ) ),
          comm( std::move( comm_ ) )
    {
    }
    ~IOWorkItem() {}
    virtual void run()
    {
        PROFILE_START( "Save Vis", 1 );

        auto color_db = input_db->getDatabase( "Color" );
        auto vis_db   = input_db->getDatabase( "Visualization" );
        // int timestep = color_db->getWithDefault<int>( "timestep", 0 );

        fillHalo<double> fillData( comm.comm, rank_info, n, { 1, 1, 1 }, 0, 1 );

        if ( vis_db->getWithDefault<bool>( "save_phase_field", true ) ) {
            ASSERT( visData[0].vars[0]->name == "phase" );
            Array<double> &PhaseData = visData[0].vars[0]->data;
            fillData.copy( Averages.Phi, PhaseData );
        }

        if ( vis_db->getWithDefault<bool>( "save_pressure", false ) ) {
            ASSERT( visData[0].vars[1]->name == "Pressure" );
            Array<double> &PressData = visData[0].vars[1]->data;
            fillData.copy( Averages.Pressure, PressData );
        }

        if ( vis_db->getWithDefault<bool>( "save_velocity", false ) ) {
            ASSERT( visData[0].vars[2]->name == "Velocity_x" );
            ASSERT( visData[0].vars[3]->name == "Velocity_y" );
            ASSERT( visData[0].vars[4]->name == "Velocity_z" );
            Array<double> &VelxData = visData[0].vars[2]->data;
            Array<double> &VelyData = visData[0].vars[3]->data;
            Array<double> &VelzData = visData[0].vars[4]->data;
            fillData.copy( Averages.Vel_x, VelxData );
            fillData.copy( Averages.Vel_y, VelyData );
            fillData.copy( Averages.Vel_z, VelzData );
        }

        if ( vis_db->getWithDefault<bool>( "save_distance", false ) ) {
            ASSERT( visData[0].vars[5]->name == "SignDist" );
            Array<double> &SignData = visData[0].vars[5]->data;
            fillData.copy( Averages.SDs, SignData );
        }

        if ( vis_db->getWithDefault<bool>( "save_connected_components", false ) ) {
            ASSERT( visData[0].vars[6]->name == "BlobID" );
            Array<double> &BlobData = visData[0].vars[6]->data;
            fillData.copy( Averages.morph_n->label, BlobData );
        }

        if ( vis_db->getWithDefault<bool>( "write_silo", true ) )
            IO::writeData( timestep, visData, comm.comm );

        if ( vis_db->getWithDefault<bool>( "save_8bit_raw", true ) ) {
            char CurrentIDFilename[40];
            sprintf( CurrentIDFilename, "id_t%d.raw", timestep );
            Averages.AggregateLabels( CurrentIDFilename );
        }

        PROFILE_STOP( "Save Vis", 1 );
    };

private:
    IOWorkItem();
    int timestep;
    std::array<int, 3> n;
    RankInfoStruct rank_info;
    std::shared_ptr<Database> input_db;
    std::vector<IO::MeshDataStruct> &visData;
    SubPhase &Averages;
    runAnalysis::commWrapper comm;
};


// Helper class to run the analysis from within a thread
// Note: Averages will be modified after the constructor is called
class AnalysisWorkItem : public ThreadPool::WorkItemRet<void>
{
public:
    AnalysisWorkItem( AnalysisType type_, int timestep_, TwoPhase &Averages_, BlobIDstruct ids,
        BlobIDList id_list_, double beta_ )
        : type( type_ ),
          timestep( timestep_ ),
          Averages( Averages_ ),
          blob_ids( ids ),
          id_list( id_list_ ),
          beta( beta_ )
    {
    }
    ~AnalysisWorkItem() {}
    virtual void run()
    {
        Averages.NumberComponents_NWP = blob_ids->first;
        Averages.Label_NWP            = blob_ids->second;
        Averages.Label_NWP_map        = *id_list;
        Averages.NumberComponents_WP  = 1;
        Averages.Label_WP.fill( 0.0 );
        if ( matches( type, AnalysisType::CopyPhaseIndicator ) ) {
            // Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
        }
        if ( matches( type, AnalysisType::ComputeAverages ) ) {
            PROFILE_START( "Compute dist", 1 );
            Averages.Initialize();
            Averages.ComputeDelPhi();
            Averages.ColorToSignedDistance( beta, Averages.Phase, Averages.SDn );
            Averages.ColorToSignedDistance( beta, Averages.Phase_tminus, Averages.Phase_tminus );
            Averages.ColorToSignedDistance( beta, Averages.Phase_tplus, Averages.Phase_tplus );
            Averages.UpdateMeshValues();
            Averages.ComputeLocal();
            Averages.Reduce();
            Averages.PrintAll( timestep );
            Averages.Initialize();
            Averages.ComponentAverages();
            Averages.SortBlobs();
            Averages.PrintComponents( timestep );
            PROFILE_STOP( "Compute dist", 1 );
        }
    }

private:
    AnalysisWorkItem();
    AnalysisType type;
    int timestep;
    TwoPhase &Averages;
    BlobIDstruct blob_ids;
    BlobIDList id_list;
    double beta;
};


class TCATWorkItem : public ThreadPool::WorkItemRet<void>
{
public:
    TCATWorkItem( AnalysisType type_, int timestep_, TwoPhase &Averages_, BlobIDstruct ids,
        BlobIDList id_list_, double beta_ )
        : type( type_ ),
          timestep( timestep_ ),
          Averages( Averages_ ),
          blob_ids( ids ),
          id_list( id_list_ ),
          beta( beta_ )
    {
    }
    ~TCATWorkItem() {}
    virtual void run()
    {
        Averages.NumberComponents_NWP = blob_ids->first;
        Averages.Label_NWP            = blob_ids->second;
        Averages.Label_NWP_map        = *id_list;
        Averages.NumberComponents_WP  = 1;
        Averages.Label_WP.fill( 0.0 );
        if ( matches( type, AnalysisType::CopyPhaseIndicator ) ) {
            // Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
        }
        if ( matches( type, AnalysisType::ComputeAverages ) ) {
            PROFILE_START( "Compute TCAT", 1 );
            Averages.Initialize();
            Averages.ComputeDelPhi();
            Averages.ColorToSignedDistance( beta, Averages.Phase, Averages.SDn );
            Averages.ColorToSignedDistance( beta, Averages.Phase_tminus, Averages.Phase_tminus );
            Averages.ColorToSignedDistance( beta, Averages.Phase_tplus, Averages.Phase_tplus );
            Averages.UpdateMeshValues();
            Averages.ComputeLocal();
            Averages.Reduce();
            Averages.PrintAll( timestep );
            PROFILE_STOP( "Compute TCAT", 1 );
        }
    }

private:
    TCATWorkItem();
    AnalysisType type;
    int timestep;
    TwoPhase &Averages;
    BlobIDstruct blob_ids;
    BlobIDList id_list;
    double beta;
};


class GanglionTrackingWorkItem : public ThreadPool::WorkItemRet<void>
{
public:
    GanglionTrackingWorkItem( AnalysisType type_, int timestep_, TwoPhase &Averages_,
        BlobIDstruct ids, BlobIDList id_list_, double beta_ )
        : type( type_ ),
          timestep( timestep_ ),
          Averages( Averages_ ),
          blob_ids( ids ),
          id_list( id_list_ ),
          beta( beta_ )
    {
    }
    ~GanglionTrackingWorkItem() {}
    virtual void run()
    {
        Averages.NumberComponents_NWP = blob_ids->first;
        Averages.Label_NWP            = blob_ids->second;
        Averages.Label_NWP_map        = *id_list;
        Averages.NumberComponents_WP  = 1;
        Averages.Label_WP.fill( 0.0 );
        if ( matches( type, AnalysisType::CopyPhaseIndicator ) ) {
            // Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
        }
        if ( matches( type, AnalysisType::ComputeAverages ) ) {
            PROFILE_START( "Compute ganglion", 1 );
            Averages.Initialize();
            Averages.ComputeDelPhi();
            Averages.ColorToSignedDistance( beta, Averages.Phase, Averages.SDn );
            Averages.ColorToSignedDistance( beta, Averages.Phase_tminus, Averages.Phase_tminus );
            Averages.ColorToSignedDistance( beta, Averages.Phase_tplus, Averages.Phase_tplus );
            Averages.UpdateMeshValues();
            Averages.ComponentAverages();
            Averages.SortBlobs();
            Averages.PrintComponents( timestep );
            PROFILE_STOP( "Compute ganglion", 1 );
        }
    }

private:
    GanglionTrackingWorkItem();
    AnalysisType type;
    int timestep;
    TwoPhase &Averages;
    BlobIDstruct blob_ids;
    BlobIDList id_list;
    double beta;
};


class BasicWorkItem : public ThreadPool::WorkItemRet<void>
{
public:
    BasicWorkItem( AnalysisType type_, int timestep_, SubPhase &Averages_ )
        : type( type_ ), timestep( timestep_ ), Averages( Averages_ )
    {
    }
    ~BasicWorkItem() {}
    virtual void run()
    {

        if ( matches( type, AnalysisType::CopyPhaseIndicator ) ) {
            // Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
        }
        if ( matches( type, AnalysisType::ComputeAverages ) ) {
            PROFILE_START( "Compute basic averages", 1 );
            Averages.Basic();
            PROFILE_STOP( "Compute basic averages", 1 );
        }
    }

private:
    BasicWorkItem();
    AnalysisType type;
    int timestep;
    SubPhase &Averages;
    double beta;
};

class SubphaseWorkItem : public ThreadPool::WorkItemRet<void>
{
public:
    SubphaseWorkItem( AnalysisType type_, int timestep_, SubPhase &Averages_ )
        : type( type_ ), timestep( timestep_ ), Averages( Averages_ )
    {
    }
    ~SubphaseWorkItem() {}
    virtual void run()
    {

        PROFILE_START( "Compute subphase", 1 );
        Averages.Full();
        Averages.Write( timestep );
        PROFILE_STOP( "Compute subphase", 1 );
    }

private:
    SubphaseWorkItem();
    AnalysisType type;
    int timestep;
    SubPhase &Averages;
    double beta;
};


/******************************************************************
 *  MPI comm wrapper for use with analysis                         *
 ******************************************************************/
runAnalysis::commWrapper::commWrapper(
    int tag_, const Utilities::MPI &comm_, runAnalysis *analysis_ )
    : comm( comm_ ), tag( tag_ ), analysis( analysis_ )
{
}
runAnalysis::commWrapper::commWrapper( commWrapper &&rhs )
    : comm( rhs.comm ), tag( rhs.tag ), analysis( rhs.analysis )
{
    rhs.tag = -1;
}
runAnalysis::commWrapper::~commWrapper()
{
    if ( tag == -1 )
        return;
    comm.barrier();
    analysis->d_comm_used[tag] = false;
}
runAnalysis::commWrapper runAnalysis::getComm()
{
    // Get a tag from root
    int tag = -1;
    if ( d_rank == 0 ) {
        for ( int i = 0; i < 1024; i++ ) {
            if ( !d_comm_used[i] ) {
                tag = i;
                break;
            }
        }
        if ( tag == -1 )
            ERROR( "Unable to get comm" );
    }
    tag              = d_comm.bcast( tag, 0 );
    d_comm_used[tag] = true;
    if ( d_comms[tag].isNull() )
        d_comms[tag] = d_comm.dup();
    return commWrapper( tag, d_comms[tag], this );
}


/******************************************************************
 *  Constructor/Destructors                                        *
 ******************************************************************/
runAnalysis::runAnalysis( std::shared_ptr<Database> input_db, const RankInfoStruct &rank_info,
    std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm, std::shared_ptr<Domain> Dm, int Np,
    bool Regular, IntArray Map )
    : d_Np( Np ),
      d_regular( Regular ),
      d_rank_info( rank_info ),
      d_Map( Map ),
      d_comm( Dm->Comm.dup() ),
      d_ScaLBL_Comm( ScaLBL_Comm )
{

    auto db     = input_db->getDatabase( "Analysis" );
    auto vis_db = input_db->getDatabase( "Visualization" );

    // Ids of work items to use for dependencies
    ThreadPool::thread_id_t d_wait_blobID;
    ThreadPool::thread_id_t d_wait_analysis;
    ThreadPool::thread_id_t d_wait_vis;
    ThreadPool::thread_id_t d_wait_restart;
    ThreadPool::thread_id_t d_wait_subphase;

    char rankString[20];
    sprintf( rankString, "%05d", Dm->rank() );
    d_n[0] = Dm->Nx - 2;
    d_n[1] = Dm->Ny - 2;
    d_n[2] = Dm->Nz - 2;
    d_N[0] = Dm->Nx;
    d_N[1] = Dm->Ny;
    d_N[2] = Dm->Nz;

    d_restart_interval           = db->getScalar<int>( "restart_interval" );
    d_analysis_interval          = db->getScalar<int>( "analysis_interval" );
    d_subphase_analysis_interval = INT_MAX;
    d_visualization_interval     = INT_MAX;
    d_blobid_interval            = INT_MAX;
    if ( db->keyExists( "blobid_interval" ) ) {
        d_blobid_interval = db->getScalar<int>( "blobid_interval" );
    }
    if ( db->keyExists( "visualization_interval" ) ) {
        d_visualization_interval = db->getScalar<int>( "visualization_interval" );
    }
    if ( db->keyExists( "subphase_analysis_interval" ) ) {
        d_subphase_analysis_interval = db->getScalar<int>( "subphase_analysis_interval" );
    }

    auto restart_file = db->getScalar<std::string>( "restart_file" );
    d_restartFile     = restart_file + "." + rankString;


    d_rank = d_comm.getRank();
    writeIDMap( ID_map_struct(), 0, id_map_filename );
    // Initialize IO for silo
    IO::initialize( "", "silo", "false" );
    // Create the MeshDataStruct
    d_meshData.resize( 1 );

    d_meshData[0].meshName = "domain";
    d_meshData[0].mesh     = std::make_shared<IO::DomainMesh>(
        d_rank_info, d_n[0], d_n[1], d_n[2], Dm->Lx, Dm->Ly, Dm->Lz );
    auto PhaseVar    = std::make_shared<IO::Variable>();
    auto PressVar    = std::make_shared<IO::Variable>();
    auto VxVar       = std::make_shared<IO::Variable>();
    auto VyVar       = std::make_shared<IO::Variable>();
    auto VzVar       = std::make_shared<IO::Variable>();
    auto SignDistVar = std::make_shared<IO::Variable>();
    auto BlobIDVar   = std::make_shared<IO::Variable>();

    if ( vis_db->getWithDefault<bool>( "save_phase_field", true ) ) {
        PhaseVar->name = "phase";
        PhaseVar->type = IO::VariableType::VolumeVariable;
        PhaseVar->dim  = 1;
        PhaseVar->data.resize( d_n[0], d_n[1], d_n[2] );
        d_meshData[0].vars.push_back( PhaseVar );
    }

    if ( vis_db->getWithDefault<bool>( "save_pressure", false ) ) {
        PressVar->name = "Pressure";
        PressVar->type = IO::VariableType::VolumeVariable;
        PressVar->dim  = 1;
        PressVar->data.resize( d_n[0], d_n[1], d_n[2] );
        d_meshData[0].vars.push_back( PressVar );
    }

    if ( vis_db->getWithDefault<bool>( "save_velocity", false ) ) {
        VxVar->name = "Velocity_x";
        VxVar->type = IO::VariableType::VolumeVariable;
        VxVar->dim  = 1;
        VxVar->data.resize( d_n[0], d_n[1], d_n[2] );
        d_meshData[0].vars.push_back( VxVar );
        VyVar->name = "Velocity_y";
        VyVar->type = IO::VariableType::VolumeVariable;
        VyVar->dim  = 1;
        VyVar->data.resize( d_n[0], d_n[1], d_n[2] );
        d_meshData[0].vars.push_back( VyVar );
        VzVar->name = "Velocity_z";
        VzVar->type = IO::VariableType::VolumeVariable;
        VzVar->dim  = 1;
        VzVar->data.resize( d_n[0], d_n[1], d_n[2] );
        d_meshData[0].vars.push_back( VzVar );
    }

    if ( vis_db->getWithDefault<bool>( "save_distance", false ) ) {
        SignDistVar->name = "SignDist";
        SignDistVar->type = IO::VariableType::VolumeVariable;
        SignDistVar->dim  = 1;
        SignDistVar->data.resize( d_n[0], d_n[1], d_n[2] );
        d_meshData[0].vars.push_back( SignDistVar );
    }

    if ( vis_db->getWithDefault<bool>( "save_connected_components", false ) ) {
        BlobIDVar->name = "BlobID";
        BlobIDVar->type = IO::VariableType::VolumeVariable;
        BlobIDVar->dim  = 1;
        BlobIDVar->data.resize( d_n[0], d_n[1], d_n[2] );
        d_meshData[0].vars.push_back( BlobIDVar );
    }


    // Initialize the comms
    for ( int i = 0; i < 1024; i++ )
        d_comm_used[i] = false;
    // Initialize the threads
    int N_threads = db->getWithDefault<int>( "N_threads", 4 );
    auto method   = db->getWithDefault<std::string>( "load_balance", "default" );
    createThreads( method, N_threads );
}
runAnalysis::~runAnalysis()
{
    // Finish processing analysis
    finish();
}
void runAnalysis::finish()
{
    PROFILE_START( "finish" );
    // Wait for the work items to finish
    d_tpool.wait_pool_finished();
    // Clear the wait ids
    d_wait_blobID.reset();
    d_wait_analysis.reset();
    d_wait_vis.reset();
    d_wait_subphase.reset();
    d_wait_restart.reset();
    // Syncronize
    d_comm.barrier();
    PROFILE_STOP( "finish" );
}


/******************************************************************
 *  Set the thread affinities                                      *
 ******************************************************************/
void print( const std::vector<int> &ids )
{
    if ( ids.empty() )
        return;
    printf( "%i", ids[0] );
    for ( size_t i = 1; i < ids.size(); i++ )
        printf( ", %i", ids[i] );
    printf( "\n" );
}
void runAnalysis::createThreads( const std::string &method, int N_threads )
{
    // Check if we are not using analysis threads
    if ( method == "none" )
        return;
    // Check if we have thread support
    auto thread_support = Utilities::MPI::queryThreadSupport();
    if ( thread_support != Utilities::MPI::ThreadSupport::MULTIPLE && N_threads > 0 )
        std::cerr
            << "Warning: Failed to start MPI with necessary thread support, errors may occur\n";
    // Create the threads
    const auto cores = d_tpool.getProcessAffinity();
    if ( N_threads == 0 ) {
        // Special case to serials the analysis for debugging
        d_tpool.setNumThreads( 0 );
    } else if ( cores.empty() ) {
        // We were not able to get the cores for the process
        d_tpool.setNumThreads( N_threads );
    } else if ( method == "default" ) {
        // Create the given number of threads, but let the OS manage affinities
        d_tpool.setNumThreads( N_threads );
    } else if ( method == "independent" ) {
        int N = cores.size() - 1;
        d_tpool.setNumThreads( N );
        d_tpool.setThreadAffinity( { cores[0] } );
        for ( int i = 0; i < N; i++ )
            d_tpool.setThreadAffinity( i, { cores[i + 1] } );
    }
    // Print the current affinities
    if ( d_rank == 0 ) {
        printf( "Affinities - rank 0:\n" );
        printf( "Main: " );
        print( d_tpool.getProcessAffinity() );
        for ( int i = 0; i < d_tpool.getNumThreads(); i++ ) {
            printf( "Thread %i: ", i + 1 );
            print( d_tpool.getThreadAffinity( i ) );
        }
    }
}


/******************************************************************
 *  Check which analysis we want to perform                        *
 ******************************************************************/
AnalysisType runAnalysis::computeAnalysisType( int timestep )
{
    AnalysisType type = AnalysisType::AnalyzeNone;
    if ( timestep % d_analysis_interval + 8 == d_analysis_interval ) {
        // Copy the phase indicator field for the earlier timestep
        // printf("Copy phase indicator,timestep=%i\n",timestep);
        type |= AnalysisType::CopyPhaseIndicator;
    }
    if ( timestep % d_blobid_interval == 0 ) {
        // Identify blobs and update global ids in time
        type |= AnalysisType::IdentifyBlobs;
    }
    /*#ifdef USE_CUDA
        if ( tpool.getQueueSize()<=3 && tpool.getNumThreads()>0 && timestep%50==0 ) {
            // Keep a few blob identifications queued up to keep the processors busy,
            // allowing us to track the blobs as fast as possible
            // Add more detailed estimates of the update frequency required to track blobs
            type |= AnalysisType::IdentifyBlobs;
        }
    #endif */
    if ( timestep % d_analysis_interval + 4 == d_analysis_interval ) {
        // Copy the averages to the CPU (and identify blobs)
        // printf("Copy sim state, timestep=%i \n",timestep);
        type |= AnalysisType::CopySimState;
        type |= AnalysisType::IdentifyBlobs;
    }
    if ( timestep % d_analysis_interval == 0 ) {
        // Run the analysis
        // printf("Compute averages, timestep=%i \n",timestep);
        type |= AnalysisType::ComputeAverages;
    }
    if ( timestep % d_restart_interval == 0 ) {
        // Write the restart file
        type |= AnalysisType::CreateRestart;
    }
    if ( timestep % d_visualization_interval == 0 ) {
        // Write the visualization data
        type |= AnalysisType::WriteVis;
        type |= AnalysisType::CopySimState;
        type |= AnalysisType::IdentifyBlobs;
    }
    return type;
}


/******************************************************************
 *  Run the analysis                                               *
 ******************************************************************/
void runAnalysis::run( int timestep, std::shared_ptr<Database> input_db, TwoPhase &Averages,
    const double *Phi, double *Pressure, double *Velocity, double *fq, double *Den )
{
    int N = d_N[0] * d_N[1] * d_N[2];
    NULL_USE( N );
    NULL_USE( Phi );

    auto db = input_db->getDatabase( "Analysis" );
    // int timestep = db->getWithDefault<int>( "timestep", 0 );

    // Check which analysis steps we need to perform
    auto type = computeAnalysisType( timestep );
    if ( type == AnalysisType::AnalyzeNone )
        return;

    // Check how may queued items we have
    if ( d_tpool.N_queued() > 20 ) {
        std::cerr << "Analysis queue is getting behind, waiting ...\n";
        finish();
    }

    PROFILE_START( "run" );

    // Copy the appropriate variables to the host (so we can spawn new threads)
    ScaLBL_DeviceBarrier();
    PROFILE_START( "Copy data to host", 1 );
    std::shared_ptr<DoubleArray> phase;
    /*   if ( matches(type,AnalysisType::CopyPhaseIndicator) ||
            matches(type,AnalysisType::ComputeAverages) ||
            matches(type,AnalysisType::CopySimState) ||
            matches(type,AnalysisType::IdentifyBlobs) )
    {
        phase = std::make_shared<DoubleArray>(d_N[0],d_N[1],d_N[2]);
        //ScaLBL_CopyToHost(phase->data(),Phi,N*sizeof(double));
        //   try 2 d_ScaLBL_Comm.RegulLayout(d_Map,Phi,Averages.Phase);
        //   memcpy(Averages.Phase.data(),phase->data(),N*sizeof(double));
        int Nx = d_N[0];
        int Ny = d_N[1];
        int Nz = d_N[2];
        double *TmpDat;
        TmpDat = new double [d_Np];
        ScaLBL_CopyToHost(&TmpDat[0],&Phi[0], d_Np*sizeof(double));
        for (int k=0; k<Nz; k++){
            for (int j=0; j<Ny; j++){
                for (int i=0; i<Nx; i++){
                    int n=k*Nx*Ny+j*Nx+i;
                    int idx=d_Map(i,j,k);
                    if (!(idx<0)){
                        double value=TmpDat[idx];
                        //regdata(i,j,k)=value;
                        phase->data()[n]=value;
                    }
                }
            }
        }
        delete [] TmpDat;
    }
    */
    // if ( matches(type,AnalysisType::CopyPhaseIndicator) ) {
    if ( timestep % d_analysis_interval + 8 == d_analysis_interval ) {
        if ( d_regular )
            d_ScaLBL_Comm->RegularLayout( d_Map, Phi, Averages.Phase_tplus );
        else
            ScaLBL_CopyToHost( Averages.Phase_tplus.data(), Phi, N * sizeof( double ) );
        // memcpy(Averages.Phase_tplus.data(),phase->data(),N*sizeof(double));
    }
    if ( timestep % d_analysis_interval == 0 ) {
        if ( d_regular )
            d_ScaLBL_Comm->RegularLayout( d_Map, Phi, Averages.Phase_tminus );
        else
            ScaLBL_CopyToHost( Averages.Phase_tminus.data(), Phi, N * sizeof( double ) );
        // memcpy(Averages.Phase_tminus.data(),phase->data(),N*sizeof(double));
    }
    // if ( matches(type,AnalysisType::CopySimState) ) {
    if ( timestep % d_analysis_interval + 4 == d_analysis_interval ) {
        // Copy the members of Averages to the cpu (phase was copied above)
        PROFILE_START( "Copy-Pressure", 1 );
        ScaLBL_D3Q19_Pressure( fq, Pressure, d_Np );
        // ScaLBL_D3Q19_Momentum(fq,Velocity,d_Np);
        ScaLBL_DeviceBarrier();
        PROFILE_STOP( "Copy-Pressure", 1 );
        PROFILE_START( "Copy-Wait", 1 );
        PROFILE_STOP( "Copy-Wait", 1 );
        PROFILE_START( "Copy-State", 1 );
        // memcpy(Averages.Phase.data(),phase->data(),N*sizeof(double));
        if ( d_regular )
            d_ScaLBL_Comm->RegularLayout( d_Map, Phi, Averages.Phase );
        else
            ScaLBL_CopyToHost( Averages.Phase.data(), Phi, N * sizeof( double ) );
        // copy other variables
        d_ScaLBL_Comm->RegularLayout( d_Map, Pressure, Averages.Press );
        d_ScaLBL_Comm->RegularLayout( d_Map, &Velocity[0], Averages.Vel_x );
        d_ScaLBL_Comm->RegularLayout( d_Map, &Velocity[d_Np], Averages.Vel_y );
        d_ScaLBL_Comm->RegularLayout( d_Map, &Velocity[2 * d_Np], Averages.Vel_z );
        PROFILE_STOP( "Copy-State", 1 );
    }
    std::shared_ptr<double> cfq, cDen;
    // if ( matches(type,AnalysisType::CreateRestart) ) {
    if ( timestep % d_restart_interval == 0 ) {
        // Copy restart data to the CPU
        cDen = make_shared_array<double>( 2 * d_Np );
        cfq  = make_shared_array<double>( 19 * d_Np );
        ScaLBL_CopyToHost( cfq.get(), fq, 19 * d_Np * sizeof( double ) );
        ScaLBL_CopyToHost( cDen.get(), Den, 2 * d_Np * sizeof( double ) );
    }
    PROFILE_STOP( "Copy data to host", 1 );

    // Spawn threads to do blob identification work
    if ( matches( type, AnalysisType::IdentifyBlobs ) ) {
        phase = std::make_shared<DoubleArray>( d_N[0], d_N[1], d_N[2] );
        if ( d_regular )
            d_ScaLBL_Comm->RegularLayout( d_Map, Phi, *phase );
        else
            ScaLBL_CopyToHost( phase->data(), Phi, N * sizeof( double ) );

        auto new_index = std::make_shared<std::pair<int, IntArray>>( 0, IntArray() );
        auto new_ids   = std::make_shared<std::pair<int, IntArray>>( 0, IntArray() );
        auto new_list  = std::make_shared<std::vector<BlobIDType>>();
        auto work1 = new BlobIdentificationWorkItem1( timestep, d_N[0], d_N[1], d_N[2], d_rank_info,
            phase, Averages.SDs, d_last_ids, new_index, new_ids, new_list, getComm() );
        auto work2 = new BlobIdentificationWorkItem2( timestep, d_N[0], d_N[1], d_N[2], d_rank_info,
            phase, Averages.SDs, d_last_ids, new_index, new_ids, new_list, getComm() );
        work1->add_dependency( d_wait_blobID );
        work2->add_dependency( d_tpool.add_work( work1 ) );
        d_wait_blobID = d_tpool.add_work( work2 );
        d_last_index  = new_index;
        d_last_ids    = new_ids;
        d_last_id_map = new_list;
    }

    // Spawn threads to do the analysis work
    // if (timestep%d_restart_interval==0){
    // if ( matches(type,AnalysisType::ComputeAverages) ) {
    if ( timestep % d_analysis_interval == 0 ) {
        auto work =
            new AnalysisWorkItem( type, timestep, Averages, d_last_index, d_last_id_map, d_beta );
        work->add_dependency( d_wait_blobID );
        work->add_dependency( d_wait_analysis );
        work->add_dependency( d_wait_vis ); // Make sure we are done using analysis before modifying
        d_wait_analysis = d_tpool.add_work( work );
    }

    // Spawn a thread to write the restart file
    //    if ( matches(type,AnalysisType::CreateRestart) ) {
    if ( timestep % d_restart_interval == 0 ) {

        if ( d_rank == 0 ) {
            input_db->putScalar<bool>( "Restart", true );
            std::ofstream OutStream( "Restart.db" );
            input_db->print( OutStream, "" );
            OutStream.close();
        }
        // Write the restart file (using a seperate thread)
        auto work = new WriteRestartWorkItem( d_restartFile.c_str(), cDen, cfq, d_Np );
        work->add_dependency( d_wait_restart );
        d_wait_restart = d_tpool.add_work( work );
    }

    // Save the results for visualization
    //    if ( matches(type,AnalysisType::CreateRestart) ) {
    if ( timestep % d_restart_interval == 0 ) {
        // Write the vis files
        auto work =
            new WriteVisWorkItem( timestep, d_meshData, Averages, d_n, d_rank_info, getComm() );
        work->add_dependency( d_wait_blobID );
        work->add_dependency( d_wait_analysis );
        work->add_dependency( d_wait_vis );
        d_wait_vis = d_tpool.add_work( work );
    }
    PROFILE_STOP( "run" );
}


/******************************************************************
 *  Run the analysis                                               *
 ******************************************************************/
void runAnalysis::basic( int timestep, std::shared_ptr<Database> input_db, SubPhase &Averages,
    const double *Phi, double *Pressure, double *Velocity, double *fq, double *Den )
{
    int Nx = d_N[0];
    int Ny = d_N[1];
    int Nz = d_N[2];
    int N  = Nx * Ny * Nz;
    NULL_USE( N );
    // Check which analysis steps we need to perform
    auto color_db = input_db->getDatabase( "Color" );
    auto vis_db   = input_db->getDatabase( "Visualization" );

    // int timestep = color_db->getWithDefault<int>( "timestep", 0 );
    auto type = computeAnalysisType( timestep );
    if ( type == AnalysisType::AnalyzeNone )
        return;

    // Check how may queued items we have
    if ( d_tpool.N_queued() > 20 ) {
        std::cerr << "Analysis queue is getting behind, waiting ...\n";
        finish();
    }

    PROFILE_START( "basic" );

    // Copy the appropriate variables to the host (so we can spawn new threads)
    ScaLBL_DeviceBarrier();
    PROFILE_START( "Copy data to host", 1 );

    // if ( matches(type,AnalysisType::CopySimState) ) {
    if ( timestep % d_analysis_interval == 0 ) {
        finish(); // can't copy if threads are still working on data
        // Copy the members of Averages to the cpu (phase was copied above)
        PROFILE_START( "Copy-Pressure", 1 );
        ScaLBL_D3Q19_Pressure( fq, Pressure, d_Np );
        // ScaLBL_D3Q19_Momentum(fq,Velocity,d_Np);
        ScaLBL_DeviceBarrier();
        PROFILE_STOP( "Copy-Pressure", 1 );
        PROFILE_START( "Copy-Wait", 1 );
        PROFILE_STOP( "Copy-Wait", 1 );
        PROFILE_START( "Copy-State", 1 );
        /*if (d_regular)
            d_ScaLBL_Comm->RegularLayout(d_Map,Phi,Averages.Phi);
        else */
        ScaLBL_CopyToHost( Averages.Phi.data(), Phi, N * sizeof( double ) );
        // copy other variables
        d_ScaLBL_Comm->RegularLayout( d_Map, Pressure, Averages.Pressure );
        d_ScaLBL_Comm->RegularLayout( d_Map, &Den[0], Averages.Rho_n );
        d_ScaLBL_Comm->RegularLayout( d_Map, &Den[d_Np], Averages.Rho_w );
        d_ScaLBL_Comm->RegularLayout( d_Map, &Velocity[0], Averages.Vel_x );
        d_ScaLBL_Comm->RegularLayout( d_Map, &Velocity[d_Np], Averages.Vel_y );
        d_ScaLBL_Comm->RegularLayout( d_Map, &Velocity[2 * d_Np], Averages.Vel_z );
        PROFILE_STOP( "Copy-State", 1 );
    }
    PROFILE_STOP( "Copy data to host" );

    // Spawn threads to do the analysis work
    // if (timestep%d_restart_interval==0){
    // if ( matches(type,AnalysisType::ComputeAverages) ) {
    if ( timestep % d_analysis_interval == 0 ) {
        auto work = new BasicWorkItem( type, timestep, Averages );
        work->add_dependency(
            d_wait_subphase ); // Make sure we are done using analysis before modifying
        work->add_dependency( d_wait_analysis );
        work->add_dependency( d_wait_vis );
        d_wait_analysis = d_tpool.add_work( work );
    }

    if ( timestep % d_subphase_analysis_interval == 0 ) {
        auto work = new SubphaseWorkItem( type, timestep, Averages );
        work->add_dependency(
            d_wait_subphase ); // Make sure we are done using analysis before modifying
        work->add_dependency( d_wait_analysis );
        work->add_dependency( d_wait_vis );
        d_wait_subphase = d_tpool.add_work( work );
    }

    if ( timestep % d_restart_interval == 0 ) {
        std::shared_ptr<double> cfq, cDen;
        // Copy restart data to the CPU
        cDen = make_shared_array<double>( 2 * d_Np );
        cfq  = make_shared_array<double>( 19 * d_Np );
        ScaLBL_CopyToHost( cfq.get(), fq, 19 * d_Np * sizeof( double ) );
        ScaLBL_CopyToHost( cDen.get(), Den, 2 * d_Np * sizeof( double ) );

        if ( d_rank == 0 ) {
            color_db->putScalar<int>( "timestep", timestep );
            color_db->putScalar<bool>( "Restart", true );
            input_db->putDatabase( "Color", color_db );
            std::ofstream OutStream( "Restart.db" );
            input_db->print( OutStream, "" );
            OutStream.close();
        }
        // Write the restart file (using a seperate thread)
        auto work1 = new WriteRestartWorkItem( d_restartFile.c_str(), cDen, cfq, d_Np );
        work1->add_dependency( d_wait_restart );
        d_wait_restart = d_tpool.add_work( work1 );
    }

    if ( timestep % d_visualization_interval == 0 ) {
        // Write the vis files
        auto work =
            new IOWorkItem( timestep, input_db, d_meshData, Averages, d_n, d_rank_info, getComm() );
        work->add_dependency( d_wait_analysis );
        work->add_dependency( d_wait_subphase );
        work->add_dependency( d_wait_vis );
        d_wait_vis = d_tpool.add_work( work );
    }

    PROFILE_STOP( "basic" );
}

void runAnalysis::WriteVisData( int timestep, std::shared_ptr<Database> input_db,
    SubPhase &Averages, const double *Phi, double *Pressure, double *Velocity, double *fq,
    double *Den )
{
    auto color_db = input_db->getDatabase( "Color" );
    auto vis_db   = input_db->getDatabase( "Visualization" );
    // int timestep = color_db->getWithDefault<int>( "timestep", 0 );

    // Check which analysis steps we need to perform
    auto type = computeAnalysisType( timestep );
    if ( type == AnalysisType::AnalyzeNone )
        return;

    // Check how may queued items we have
    if ( d_tpool.N_queued() > 20 ) {
        std::cerr << "Analysis queue is getting behind, waiting ...\n";
        finish();
    }

    // Copy the appropriate variables to the host (so we can spawn new threads)
    ScaLBL_DeviceBarrier();

    PROFILE_START( "write vis", 1 );

    // if (Averages.WriteVis == true){
    auto work2 =
        new IOWorkItem( timestep, input_db, d_meshData, Averages, d_n, d_rank_info, getComm() );
    work2->add_dependency( d_wait_vis );
    d_wait_vis = d_tpool.add_work( work2 );

    // Averages.WriteVis = false;

    PROFILE_STOP( "write vis" );
}