// 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_Helpers.h"
#include "common/ScaLBL.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;
}


template<class TYPE>
void DeleteArray( 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 char* filename_, const DoubleArray& phase_, const DoubleArray& dist_, int N_ ):
        filename(filename_), phase(phase_), dist(dist_), N(N_) {}
    virtual void run() {
        PROFILE_START("Save Checkpoint",1);
        char *IDS;
        IDS = new char [N];
        char local_id=0;
        for (int idx=0; idx<N; idx++){
        	if (dist(idx) < 0.f ) local_id = 0; 
        	else if (phase(idx) > 0.f) local_id = 1;
        	else local_id=2;
        	IDS[idx] = local_id;
        }
		FILE *RESTART = fopen(filename,"wb");
		fwrite(IDS,1,N,RESTART);
		//    fwrite(Distance.get(),8,Distance.length(),ID);
		fclose(RESTART);
		PROFILE_STOP("Save Checkpoint",1);
	
    };
private:
    WriteRestartWorkItem();
    const char* filename;
    // std::shared_ptr<double> cPhi, cDist;
    const DoubleArray& phase;
    const DoubleArray& dist;
    const int N;
};


// Helper class to compute the blob ids
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_, fillHalo<double>& fillData_, runAnalysis::commWrapper&& comm_ ):
        timestep(timestep_), visData(visData_), Averages(Avgerages_), fillData(fillData_), comm(std::move(comm_))
        {
        }
    ~WriteVisWorkItem() { }
    virtual void run() {
        PROFILE_START("Save Vis",1);
        ASSERT(visData[0].vars[0]->name=="phase");
        ASSERT(visData[0].vars[1]->name=="Pressure");
        ASSERT(visData[0].vars[2]->name=="SignDist");
        ASSERT(visData[0].vars[3]->name=="BlobID");
        Array<double>& PhaseData = visData[0].vars[0]->data;
        Array<double>& PressData = visData[0].vars[1]->data;
        Array<double>& SignData  = visData[0].vars[2]->data;
        Array<double>& BlobData  = visData[0].vars[3]->data;
        fillData.copy(Averages.SDn,PhaseData);
        fillData.copy(Averages.Press,PressData);
        fillData.copy(Averages.SDs,SignData);
        fillData.copy(Averages.Label_NWP,BlobData);
        IO::writeData( timestep, visData, comm.comm );
        PROFILE_STOP("Save Vis",1);
    };
private:
    WriteVisWorkItem();
    int timestep;
    std::vector<IO::MeshDataStruct>& visData;
    TwoPhase& Averages;
    fillHalo<double>& fillData;
    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;
};


/******************************************************************
 *  MPI comm wrapper for use with analysis                         *
 ******************************************************************/
runAnalysis::commWrapper::commWrapper( int tag_, MPI_Comm 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;
    MPI_Barrier( comm );
    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");
    }
    MPI_Bcast( &tag, 1, MPI_INT, 0, d_comm );
    d_comm_used[tag] = true;
    if ( d_comms[tag] == MPI_COMM_NULL )
        MPI_Comm_dup( MPI_COMM_WORLD, &d_comms[tag] );
    return commWrapper(tag,d_comms[tag],this);
}


/******************************************************************
 *  Constructor/Destructors                                        *
 ******************************************************************/
runAnalysis::runAnalysis( std::shared_ptr<Database> db,
    const RankInfoStruct& rank_info, std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm, std::shared_ptr <Domain> Dm,
    int Np, bool pBC, double beta, IntArray Map ):
    d_Np( Np ),
    d_beta( beta ),
    d_rank_info( rank_info ),
    d_Map( Map ),
    d_ScaLBL_Comm( ScaLBL_Comm),
    d_fillData(Dm->Comm,Dm->rank_info,{Dm->Nx-2,Dm->Ny-2,Dm->Nz-2},{1,1,1},0,1)
{
    NULL_USE( pBC );
    INSIST( db, "Input database is empty" );
	char rankString[20];
	sprintf(rankString,"%05d",Dm->rank());
    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_blobid_interval = db->getScalar<int>( "blobid_interval" );
    d_visualization_interval = db->getScalar<int>( "visualization_interval" );
    auto restart_file = db->getScalar<std::string>( "restart_file" );
    d_restartFile = restart_file + "." + rankString;
    d_rank = MPI_WORLD_RANK();
	writeIDMap(ID_map_struct(),0,id_map_filename);
	// Create the MeshDataStruct
	d_meshData.resize(1);
	d_meshData[0].meshName = "domain";
	d_meshData[0].mesh = std::make_shared<IO::DomainMesh>( Dm->rank_info,Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->Lx,Dm->Ly,Dm->Lz );
	auto PhaseVar = std::make_shared<IO::Variable>();
	auto PressVar = std::make_shared<IO::Variable>();
	auto SignDistVar = std::make_shared<IO::Variable>();
	auto BlobIDVar = std::make_shared<IO::Variable>();
	PhaseVar->name = "phase";
	PhaseVar->type = IO::VariableType::VolumeVariable;
	PhaseVar->dim = 1;
	PhaseVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
	d_meshData[0].vars.push_back(PhaseVar);
	PressVar->name = "Pressure";
	PressVar->type = IO::VariableType::VolumeVariable;
	PressVar->dim = 1;
	PressVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
	d_meshData[0].vars.push_back(PressVar);
	SignDistVar->name = "SignDist";
	SignDistVar->type = IO::VariableType::VolumeVariable;
	SignDistVar->dim = 1;
	SignDistVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
	d_meshData[0].vars.push_back(SignDistVar);
	BlobIDVar->name = "BlobID";
	BlobIDVar->type = IO::VariableType::VolumeVariable;
	BlobIDVar->dim = 1;
	BlobIDVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
	d_meshData[0].vars.push_back(BlobIDVar);
    // Initialize the comms
    MPI_Comm_dup(MPI_COMM_WORLD,&d_comm);
    for (int i=0; i<1024; i++) {
        d_comms[i] = MPI_COMM_NULL;
        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();
    // Clear internal data
    MPI_Comm_free( &d_comm );
    for (int i=0; i<1024; i++) {
        if ( d_comms[i] != MPI_COMM_NULL )
            MPI_Comm_free(&d_comms[i]);
    }
}
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_restart.reset();
    // Syncronize
    MPI_Barrier( d_comm );
    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
    int thread_support;
    MPI_Query_thread( &thread_support );
	if ( thread_support < MPI_THREAD_MULTIPLE ) {
		std::cerr << "Warning: Failed to start MPI with necessary thread support, thread support will be disabled" << std::endl;
        return;
    }
    // Create the threads
    const auto cores = d_tpool.getProcessAffinity();
    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, TwoPhase& Averages, const double *Phi,
		       double *Pressure, double *Velocity, double *fq, double *Den)
{
    int N = d_N[0]*d_N[1]*d_N[2];

    // 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::shared_ptr<DoubleArray>(new DoubleArray(d_N[0],d_N[1],d_N[2]));
    	//ScaLBL_CopyToHost(phase->data(),Phi,N*sizeof(double));
    	//   try 2 d_ScaLBL_Comm.RegularLayout(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;
    	double value;
    	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) ) {
        memcpy(Averages.Phase_tplus.data(),phase->data(),N*sizeof(double));
        //Averages.ColorToSignedDistance(d_beta,Averages.Phase,Averages.Phase_tplus);
    }
    if ( matches(type,AnalysisType::ComputeAverages) ) {
        memcpy(Averages.Phase_tminus.data(),phase->data(),N*sizeof(double));
        //Averages.ColorToSignedDistance(d_beta,Averages.Phase,Averages.Phase_tminus);
    }
    if ( matches(type,AnalysisType::CopySimState) ) {
        // 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));
        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> cDen, cfq;
    if ( matches(type,AnalysisType::CreateRestart) ) {
        // Copy restart data to the CPU
        //cDen = std::shared_ptr<double>(new double[2*d_Np],DeleteArray<double>);
        //cfq = std::shared_ptr<double>(new double[19*d_Np],DeleteArray<double>);
        //ScaLBL_CopyToHost(cfq.get(),fq,19*d_Np*sizeof(double));
        //ScaLBL_CopyToHost(cDen.get(),Den,2*d_Np*sizeof(double));
        //cPhi = std::shared_ptr<double>(new double[N],DeleteArray<double>);
        //cDist = std::shared_ptr<double>(new double[N],DeleteArray<double>);
        //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) ) {
        BlobIDstruct new_index(new std::pair<int,IntArray>(0,IntArray()));
        BlobIDstruct new_ids(new std::pair<int,IntArray>(0,IntArray()));
        BlobIDList new_list(new 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 (pBC) {
            err = fabs(sat_w - sat_w_previous);
            sat_w_previous = sat_w;
            if (rank==0){
               printf("Timestep %i: change in saturation since last checkpoint is %f \n",timestep,err);
           }
        } */
        // Retain the timestep associated with the restart files
        if (d_rank==0) {
            FILE *Rst = fopen("Restart.txt","w");
            fprintf(Rst,"%i\n",timestep+4);
            fclose(Rst);
        }
        // Write the restart file (using a seperate thread)
        auto work = new WriteRestartWorkItem(d_restartFile.c_str(),*phase,Averages.SDs,N);
        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_fillData, 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");
}