AMReX_WriteBinaryParticleData.H

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#ifndef AMREX_WRITE_BINARY_PARTICLE_DATA_H
#define AMREX_WRITE_BINARY_PARTICLE_DATA_H
#include <AMReX_Config.H>
 
#include <AMReX_TypeTraits.H>
#include <AMReX_ParticleUtil.H>
#include <AMReX_GpuDevice.H>
 
struct KeepValidFilter
{
    template <typename SrcData>
    AMREX_GPU_HOST_DEVICE
    int operator() (const SrcData& src, int i) const noexcept
    {
        return (src.id(i) > 0);
    }
};
 
namespace particle_detail {
 
template <typename ParticleReal>
std::size_t PSizeInFile (const Vector<int>& wrc, const Vector<int>& wic)
{
    std::size_t rsize = sizeof(ParticleReal)*std::accumulate(wrc.begin(), wrc.end(), 0);
    std::size_t isize = sizeof(int)*std::accumulate(wic.begin(), wic.end(), 0);
    return rsize + isize + AMREX_SPACEDIM*sizeof(ParticleReal) + 2*sizeof(int);
}
 
template <template <class, class> class Container,
          class Allocator,
          class PTile,
          class F>
std::enable_if_t<RunOnGpu<typename Container<int, Allocator>::allocator_type>::value>
fillFlags (Container<int, Allocator>& pflags, const PTile& ptile, F const& f)
{
    const auto& ptd = ptile.getConstParticleTileData();
    const auto np = ptile.numParticles();
    pflags.resize(np, 0);
    auto flag_ptr = pflags.data();
    amrex::ParallelForRNG(np,
        [=] AMREX_GPU_DEVICE (int k, amrex::RandomEngine const& engine) noexcept
        {
            const auto p = ptd.getSuperParticle(k);
            amrex::ignore_unused(flag_ptr, f, engine);
            if constexpr (IsCallable<F,decltype(p),RandomEngine>::value) {
                flag_ptr[k] = f(p,engine);
            } else {
                flag_ptr[k] = f(p);
            }
        });
}
 
template <template <class, class> class Container,
          class Allocator,
          class PTile,
          class F>
std::enable_if_t<!RunOnGpu<typename Container<int, Allocator>::allocator_type>::value>
fillFlags (Container<int, Allocator>& pflags, const PTile& ptile, F const& f)
{
    const auto& ptd = ptile.getConstParticleTileData();
    const auto np = ptile.numParticles();
    pflags.resize(np, 0);
    auto flag_ptr = pflags.data();
    for (int k = 0; k < np; ++k) {
        const auto p = ptd.getSuperParticle(k);
        if constexpr (IsCallable<F,decltype(p),RandomEngine>::value) {
            flag_ptr[k] = f(p,RandomEngine{});
        } else {
            flag_ptr[k] = f(p);
        }
    }
}
 
template <template <class, class> class Container, class Allocator, class PC>
std::enable_if_t<RunOnGpu<typename Container<int, Allocator>::allocator_type>::value, amrex::Long>
countFlags (const Vector<std::map<std::pair<int,int>,Container<int,Allocator>>>& particle_io_flags, const PC& pc)
{
    ReduceOps<ReduceOpSum> reduce_op;
    ReduceData<Long> reduce_data(reduce_op);
    using ReduceTuple = typename decltype(reduce_data)::Type;
 
    for (int lev = 0; lev < pc.GetParticles().size();  lev++)
    {
        const auto& pmap = pc.GetParticles(lev);
        for (const auto& kv : pmap)
        {
            const auto& pflags = particle_io_flags[lev].at(kv.first);
            const auto flag_ptr = pflags.data();
            reduce_op.eval(pflags.size(), reduce_data,
                [=] AMREX_GPU_DEVICE (const int i) -> ReduceTuple
                {
                    return flag_ptr[i] ? 1 : 0;
                });
        }
    }
    ReduceTuple hv = reduce_data.value(reduce_op);
    return amrex::get<0>(hv);
}
 
template <template <class, class> class Container, class Allocator>
std::enable_if_t<RunOnGpu<typename Container<int, Allocator>::allocator_type>::value, int>
countFlags (const Container<int,Allocator>& pflags)
{
    ReduceOps<ReduceOpSum> reduce_op;
    ReduceData<Long> reduce_data(reduce_op);
    using ReduceTuple = typename decltype(reduce_data)::Type;
 
    const auto flag_ptr = pflags.data();
    reduce_op.eval(pflags.size(), reduce_data,
        [=] AMREX_GPU_DEVICE (const int i) -> ReduceTuple
        {
            return flag_ptr[i] ? 1 : 0;
        });
    ReduceTuple hv = reduce_data.value(reduce_op);
    return amrex::get<0>(hv);
}
 
template <template <class, class> class Container, class Allocator, class PC>
std::enable_if_t<!RunOnGpu<typename Container<int, Allocator>::allocator_type>::value, amrex::Long>
countFlags (const Vector<std::map<std::pair<int,int>,Container<int,Allocator>>>& particle_io_flags, const PC& pc)
{
    amrex::Long nparticles = 0;
    for (int lev = 0; lev < pc.GetParticles().size();  lev++)
    {
        const auto& pmap = pc.GetParticles(lev);
        for (const auto& kv : pmap)
        {
            const auto& pflags = particle_io_flags[lev].at(kv.first);
            for (int k = 0; k < kv.second.numParticles(); ++k)
            {
                if (pflags[k]) { nparticles++; }
            }
        }
    }
    return nparticles;
}
 
template <template <class, class> class Container, class Allocator>
std::enable_if_t<!RunOnGpu<typename Container<int, Allocator>::allocator_type>::value, int>
countFlags (const Container<int,Allocator>& pflags)
{
    int nparticles = 0;
    for (std::size_t k = 0; k < pflags.size(); ++k)
    {
        if (pflags[k]) { nparticles++; }
    }
    return nparticles;
}
 
template <typename P, typename I>
AMREX_GPU_HOST_DEVICE
void packParticleIDs (I* idata, const P& p, bool is_checkpoint) noexcept
{
    if (is_checkpoint) {
        std::int32_t  xi, yi;
        std::uint32_t xu, yu;
        xu = (std::uint32_t)((p.m_idcpu & 0xFFFFFFFF00000000LL) >> 32);
        yu = (std::uint32_t)( p.m_idcpu & 0xFFFFFFFFLL);
        amrex::Gpu::memcpy(&xi, &xu, sizeof(xu));
        amrex::Gpu::memcpy(&yi, &yu, sizeof(yu));
        idata[0] = xi;
        idata[1] = yi;
    } else {
        idata[0] = p.id();
        idata[1] = p.cpu();
    }
}
 
template <class PC>
std::enable_if_t<RunOnGpu<typename PC::template AllocatorType<int>>::value>
packIOData (Vector<int>& idata, Vector<ParticleReal>& rdata, const PC& pc, int lev, int grid,
            const Vector<int>& write_real_comp, const Vector<int>& write_int_comp,
            const Vector<std::map<std::pair<int, int>, typename PC::IntVector>>& particle_io_flags,
            const Vector<int>& tiles, int np, bool is_checkpoint)
{
    int num_output_int = 0;
    for (int i = 0; i < pc.NumIntComps() + PC::NStructInt; ++i) {
        if (write_int_comp[i]) { ++num_output_int; }
    }
 
    const Long iChunkSize = 2 + num_output_int;
    idata.resize(np*iChunkSize);
 
    int num_output_real = 0;
    for (int i : write_real_comp) {
        if (i) { ++num_output_real; }
    }
 
    const Long rChunkSize = AMREX_SPACEDIM + num_output_real;
    rdata.resize(np*rChunkSize);
 
    typename PC::IntVector write_int_comp_d(write_int_comp.size());
    typename PC::IntVector write_real_comp_d(write_real_comp.size());
    Gpu::copyAsync(Gpu::hostToDevice, write_int_comp.begin(), write_int_comp.end(),
                   write_int_comp_d.begin());
    Gpu::copyAsync(Gpu::hostToDevice, write_real_comp.begin(), write_real_comp.end(),
                   write_real_comp_d.begin());
 
    const auto write_int_comp_d_ptr = write_int_comp_d.data();
    const auto write_real_comp_d_ptr = write_real_comp_d.data();
 
    std::size_t poffset = 0;
    for (int tile : tiles) {
        const auto& ptile = pc.ParticlesAt(lev, grid, tile);
        const auto& pflags = particle_io_flags[lev].at(std::make_pair(grid, tile));
        int np_tile = ptile.numParticles();
        typename PC::IntVector offsets(np_tile);
        int num_copies = Scan::ExclusiveSum(np_tile, pflags.begin(), offsets.begin(), Scan::retSum);
 
        typename PC::IntVector  idata_d(num_copies*iChunkSize);
        typename PC::RealVector rdata_d(num_copies*rChunkSize);
 
        const auto flag_ptr = pflags.data();
 
        auto idata_d_ptr = idata_d.data();
        auto rdata_d_ptr = rdata_d.data();
 
        const auto& ptd = ptile.getConstParticleTileData();
        amrex::ParallelFor(num_copies,
        [=] AMREX_GPU_DEVICE (int pindex) noexcept
        {
            // might be worth using shared memory here
            const auto p = ptd.getSuperParticle(pindex);
 
            if (flag_ptr[pindex]) {
                std::size_t iout_index = pindex*iChunkSize;
                packParticleIDs(&idata_d_ptr[iout_index], p, is_checkpoint);
                iout_index += 2;
 
                std::size_t rout_index = pindex*rChunkSize;
                for (int j = 0; j < AMREX_SPACEDIM; j++) {
                  rdata_d_ptr[rout_index] = p.pos(j);
                  rout_index++;
                }
 
                for (int j = 0; j < PC::SuperParticleType::NInt; j++) {
                    if (write_int_comp_d_ptr[j]) {
                        idata_d_ptr[iout_index] = p.idata(j);
                        iout_index++;
                    }
                }
 
                for (int j = 0; j < ptd.m_num_runtime_int; j++) {
                    if (write_int_comp_d_ptr[PC::SuperParticleType::NInt + j]) {
                        idata_d_ptr[iout_index] = ptd.m_runtime_idata[j][pindex];
                        iout_index++;
                    }
                }
 
                // extra SoA Real components
                const int real_start_offset = PC::ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0; // pure SoA: skip positions
                for (int j = real_start_offset; j < PC::SuperParticleType::NReal; j++) {
                    const int write_comp_index = j-real_start_offset;
                    if (write_real_comp_d_ptr[write_comp_index]) {
                        rdata_d_ptr[rout_index] = p.rdata(j);
                        rout_index++;
                    }
                }
 
                for (int j = 0; j < ptd.m_num_runtime_real; j++) {
                    if (write_real_comp_d_ptr[PC::SuperParticleType::NReal+j-real_start_offset]) {
                        rdata_d_ptr[rout_index] = ptd.m_runtime_rdata[j][pindex];
                        rout_index++;
                    }
                }
            }
        });
 
        Gpu::copyAsync(Gpu::deviceToHost, idata_d.begin(), idata_d.end(),
                       idata.begin() + typename PC::IntVector::difference_type(poffset));
        Gpu::copyAsync(Gpu::deviceToHost, rdata_d.begin(), rdata_d.end(),
                       rdata.begin() + typename PC::RealVector::difference_type(poffset));
        Gpu::Device::streamSynchronize();
 
        poffset += num_copies;
    }
}
 
template <class PC>
std::enable_if_t<!RunOnGpu<typename PC::template AllocatorType<int>>::value>
packIOData (Vector<int>& idata, Vector<ParticleReal>& rdata, const PC& pc, int lev, int grid,
            const Vector<int>& write_real_comp, const Vector<int>& write_int_comp,
            const Vector<std::map<std::pair<int, int>, typename PC::IntVector>>& particle_io_flags,
            const Vector<int>& tiles, int np, bool is_checkpoint)
{
    int num_output_int = 0;
    for (int i = 0; i < pc.NumIntComps() + PC::NStructInt; ++i) {
        if (write_int_comp[i]) { ++num_output_int; }
    }
 
    const Long iChunkSize = 2 + num_output_int;
    idata.resize(np*iChunkSize);
 
    int num_output_real = 0;
    for (int i : write_real_comp) {
        if (i) { ++num_output_real; }
    }
 
    const Long rChunkSize = AMREX_SPACEDIM + num_output_real;
    rdata.resize(np*rChunkSize);
 
    int* iptr = idata.dataPtr();
    ParticleReal* rptr = rdata.dataPtr();
    for (int tile : tiles) {
        const auto& ptile = pc.ParticlesAt(lev, grid, tile);
        const auto& pflags = particle_io_flags[lev].at(std::make_pair(grid, tile));
        for (int pindex = 0; pindex < ptile.numParticles(); ++pindex) {
            if (pflags[pindex]) {
                const auto& soa  = ptile.GetStructOfArrays();
 
                // note: for pure SoA particle layouts, we do write the id, cpu and positions as a struct
                //       for backwards compatibility with readers
                if constexpr(!PC::ParticleType::is_soa_particle)
                {
                    const auto& aos = ptile.GetArrayOfStructs();
                    const auto& p = aos[pindex];
 
                    // Int: id, cpu
                    packParticleIDs(iptr, p, is_checkpoint);
                    iptr += 2;
 
                    // Real: positions
                    for (int j = 0; j < AMREX_SPACEDIM; j++) { rptr[j] = p.pos(j); }
                    rptr += AMREX_SPACEDIM;
 
                    // extra AoS Int components
                    for (int j = 0; j < PC::NStructInt; j++) {
                        if (write_int_comp[j]) {
                            *iptr = p.idata(j);
                            ++iptr;
                        }
                    }
                    // extra AoS Real components
                    for (int j = 0; j < PC::NStructReal; j++) {
                        if (write_real_comp[j]) {
                            *rptr = p.rdata(j);
                            ++rptr;
                        }
                    }
                }
                else {
                    uint64_t idcpu = soa.GetIdCPUData()[pindex];
                    if (is_checkpoint) {
                        std::int32_t  xi, yi;
                        std::uint32_t xu, yu;
                        xu = (std::uint32_t)((idcpu & 0xFFFFFFFF00000000LL) >> 32);
                        yu = (std::uint32_t)( idcpu & 0xFFFFFFFFLL);
                        std::memcpy(&xi, &xu, sizeof(xu));
                        std::memcpy(&yi, &yu, sizeof(yu));
                        *iptr = xi;
                        iptr += 1;
                        *iptr = yi;
                        iptr += 1;
                    } else {
                        // Int: id, cpu
                        *iptr = (int) ParticleIDWrapper(idcpu);
                        iptr += 1;
                        *iptr = (int) ParticleCPUWrapper(idcpu);
                        iptr += 1;
                    }
 
                    // Real: position
                    for (int j = 0; j < AMREX_SPACEDIM; j++) { rptr[j] = soa.GetRealData(j)[pindex]; }
                    rptr += AMREX_SPACEDIM;
                }
 
                // SoA int data
                const int int_start_offset = 0;
                for (int j = int_start_offset; j < pc.NumIntComps(); j++) {
                    if (write_int_comp[PC::NStructInt+j]) {
                        *iptr = soa.GetIntData(j)[pindex];
                        ++iptr;
                    }
                }
 
                // extra SoA Real components
                const int real_start_offset = PC::ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0; // pure SoA: skip positions
                for (int j = real_start_offset; j < pc.NumRealComps(); j++) {
                    const int write_comp_index = PC::NStructReal+j-real_start_offset;
                    if (write_real_comp[write_comp_index]) {
                        *rptr = (ParticleReal) soa.GetRealData(j)[pindex];
                        ++rptr;
                    }
                }
            }
        }
    }
}
}
 
template <class PC, class F, std::enable_if_t<IsParticleContainer<PC>::value, int> foo = 0>
void WriteBinaryParticleDataSync (PC const& pc,
                                  const std::string& dir, const std::string& name,
                                  const Vector<int>& write_real_comp,
                                  const Vector<int>& write_int_comp,
                                  const Vector<std::string>& real_comp_names,
                                  const Vector<std::string>& int_comp_names,
                                  F const& f, bool is_checkpoint)
{
    BL_PROFILE("WriteBinaryParticleData()");
    AMREX_ASSERT(pc.OK());
 
    AMREX_ASSERT(sizeof(typename PC::ParticleType::RealType) == 4 ||
                 sizeof(typename PC::ParticleType::RealType) == 8);
 
    constexpr int NStructReal = PC::NStructReal;
    constexpr int NStructInt  = PC::NStructInt;
 
    const int NProcs = ParallelDescriptor::NProcs();
    const int IOProcNumber = ParallelDescriptor::IOProcessorNumber();
 
    if constexpr(PC::ParticleType::is_soa_particle) {
        AMREX_ALWAYS_ASSERT(real_comp_names.size() == pc.NumRealComps() + NStructReal - AMREX_SPACEDIM); // pure SoA: skip positions
    } else {
        AMREX_ALWAYS_ASSERT(real_comp_names.size() == pc.NumRealComps() + NStructReal);
    }
    AMREX_ALWAYS_ASSERT( int_comp_names.size() == pc.NumIntComps() + NStructInt);
 
    std::string pdir = dir;
    if ( ! pdir.empty() && pdir[pdir.size()-1] != '/') { pdir += '/'; }
    pdir += name;
 
    if ( ! pc.GetLevelDirectoriesCreated()) {
        if (ParallelDescriptor::IOProcessor())
        {
            if ( ! amrex::UtilCreateDirectory(pdir, 0755))
            {
                amrex::CreateDirectoryFailed(pdir);
            }
        }
        ParallelDescriptor::Barrier();
    }
 
    std::ofstream HdrFile;
 
    Long nparticles = 0;
    Long maxnextid;
 
    // evaluate f for every particle to determine which ones to output
    Vector<std::map<std::pair<int, int>, typename PC::IntVector > >
        particle_io_flags(pc.GetParticles().size());
    for (int lev = 0; lev < pc.GetParticles().size();  lev++)
    {
        const auto& pmap = pc.GetParticles(lev);
        for (const auto& kv : pmap)
        {
            auto& flags = particle_io_flags[lev][kv.first];
            particle_detail::fillFlags(flags, kv.second, f);
        }
    }
 
    Gpu::Device::streamSynchronize();
 
    if(pc.GetUsePrePost())
    {
        nparticles = pc.GetNParticlesPrePost();
        maxnextid  = pc.GetMaxNextIDPrePost();
    }
    else
    {
        nparticles = particle_detail::countFlags(particle_io_flags, pc);
        maxnextid  = PC::ParticleType::NextID();
        ParallelDescriptor::ReduceLongSum(nparticles, IOProcNumber);
        PC::ParticleType::NextID(maxnextid);
        ParallelDescriptor::ReduceLongMax(maxnextid, IOProcNumber);
    }
 
    if (ParallelDescriptor::IOProcessor())
    {
        std::string HdrFileName = pdir;
 
        if ( ! HdrFileName.empty() && HdrFileName[HdrFileName.size()-1] != '/') {
            HdrFileName += '/';
        }
 
        HdrFileName += "Header";
        pc.HdrFileNamePrePost = HdrFileName;
 
        HdrFile.open(HdrFileName.c_str(), std::ios::out|std::ios::trunc);
 
        if ( ! HdrFile.good()) { amrex::FileOpenFailed(HdrFileName); }
 
        //
        // First thing written is our version string.
        // We append "_single" or "_double" to the version string indicating
        // whether we're using "float" or "double" floating point data.
        //
        std::string version_string = is_checkpoint ? PC::CheckpointVersion() : PC::PlotfileVersion();
        if (sizeof(typename PC::ParticleType::RealType) == 4)
        {
            HdrFile << version_string << "_single" << '\n';
        }
        else
        {
            HdrFile << version_string << "_double" << '\n';
        }
 
        int num_output_real = 0;
        for (int i : write_real_comp) {
            if (i) { ++num_output_real; }
        }
 
        int num_output_int = 0;
        for (int i = 0; i < pc.NumIntComps() + NStructInt; ++i) {
            if (write_int_comp[i]) { ++num_output_int; }
        }
 
        // AMREX_SPACEDIM and N for sanity checking.
        HdrFile << AMREX_SPACEDIM << '\n';
 
        // The number of extra real parameters
        HdrFile << num_output_real << '\n';
 
        // Real component names
        for (int i = 0; i < (int) real_comp_names.size(); ++i ) {
            if (write_real_comp[i]) { HdrFile << real_comp_names[i] << '\n'; }
        }
 
        // The number of extra int parameters
        HdrFile << num_output_int << '\n';
 
        // int component names
        for (int i = 0; i < NStructInt + pc.NumIntComps(); ++i ) {
            if (write_int_comp[i]) { HdrFile << int_comp_names[i] << '\n'; }
        }
 
        bool is_checkpoint_legacy = true; // legacy
        HdrFile << is_checkpoint_legacy << '\n';
 
        // The total number of particles.
        HdrFile << nparticles << '\n';
 
        // The value of nextid that we need to restore on restart.
        HdrFile << maxnextid << '\n';
 
        // Then the finest level of the AMR hierarchy.
        HdrFile << pc.finestLevel() << '\n';
 
        // Then the number of grids at each level.
        for (int lev = 0; lev <= pc.finestLevel(); lev++) {
            HdrFile << pc.ParticleBoxArray(lev).size() << '\n';
        }
    }
 
    // We want to write the data out in parallel.
    // We'll allow up to nOutFiles active writers at a time.
    int nOutFiles(256);
 
    ParmParse pp("particles");
    pp.queryAdd("particles_nfiles",nOutFiles);
    if(nOutFiles == -1) { nOutFiles = NProcs; }
    nOutFiles = std::max(1, std::min(nOutFiles,NProcs));
    pc.nOutFilesPrePost = nOutFiles;
 
    for (int lev = 0; lev <= pc.finestLevel(); lev++)
    {
        bool gotsome;
        if(pc.usePrePost)
        {
            gotsome = (pc.nParticlesAtLevelPrePost[lev] > 0);
        }
        else
        {
            gotsome = (pc.NumberOfParticlesAtLevel(lev) > 0);
        }
 
        // We store the particles at each level in their own subdirectory.
        std::string LevelDir = pdir;
 
        if (gotsome)
        {
            if ( ! LevelDir.empty() && LevelDir[LevelDir.size()-1] != '/') { LevelDir += '/'; }
 
            LevelDir = amrex::Concatenate(LevelDir.append("Level_"), lev, 1);
 
            if ( ! pc.GetLevelDirectoriesCreated())
            {
                if (ParallelDescriptor::IOProcessor()) {
                    if ( ! amrex::UtilCreateDirectory(LevelDir, 0755)) {
                        amrex::CreateDirectoryFailed(LevelDir);
                    }
                }
                ParallelDescriptor::Barrier();
            }
        }
 
        // Write out the header for each particle
        if (gotsome && ParallelDescriptor::IOProcessor()) {
            std::string HeaderFileName = LevelDir;
            HeaderFileName += "/Particle_H";
            std::ofstream ParticleHeader(HeaderFileName);
 
            pc.ParticleBoxArray(lev).writeOn(ParticleHeader);
            ParticleHeader << '\n';
 
            ParticleHeader.flush();
            ParticleHeader.close();
        }
 
        MFInfo info;
        info.SetAlloc(false);
        MultiFab state(pc.ParticleBoxArray(lev),
                       pc.ParticleDistributionMap(lev),
                       1,0,info);
 
        // We eventually want to write out the file name and the offset
        // into that file into which each grid of particles is written.
        Vector<int>  which(state.size(),0);
        Vector<int > count(state.size(),0);
        Vector<Long> where(state.size(),0);
 
        std::string filePrefix(LevelDir);
        filePrefix += '/';
        filePrefix += PC::DataPrefix();
        if(pc.usePrePost) {
            pc.filePrefixPrePost[lev] = filePrefix;
        }
        bool groupSets(false), setBuf(true);
 
        if (gotsome)
        {
            for(NFilesIter nfi(nOutFiles, filePrefix, groupSets, setBuf); nfi.ReadyToWrite(); ++nfi)
            {
                auto& myStream = (std::ofstream&) nfi.Stream();
                pc.WriteParticles(lev, myStream, nfi.FileNumber(), which, count, where,
                                  write_real_comp, write_int_comp, particle_io_flags, is_checkpoint);
            }
 
            if(pc.usePrePost) {
                pc.whichPrePost[lev] = which;
                pc.countPrePost[lev] = count;
                pc.wherePrePost[lev] = where;
            } else {
                ParallelDescriptor::ReduceIntSum (which.dataPtr(), static_cast<int>(which.size()), IOProcNumber);
                ParallelDescriptor::ReduceIntSum (count.dataPtr(), static_cast<int>(count.size()), IOProcNumber);
                ParallelDescriptor::ReduceLongSum(where.dataPtr(), static_cast<int>(where.size()), IOProcNumber);
            }
        }
 
        if (ParallelDescriptor::IOProcessor())
        {
            if(pc.GetUsePrePost()) {
                // ---- write to the header and unlink in CheckpointPost
            } else {
                for (int j = 0; j < state.size(); j++)
                {
                    HdrFile << which[j] << ' ' << count[j] << ' ' << where[j] << '\n';
                }
 
                if (gotsome && pc.doUnlink)
                {
                    // Unlink any zero-length data files.
                    Vector<Long> cnt(nOutFiles,0);
 
                    for (int i = 0, N=static_cast<int>(count.size()); i < N; i++) {
                        cnt[which[i]] += count[i];
                    }
 
                    for (int i = 0, N=static_cast<int>(cnt.size()); i < N; i++)
                    {
                        if (cnt[i] == 0)
                        {
                            std::string FullFileName = NFilesIter::FileName(i, filePrefix);
                            FileSystem::Remove(FullFileName);
                        }
                    }
                }
            }
        }
    }
 
    if (ParallelDescriptor::IOProcessor())
    {
        HdrFile.flush();
        HdrFile.close();
        if ( ! HdrFile.good())
        {
            amrex::Abort("amrex::WriteBinaryParticleDataSync(): problem writing HdrFile");
        }
    }
}
 
template <class PC, std::enable_if_t<IsParticleContainer<PC>::value, int> foo = 0>
void WriteBinaryParticleDataAsync (PC const& pc,
                                   const std::string& dir, const std::string& name,
                                   const Vector<int>& write_real_comp,
                                   const Vector<int>& write_int_comp,
                                   const Vector<std::string>& real_comp_names,
                                   const Vector<std::string>& int_comp_names, bool is_checkpoint)
{
    BL_PROFILE("WriteBinaryParticleDataAsync");
    AMREX_ASSERT(pc.OK());
 
    AMREX_ASSERT(sizeof(typename PC::ParticleType::RealType) == 4 ||
                 sizeof(typename PC::ParticleType::RealType) == 8);
 
    constexpr int NStructReal = PC::NStructReal;
    constexpr int NStructInt  = PC::NStructInt;
    constexpr int NArrayReal  = PC::NArrayReal;
    constexpr int NArrayInt   = PC::NArrayInt;
 
    const int MyProc = ParallelDescriptor::MyProc();
    const int NProcs = ParallelDescriptor::NProcs();
    const int IOProcNumber = NProcs - 1;
 
    if constexpr(PC::ParticleType::is_soa_particle) {
        AMREX_ALWAYS_ASSERT(real_comp_names.size() == pc.NumRealComps() + NStructReal - AMREX_SPACEDIM); // pure SoA: skip positions
    } else {
        AMREX_ALWAYS_ASSERT(real_comp_names.size() == pc.NumRealComps() + NStructReal);
    }
    AMREX_ALWAYS_ASSERT( int_comp_names.size() == pc.NumIntComps() + NStructInt);
 
    Vector<LayoutData<Long> > np_per_grid_local(pc.finestLevel()+1);
    for (int lev = 0; lev <= pc.finestLevel(); lev++)
    {
        np_per_grid_local[lev].define(pc.ParticleBoxArray(lev), pc.ParticleDistributionMap(lev));
        using ParIter = typename PC::ParConstIterType;
        for (ParIter pti(pc, lev); pti.isValid(); ++pti)
        {
            int gid = pti.index();
            const auto& ptile = pc.ParticlesAt(lev, pti);
            const auto& ptd = ptile.getConstParticleTileData();
            const int np = ptile.numParticles();
 
            ReduceOps<ReduceOpSum> reduce_op;
            ReduceData<int> reduce_data(reduce_op);
            using ReduceTuple = typename decltype(reduce_data)::Type;
 
            reduce_op.eval(np, reduce_data,
            [=] AMREX_GPU_DEVICE (int i) -> ReduceTuple
            {
                return (ptd.id(i) > 0) ? 1 : 0;
            });
 
            int np_valid = amrex::get<0>(reduce_data.value(reduce_op));
            np_per_grid_local[lev][gid] += np_valid;
        }
    }
 
    Vector<Vector<Long> > np_per_grid_global(pc.finestLevel()+1);
    Long total_np = 0;
    Vector<Long> np_per_level(pc.finestLevel()+1);
    for (int lev = 0; lev <= pc.finestLevel(); lev++)
    {
        np_per_grid_global[lev].resize(np_per_grid_local[lev].size());
        ParallelDescriptor::GatherLayoutDataToVector(np_per_grid_local[lev],
                                                     np_per_grid_global[lev],
                                                     IOProcNumber);
        np_per_level[lev] = std::accumulate(np_per_grid_global[lev].begin(),
                                            np_per_grid_global[lev].end(), 0L);
        total_np += np_per_level[lev];
    }
 
    std::string pdir = dir;
    if ( ! pdir.empty() && pdir[pdir.size()-1] != '/') { pdir += '/'; }
    pdir += name;
 
    if (MyProc == IOProcNumber)
    {
        if ( ! pc.GetLevelDirectoriesCreated())
        {
            if ( ! amrex::UtilCreateDirectory(pdir, 0755))
            {
                amrex::CreateDirectoryFailed(pdir);
            }
        }
 
        for (int lev = 0; lev <= pc.finestLevel(); lev++)
        {
            std::string LevelDir = pdir;
            bool gotsome = np_per_level[lev];
 
            if (gotsome)
            {
                if ( ! LevelDir.empty() && LevelDir[LevelDir.size()-1] != '/') { LevelDir += '/'; }
 
                LevelDir = amrex::Concatenate(LevelDir.append("Level_"), lev, 1);
 
                if ( ! pc.GetLevelDirectoriesCreated())
                {
                    if ( ! amrex::UtilCreateDirectory(LevelDir, 0755))
                    {
                        amrex::CreateDirectoryFailed(LevelDir);
                    }
                }
 
                std::string HeaderFileName = LevelDir;
                HeaderFileName += "/Particle_H";
                std::ofstream ParticleHeader(HeaderFileName);
 
                pc.ParticleBoxArray(lev).writeOn(ParticleHeader);
                ParticleHeader << '\n';
 
                ParticleHeader.flush();
                ParticleHeader.close();
            }
        }
    }
    ParallelDescriptor::Barrier();
 
    Long maxnextid = PC::ParticleType::NextID();
    ParallelDescriptor::ReduceLongMax(maxnextid, IOProcNumber);
 
    Vector<Long> np_on_rank(NProcs, 0L);
    std::size_t psize = particle_detail::PSizeInFile<ParticleReal>(write_real_comp, write_int_comp);
    Vector<int64_t> rank_start_offset(NProcs);
    if (MyProc == IOProcNumber)
    {
        for (int lev = 0; lev <= pc.finestLevel(); lev++)
        {
            for (int k = 0; k < pc.ParticleBoxArray(lev).size(); ++k)
            {
                int rank = pc.ParticleDistributionMap(lev)[k];
                np_on_rank[rank] += np_per_grid_global[lev][k];
            }
        }
 
        for (int ip = 0; ip < NProcs; ++ip)
        {
            auto info = AsyncOut::GetWriteInfo(ip);
            rank_start_offset[ip] = (info.ispot == 0) ? 0 : static_cast<int64_t>(rank_start_offset[ip-1] + np_on_rank[ip-1]*psize);
        }
    }
 
    // make tmp particle tiles in pinned memory to write
    using PinnedPTile = ParticleTile<typename PC::ParticleType, NArrayReal, NArrayInt,
                                     PinnedArenaAllocator>;
    auto myptiles = std::make_shared<Vector<std::map<std::pair<int, int>,PinnedPTile> > >();
    myptiles->resize(pc.finestLevel()+1);
    for (int lev = 0; lev <= pc.finestLevel(); lev++)
    {
        for (MFIter mfi = pc.MakeMFIter(lev); mfi.isValid(); ++mfi)
        {
            auto& new_ptile = (*myptiles)[lev][std::make_pair(mfi.index(),
                                                              mfi.LocalTileIndex())];
 
            if (np_per_grid_local[lev][mfi.index()] > 0)
            {
                const auto& ptile = pc.ParticlesAt(lev, mfi);
 
                const auto np = np_per_grid_local[lev][mfi.index()];
 
                new_ptile.resize(np);
 
                const auto runtime_real_comps = ptile.NumRuntimeRealComps();
                const auto runtime_int_comps = ptile.NumRuntimeIntComps();
 
                new_ptile.define(runtime_real_comps, runtime_int_comps);
 
                for (auto comp(0); comp < runtime_real_comps; ++comp) {
                    new_ptile.push_back_real(NArrayReal+comp, np, 0.);
                }
 
                for (auto comp(0); comp < runtime_int_comps; ++comp) {
                    new_ptile.push_back_int(NArrayInt+comp, np, 0);
                }
 
                amrex::filterParticles(new_ptile, ptile, KeepValidFilter());
            }
        }
    }
 
    int finest_level = pc.finestLevel();
    Vector<BoxArray> bas;
    Vector<DistributionMapping> dms;
    for (int lev = 0; lev <= pc.finestLevel(); lev++)
    {
        bas.push_back(pc.ParticleBoxArray(lev));
        dms.push_back(pc.ParticleDistributionMap(lev));
    }
 
    int nrc = pc.NumRealComps();
    int nic = pc.NumIntComps();
    int rnames_size = (int) real_comp_names.size();
 
    auto RD = pc.ParticleRealDescriptor;
 
    AsyncOut::Submit([=] ()
#if defined(__GNUC__) && (__GNUC__ == 8) && (__GNUC_MINOR__ == 1)
                     mutable // workaround for bug in gcc 8.1
#endif
    {
        if (MyProc == IOProcNumber)
        {
            std::string HdrFileName = pdir;
            std::ofstream HdrFile;
 
            if ( ! HdrFileName.empty() && HdrFileName[HdrFileName.size()-1] != '/') {
                HdrFileName += '/';
            }
 
            HdrFileName += "Header";
 
            HdrFile.open(HdrFileName.c_str(), std::ios::out|std::ios::trunc);
 
            if ( ! HdrFile.good()) { amrex::FileOpenFailed(HdrFileName); }
 
            std::string version_string = is_checkpoint ? PC::CheckpointVersion() : PC::PlotfileVersion();
            if (sizeof(typename PC::ParticleType::RealType) == 4)
            {
                HdrFile << version_string << "_single" << '\n';
            }
            else
            {
                HdrFile << version_string << "_double" << '\n';
            }
 
            int num_output_real = 0;
            for (int i = 0; i < rnames_size; ++i) {
                if (write_real_comp[i]) { ++num_output_real; }
            }
 
            int num_output_int = 0;
            for (int i = 0; i < nic + NStructInt; ++i) {
                if (write_int_comp[i]) { ++num_output_int; }
            }
 
            // AMREX_SPACEDIM and N for sanity checking.
            HdrFile << AMREX_SPACEDIM << '\n';
 
            // The number of extra real parameters
            HdrFile << num_output_real << '\n';
 
            // Real component names
            for (int i = 0; i < rnames_size; ++i ) {
                if (write_real_comp[i]) { HdrFile << real_comp_names[i] << '\n'; }
            }
 
            // The number of extra int parameters
            HdrFile << num_output_int << '\n';
 
            // int component names
            for (int i = 0; i < NStructInt + nic; ++i ) {
                if (write_int_comp[i]) { HdrFile << int_comp_names[i] << '\n'; }
            }
 
            bool is_checkpoint_legacy = true; // legacy
            HdrFile << is_checkpoint_legacy << '\n';
 
            // The total number of particles.
            HdrFile << total_np << '\n';
 
            // The value of nextid that we need to restore on restart.
            HdrFile << maxnextid << '\n';
 
            // Then the finest level of the AMR hierarchy.
            HdrFile << finest_level << '\n';
 
            // Then the number of grids at each level.
            for (int lev = 0; lev <= finest_level; lev++) {
                HdrFile << dms[lev].size() << '\n';
            }
 
            for (int lev = 0; lev <= finest_level; lev++)
            {
                Vector<int64_t> grid_offset(NProcs, 0);
                for (int k = 0; k < bas[lev].size(); ++k)
                {
                    int rank = dms[lev][k];
                    auto info = AsyncOut::GetWriteInfo(rank);
                    HdrFile << info.ifile << ' '
                            << np_per_grid_global[lev][k] << ' '
                            << grid_offset[rank] + rank_start_offset[rank] << '\n';
                    grid_offset[rank] += static_cast<int64_t>(np_per_grid_global[lev][k]*psize);
                }
            }
 
            HdrFile.flush();
            HdrFile.close();
            if ( ! HdrFile.good())
            {
                amrex::Abort("amrex::WriteBinaryParticleDataAsync(): problem writing HdrFile");
            }
        }
 
        AsyncOut::Wait();  // Wait for my turn
 
        for (int lev = 0; lev <= finest_level; lev++)
        {
            // For a each grid, the tiles it contains
            std::map<int, Vector<int> > tile_map;
 
            for (const auto& kv : (*myptiles)[lev])
            {
                const int grid = kv.first.first;
                const int tile = kv.first.second;
                tile_map[grid].push_back(tile);
            }
 
            std::string LevelDir = pdir;
            if ( ! LevelDir.empty() && LevelDir[LevelDir.size()-1] != '/') { LevelDir += '/'; }
            LevelDir = amrex::Concatenate(LevelDir.append("Level_"), lev, 1);
            std::string filePrefix(LevelDir);
            filePrefix += '/';
            filePrefix += PC::DataPrefix();
            auto info = AsyncOut::GetWriteInfo(MyProc);
            std::string file_name = amrex::Concatenate(filePrefix, info.ifile, 5);
            std::ofstream ofs;
            ofs.open(file_name.c_str(), (info.ispot == 0) ? (std::ios::binary | std::ios::trunc)
                     : (std::ios::binary | std::ios::app));
 
            for (int k = 0; k < bas[lev].size(); ++k)
            {
                int rank = dms[lev][k];
                if (rank != MyProc) { continue; }
                const int grid = k;
                if (np_per_grid_local[lev][grid] == 0) { continue; }
 
                // First write out the integer data in binary.
                int num_output_int = 0;
                for (int i = 0; i < nic + NStructInt; ++i) {
                    if (write_int_comp[i]) { ++num_output_int; }
                }
 
                const Long iChunkSize = 2 + num_output_int;
                Vector<int> istuff(np_per_grid_local[lev][grid]*iChunkSize);
                int* iptr = istuff.dataPtr();
 
                for (unsigned i = 0; i < tile_map[grid].size(); i++) {
                    auto ptile_index = std::make_pair(grid, tile_map[grid][i]);
                    const auto& pbox = (*myptiles)[lev][ptile_index];
                    const auto& ptd = pbox.getConstParticleTileData();
                    for (int pindex = 0; pindex < pbox.numParticles(); ++pindex)
                    {
                        const auto& soa  = pbox.GetStructOfArrays();
 
                        const auto& p = make_particle<typename PC::ConstParticleType>{}(ptd, pindex);
                        if (p.id() <= 0) { continue; }
 
                        // note: for pure SoA particle layouts, we do write the id, cpu and positions as a struct
                        //       for backwards compatibility with readers
                        if constexpr(!PC::ParticleType::is_soa_particle)
                        {
                            // Ints: id, cpu
                            particle_detail::packParticleIDs(iptr, p, is_checkpoint);
                            iptr += 2;
 
                            // extra AoS Int components
                            for (int j = 0; j < NStructInt; j++)
                            {
                                if (write_int_comp[j])
                                {
                                    *iptr = p.idata(j);
                                    ++iptr;
                                }
                            }
                        }
                        else {
                            uint64_t idcpu = soa.GetIdCPUData()[pindex];
                            if (is_checkpoint) {
                                std::int32_t  xi, yi;
                                std::uint32_t xu, yu;
                                xu = (std::uint32_t)((idcpu & 0xFFFFFFFF00000000LL) >> 32);
                                yu = (std::uint32_t)( idcpu & 0xFFFFFFFFLL);
                                std::memcpy(&xi, &xu, sizeof(xu));
                                std::memcpy(&yi, &yu, sizeof(yu));
                                *iptr = xi;
                                iptr += 1;
                                *iptr = yi;
                                iptr += 1;
                            } else {
                                // Int: id, cpu
                                *iptr = (int) ParticleIDWrapper(idcpu);
                                iptr += 1;
                                *iptr = (int) ParticleCPUWrapper(idcpu);
                                iptr += 1;
                            }
                        }
 
                        // extra SoA Ints
                        const int int_start_offset = 0;
                        for (int j = int_start_offset; j < nic; j++)
                        {
                            if (write_int_comp[NStructInt+j])
                            {
                                *iptr = soa.GetIntData(j)[pindex];
                                ++iptr;
                            }
                        }
                    }
                }
 
                writeIntData(istuff.dataPtr(), istuff.size(), ofs);
                ofs.flush();  // Some systems require this flush() (probably due to a bug)
 
                // Write the Real data in binary.
                int num_output_real = 0;
                for (int i = 0; i < rnames_size; ++i) {
                    if (write_real_comp[i]) { ++num_output_real; }
                }
 
                const Long rChunkSize = AMREX_SPACEDIM + num_output_real;
                Vector<typename PC::ParticleType::RealType> rstuff(np_per_grid_local[lev][grid]*rChunkSize);
                typename PC::ParticleType::RealType* rptr = rstuff.dataPtr();
 
                for (unsigned i = 0; i < tile_map[grid].size(); i++) {
                    auto ptile_index = std::make_pair(grid, tile_map[grid][i]);
                    const auto& pbox = (*myptiles)[lev][ptile_index];
                    const auto& ptd = pbox.getConstParticleTileData();
                    for (int pindex = 0;
                         pindex < pbox.numParticles(); ++pindex)
                    {
                        const auto& soa  = pbox.GetStructOfArrays();
                        const auto& p = make_particle<typename PC::ConstParticleType>{}(ptd, pindex);
 
                        if (p.id() <= 0) { continue; }
 
                        if constexpr(!PC::ParticleType::is_soa_particle)
                        {
                            // Real: position
                            for (int j = 0; j < AMREX_SPACEDIM; j++) { rptr[j] = p.pos(j); }
                            rptr += AMREX_SPACEDIM;
 
                            // extra AoS real
                            for (int j = 0; j < NStructReal; j++)
                            {
                                if (write_real_comp[j])
                                {
                                    *rptr = p.rdata(j);
                                    ++rptr;
                                }
                            }
                        }
                        else {
                            // Real: position
                            for (int j = 0; j < AMREX_SPACEDIM; j++) { rptr[j] = soa.GetRealData(j)[pindex]; }
                            rptr += AMREX_SPACEDIM;
                        }
 
                        // extra SoA real
                        const int real_start_offset = PC::ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0; // pure SoA: positions
                        for (int j = real_start_offset; j < nrc; j++)
                        {
                    const int write_comp_offset = PC::ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0; // pure SoA: skip positions
                    const int write_comp_index = PC::NStructReal+j-write_comp_offset;
                            if (write_real_comp[write_comp_index])
                            {
                                *rptr = (typename PC::ParticleType::RealType) soa.GetRealData(j)[pindex];
                                ++rptr;
                            }
                        }
                    }
                }
 
                if (sizeof(typename PC::ParticleType::RealType) == 4) {
                    writeFloatData((float*) rstuff.dataPtr(), rstuff.size(), ofs, RD);
                }
                else if (sizeof(typename PC::ParticleType::RealType) == 8) {
                    writeDoubleData((double*) rstuff.dataPtr(), rstuff.size(), ofs, RD);
                }
 
                ofs.flush();  // Some systems require this flush() (probably due to a bug)
            }
        }
        AsyncOut::Notify();  // Notify others I am done
    });
}
 
#ifdef AMREX_USE_HDF5
#include <AMReX_WriteBinaryParticleDataHDF5.H>
#endif
 
#endif /*AMREX_WRITE_BINARY_PARTICLE_DATA_H*/