particles_container.hpp

#ifndef __PARTICLES_CONTAINER_HPP__
#define __PARTICLES_CONTAINER_HPP__
 
#include "Kokkos_Macros.hpp"
#include "common/alg.hpp"
#include <Kokkos_Core.hpp>
#include <biocma_cst_config.hpp>
#include <cmath>
#include <common/common.hpp>
#include <common/env_var.hpp>
#include <common/has_serialize.hpp>
#include <cstdint>
#include <mc/alias.hpp>
#include <mc/prng/prng.hpp>
#include <mc/traits.hpp>
 
#include <Kokkos_Sort.hpp>
#include <sorting/Kokkos_BinSortPublicAPI.hpp>
#include <sorting/impl/Kokkos_CopyOpsForBinSortImpl.hpp>
#include <sorting/impl/Kokkos_SortByKeyImpl.hpp>
#include <utility>
namespace MC
{
 
  struct RuntimeParameters
  {
    uint64_t minimum_dead_particle_removal{};
    double buffer_ratio{};
    double allocation_factor = {};
    double shink_ratio{};
    double dead_particle_ratio_threshold{};
 
    template <class Archive>
    void
    serialize(Archive& ar)
    {
      ar(minimum_dead_particle_removal,
         buffer_ratio,
         allocation_factor,
         shink_ratio,
         dead_particle_ratio_threshold);
    }
  };

  template <ModelType Model> class ParticlesContainer
  {
  public:
    using UsedModel = Model;

 
    explicit ParticlesContainer(RuntimeParameters rt_param,
                                std::size_t n_particle,
                                std::size_t _n_samples);
    ParticlesContainer(); //=default;
    ParticlesContainer(const ParticlesContainer&) = default;
    ParticlesContainer(ParticlesContainer&&) = default;
    ParticlesContainer& operator=(const ParticlesContainer&) = default;
    ParticlesContainer& operator=(ParticlesContainer&&) = default;

    ~ParticlesContainer() = default;
 
    // NOLINTBEGIN(cppcoreguidelines-non-private-member-variables-in-classes)
    Model::SelfParticle model;
    MC::ParticlePositions position;
    MC::ParticleStatus status;
    ParticleWeigths weights;
    ParticleAges ages;
    ParticleSamples random;
    // NOLINTEND(cppcoreguidelines-non-private-member-variables-in-classes)

    KOKKOS_INLINE_FUNCTION auto sample(std::size_t idx,
                                       std::size_t i_sample) const;

    KOKKOS_INLINE_FUNCTION auto samples();

    template <typename CviewType>
    KOKKOS_INLINE_FUNCTION void
    get_contributions(const std::size_t idx,
                      const CviewType& contributions) const
    {
      if (begin < end)
      {
        static_assert(ConstWeightModelType<Model>,
                      "ModelType: Constapply_weight()");
 
        const double weight = get_weight(idx);
        const auto pos = position(idx);
        auto access = contributions.access();
 
        for (int i = begin; i < end; ++i)
        {
          const int rel = i - begin;
          access(rel, pos) += weight * model(idx, i);
        }
      }
    }

    [[nodiscard]] KOKKOS_INLINE_FUNCTION bool
    handle_division(const MC::pool_type& random_pool, std::size_t idx1) const;

    [[nodiscard]] KOKKOS_INLINE_FUNCTION double
    get_weight(std::size_t idx) const;
 
    // HOST

    void force_remove_dead();

    void merge_buffer();

    template <class Archive> void save(Archive& ar) const;

    template <class Archive> void load(Archive& ar);

    [[nodiscard]] double get_allocation_factor() const noexcept;
 
    void change_nsample(std::size_t new_n_sample);
    [[nodiscard]] std::size_t capacity() const noexcept;

    [[nodiscard]] std::size_t get_inactive() const noexcept;

    void update_and_remove_inactive(std::size_t out, std::size_t dead);

    [[nodiscard]] KOKKOS_INLINE_FUNCTION std::size_t n_particles() const;
 
    void change_runtime(RuntimeParameters&& parameters) noexcept;
 
    void _sort(size_t n_c);

    void remove_inactive_particles(std::size_t to_remove);
 
// FIXME: used only in unit test
#ifndef NDEBUG
    [[maybe_unused]] [[nodiscard]] auto get_buffer_index() const;
#endif
 
  private:
    Model::SelfParticle buffer_model;
    ParticlePositions buffer_position;
    Kokkos::View<uint64_t, Kokkos::SharedSpace> buffer_index;
    std::size_t n_allocated_elements;
    uint64_t n_used_elements;
    std::size_t inactive_counter;
 
    void __allocate_buffer__();
    void _resize(std::size_t new_size, bool force = false);
    std::size_t n_samples;
    RuntimeParameters rt_params;
 
    int begin;
    int end;
  };
 
} // namespace MC
 
/*
 * IMPLEMENTATION
 */
namespace MC
{
  namespace
  {
 
    using TeamPolicy = Kokkos::TeamPolicy<ComputeSpace>;
    using TeamMember = TeamPolicy::member_type;

    template <ModelType M> struct CompactParticlesFunctor
    {
 
      CompactParticlesFunctor(MC::ParticleStatus _status,
                              M::SelfParticle _model,
                              MC::ParticlePositions _position,
                              MC::ParticleAges _ages,
                              std::size_t _to_remove,
                              std::size_t _last_used_index)
          : status(std::move(_status)), model(std::move(_model)),
            position(std::move(_position)), ages(std::move(_ages)),
            offset("offset"), to_remove(_to_remove),
            last_used_index(_last_used_index)
      {
 
        Kokkos::deep_copy(offset, 0);
      }
 
      KOKKOS_INLINE_FUNCTION void
      operator()(const int i, std::size_t& update, const bool final) const
      {

 
        // Check if the particle is non-idle.
        const bool is_inactive = (status(i) != MC::Status::Idle);
 
        // Capture the current prefix sum of inactive particles.
        const std::size_t scan_index = update;
 
        // Increment the shared counter if the particle is inactive.
        update += is_inactive ? 1 : 0;
 
        // Final pass: Compact the container by replacing inactive particles.
        if (final && is_inactive && scan_index < to_remove)
        {
 
          const auto inactive_slot = i; // Index of the "gap" to fill
 
          // Atomically find a replacement particle from the end of the
          // container. The replacement must be alive (idle) and not the same as
          // the particle being removed.
          // Index of the particle that will "fill" the inactive slot
          auto replacement_index
              = last_used_index - Kokkos::atomic_fetch_add(&offset(), 1);
          while (status(replacement_index) != MC::Status::Idle
                 || replacement_index
                        == static_cast<std::size_t>(inactive_slot))
          {
            replacement_index
                = last_used_index - Kokkos::atomic_fetch_add(&offset(), 1);
          }
 
          // Mark the removed particle's position as idle.
          status(inactive_slot) = MC::Status::Idle;
 
          // Merge position EZ
          // No need atomic: final executed exactly once
          Kokkos::atomic_exchange(&position(inactive_slot),
                                  position(replacement_index));
 
          // TODO Use hierachical parallism here, thread range is likely to work
          for (std::size_t i_properties = 0; i_properties < M::n_var;
               ++i_properties)
          {
            model(inactive_slot, i_properties)
                = model(replacement_index, i_properties);
          }
          ages(inactive_slot, 0) = ages(replacement_index, 0);
          ages(inactive_slot, 1) = ages(replacement_index, 1);
        }
      }
 
      MC::ParticleStatus status;
      M::SelfParticle model;
      MC::ParticlePositions position;
      MC::ParticleAges ages;
      Kokkos::View<std::size_t, ComputeSpace> offset;
      std::size_t to_remove;
      std::size_t last_used_index;
    };

    template <ModelType M> struct InsertFunctor
    {
      InsertFunctor(std::size_t _original_size,
                    M::SelfParticle _model,
                    MC::ParticlePositions _position,
                    MC::ParticleAges _ages,
                    M::SelfParticle _buffer_model,
                    MC::ParticlePositions _buffer_position)
          : original_size(_original_size), model(std::move(_model)),
            ages(std::move(_ages)), position(std::move(_position)),
            buffer_model(std::move(_buffer_model)),
            buffer_position(std::move(_buffer_position))
      {
      }
 
      // KOKKOS_INLINE_FUNCTION void operator()(const int i) const
      // {
      //   position(original_size + i) = buffer_position(i);
      //   for (std::size_t j = 0; j < M::n_var; ++j)
      //   {
      //     model(original_size + i, j) = buffer_model(i, j);
      //   }
      // }
 
      // TODO try this functor
      // TODO find a way to organise data to not copy non needed  data (like
      // contribs). Split model in two arrays?
 
      KOKKOS_INLINE_FUNCTION
      void
      operator()(const TeamMember& team) const
      {
        auto range = M::n_var;
        const int i = team.league_rank();
 
        Kokkos::parallel_for(
            Kokkos::TeamVectorRange(team, range),
            [&](const int& j)
            { model(original_size + i, j) = buffer_model(i, j); });
        position(original_size + i) = buffer_position(i);
 
        // Actually needs buffer to store mother's hydraulic time
        // But set new hydraulic time to 0 to not create new buffer a save
        // memory usage
        ages(original_size + i, 0) = 0;
        ages(original_size + i, 1) = 0;
      }
 
      std::size_t original_size;
      M::SelfParticle model;
      MC::ParticleAges ages;
      MC::ParticlePositions position;
      M::SelfParticle buffer_model;
      MC::ParticlePositions buffer_position;
    };
 
  }; // namespace
 
  template <ModelType Model>
  [[nodiscard]] KOKKOS_INLINE_FUNCTION std::size_t
  ParticlesContainer<Model>::n_particles() const
  {
    return n_used_elements;
  };
 
  template <ModelType Model>
  [[nodiscard]] std::size_t
  ParticlesContainer<Model>::get_inactive() const noexcept
  {
    return inactive_counter;
  }
 
  template <ModelType Model>
  void
  ParticlesContainer<Model>::force_remove_dead()
  {
    this->remove_inactive_particles(this->inactive_counter);
  }
#ifndef NDEBUG
 
  template <ModelType Model>
  [[maybe_unused]] [[nodiscard]] auto
  ParticlesContainer<Model>::get_buffer_index() const
  {
    return buffer_index();
  }
#endif
 
  template <ModelType Model>
  [[nodiscard]] double
  ParticlesContainer<Model>::get_allocation_factor() const noexcept
  {
    return rt_params.allocation_factor;
  }
 
  template <ModelType Model>
  [[nodiscard]] std::size_t
  ParticlesContainer<Model>::capacity() const noexcept
  {
    return n_allocated_elements;
  }
 
  template <ModelType Model>
  KOKKOS_INLINE_FUNCTION auto
  ParticlesContainer<Model>::samples()
  {
    return random;
  }
  template <ModelType Model>
  KOKKOS_INLINE_FUNCTION auto
  ParticlesContainer<Model>::sample(const std::size_t idx,
                                    const std::size_t i_sample) const
  {
    return random(idx, i_sample);
  }
 
  template <ModelType Model>
  template <class Archive>
  void
  ParticlesContainer<Model>::load(Archive& ar)
  {
    // Basically store everything that is usefull
    ar(n_allocated_elements, n_used_elements, rt_params);
 
    // Allocation is done in the deserialize
    deserialize_view(ar, weights);
    deserialize_view(ar, position);
    deserialize_view(ar, status);
    deserialize_view(ar, model);
    deserialize_view(ar, ages);
#ifndef NDEBUG
    Kokkos::printf("ParticlesContainer::load: Check if load_tuning_constant "
                   "works with different value");
#endif
 
    __allocate_buffer__(); // Dont forget to allocate buffer
  }
 
  template <ModelType Model>
  template <class Archive>
  void
  ParticlesContainer<Model>::save(Archive& ar) const
  {
 
    // Basically store everything that is usefull
    ar(n_allocated_elements, n_used_elements, rt_params);
    serialize_view(ar, weights);
    serialize_view(ar, position);
    serialize_view(ar, status);
    serialize_view(ar, model);
    serialize_view(ar, ages);
  }
 
  template <ModelType Model>
  void
  ParticlesContainer<Model>::change_nsample(const std::size_t new_n_sample)
  {
    if (new_n_sample != n_samples)
    {
      n_samples = new_n_sample;
      Kokkos::resize(random, n_allocated_elements, n_samples);
    }
  }
 
  template <ModelType Model>
  void
  ParticlesContainer<Model>::update_and_remove_inactive(const std::size_t out,
                                                        const std::size_t dead)
  {
    // Actually out particle and dead ones are just inactive
    inactive_counter += out;
    inactive_counter += dead;
 
    const auto _threshold = std::max(
        rt_params.minimum_dead_particle_removal,
        static_cast<uint64_t>(static_cast<double>(n_used_elements)
                              * rt_params.dead_particle_ratio_threshold));
 
    // TODO: May change threshold as container is now cleaned before exporting,
    if (inactive_counter > _threshold)
    {
      this->remove_inactive_particles(inactive_counter);
    }
  }
 
  template <ModelType Model>
  KOKKOS_INLINE_FUNCTION bool
  ParticlesContainer<Model>::handle_division(const MC::pool_type& random_pool,
                                             std::size_t idx1) const
  {
    if (Kokkos::atomic_load(&buffer_index()) < buffer_model.extent(0))
    {
      const auto idx2 = Kokkos::atomic_fetch_add(&buffer_index(), 1);
      Model::division(random_pool, idx1, idx2, model, buffer_model);
      buffer_position(idx2) = position(idx1);
      ages(idx1, 1) = 0;
      return true;
    }
    return false;
  }
 
  template <ModelType Model>
  void
  ParticlesContainer<Model>::merge_buffer()
  {
    PROFILE_SECTION("ParticlesContainer::merge_buffer")
    const auto original_size = n_used_elements;
    const auto n_add_item = buffer_index();
    if (n_add_item == 0)
    {
      return;
    }
    _resize(original_size + n_add_item);
    Kokkos::parallel_for("insert_merge",
                         TeamPolicy(n_add_item, Kokkos::AUTO, Model::n_var),
                         InsertFunctor<Model>(original_size,
                                              model,
                                              position,
                                              ages,
                                              buffer_model,
                                              buffer_position));
 
    buffer_index() = 0;
    n_used_elements += n_add_item;
    __allocate_buffer__();
  }
 
  template <ModelType Model>
  void
  ParticlesContainer<Model>::_resize(std::size_t new_size, bool force)
  {
    PROFILE_SECTION("ParticlesContainer::_resize")
 
    // Ensure new_size is greater than zero
    if (new_size > 0)
    {
      // Determine if resizing is necessary based on the condition
      if (new_size > n_allocated_elements || force)
      {
        // Calculate the new allocated size
        const auto new_allocated_size = static_cast<std::size_t>(std::ceil(
            static_cast<double>(new_size) * rt_params.allocation_factor));
 
        // Update the allocated size
        n_allocated_elements = new_allocated_size;
 
        // Perform the resizing on all relevant data containers
        Kokkos::resize(position, n_allocated_elements);
        Kokkos::resize(model,
                       n_allocated_elements,
                       Model::n_var); // use 2nd dim resize if dynamic
        Kokkos::resize(status, n_allocated_elements);
        Kokkos::resize(ages, n_allocated_elements);
 
        if (n_samples != 0)
        {
          Kokkos::resize(random, n_allocated_elements, n_samples);
        }
 
        // Handle resizing for weights based on model type
        if constexpr (ConstWeightModelType<Model>)
        {
          Kokkos::resize(weights,
                         1); // Fixed size for ConstWeightModelType
        }
        else
        {
          Kokkos::resize(weights, n_allocated_elements);
        }
      }
    }
  }
 
  template <ModelType Model>
  void
  ParticlesContainer<Model>::__allocate_buffer__()
  {
    PROFILE_SECTION("ParticlesContainer::__allocate_buffer__")
    auto buffer_size = buffer_position.extent(0);
    const auto buffer_ratio = rt_params.buffer_ratio;
    if (static_cast<double>(buffer_size)
            / static_cast<double>(n_allocated_elements)
        < buffer_ratio)
    {
      buffer_size = static_cast<std::size_t>(
          std::ceil(static_cast<double>(n_allocated_elements) * buffer_ratio));
 
      // Realloc because not needed to keep buffer as it has been copied
      Kokkos::realloc(buffer_position, buffer_size);
      Kokkos::realloc(buffer_model,
                      buffer_size,
                      Model::n_var); // use 2nd dim resize if dynamic
      buffer_index() = 0;
    }
  }
 
  template <ModelType M>
  ParticlesContainer<M>::ParticlesContainer(RuntimeParameters rt_param,
                                            std::size_t n_particle,
                                            std::size_t _n_samples)
      : model(Kokkos::view_alloc(Kokkos::WithoutInitializing, "particle_model"),
              0,
              0),
        position(Kokkos::view_alloc(Kokkos::WithoutInitializing,
                                    "particle_position"),
                 0),
        status(
            Kokkos::view_alloc(Kokkos::WithoutInitializing, "particle_status"),
            0),
        weights(
            Kokkos::view_alloc(Kokkos::WithoutInitializing, "particle_weigth"),
            0),
        ages(Kokkos::view_alloc(Kokkos::WithoutInitializing, "particle_age"),
             0),
        random(
            Kokkos::view_alloc(Kokkos::WithoutInitializing, "particle_random"),
            0,
            0),
        buffer_model("buffer_particle_model", 0),
        buffer_position("buffer_particle_position", 0),
        buffer_index("buffer_index"), n_allocated_elements(0),
        n_used_elements(n_particle), inactive_counter(0), n_samples(_n_samples),
        rt_params(rt_param), begin(0), end(0)
  {
 
    // load_tuning_constant();
 
    if (n_particle != 0)
    {
      _resize(n_particle);
      __allocate_buffer__();
    }
 
    const auto bounds = M::get_bounds();
    begin = bounds.begin;
    end = bounds.end;
  }
 
  template <ModelType M>
  ParticlesContainer<M>::ParticlesContainer()
      : ParticlesContainer(RuntimeParameters{}, 0, 0)
  {
  }
 
  template <ModelType M>
  void
  ParticlesContainer<M>::remove_inactive_particles(std::size_t to_remove)
  {
 
    PROFILE_SECTION("ParticlesContainer::remove_inactive_particles")
    if (to_remove == 0)
    {
      return;
    }
 
    if (to_remove == n_used_elements)
    {
      _resize(0, true);
      n_used_elements = 0;
      inactive_counter = 0;
    }
    else if (to_remove > n_used_elements)
    {
      throw std::runtime_error(
          "remove_inactive_particles: Error in kernel cannot remove more "
          "element than existing");
    }
    else
    {
 
      const auto new_used_item = n_used_elements - to_remove;
 
      const auto last_used_index = n_used_elements - 1;
      Kokkos::parallel_scan(
          "find_and_fill_gap",
          Kokkos::RangePolicy<ComputeSpace>(0, n_used_elements),
          CompactParticlesFunctor<M>(
              status, model, position, ages, to_remove, last_used_index));
 
      Kokkos::fence();
      KOKKOS_ASSERT(this->position.extent(0) == n_allocated_elements);
      KOKKOS_ASSERT(this->model.extent(0) == n_allocated_elements);
      KOKKOS_ASSERT(this->status.extent(0) == n_allocated_elements);
      if (n_samples != 0)
      {
        KOKKOS_ASSERT(this->random.extent(0) == n_allocated_elements);
        KOKKOS_ASSERT(this->random.extent(1) == n_samples);
      }
 
      n_used_elements = new_used_item;
      if (static_cast<double>(n_used_elements)
              / static_cast<double>(n_allocated_elements)
          <= rt_params.shink_ratio)
      {
        //        Kokkos::printf("SHRINK \r\n");
        // force to true if we want to shrink
        _resize(n_used_elements * rt_params.allocation_factor, true);
      }
      inactive_counter = inactive_counter - to_remove;
    };
  }
 
  template <ModelType M>
  [[nodiscard]] KOKKOS_INLINE_FUNCTION double
  ParticlesContainer<M>::get_weight(std::size_t idx) const
  {
    if constexpr (ConstWeightModelType<M>)
    {
      return weights(0);
    }
    else
    {
      return weights(idx);
    }
  }
 
  template <ModelType M>
  void
  ParticlesContainer<M>::change_runtime(RuntimeParameters&& parameters) noexcept
  {
    this->rt_params = parameters;
  }
 
  template <ModelType M>
  void
  ParticlesContainer<M>::_sort(std::size_t n_c)
  {
    Sorting::sort_soa(0,
                      n_c,
                      n_used_elements,
                      n_allocated_elements,
                      position, // ref
                      position,
                      model,
                      status);
  }
 
} // namespace MC
 
#endif