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@abkein
abkein committed Dec 3, 2024
1 parent 1b6164d commit 94ccab3
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Showing 4 changed files with 449 additions and 169 deletions.
62 changes: 42 additions & 20 deletions src/compute_cluster_size_ext.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,13 +61,13 @@ ComputeClusterSizeExt::ComputeClusterSizeExt(LAMMPS *lmp, int narg, char **arg)
error->all(FLERR, "size_cutoff for compute cluster/size must be greater than 0");
}

// alloc = new CustomAllocator<std::pair<const int, cluster_ptr>>(1024, memory, keeper);
// cluster_map =
// new std::u
// keeper = new MemoryKeeper(memory);
// alloc = new CustomAllocator<std::pair<const int, cluster_ptr>>(1024, memory, keeper);
// cluster_map =
// new std::unordered_map<int, cluster_ptr, std::hash<int>, std::equal_to<int>, CustomAllocator<std::pair<const int, cluster_ptr>>>(*alloc);
keeper = new MemoryKeeper(memory);

alloc = new CustomAllocator<std::pair<const int, int>>(memory, keeper);
cluster_map = new Cluster_map_t(*alloc);

alloc_vector = new Allocator_map_vector(memory, keeper);
cIDs_by_size = new Sizes_map_t(*alloc_vector);

size_vector = size_cutoff + 1;
}
Expand All @@ -83,10 +83,14 @@ ComputeClusterSizeExt::~ComputeClusterSizeExt() noexcept(true)
if (clusters != nullptr) { memory->destroy(clusters); }
if (ns != nullptr) { memory->destroy(ns); }
if (gathered != nullptr) { memory->destroy(gathered); }
if (monomers != nullptr) { memory->destroy(monomers); }

// delete cluster_map;
// delete alloc;
// delete keeper;
delete cIDs_by_size;
delete alloc_vector;

delete cluster_map;
delete alloc;
delete keeper;
}

/* ---------------------------------------------------------------------- */
Expand All @@ -105,13 +109,17 @@ void ComputeClusterSizeExt::init()
vector = dist;

nloc = static_cast<int>(atom->nlocal * LMP_NUCC_ALLOC_COEFF);
cluster_map.reserve(nloc);
// cluster_map->reserve(nloc);
// alloc->pool_size_ = nloc;
// cluster_map.reserve(nloc);
cluster_map->reserve(nloc);
cIDs_by_size->reserve(nloc);
keeper->pool_size(nloc);

memory->create(clusters, nloc, "clusters");
memory->create(ns, 2 * nloc, "ns");
memory->create(monomers, nloc, "monomers");

natom_loc = static_cast<int>(2 * atom->natoms * LMP_NUCC_ALLOC_COEFF);
natom_loc =
static_cast<bigint>(static_cast<long double>(2 * atom->natoms) * LMP_NUCC_ALLOC_COEFF);
memory->create(gathered, natom_loc, "gathered");

initialized_flag = 1;
Expand Down Expand Up @@ -148,7 +156,7 @@ void ComputeClusterSizeExt::compute_vector()
{
invoked_vector = update->ntimestep;

auto &cmap = cluster_map;
auto &cmap = *cluster_map;

if (compute_cluster_atom->invoked_peratom != update->ntimestep) {
compute_cluster_atom->compute_peratom();
Expand All @@ -163,10 +171,13 @@ void ComputeClusterSizeExt::compute_vector()

if (atom->nlocal > nloc) {
nloc = static_cast<int>(atom->nlocal * LMP_NUCC_ALLOC_COEFF);
keeper->pool_size(nloc);
cmap.reserve(nloc);
// alloc->pool_size_ = nloc;
cIDs_by_size->reserve(nloc);

memory->grow(clusters, nloc, "clusters");
memory->grow(ns, 2 * nloc, "ns");
memory->grow(monomers, nloc, "monomers");
}

// Sort atom IDs by cluster IDs
Expand All @@ -178,7 +189,7 @@ void ComputeClusterSizeExt::compute_vector()
cmap[clid] = clidx;
ns[clidx] = clid;
ns[clidx + 1] = 0;
clusters[clidx] = {0, 0, -1, 0, 0, 0};
clusters[clidx] = cluster_data(clid);
}
// possible segfault if actual cluster size exceeds LMP_NUCC_CLUSTER_MAX_SIZE + LMP_NUCC_CLUSTER_MAX_GHOST
const int clidx = cmap[clid];
Expand All @@ -189,7 +200,7 @@ void ComputeClusterSizeExt::compute_vector()
// add ghost atoms
for (int i = atom->nlocal; i < atom->nmax; ++i) {
if ((atom->mask[i] & groupbit) != 0) {
int const clid = static_cast<int>(cluster_ids[i]);
const auto clid = static_cast<bigint>(cluster_ids[i]);
if (cmap.count(clid) > 0) {
cluster_data &clstr = clusters[cmap[clid]];
// also possible segfault if number of ghost exceeds LMP_NUCC_CLUSTER_MAX_GHOST
Expand Down Expand Up @@ -222,7 +233,7 @@ void ComputeClusterSizeExt::compute_vector()
int const k = displs[i] + j;
if (cmap.count(gathered[k]) > 0) {
cluster_data &clstr = clusters[cmap[gathered[k]]];
clstr.owners[clstr.nowners++] = i;
if (i != comm->me) { clstr.owners[clstr.nowners++] = i; }
clstr.g_size += gathered[k + 1];
if (gathered[k + 1] > clstr.nhost) {
clstr.host = i;
Expand All @@ -233,11 +244,22 @@ void ComputeClusterSizeExt::compute_vector()
}

// adjust local data and fill local size distribution
nonexclusive = 0;
nmono = 0;
for (auto &[clid, clidx] : cmap) {
cluster_data &clstr = clusters[clidx];
clstr.l_size = ns[static_cast<ptrdiff_t>(2) * clidx];
::memcpy(clstr.atoms + clstr.l_size, clstr.ghost, clstr.nghost * sizeof(int));
if ((clstr.host < 0) && (clstr.g_size < size_cutoff)) { dist_local[clstr.g_size] += 1; }
if (clstr.host == comm->me) {
if (clstr.g_size < size_cutoff) { dist_local[clstr.g_size] += 1; }
if (clstr.g_size == 1) {
monomers[nmono++];
} else {
(*cIDs_by_size)[clstr.g_size].push_back(clidx);
}
} else {
++nonexclusive;
}
}

::MPI_Allreduce(dist_local, dist, size_vector, MPI_DOUBLE, MPI_SUM, world);
Expand Down
53 changes: 37 additions & 16 deletions src/compute_cluster_size_ext.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,24 +24,38 @@ ComputeStyle(cluster/size/ext,ComputeClusterSizeExt);
#define LMP_NUCC_CLUSTER_MAX_OWNERS 128
#define LMP_NUCC_CLUSTER_MAX_SIZE 300
#define LMP_NUCC_CLUSTER_MAX_GHOST 30
#include "compute.h"

#include "compute.h"
#include "nucc_allocator.hpp"
#include <scoped_allocator>
#include <unordered_map>
#include <vector>

namespace LAMMPS_NS {

class ComputeClusterVolume;
using Cluster_map_t =
std::unordered_map<int, int, std::hash<int>, std::equal_to<int>,
std::scoped_allocator_adaptor<CustomAllocator<std::pair<const int, int>>>>;
using Allocator_map_vector =
CustomAllocator<std::pair<const int, std::vector<int, CustomAllocator<int>>>>;
using Sizes_map_t =
std::unordered_map<int, std::vector<int, CustomAllocator<int>>, std::hash<int>,
std::equal_to<int>, std::scoped_allocator_adaptor<Allocator_map_vector>>;

struct cluster_data {
int l_size = 0; // local size
int g_size = 0; // global size
int host = -1; // host proc (me if <0)
int nhost = 0; // local cluster size of host proc
int nowners = 0; // number of owners
int nghost = 0; // number of ghost atoms in cluster
int owners[LMP_NUCC_CLUSTER_MAX_OWNERS];
int atoms[LMP_NUCC_CLUSTER_MAX_SIZE]; // local ids of atoms
int ghost[LMP_NUCC_CLUSTER_MAX_GHOST]; // local ids of ghost atoms
cluster_data(const bigint clid = 0) : clid(clid) {}

bigint clid = 0; // cluster ID
int l_size = 0; // local size
int g_size = 0; // global size
int host = -1; // host proc (me if <0)
int nhost = 0; // local cluster size of host proc
int nowners = 0; // number of owners
int nghost = 0; // number of ghost atoms in cluster
int owners[LMP_NUCC_CLUSTER_MAX_OWNERS]; // procs owning some cluster's atoms
int atoms[LMP_NUCC_CLUSTER_MAX_SIZE]; // local ids of atoms
int ghost[LMP_NUCC_CLUSTER_MAX_GHOST]; // local ids of ghost atoms
};

class ComputeClusterSizeExt : public Compute {
Expand All @@ -53,15 +67,18 @@ class ComputeClusterSizeExt : public Compute {
void compute_vector() override;
double memory_usage() override;

inline int get_size_cutoff() const noexcept(true) { return size_cutoff; }
int get_size_cutoff() const noexcept(true) { return size_cutoff; }

private:
int size_cutoff; // number of elements reserved in dist

// MemoryKeeper* keeper;
// CustomAllocator<std::pair<const int, cluster_ptr>>* alloc;
// std::unordered_map<int, cluster_ptr, std::hash<int>, std::equal_to<int>, CustomAllocator<std::pair<const int, cluster_ptr>>>* cluster_map;
std::unordered_map<int, int> cluster_map;
MemoryKeeper *keeper;
CustomAllocator<std::pair<const int, int>> *alloc;
Cluster_map_t *cluster_map;
// std::unordered_map<bigint, int> cluster_map; // clid -> idx
Allocator_map_vector *alloc_vector;
Sizes_map_t *cIDs_by_size;
// std::unordered_map<int, std::vector<int>> cIDs_by_size; // size -> vector(idx)

int nloc; // number of reserved elements in atoms_by_cID and cIDs_by_size
double *dist; // cluster size distribution (vector == dist)
Expand All @@ -72,7 +89,11 @@ class ComputeClusterSizeExt : public Compute {
cluster_data *clusters{};
int *ns{};
int *gathered{};
int natom_loc;
bigint natom_loc;
int nonexclusive;

int *monomers;
int nmono;

Compute *compute_cluster_atom = nullptr;
// void test_allocator() const;
Expand Down
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