Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Cut peak memory footprint in graph creation #3966

Merged
merged 5 commits into from
Nov 1, 2023
Merged

Cut peak memory footprint in graph creation #3966

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
46e8256
cut peak memory usage in computing global vertex degrees in renumbering
seunghwak Oct 31, 2023
2235e5e
cut peak memory usage in edge list compression (and switch from the p…
seunghwak Oct 31, 2023
016bed8
remove debug std::cout
seunghwak Oct 31, 2023
4727508
tweak tuning parameters and clang-format
seunghwak Oct 31, 2023
80ea981
Merge branch 'branch-23.12' of https://github.com/rapidsai/cugraph in…
seunghwak Oct 31, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion cpp/src/c_api/capi_helper.cu
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ shuffle_vertex_ids_and_offsets(raft::handle_t const& handle,
thrust::make_zip_iterator(ids.end(), vertices.end()));

auto return_offsets = cugraph::detail::compute_sparse_offsets<size_t>(
ids.begin(), ids.end(), size_t{0}, size_t{offsets.size() - 1}, handle.get_stream());
ids.begin(), ids.end(), size_t{0}, size_t{offsets.size() - 1}, true, handle.get_stream());

return std::make_tuple(std::move(vertices), std::move(return_offsets));
}
Expand Down
425 changes: 180 additions & 245 deletions cpp/src/structure/create_graph_from_edgelist_impl.cuh
View file
Open in desktop

Large diffs are not rendered by default.

281 changes: 146 additions & 135 deletions cpp/src/structure/detail/structure_utils.cuh
View file
Open in desktop

Large diffs are not rendered by default.

2 changes: 2 additions & 0 deletions cpp/src/structure/induced_subgraph_impl.cuh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -196,6 +196,7 @@ extract_induced_subgraphs(
graph_ids_v.end(),
size_t{0},
size_t{subgraph_offsets.size() - 1},
true,
handle.get_stream());

dst_subgraph_offsets =
Expand Down Expand Up @@ -290,6 +291,7 @@ extract_induced_subgraphs(
subgraph_edge_graph_ids.end(),
size_t{0},
size_t{subgraph_offsets.size() - 1},
true,
handle.get_stream());

#ifdef TIMING
Expand Down
100 changes: 54 additions & 46 deletions cpp/src/structure/renumber_edgelist_impl.cuh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -367,18 +367,19 @@ std::tuple<rmm::device_uvector<vertex_t>, std::vector<vertex_t>, vertex_t> compu
rmm::device_uvector<edge_t> sorted_local_vertex_degrees(0, handle.get_stream());
std::optional<std::vector<size_t>> stream_pool_indices{
std::nullopt}; // FIXME: move this inside the if statement

auto constexpr num_chunks = size_t{
2}; // tuning parameter, this trade-offs # binary searches (up to num_chunks times more binary
// searches can be necessary if num_unique_majors << edgelist_edge_counts[i]) and temporary
// buffer requirement (cut by num_chunks times), currently set to 2 to avoid peak memory
// usage happening in this part (especially when minor_comm_size is small)

if constexpr (multi_gpu) {
auto& comm = handle.get_comms();
auto& minor_comm = handle.get_subcomm(cugraph::partition_manager::minor_comm_name());
auto const minor_comm_rank = minor_comm.get_rank();
auto const minor_comm_size = minor_comm.get_size();

auto constexpr num_chunks = size_t{
2}; // tuning parameter, this trade-offs # binary searches (up to num_chunks times more
// binary searches can be necessary if num_unique_majors << edgelist_edge_counts[i]) and
// temporary buffer requirement (cut by num_chunks times), currently set to 2 to avoid
// peak memory usage happening in this part (especially when minor_comm_size is small)

assert(edgelist_majors.size() == minor_comm_size);

auto edge_partition_major_range_sizes =
Expand Down Expand Up @@ -433,29 +434,30 @@ std::tuple<rmm::device_uvector<vertex_t>, std::vector<vertex_t>, vertex_t> compu
sorted_major_degrees.end(),
edge_t{0});

rmm::device_uvector<vertex_t> tmp_majors(
rmm::device_uvector<vertex_t> tmp_majors(0, loop_stream);
tmp_majors.reserve(
(static_cast<size_t>(edgelist_edge_counts[i]) + (num_chunks - 1)) / num_chunks,
handle.get_stream());
loop_stream);
size_t offset{0};
for (size_t j = 0; j < num_chunks; ++j) {
size_t this_chunk_size =
std::min(tmp_majors.size(), static_cast<size_t>(edgelist_edge_counts[i]) - offset);
std::min(tmp_majors.capacity(), static_cast<size_t>(edgelist_edge_counts[i]) - offset);
tmp_majors.resize(this_chunk_size, loop_stream);
thrust::copy(rmm::exec_policy(loop_stream),
edgelist_majors[i] + offset,
edgelist_majors[i] + offset + this_chunk_size,
edgelist_majors[i] + offset + tmp_majors.size(),
tmp_majors.begin());
thrust::sort(
rmm::exec_policy(loop_stream), tmp_majors.begin(), tmp_majors.begin() + this_chunk_size);
thrust::sort(rmm::exec_policy(loop_stream), tmp_majors.begin(), tmp_majors.end());
auto num_unique_majors =
thrust::count_if(rmm::exec_policy(loop_stream),
thrust::make_counting_iterator(size_t{0}),
thrust::make_counting_iterator(this_chunk_size),
thrust::make_counting_iterator(tmp_majors.size()),
is_first_in_run_t<vertex_t const*>{tmp_majors.data()});
rmm::device_uvector<vertex_t> tmp_keys(num_unique_majors, loop_stream);
rmm::device_uvector<edge_t> tmp_values(num_unique_majors, loop_stream);
thrust::reduce_by_key(rmm::exec_policy(loop_stream),
tmp_majors.begin(),
tmp_majors.begin() + this_chunk_size,
tmp_majors.end(),
thrust::make_constant_iterator(edge_t{1}),
tmp_keys.begin(),
tmp_values.begin());
Expand Down Expand Up @@ -486,44 +488,50 @@ std::tuple<rmm::device_uvector<vertex_t>, std::vector<vertex_t>, vertex_t> compu
} else {
assert(edgelist_majors.size() == 1);

rmm::device_uvector<vertex_t> tmp_majors(edgelist_edge_counts[0], handle.get_stream());
thrust::copy(handle.get_thrust_policy(),
edgelist_majors[0],
edgelist_majors[0] + edgelist_edge_counts[0],
tmp_majors.begin());
thrust::sort(handle.get_thrust_policy(), tmp_majors.begin(), tmp_majors.end());
auto num_unique_majors =
thrust::count_if(handle.get_thrust_policy(),
thrust::make_counting_iterator(size_t{0}),
thrust::make_counting_iterator(tmp_majors.size()),
is_first_in_run_t<vertex_t const*>{tmp_majors.data()});
rmm::device_uvector<vertex_t> tmp_keys(num_unique_majors, handle.get_stream());
rmm::device_uvector<edge_t> tmp_values(num_unique_majors, handle.get_stream());
thrust::reduce_by_key(handle.get_thrust_policy(),
tmp_majors.begin(),
tmp_majors.end(),
thrust::make_constant_iterator(edge_t{1}),
tmp_keys.begin(),
tmp_values.begin());

tmp_majors.resize(0, handle.get_stream());
tmp_majors.shrink_to_fit(handle.get_stream());

sorted_local_vertex_degrees.resize(sorted_local_vertices.size(), handle.get_stream());
thrust::fill(handle.get_thrust_policy(),
sorted_local_vertex_degrees.begin(),
sorted_local_vertex_degrees.end(),
edge_t{0});

auto kv_pair_first =
thrust::make_zip_iterator(thrust::make_tuple(tmp_keys.begin(), tmp_values.begin()));
thrust::for_each(handle.get_thrust_policy(),
kv_pair_first,
kv_pair_first + tmp_keys.size(),
search_and_increment_degree_t<vertex_t, edge_t>{
sorted_local_vertices.data(),
static_cast<vertex_t>(sorted_local_vertices.size()),
sorted_local_vertex_degrees.data()});
rmm::device_uvector<vertex_t> tmp_majors(0, handle.get_stream());
tmp_majors.reserve(static_cast<size_t>(edgelist_edge_counts[0] + (num_chunks - 1)) / num_chunks,
handle.get_stream());
size_t offset{0};
for (size_t i = 0; i < num_chunks; ++i) {
size_t this_chunk_size =
std::min(tmp_majors.capacity(), static_cast<size_t>(edgelist_edge_counts[0]) - offset);
tmp_majors.resize(this_chunk_size, handle.get_stream());
thrust::copy(handle.get_thrust_policy(),
edgelist_majors[0] + offset,
edgelist_majors[0] + offset + tmp_majors.size(),
tmp_majors.begin());
thrust::sort(handle.get_thrust_policy(), tmp_majors.begin(), tmp_majors.end());
auto num_unique_majors =
thrust::count_if(handle.get_thrust_policy(),
thrust::make_counting_iterator(size_t{0}),
thrust::make_counting_iterator(tmp_majors.size()),
is_first_in_run_t<vertex_t const*>{tmp_majors.data()});
rmm::device_uvector<vertex_t> tmp_keys(num_unique_majors, handle.get_stream());
rmm::device_uvector<edge_t> tmp_values(num_unique_majors, handle.get_stream());
thrust::reduce_by_key(handle.get_thrust_policy(),
tmp_majors.begin(),
tmp_majors.end(),
thrust::make_constant_iterator(edge_t{1}),
tmp_keys.begin(),
tmp_values.begin());

auto kv_pair_first =
thrust::make_zip_iterator(thrust::make_tuple(tmp_keys.begin(), tmp_values.begin()));
thrust::for_each(handle.get_thrust_policy(),
kv_pair_first,
kv_pair_first + tmp_keys.size(),
search_and_increment_degree_t<vertex_t, edge_t>{
sorted_local_vertices.data(),
static_cast<vertex_t>(sorted_local_vertices.size()),
sorted_local_vertex_degrees.data()});
offset += this_chunk_size;
}
}

// 4. sort local vertices by degree (descending)
Expand Down
1 change: 1 addition & 0 deletions cpp/tests/community/mg_egonet_test.cu
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -215,6 +215,7 @@ class Tests_MGEgonet
graph_ids_v.end(),
size_t{0},
d_mg_edgelist_offsets.size() - 1,
true,
handle_->get_stream());

auto [d_reference_src, d_reference_dst, d_reference_wgt, d_reference_offsets] =
Expand Down
1 change: 1 addition & 0 deletions cpp/tests/structure/mg_induced_subgraph_test.cu
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -210,6 +210,7 @@ class Tests_MGInducedSubgraph
graph_ids_v.end(),
size_t{0},
size_t{d_subgraph_offsets.size() - 1},
true,
handle_->get_stream());

auto [sg_graph, sg_edge_weights, sg_number_map] = cugraph::test::mg_graph_to_sg_graph(
Expand Down
61 changes: 30 additions & 31 deletions cpp/tests/utilities/test_utilities_impl.cuh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -183,43 +183,42 @@ graph_to_host_csr(
}
}

auto total_global_mem = handle.get_device_properties().totalGlobalMem;
size_t element_size = sizeof(vertex_t) * 2;
if (d_wgt) { element_size += sizeof(weight_t); }
auto constexpr mem_frugal_ratio =
0.25; // if the expected temporary buffer size exceeds the mem_frugal_ratio of the
// total_global_mem, switch to the memory frugal approach
auto mem_frugal_threshold =
static_cast<size_t>(static_cast<double>(total_global_mem / element_size) * mem_frugal_ratio);

rmm::device_uvector<edge_t> d_offsets(0, handle.get_stream());

if (d_wgt) {
std::tie(d_offsets, d_dst, *d_wgt, std::ignore) =
detail::compress_edgelist<edge_t, store_transposed>(d_src.begin(),
d_src.end(),
d_dst.begin(),
d_wgt->begin(),
vertex_t{0},
std::optional<vertex_t>{std::nullopt},
graph_view.number_of_vertices(),
vertex_t{0},
graph_view.number_of_vertices(),
handle.get_stream());

// segmented sort neighbors
detail::sort_adjacency_list(handle,
raft::device_span<edge_t const>(d_offsets.data(), d_offsets.size()),
d_dst.begin(),
d_dst.end(),
d_wgt->begin());
detail::sort_and_compress_edgelist<vertex_t, edge_t, weight_t, store_transposed>(
std::move(d_src),
std::move(d_dst),
std::move(*d_wgt),
vertex_t{0},
std::optional<vertex_t>{std::nullopt},
graph_view.number_of_vertices(),
vertex_t{0},
graph_view.number_of_vertices(),
mem_frugal_threshold,
handle.get_stream());
} else {
std::tie(d_offsets, d_dst, std::ignore) =
detail::compress_edgelist<edge_t, store_transposed>(d_src.begin(),
d_src.end(),
d_dst.begin(),
vertex_t{0},
std::optional<vertex_t>{std::nullopt},
graph_view.number_of_vertices(),
vertex_t{0},
graph_view.number_of_vertices(),
handle.get_stream());
// segmented sort neighbors
detail::sort_adjacency_list(handle,
raft::device_span<edge_t const>(d_offsets.data(), d_offsets.size()),
d_dst.begin(),
d_dst.end());
detail::sort_and_compress_edgelist<vertex_t, edge_t, store_transposed>(
std::move(d_src),
std::move(d_dst),
vertex_t{0},
std::optional<vertex_t>{std::nullopt},
graph_view.number_of_vertices(),
vertex_t{0},
graph_view.number_of_vertices(),
mem_frugal_threshold,
handle.get_stream());
}

return std::make_tuple(
Expand Down