From d6c47f29569f416beae65e314b5f381f31a641d9 Mon Sep 17 00:00:00 2001 From: Meyer Zinn Date: Tue, 19 Mar 2024 01:00:10 +0000 Subject: [PATCH 1/2] reduce vertex metadata size --- libgalois/include/galois/graphs/LS_LC_CSR_Graph.h | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/libgalois/include/galois/graphs/LS_LC_CSR_Graph.h b/libgalois/include/galois/graphs/LS_LC_CSR_Graph.h index c49e504ab..ec4fcd236 100644 --- a/libgalois/include/galois/graphs/LS_LC_CSR_Graph.h +++ b/libgalois/include/galois/graphs/LS_LC_CSR_Graph.h @@ -259,7 +259,8 @@ class LS_LC_CSR_Graph : private boost::noncopyable { } private: - struct VertexMetadata : public SpinLock { + struct VertexMetadata { + std::atomic_uint8_t spinlock = ATOMIC_VAR_INIT(0); uint8_t buffer : 1; uint64_t begin : 48; // inclusive uint64_t end : 48; // exclusive @@ -274,6 +275,13 @@ class LS_LC_CSR_Graph : private boost::noncopyable { VertexMetadata(VertexMetadata&& other) : buffer(std::move(other.buffer)), begin(std::move(other.begin)), end(std::move(other.end)), degree(std::move(other.degree)) {} + + inline void lock() { + while (spinlock.exchange(1, std::memory_order_acquire)) + ; + } + + inline void unlock() { spinlock.store(0, std::memory_order_release); } }; struct EdgeMetadata { From d6cace4fc6286c6cad60232f2a304c3ba6f8825e Mon Sep 17 00:00:00 2001 From: Meyer Zinn Date: Tue, 19 Mar 2024 17:01:30 +0000 Subject: [PATCH 2/2] remove vertex locks --- .../include/galois/graphs/LS_LC_CSR_Graph.h | 132 +++++++----------- 1 file changed, 51 insertions(+), 81 deletions(-) diff --git a/libgalois/include/galois/graphs/LS_LC_CSR_Graph.h b/libgalois/include/galois/graphs/LS_LC_CSR_Graph.h index ec4fcd236..8de92e2d5 100644 --- a/libgalois/include/galois/graphs/LS_LC_CSR_Graph.h +++ b/libgalois/include/galois/graphs/LS_LC_CSR_Graph.h @@ -72,13 +72,8 @@ class LS_LC_CSR_Graph : private boost::noncopyable { using EdgeRange = boost::iterator_range; std::vector m_vertices; - LargeVector m_edges[2]; - - // To avoid deadlock between updates and compaction, at least one vertex lock - // must be held to acquire m_edges_lock. - SpinLock m_edges_lock; - + SpinLock m_edges_lock; // guards resizing of edges vectors std::atomic_uint64_t m_edges_tail = ATOMIC_VAR_INIT(0); // returns a reference to the metadata for the pointed-to edge @@ -116,46 +111,43 @@ class LS_LC_CSR_Graph : private boost::noncopyable { int addEdgesTopologyOnly(VertexTopologyID src, const std::vector dsts) { - auto& vertex_meta = m_vertices[src]; // Copies the edge list to the end of m_edges[1], prepending // the new edges. - vertex_meta.lock(); // prevents compaction - { - uint64_t const new_degree = vertex_meta.degree + dsts.size(); - uint64_t const new_begin = - m_edges_tail.fetch_add(new_degree, std::memory_order_relaxed); - uint64_t const new_end = new_begin + new_degree; - - if (m_edges[1].size() < new_end) { - m_edges_lock.lock(); - { - if (m_edges[1].size() < new_end) - m_edges[1].resize(std::max(m_edges[1].size() * 2, new_end)); - } - m_edges_lock.unlock(); - } + auto& vertex_meta = m_vertices[src]; + + uint64_t const new_degree = vertex_meta.degree + dsts.size(); + uint64_t const new_begin = + m_edges_tail.fetch_add(new_degree, std::memory_order_relaxed); + uint64_t const new_end = new_begin + new_degree; - // insert new edges - std::transform(dsts.begin(), dsts.end(), &getEdgeMetadata(1, new_begin), - [](VertexTopologyID dst) { - return EdgeMetadata{.flags = 0, .dst = dst}; - }); - - // copy old, non-tombstoned edges - std::copy_if(&getEdgeMetadata(vertex_meta.buffer, vertex_meta.begin), - &getEdgeMetadata(vertex_meta.buffer, vertex_meta.end), - &getEdgeMetadata(1, new_begin + dsts.size()), - [](EdgeMetadata& edge) { return !edge.is_tomb(); }); - - // update vertex metadata - vertex_meta.buffer = 1; - vertex_meta.begin = new_begin; - vertex_meta.end = new_end; - vertex_meta.degree += dsts.size(); + if (m_edges[1].size() < new_end) { + m_edges_lock.lock(); + { + if (m_edges[1].size() < new_end) + m_edges[1].resize(std::max(m_edges[1].size() * 2, new_end)); + } + m_edges_lock.unlock(); } - vertex_meta.unlock(); + + // insert new edges + std::transform(dsts.begin(), dsts.end(), &getEdgeMetadata(1, new_begin), + [](VertexTopologyID dst) { + return EdgeMetadata{.flags = 0, .dst = dst}; + }); + + // copy old, non-tombstoned edges + std::copy_if(&getEdgeMetadata(vertex_meta.buffer, vertex_meta.begin), + &getEdgeMetadata(vertex_meta.buffer, vertex_meta.end), + &getEdgeMetadata(1, new_begin + dsts.size()), + [](EdgeMetadata& edge) { return !edge.is_tomb(); }); + + // update vertex metadata + vertex_meta.buffer = 1; + vertex_meta.begin = new_begin; + vertex_meta.end = new_end; + vertex_meta.degree += dsts.size(); return 0; } @@ -165,32 +157,28 @@ class LS_LC_CSR_Graph : private boost::noncopyable { std::unordered_set edges_set(edges.begin(), edges.end()); auto& vertex_meta = m_vertices[src]; - vertex_meta.lock(); - { - for (auto i = vertex_meta.begin; i < vertex_meta.end; ++i) { - EdgeMetadata& edge_meta = - getEdgeMetadata(EdgeHandle(vertex_meta.buffer, i)); - if (!edge_meta.is_tomb() && - edges_set.find(edge_meta.dst) != edges_set.end()) { - edge_meta.tomb(); - --vertex_meta.degree; - // remove tombstoned edges from the start of the edge list - if (i == vertex_meta.begin) - ++vertex_meta.begin; - } + for (auto i = vertex_meta.begin; i < vertex_meta.end; ++i) { + EdgeMetadata& edge_meta = + getEdgeMetadata(EdgeHandle(vertex_meta.buffer, i)); + if (!edge_meta.is_tomb() && + edges_set.find(edge_meta.dst) != edges_set.end()) { + edge_meta.tomb(); + --vertex_meta.degree; + // remove tombstoned edges from the start of the edge list + if (i == vertex_meta.begin) + ++vertex_meta.begin; } + } - // remove tombstoned edges from the end of the edge list - for (auto i = vertex_meta.end; i > vertex_meta.begin; --i) { - if (getEdgeMetadata(EdgeHandle(vertex_meta.buffer, i - 1)).is_tomb()) { - --vertex_meta.end; - --vertex_meta.degree; - } else { - break; - } + // remove tombstoned edges from the end of the edge list + for (auto i = vertex_meta.end; i > vertex_meta.begin; --i) { + if (getEdgeMetadata(EdgeHandle(vertex_meta.buffer, i - 1)).is_tomb()) { + --vertex_meta.end; + --vertex_meta.degree; + } else { + break; } } - vertex_meta.unlock(); return 0; } @@ -202,7 +190,7 @@ class LS_LC_CSR_Graph : private boost::noncopyable { // Performs the compaction algorithm by copying any vertices left in buffer 0 // to buffer 1, then swapping the buffers. // - // Should not be called from within a Galois parallel kernel. + // Not safe to call in parallel with insertions/deletions. void compact() { using std::swap; @@ -210,7 +198,6 @@ class LS_LC_CSR_Graph : private boost::noncopyable { galois::do_all(galois::iterate(vertices().begin(), vertices().end()), [&](VertexTopologyID vertex_id) { VertexMetadata& vertex_meta = m_vertices[vertex_id]; - vertex_meta.lock(); if (vertex_meta.buffer == 0) { uint64_t new_begin; @@ -237,14 +224,9 @@ class LS_LC_CSR_Graph : private boost::noncopyable { // we are about to swap the buffers, so all vertices will // be in buffer 0 vertex_meta.buffer = 0; - - // don't release the vertex lock until after the edge - // arrays are swapped }); // At this point, there are no more live edges in buffer 0. - // We also hold the lock for all vertices, so nobody else can hold - // m_edges_lock. m_edges_lock.lock(); { m_edges[0].resize(0); @@ -252,15 +234,10 @@ class LS_LC_CSR_Graph : private boost::noncopyable { m_edges_tail.store(0, std::memory_order_relaxed); // fine because lock } m_edges_lock.unlock(); - - galois::do_all( - galois::iterate(vertices().begin(), vertices().end()), - [&](VertexTopologyID vertex_id) { m_vertices[vertex_id].unlock(); }); } private: struct VertexMetadata { - std::atomic_uint8_t spinlock = ATOMIC_VAR_INIT(0); uint8_t buffer : 1; uint64_t begin : 48; // inclusive uint64_t end : 48; // exclusive @@ -275,13 +252,6 @@ class LS_LC_CSR_Graph : private boost::noncopyable { VertexMetadata(VertexMetadata&& other) : buffer(std::move(other.buffer)), begin(std::move(other.begin)), end(std::move(other.end)), degree(std::move(other.degree)) {} - - inline void lock() { - while (spinlock.exchange(1, std::memory_order_acquire)) - ; - } - - inline void unlock() { spinlock.store(0, std::memory_order_release); } }; struct EdgeMetadata {