🐛 setup batch update experiment

Also: - rename to setDegreeUnsafe() - rename to addEdgeUnsafe() - fix get/set/clearBit() - use GCC13
puzzlef · Jan 26, 2025 · 36fdb37 · 36fdb37
1 parent 3eaf351
commit 36fdb37
Show file tree

Hide file tree

Showing 5 changed files with 157 additions and 28 deletions.
diff --git a/inc/Graph.hxx b/inc/Graph.hxx
@@ -722,12 +722,12 @@ class ArenaDiGraph {
 
 
   /**
-   * Set the degree of a vertex in the graph.
+   * Set the degree of a vertex in the graph, without "any" checks.
    * @param u vertex id
    * @param d new degree of the vertex
-   * @note `update()` must be called after all degrees are set.
+   * @note Ensure that the vertex exists, and it has at least `d` edges.
    */
-  inline void setDegreeUnchecked(K u, K d) {
+  inline void setDegreeUnsafe(K u, K d) {
     degrees[u] = d;
   }
 
@@ -737,10 +737,12 @@ class ArenaDiGraph {
    * @param u source vertex id
    * @param v target vertex id
    * @param w associated weight of the edge
+   * @note Ensure that the vertex exists, and enough capacity is reserved.
    */
-  inline void addEdgeUnchecked(K u, K v, E w=E()) {
+  inline void addEdgeUnsafe(K u, K v, E w=E()) {
     auto *ptr = edges[u];
-    ptr[degrees[u]++] = {v, w};
+    K i = degrees[u]++;
+    ptr[i] = {v, w};
   }
 
 
@@ -749,8 +751,9 @@ class ArenaDiGraph {
    * @param u source vertex id
    * @param v target vertex id
    * @param w associated weight of the edge
+   * @note Ensure that the vertex exists, and enough capacity is reserved.
    */
-  inline void addEdgeUncheckedOmp(K u, K v, E w=E()) {
+  inline void addEdgeUnsafeOmp(K u, K v, E w=E()) {
     auto *ptr = edges[u];
     K i = K();
     #pragma omp atomic capture
@@ -759,6 +762,30 @@ class ArenaDiGraph {
   }
 
 
+  /**
+   * Add an outgoing edge to the graph, without uniqueness check.
+   * @param u source vertex id
+   * @param v target vertex id
+   * @param w associated weight of the edge
+   * @note Ensure that the span of the graph is sufficient.
+   */
+  inline void addEdgeUnchecked(K u, K v, E w=E()) {
+    if (!getBit(exists, u)) setBit(exists, u);
+    if (!getBit(exists, v)) setBit(exists, v);
+    K i = degrees[u]++;
+    if (i >= capacities[u]) {
+      K cap = allocationCapacity(degrees[u]);
+      pair<K, E> *tmp = allocate(cap);
+      if (i>0) memcpy(tmp, edges[u], i*EDGE);
+      if (i>0) deallocate(edges[u], capacities[u]);
+      edges[u] = tmp;
+      capacities[u] = cap;
+    }
+    pair<K, E> *ptr = edges[u];
+    ptr[i] = {v, w};
+  }
+
+
   /**
    * Remove outgoing edges from a vertex in the graph.
    * @param u source vertex id
@@ -797,7 +824,7 @@ class ArenaDiGraph {
    * @param ie end iterator of edges to add
    * @note [ib, ie) must be sorted and unique.
    */
-  template <class I, class FL>
+  template <class I>
   inline void addEdges(K u, I ib, I ie) {
     if (!hasVertex(u) || ib==ie) return;
     auto *eb = edges[u], *ee = edges[u] + degrees[u];
@@ -1590,7 +1617,7 @@ inline void subtractGraphW(H& a, const GX& x, const GY& y) {
     auto xb = x.beginEdges(u), xe = x.endEdges(u);
     auto ab = a.beginEdges(u);
     auto it = copy(xb, xe, ab);
-    a.setDegreeUnchecked(u, it - ab);
+    a.setDegreeUnsafe(u, it - ab);
   });
   // Now add edges of vertices that are touched.
   y.forEachVertexKey([&](auto u) {
@@ -1600,7 +1627,7 @@ inline void subtractGraphW(H& a, const GX& x, const GY& y) {
     auto ab = a.beginEdges(u);
     auto fl = [](const auto& a, const auto& b) { return a.first < b.first; };
     auto it = set_difference(xb, xe, yb, ye, ab, fl);
-    a.setDegreeUnchecked(u, it - ab);
+    a.setDegreeUnsafe(u, it - ab);
   });
   a.update(true, true);
 }
@@ -1638,7 +1665,7 @@ inline void subtractGraphOmpW(H& a, const GX& x, const GY& y) {
     auto xb = x.beginEdges(u), xe = x.endEdges(u);
     auto ab = a.beginEdges(u);
     auto it = copy(xb, xe, ab);
-    a.setDegreeUnchecked(u, it - ab);
+    a.setDegreeUnsafe(u, it - ab);
   }
   // Now add edges of vertices that are touched.
   #pragma omp parallel for schedule(dynamic, 2048)
@@ -1649,7 +1676,7 @@ inline void subtractGraphOmpW(H& a, const GX& x, const GY& y) {
     auto ab = a.beginEdges(u);
     auto fl = [](const auto& a, const auto& b) { return a.first < b.first; };
     auto it = set_difference(xb, xe, yb, ye, ab, fl);
-    a.setDegreeUnchecked(u, it - ab);
+    a.setDegreeUnsafe(u, it - ab);
   }
   a.updateOmp(true, true);
 }
@@ -1738,7 +1765,7 @@ inline void addGraphW(H& a, const GX& x, const GY& y) {
     auto ab = a.beginEdges(u);
     auto fl = [](const auto& a, const auto& b) { return a.first < b.first; };
     auto it = set_union(xb, xe, yb, ye, ab, fl);
-    a.setDegreeUnchecked(u, it - ab);
+    a.setDegreeUnsafe(u, it - ab);
   }
   a.update(true, true);
 }
@@ -1779,7 +1806,7 @@ inline void addGraphOmpW(H& a, const GX& x, const GY& y) {
     auto ab = a.beginEdges(u);
     auto fl = [](const auto& a, const auto& b) { return a.first < b.first; };
     auto it = set_union(xb, xe, yb, ye, ab, fl);
-    a.setDegreeUnchecked(u, it - ab);
+    a.setDegreeUnsafe(u, it - ab);
   }
   a.updateOmp(true, true);
 }

diff --git a/inc/_vector.hxx b/inc/_vector.hxx
@@ -40,7 +40,7 @@ using vector2d = vector<vector<T>>;
 template <class T>
 inline bool getBit(const T *x, size_t i) {
   constexpr size_t WORD = 8 * sizeof(T);
-  return x[i / WORD] & (1 << (i % WORD));
+  return (x[i / WORD] & (T(1) << (i % WORD))) != 0;
 }
 
 
@@ -52,7 +52,7 @@ inline bool getBit(const T *x, size_t i) {
 template <class T>
 inline void setBit(T *x, size_t i) {
   constexpr size_t WORD = 8 * sizeof(T);
-  x[i / WORD] |= (1 << (i % WORD));
+  x[i / WORD] |= (T(1) << (i % WORD));
 }
 
 
@@ -64,7 +64,7 @@ inline void setBit(T *x, size_t i) {
 template <class T>
 inline void clearBit(T *x, size_t i) {
   constexpr size_t WORD = 8 * sizeof(T);
-  x[i / WORD] &= ~(1 << (i % WORD));
+  x[i / WORD] &= ~(T(1) << (i % WORD));
 }
 #pragma endregion
 

diff --git a/inc/duplicate.hxx b/inc/duplicate.hxx
@@ -173,36 +173,36 @@ inline void duplicateArenaOmpW(H& a, const G& x) {
   // Delete existing data.
   a.clear();
   // Add vertices and reserve space for edges.
-  auto t0 = timeNow();
+  // auto t0 = timeNow();
   a.reserveOmp(S);
-  auto t1 = timeNow();
+  // auto t1 = timeNow();
   #pragma omp parallel for schedule(static, 2048)
   for (K u=0; u<S; ++u) {
     if (!x.hasVertex(u)) continue;
     a.addVertex(u, x.vertexValue(u));
   }
-  auto t2 = timeNow();
+  // auto t2 = timeNow();
   #pragma omp parallel for schedule(dynamic, 2048)
   for (K u=0; u<S; ++u) {
     if (!x.hasVertex(u)) continue;
     a.allocateEdges(u, x.degree(u));
   }
-  auto t3 = timeNow();
+  // auto t3 = timeNow();
   // Populate the edges.
   #pragma omp parallel for schedule(dynamic, 1024)
   for (K u=0; u<S; ++u) {
     if (!x.hasVertex(u)) continue;
     x.forEachEdge(u, [&](auto v, auto w) {
-      a.addEdgeUnchecked(u, v, w);
+      a.addEdgeUnsafe(u, v, w);
     });
   }
-  auto t4 = timeNow();
+  // auto t4 = timeNow();
   a.updateOmp(true, false);
-  auto t5 = timeNow();
-  printf("duplicateArenaOmpW: Reserve space = %.3f ms\n", duration(t0, t1));
-  printf("duplicateArenaOmpW: Add vertices  = %.3f ms\n", duration(t1, t2));
-  printf("duplicateArenaOmpW: Reserve edges = %.3f ms\n", duration(t2, t3));
-  printf("duplicateArenaOmpW: Add edges     = %.3f ms\n", duration(t3, t4));
-  printf("duplicateArenaOmpW: Update        = %.3f ms\n", duration(t4, t5));
+  // auto t5 = timeNow();
+  // printf("duplicateArenaOmpW: Reserve space = %.3f ms\n", duration(t0, t1));
+  // printf("duplicateArenaOmpW: Add vertices  = %.3f ms\n", duration(t1, t2));
+  // printf("duplicateArenaOmpW: Reserve edges = %.3f ms\n", duration(t2, t3));
+  // printf("duplicateArenaOmpW: Add edges     = %.3f ms\n", duration(t3, t4));
+  // printf("duplicateArenaOmpW: Update        = %.3f ms\n", duration(t4, t5));
 }
 #pragma endregion
diff --git a/main.cxx b/main.cxx
@@ -36,6 +36,104 @@ using namespace std;
 
 #pragma region METHODS
 #pragma region PERFORM EXPERIMENT
+/**
+ * Perform the experiment.
+ * @param x input graph
+ */
+template <class G>
+inline void runExperiment(const G& x) {
+  using K = typename G::key_type;
+  using V = typename G::vertex_value_type;
+  using E = typename G::edge_value_type;
+  printf("Running experiment ...\n");
+  // Create random number generator.
+  random_device dev;
+  default_random_engine rnd(dev());
+  // Experiment of various batch fractions.
+  for (double frac=1e-7; frac<=1e-1; frac*=10) {
+    printf("Batch fraction: %.1e\n", frac);
+    // Generate random edge deletions and insertions.
+    printf("Generating random edge deletions and insertions ...\n");
+    auto deletions  = generateEdgeDeletions (rnd, x, size_t(frac * x.size()), 0, x.span(), false);
+    auto insertions = generateEdgeInsertions(rnd, x, size_t(frac * x.size()), 0, x.span(), false, E(1));
+    printf("Edge deletions:  %zu\n", deletions.size());
+    printf("Edge insertions: %zu\n", insertions.size());
+    // Create edge deletions and insertions graph.
+    printf("Creating edge deletions and insertions graph ...\n");
+    ArenaDiGraph<K, V, E> ydel;
+    ArenaDiGraph<K, V, E> yins;
+    ydel.setAllocator(x.allocator());
+    yins.setAllocator(x.allocator());
+    ydel.reserveOmp(x.span());
+    yins.reserveOmp(x.span());
+    for (auto [u, v, w] : deletions)
+      ydel.addEdgeUnchecked(u, v, w);
+    for (auto [u, v, w] : insertions)
+      yins.addEdgeUnchecked(u, v, w);
+    printf("Updating edge counts ...\n");
+    ydel.updateOmp();
+    yins.updateOmp();
+    printf("Edge deletions:  "); println(ydel);
+    printf("Edge insertions: "); println(yins);
+    // Appy edge deletions in-place.
+    printf("Applying edge deletions in-place ...\n");
+    {
+      ArenaDiGraph<K, V, E> y;
+      y.setAllocator(x.allocator());
+      float t0 = measureDuration([&]() {
+        duplicateArenaOmpW(y, x);
+      });
+      float t1 = measureDuration([&]() {
+        subtractGraphOmpU(y, ydel);
+      });
+      println(y);
+      printf("{%09.1fms; %09.1fms duplicate} %s\n", t1, t0, "subtractGraphInplace");
+    }
+    // Apply edge insertions in-place.
+    printf("Applying edge insertions in-place ...\n");
+    {
+      ArenaDiGraph<K, V, E> y;
+      y.setAllocator(x.allocator());
+      float t0 = measureDuration([&]() {
+        duplicateArenaOmpW(y, x);
+      });
+      float t1 = measureDuration([&]() {
+        addGraphOmpU(y, yins);
+      });
+      println(y);
+      printf("{%09.1fms; %09.1fms duplicate} %s\n", t1, t0, "addGraphInplace");
+    }
+    // Apply edge deletions to a new graph.
+    {
+      ArenaDiGraph<K, V, E> y;
+      y.setAllocator(x.allocator());
+      float t = measureDuration([&]() {
+        subtractGraphOmpW(y, x, ydel);
+      });
+      println(y);
+      printf("{%09.1fms; %09.1fms duplicate} %s\n", t, 0.0, "subtractGraphNew");
+    }
+    // Apply edge insertions to a new graph.
+    {
+      ArenaDiGraph<K, V, E> y;
+      y.setAllocator(x.allocator());
+      float t = measureDuration([&]() {
+        addGraphOmpW(y, x, yins);
+      });
+      println(y);
+      printf("{%09.1fms; %09.1fms duplicate} %s\n", t, 0.0, "addGraphNew");
+    }
+    printf("\n");
+  }
+}
+
+
+/**
+ * Main function.
+ * @param argc argument count
+ * @param argv argument values
+ * @returns exit code
+ */
 int main(int argc, char **argv) {
   using K = uint32_t;
   using V = None;
@@ -58,6 +156,7 @@ int main(int argc, char **argv) {
     });
     LOG(""); println(xc);
     printf("{%09.1fms} %s\n", tr, "readMtxFormatToCsrOmpW");
+
     // DiGraph<K, V, E> x;
     // double ts = measureDuration([&]() {
     //   duplicateOmpW(x, xc);
@@ -71,6 +170,8 @@ int main(int argc, char **argv) {
     });
     LOG(""); println(xa);
     printf("{%09.1fms} %s\n", ta, "duplicateArenaOmpW");
+
+    runExperiment(xa);
   }
   printf("\n");
   return 0;

diff --git a/main.sh b/main.sh
@@ -10,6 +10,7 @@
 # module load hpcx-2.7.0/hpcx-ompi
 # module load openmpi/4.1.5
 # module load cuda/12.3
+source /opt/rh/gcc-toolset-13/enable
 src="graph-openmp"
 out="$HOME/Logs/$src$1.log"
 ulimit -s unlimited