removed pragma once from files in include/parlay, and cleaned up head…

…er files in examples

examples/3d_range.cpp

@@ -2,8 +2,9 @@
 #include <string>
 #include <random>
 
-#include "parlay/primitives.h"
-#include "parlay/random.h"
+#include <parlay/primitives.h>
+#include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "3d_range.h"
 

examples/BFS_ligra.cpp

@@ -3,6 +3,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "BFS_ligra.h"
 #include "helper/graph_utils.h"

examples/betweenness_centrality.cpp

@@ -7,6 +7,7 @@
 #include <parlay/sequence.h>
 #include <parlay/random.h>
 #include <parlay/io.h>
+#include <parlay/internal/get_time.h>
 
 #include "betweenness_centrality.h"
 #include "helper/graph_utils.h"

examples/bigint_add.cpp

@@ -5,6 +5,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "bigint_add.h"
 

examples/box_kdtree.cpp

@@ -2,9 +2,10 @@
 #include <string>
 #include <random>
 
-#include "parlay/primitives.h"
-#include "parlay/random.h"
-#include "parlay/io.h"
+#include <parlay/primitives.h>
+#include <parlay/random.h>
+#include <parlay/io.h>
+#include <parlay/internal/get_time.h>
 
 #include "box_kdtree.h"
 

examples/counting_sort.cpp

@@ -6,6 +6,7 @@
 #include <parlay/primitives.h>
 #include <parlay/random.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "counting_sort.h"
 

examples/counting_sort.h

@@ -4,6 +4,7 @@
 #include <parlay/parallel.h>
 #include <parlay/sequence.h>
 #include <parlay/primitives.h>
+#include <parlay/internal/get_time.h>
 
 // **************************************************************
 // Counting sort

examples/delaunay.cpp

@@ -5,6 +5,7 @@
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
 #include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "delaunay.h"
 

examples/filter.cpp

@@ -3,6 +3,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 // **************************************************************
 // Driver code

examples/find_if.cpp

@@ -4,6 +4,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "find_if.h"
 

examples/flatten.cpp

@@ -1,7 +1,9 @@
 #include <iostream>
 #include <string>
+#include <cmath>
 
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "flatten.h"
 

examples/integer_sort.cpp

@@ -7,6 +7,7 @@
 #include <parlay/primitives.h>
 #include <parlay/random.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "integer_sort.h"
 
@@ -21,23 +22,23 @@ int main(int argc, char* argv[]) {
     try { n = std::stol(argv[1]); }
     catch (...) { std::cout << usage << std::endl; return 1; }
 
-    using int_type = int;
+    using int_type = unsigned int;
 
     parlay::random_generator gen;
     std::uniform_int_distribution<int_type> dis(0, n-1);
     int bits = std::ceil(std::log2(n));
 
-    // generate random long values
+    // generate random int_type values between 0 and n
     parlay::sequence<int_type> data = parlay::tabulate(n, [&] (long i) {
       auto r = gen[i];
       return dis(r);});
 
     parlay::internal::timer t("Time");
     parlay::sequence<int_type> result;
-    for (int i=0; i < 5; i++) {
-      result.clear();
+    for (int i = 0; i < 5; i++) {
+      result = data;
       t.start();
-      result = ::integer_sort(data,bits);
+      ::integer_sort(result, bits);
       t.next("integer_sort");
     }
 

examples/integer_sort.h

@@ -1,14 +1,11 @@
 #include <algorithm>
 #include <functional>
-#include <random>
+#include <cmath>
 
 #include <parlay/parallel.h>
 #include <parlay/primitives.h>
-#include <parlay/random.h>
 #include <parlay/slice.h>
-#include <parlay/utilities.h>
 
-#include "helper/heap_tree.h"
 #include "counting_sort.h"
 
 // **************************************************************
@@ -19,6 +16,7 @@
 // buckets based on the high bits and then recurses on each bucket.
 // The bottom up is a standard radix sort starting on low-order bits
 // and taking advantage of the stability of each counting sort.
+// Uses counting_sort for each block of the radix.
 //
 // Flips back and forth between in and out, with "inplace" keeping track
 // of whether the result should be in in (or if false, in out).
@@ -51,36 +49,35 @@ void radix_sort(Range in, Range out, long bits, bool inplace) {
   if (n < cutoff) 
     bottom_up_radix_sort(in, out, bits, 0, inplace);
   else {
-    // number of bits in bucket count (e.g. 8 would mean 256 buckets)
-    long radix_bits = std::min<long>(bits, std::ceil(std::log2(2*n/cutoff)));
+    // number of bits in radix 
+    long radix_bits = std::min<long>(bits, std::min<long>(10l, std::ceil(std::log2(2*n/cutoff))));
     long num_buckets = 1l << radix_bits;
 
     // extract the needed bits for the keys
     auto keys = parlay::delayed::tabulate(n, [&] (long i) {
       return (in[i] >> bits - radix_bits) & (num_buckets-1);});
 
-    // sort into the buckets
+    // sort in into the out based on keys
     auto offsets = counting_sort(in.begin(), in.end(), out.begin(), keys.begin(),
 				 num_buckets);
 
     // now recursively sort each bucket
     parlay::parallel_for(0, num_buckets, [&] (long i) {
-      long first = offsets[i];   // start of region
-      long last = offsets[i+1];  // end of region
+      long first = offsets[i];   // start of bucket
+      long last = offsets[i+1];  // end of bucket
       // note that order of in and out is flipped (as is inplace)
       radix_sort(out.cut(first,last), in.cut(first,last),
 		 bits - radix_bits, !inplace);
     }, 1);
   }
 }
 
-//  A wraper that calls integer_sort_
+// An inplace (i.e., result is in the same place as the input) integer_sort
+// Requires O(n) temp space
 template <typename Range>
-parlay::sequence<typename Range::value_type>
-integer_sort(Range& in, long bits) {
-  auto out = parlay::sequence<typename Range::value_type>::uninitialized(in.size());
+void integer_sort(Range& in, long bits) {
+  auto tmp = parlay::sequence<typename Range::value_type>::uninitialized(in.size());
   auto in_slice = parlay::make_slice(in);
-  auto out_slice = parlay::make_slice(out);
-  radix_sort(in_slice, out_slice, bits, false);
-  return out;
+  auto tmp_slice = parlay::make_slice(tmp);
+  radix_sort(in_slice, tmp_slice, bits, true);
 }

examples/karatsuba.cpp

@@ -5,6 +5,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "karatsuba.h"
 

examples/kmeans_pp.cpp

@@ -5,6 +5,7 @@
 #include <parlay/primitives.h>
 #include <parlay/random.h>
 #include <parlay/delayed.h>
+#include <parlay/internal/get_time.h>
 
 #include "kmeans_pp.h"
 

examples/knn.cpp

@@ -2,9 +2,10 @@
 #include <string>
 #include <random>
 
-#include "parlay/primitives.h"
-#include "parlay/random.h"
-#include "parlay/io.h"
+#include <parlay/primitives.h>
+#include <parlay/random.h>
+#include <parlay/io.h>
+#include <parlay/internal/get_time.h>
 
 #include "knn.h"
 

examples/knuth_shuffle.cpp

@@ -4,6 +4,7 @@
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
 #include <parlay/io.h>
+#include <parlay/internal/get_time.h>
 
 #include "knuth_shuffle.h"
 

examples/kth_smallest.cpp

@@ -4,6 +4,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "kth_smallest.h"
 

examples/ldd_connectivity.cpp

@@ -3,6 +3,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "ldd_connectivity.h"
 #include "helper/graph_utils.h"

examples/ldd_connectivity.h

@@ -8,7 +8,13 @@
 #include "star_connectivity.h"
 
 // **************************************************************
-// Graph Connectivity using Low Diameter Decomposition
+// Graph Connectivity using Low Diameter Decomposition (LDD)
+// From the paper:
+//  A simple and practical linear-work parallel algorithm for connectivity
+//  Shun, Dhulipala, Blelloch
+//  SPAA '14
+// The theoretical algorithms applied LDD recursively.   This implementation
+// just uses one level, then switches to star contraction.
 // **************************************************************
 template <typename vertex>
 using graph = parlay::sequence<parlay::sequence<vertex>>;
@@ -29,7 +35,7 @@ ldd_connectivity(const graph<vertex>& G, float beta = .5) {
 
   // Extract the remaining vertices
   parlay::sequence<vertex> V_r = parlay::pack_index<vertex>(parlay::tabulate(n, [&] (vertex v) {
-							  return P[v] == v;}));
+							       return P[v] == v;}));
 
   // Finish off with star contraction on remaining graph
   auto roots = star_contract(E_r, V_r, P, parlay::random_generator(0));

examples/low_diameter_decomposition.cpp

@@ -3,6 +3,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "low_diameter_decomposition.h"
 #include "helper/graph_utils.h"

examples/maximal_independent_set.cpp

@@ -3,6 +3,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "maximal_independent_set.h"
 #include "helper/graph_utils.h"

examples/maximal_matching.cpp

@@ -5,6 +5,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "maximal_matching.h"
 #include "helper/graph_utils.h"

examples/mcss.cpp

@@ -4,6 +4,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "mcss.h"
 

examples/mergesort.cpp

@@ -6,6 +6,7 @@
 #include <parlay/primitives.h>
 #include <parlay/random.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "mergesort.h"
 

examples/minimum_edit_distance.cpp

@@ -4,6 +4,7 @@
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
 #include <parlay/io.h>
+#include <parlay/internal/get_time.h>
 
 #include "minimum_edit_distance.h"
 

examples/oct_tree.cpp

@@ -2,8 +2,9 @@
 #include <string>
 #include <random>
 
-#include "parlay/primitives.h"
-#include "parlay/random.h"
+#include <parlay/primitives.h>
+#include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "oct_tree.h"
 

examples/pagerank.cpp

@@ -4,6 +4,7 @@
 
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "pagerank.h"
 #include "helper/graph_utils.h"

examples/primes.cpp

@@ -2,6 +2,7 @@
 #include <string>
 
 #include <parlay/sequence.h>
+#include <parlay/internal/get_time.h>
 
 #include "primes.h"
 

examples/ray_trace.cpp

@@ -2,9 +2,10 @@
 #include <string>
 #include <random>
 
-#include "parlay/primitives.h"
-#include "parlay/random.h"
-#include "parlay/io.h"
+#include <parlay/primitives.h>
+#include <parlay/random.h>
+#include <parlay/io.h>
+#include <parlay/internal/get_time.h>
 
 #include "ray_trace.h"
 

examples/rectangle_intersection.cpp

@@ -2,8 +2,9 @@
 #include <string>
 #include <random>
 
-#include "parlay/primitives.h"
-#include "parlay/random.h"
+#include <parlay/primitives.h>
+#include <parlay/random.h>
+#include <parlay/internal/get_time.h>
 
 #include "rectangle_intersection.h"
 

examples/reduce.cpp

@@ -4,6 +4,7 @@
 #include <parlay/primitives.h>
 #include <parlay/sequence.h>
 #include <parlay/monoid.h>
+#include <parlay/internal/get_time.h>
 
 #include "reduce.h"