From 16e4f89c44c3be927f669c8800ba4aaa5cd3012e Mon Sep 17 00:00:00 2001
From: Apurba Das <adas@iastate.edu>
Date: Sat, 9 Jun 2018 13:45:31 -0500
Subject: [PATCH] source code update
---
.../Algorithm/parMCE/ParMCEDegeneracy.java | 92 +++--------
.../java/Algorithm/parMCE/ParMCEDegree.java | 153 ++++++------------
.../Algorithm/parMCE/ParMCETriangles.java | 90 +++--------
3 files changed, 90 insertions(+), 245 deletions(-)
diff --git a/src/main/java/Algorithm/parMCE/ParMCEDegeneracy.java b/src/main/java/Algorithm/parMCE/ParMCEDegeneracy.java
index b38bc09..ce44dce 100644
--- a/src/main/java/Algorithm/parMCE/ParMCEDegeneracy.java
+++ b/src/main/java/Algorithm/parMCE/ParMCEDegeneracy.java
@@ -88,39 +88,42 @@ public class ParMCEDegeneracy {
Collection<Integer> NghOfu = Ngh(G, u);
- Map<Integer, Integer> Ext = new HashMap<>();
+ //List<Integer> Ext = new ArrayList<>();
-
- int[] ExtForFini = new int[CAND.size()];
+ int[] Ext = new int[CAND.size()];
+
- int index = 0;
- for (int w : CAND) {
+ int index=0;
+ for(int w : CAND){
if (!NghOfu.contains(w)) {
- Ext.put(w, index);
- ExtForFini[index] = w;
- index++;
+ Ext[index++] = w;
}
}
- int size = Ext.size();
+ int size = index;
+
if (size > 0) {
- Ext.keySet().parallelStream().forEach(q -> {
+ IntStream.range(0, size).parallel().forEach(i -> {
- // long start = System.currentTimeMillis();
- int idx = Ext.get(q);
+ int q = Ext[i];
TreeSet<Integer> Kq = new TreeSet<>();
Kq.addAll(K);
Kq.add(q);
Collection<Integer> NghOfq = Ngh(G, q);
- Collection<Integer> CANDq = computeNewCand(CAND, NghOfq, Ext, idx);
- Collection<Integer> FINIq = computeNewFini(FINI, NghOfq, Ext, ExtForFini, idx);
+ HashSet<Integer> CANDq = SetOperations.intersect(CAND, NghOfq);
+
- // loopoverhead += (System.currentTimeMillis() - start);
+ HashSet<Integer> FINIq = SetOperations.intersect(FINI, NghOfq);
- // loopoverhead.addAndGet(delta);
+ for (int j = 0; j < i; j++) {
+ int p = Ext[j];
+ CANDq.remove(p);
+ if (NghOfq.contains(p))
+ FINIq.add(p);
+ }
try {
expand(Kq, CANDq, FINIq);
@@ -133,60 +136,6 @@ public class ParMCEDegeneracy {
}
}
-
- private Collection<Integer> computeNewFini(Collection<Integer> fini, Collection<Integer> nghOfq,
- Map<Integer, Integer> ext, int[] extforfini, int idx) {
-
- Collection<Integer> R = new HashSet<>();
- if (nghOfq.size() < fini.size()) {
- for (int w : nghOfq) {
- if (fini.contains(w)) {
- R.add(w);
- }
- if (ext.containsKey(w) && (ext.get(w) < idx))
- R.add(w);
- }
- }
- else {
- for (int w : fini) {
- if (nghOfq.contains(w))
- R.add(w);
- }
- for(int i=0; i< idx; i++){
- int x = extforfini[i];
- if(nghOfq.contains(x))
- R.add(x);
- }
- }
- return R;
- }
-
- private Collection<Integer> computeNewCand(Collection<Integer> cand, Collection<Integer> nghOfq,
- Map<Integer, Integer> ext, int idx) {
-
- Collection<Integer> R = new HashSet<>();
- if (cand.size() > nghOfq.size()) {
- for (int w : nghOfq) {
- if (cand.contains(w)) {
- if (ext.containsKey(w) && (ext.get(w) > idx))
- R.add(w);
- if (!ext.containsKey(w))
- R.add(w);
- }
- }
- } else {
- for (int w : cand) {
- if (nghOfq.contains(w)) {
- if (ext.containsKey(w) && (ext.get(w) > idx))
- R.add(w);
- if (!ext.containsKey(w))
- R.add(w);
- }
- }
- }
- return R;
- }
-
public Collection<Integer> Ngh(Graph G, int u) {
return G.AdjList.get(u);
}
@@ -233,6 +182,7 @@ public class ParMCEDegeneracy {
System.out.println("ParMCEDegeneracy - Degeneracy based vertex ordering");
System.out.println("Input Graph: " + args[0]);
+ System.out.println("Number of threads used: " + args[1]);
Graph G = new Graph(args[0]);
@@ -253,7 +203,7 @@ public class ParMCEDegeneracy {
// System.out.println("number of maximal cliques: " + CLQ.size());
System.out.println("number of maximal cliques: " + count.get());
System.out.println(
- "Parallel time taken to compute maximal cliques in " + args[0] + " : " + elapsed / 1000. + " sec.");
+ "Parallel time taken to compute maximal cliques in " + args[0] + " : " + elapsed / 1000 + " sec.");
// System.out.println("Total loop overhead : " + loopoverhead/1000 +
// " sec.");
} catch (IOException e) {
diff --git a/src/main/java/Algorithm/parMCE/ParMCEDegree.java b/src/main/java/Algorithm/parMCE/ParMCEDegree.java
index a4b351e..d166fe3 100644
--- a/src/main/java/Algorithm/parMCE/ParMCEDegree.java
+++ b/src/main/java/Algorithm/parMCE/ParMCEDegree.java
@@ -1,6 +1,6 @@
package Algorithm.parMCE;
-/**
- * ParMCEDegree : uses modified ParTTT along with executing on subproblems in parallel.
+/**This Algorithm generates all maximal cliques of an undirected graph G
+ * based on Tomita et al. with title "The worst-case time complexity for generating all maximal cliques and computational experiments"
* */
import java.util.*;
@@ -18,12 +18,10 @@ import java.util.concurrent.ForkJoinPool;
public class ParMCEDegree {
-
private static Collection<BitSet> CLQ;
private static ConcurrentMap<Long, Integer> timeToFrequency;
public int clqcnt;
- private FileWriter cw;
private static Graph G;
@@ -31,18 +29,12 @@ public class ParMCEDegree {
private static HashMap<Integer, HashSet<Integer>> MapVE;
- static long loopoverhead;
-
- public ParMCEDegree(Graph g, String ofname) throws IOException {
+ public ParMCEDegree(Graph g) throws IOException {
this.G = g;
count = new AtomicLong(0);
- loopoverhead = 0;
-
- CLQ = ConcurrentHashMap.newKeySet();
-
G.vertices.parallelStream().forEach(v -> {
Set<Integer> CAND = new HashSet<Integer>();
Set<Integer> FINI = new HashSet<Integer>();
@@ -72,12 +64,12 @@ public class ParMCEDegree {
e.printStackTrace();
}
});
-
+
}
public void expand(TreeSet<Integer> K, Collection<Integer> CAND, Collection<Integer> FINI) throws IOException {
if (CAND.isEmpty() && FINI.isEmpty()) {
-
+
count.incrementAndGet();
return;
@@ -87,40 +79,44 @@ public class ParMCEDegree {
int u = find_u(CAND, FINI);
Collection<Integer> NghOfu = Ngh(G, u);
-
- Map<Integer, Integer> Ext = new HashMap<>();
+ //List<Integer> Ext = new ArrayList<>();
+
- int[] ExtForFini = new int[CAND.size()];
+ int[] Ext = new int[CAND.size()];
+
int index = 0;
- for (int w : CAND) {
+ for(int w : CAND){
if (!NghOfu.contains(w)) {
- Ext.put(w, index);
- ExtForFini[index] = w;
- index++;
+ Ext[index++] = w;
}
}
- int size = Ext.size();
+ int size = index;
+
if (size > 0) {
- Ext.keySet().parallelStream().forEach(q -> {
+ IntStream.range(0, size).parallel().forEach(i -> {
- // long start = System.currentTimeMillis();
- int idx = Ext.get(q);
+ int q = Ext[i];
TreeSet<Integer> Kq = new TreeSet<>();
Kq.addAll(K);
Kq.add(q);
Collection<Integer> NghOfq = Ngh(G, q);
- Collection<Integer> CANDq = computeNewCand(CAND, NghOfq, Ext, idx);
- Collection<Integer> FINIq = computeNewFini(FINI, NghOfq, Ext, ExtForFini, idx);
+ HashSet<Integer> CANDq = SetOperations.intersect(CAND, NghOfq);
+
- // loopoverhead += (System.currentTimeMillis() - start);
+ HashSet<Integer> FINIq = SetOperations.intersect(FINI, NghOfq);
- // loopoverhead.addAndGet(delta);
+ for (int j = 0; j < i; j++) {
+ int p = Ext[j];
+ CANDq.remove(p);
+ if (NghOfq.contains(p))
+ FINIq.add(p);
+ }
try {
expand(Kq, CANDq, FINIq);
@@ -134,89 +130,38 @@ public class ParMCEDegree {
}
- private Collection<Integer> computeNewFini(Collection<Integer> fini, Collection<Integer> nghOfq,
- Map<Integer, Integer> ext, int[] extforfini, int idx) {
-
- Collection<Integer> R = new HashSet<>();
- if (nghOfq.size() < fini.size()) {
- for (int w : nghOfq) {
- if (fini.contains(w)) {
- R.add(w);
- }
- if (ext.containsKey(w) && (ext.get(w) < idx))
- R.add(w);
- }
- }
- else {
- for (int w : fini) {
- if (nghOfq.contains(w))
- R.add(w);
- }
- for(int i=0; i< idx; i++){
- int x = extforfini[i];
- if(nghOfq.contains(x))
- R.add(x);
- }
- }
- return R;
- }
-
- private Collection<Integer> computeNewCand(Collection<Integer> cand, Collection<Integer> nghOfq,
- Map<Integer, Integer> ext, int idx) {
-
- Collection<Integer> R = new HashSet<>();
- if (cand.size() > nghOfq.size()) {
- for (int w : nghOfq) {
- if (cand.contains(w)) {
- if (ext.containsKey(w) && (ext.get(w) > idx))
- R.add(w);
- if (!ext.containsKey(w))
- R.add(w);
- }
- }
- } else {
- for (int w : cand) {
- if (nghOfq.contains(w)) {
- if (ext.containsKey(w) && (ext.get(w) > idx))
- R.add(w);
- if (!ext.containsKey(w))
- R.add(w);
- }
- }
- }
- return R;
- }
-
public Collection<Integer> Ngh(Graph G, int u) {
+
return G.AdjList.get(u);
}
- public int find_u(Collection<Integer> CAND,
- Collection<Integer> FINI /*
- * Set<String> SUBG
- */) {
-
- Map<Integer, Integer> vToIntersectSize = new ConcurrentHashMap<>();
+ public int find_u(Collection<Integer> CAND, Collection<Integer> FINI /*
+ * Set<String> SUBG
+ */) {
+ Map<Integer, Integer> vToIntersectSize = new ConcurrentHashMap<>();
+
CAND.parallelStream().forEach(u -> {
-
- Collection<Integer> Q = SetOperations.intersect(Ngh(G, u), CAND);
+
+ HashSet<Integer> Q = SetOperations.intersect(Ngh(G,u), CAND);
+
vToIntersectSize.put(u, Q.size());
-
+
});
-
+
FINI.parallelStream().forEach(u -> {
-
- Collection<Integer> Q = SetOperations.intersect(Ngh(G, u), CAND);
+
+ HashSet<Integer> Q = SetOperations.intersect(Ngh(G,u), CAND);
+
vToIntersectSize.put(u, Q.size());
-
+
});
-
+
int size = -1;
int v = 0;
- for (int u : vToIntersectSize.keySet()) {
+ for(int u : vToIntersectSize.keySet()) {
int tmp = vToIntersectSize.get(u);
- if (size < tmp) {
+ if(size < tmp) {
size = tmp;
v = u;
}
@@ -230,24 +175,24 @@ public class ParMCEDegree {
// TODO Auto-generated method stub
System.setProperty("java.util.concurrent.ForkJoinPool.common.parallelism", args[1]);
-
- System.out.println("ParMCEDegree - Degree based vertex ordering");
+
+ System.out.println("ParMCEDegree : degree based vertex ordering");
System.out.println("Input Graph: " + args[0]);
+ System.out.println("Number of threads used: " + args[1]);
Graph G = new Graph(args[0]);
System.out.println("Graph Reading Complete");
+
try {
long t1 = System.currentTimeMillis();
- new ParMCEDegree(G, "output_TTT");
+ new ParMCEDegree(G);
long elapsed = System.currentTimeMillis() - t1;
- // System.out.println("number of maximal cliques: " + CLQ.size());
+
System.out.println("number of maximal cliques: " + count.get());
System.out.println(
- "Parallel time taken to compute maximal cliques in " + args[0] + " : " + elapsed / 1000. + " sec.");
- // System.out.println("Total loop overhead : " + loopoverhead/1000 +
- // " sec.");
+ "Parallel time taken to compute maximal cliques in " + args[0] + " : " + elapsed / 1000 + " sec.");
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
diff --git a/src/main/java/Algorithm/parMCE/ParMCETriangles.java b/src/main/java/Algorithm/parMCE/ParMCETriangles.java
index 11bf8b3..af9fb1c 100644
--- a/src/main/java/Algorithm/parMCE/ParMCETriangles.java
+++ b/src/main/java/Algorithm/parMCE/ParMCETriangles.java
@@ -88,39 +88,42 @@ public class ParMCETriangles {
Collection<Integer> NghOfu = Ngh(G, u);
- Map<Integer, Integer> Ext = new HashMap<>();
+ //List<Integer> Ext = new ArrayList<>();
-
- int[] ExtForFini = new int[CAND.size()];
+ int[] Ext = new int[CAND.size()];
+
int index = 0;
- for (int w : CAND) {
+ for(int w : CAND){
if (!NghOfu.contains(w)) {
- Ext.put(w, index);
- ExtForFini[index] = w;
- index++;
+ Ext[index++] = w;
}
}
- int size = Ext.size();
+ int size = index;
+
if (size > 0) {
- Ext.keySet().parallelStream().forEach(q -> {
+ IntStream.range(0, size).parallel().forEach(i -> {
- // long start = System.currentTimeMillis();
- int idx = Ext.get(q);
+ int q = Ext[i];
TreeSet<Integer> Kq = new TreeSet<>();
Kq.addAll(K);
Kq.add(q);
Collection<Integer> NghOfq = Ngh(G, q);
- Collection<Integer> CANDq = computeNewCand(CAND, NghOfq, Ext, idx);
- Collection<Integer> FINIq = computeNewFini(FINI, NghOfq, Ext, ExtForFini, idx);
+ HashSet<Integer> CANDq = SetOperations.intersect(CAND, NghOfq);
+
- // loopoverhead += (System.currentTimeMillis() - start);
+ HashSet<Integer> FINIq = SetOperations.intersect(FINI, NghOfq);
- // loopoverhead.addAndGet(delta);
+ for (int j = 0; j < i; j++) {
+ int p = Ext[j];
+ CANDq.remove(p);
+ if (NghOfq.contains(p))
+ FINIq.add(p);
+ }
try {
expand(Kq, CANDq, FINIq);
@@ -133,60 +136,6 @@ public class ParMCETriangles {
}
}
-
- private Collection<Integer> computeNewFini(Collection<Integer> fini, Collection<Integer> nghOfq,
- Map<Integer, Integer> ext, int[] extforfini, int idx) {
-
- Collection<Integer> R = new HashSet<>();
- if (nghOfq.size() < fini.size()) {
- for (int w : nghOfq) {
- if (fini.contains(w)) {
- R.add(w);
- }
- if (ext.containsKey(w) && (ext.get(w) < idx))
- R.add(w);
- }
- }
- else {
- for (int w : fini) {
- if (nghOfq.contains(w))
- R.add(w);
- }
- for(int i=0; i< idx; i++){
- int x = extforfini[i];
- if(nghOfq.contains(x))
- R.add(x);
- }
- }
- return R;
- }
-
- private Collection<Integer> computeNewCand(Collection<Integer> cand, Collection<Integer> nghOfq,
- Map<Integer, Integer> ext, int idx) {
-
- Collection<Integer> R = new HashSet<>();
- if (cand.size() > nghOfq.size()) {
- for (int w : nghOfq) {
- if (cand.contains(w)) {
- if (ext.containsKey(w) && (ext.get(w) > idx))
- R.add(w);
- if (!ext.containsKey(w))
- R.add(w);
- }
- }
- } else {
- for (int w : cand) {
- if (nghOfq.contains(w)) {
- if (ext.containsKey(w) && (ext.get(w) > idx))
- R.add(w);
- if (!ext.containsKey(w))
- R.add(w);
- }
- }
- }
- return R;
- }
-
public Collection<Integer> Ngh(Graph G, int u) {
return G.AdjList.get(u);
}
@@ -233,6 +182,7 @@ public class ParMCETriangles {
System.out.println("ParMCETriangles - Triangle count based vertex ordering");
System.out.println("Input Graph: " + args[0]);
+ System.out.println("Number of threads used: " + args[1]);
Graph G = new Graph(args[0]);
@@ -245,7 +195,7 @@ public class ParMCETriangles {
// System.out.println("number of maximal cliques: " + CLQ.size());
System.out.println("number of maximal cliques: " + count.get());
System.out.println(
- "Parallel time taken to compute maximal cliques in " + args[0] + " : " + elapsed / 1000. + " sec.");
+ "Parallel time taken to compute maximal cliques in " + args[0] + " : " + elapsed / 1000 + " sec.");
// System.out.println("Total loop overhead : " + loopoverhead/1000 +
// " sec.");
} catch (IOException e) {
--
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