add num-iteration
diff --git a/genomix/genomix-pregelix/data/webmap/part-1-out-100000 b/genomix/genomix-pregelix/data/webmap/part-1-out-100000
deleted file mode 100755
index 99d2fac..0000000
--- a/genomix/genomix-pregelix/data/webmap/part-1-out-100000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/webmap/part-1-out-200000 b/genomix/genomix-pregelix/data/webmap/part-1-out-200000
deleted file mode 100755
index 86413de..0000000
--- a/genomix/genomix-pregelix/data/webmap/part-1-out-200000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/webmap/part-1-out-25000 b/genomix/genomix-pregelix/data/webmap/part-1-out-25000
deleted file mode 100755
index 079f915..0000000
--- a/genomix/genomix-pregelix/data/webmap/part-1-out-25000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/webmap/part-1-out-50000 b/genomix/genomix-pregelix/data/webmap/part-1-out-50000
deleted file mode 100755
index d292c19..0000000
--- a/genomix/genomix-pregelix/data/webmap/part-1-out-50000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/webmap/part-1-out-500000 b/genomix/genomix-pregelix/data/webmap/part-1-out-500000
deleted file mode 100755
index 01fdc9e..0000000
--- a/genomix/genomix-pregelix/data/webmap/part-1-out-500000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/webmap/sequenceFileLongMergeTest b/genomix/genomix-pregelix/data/webmap/sequenceFileLongMergeTest
deleted file mode 100755
index ff27c48..0000000
--- a/genomix/genomix-pregelix/data/webmap/sequenceFileLongMergeTest
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/webmap/sequenceFileMergeTest b/genomix/genomix-pregelix/data/webmap/sequenceFileMergeTest
deleted file mode 100755
index b50d3f1..0000000
--- a/genomix/genomix-pregelix/data/webmap/sequenceFileMergeTest
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/webmap/sequenceShortFileMergeTest b/genomix/genomix-pregelix/data/webmap/sequenceShortFileMergeTest
deleted file mode 100755
index 96f7fc9..0000000
--- a/genomix/genomix-pregelix/data/webmap/sequenceShortFileMergeTest
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
index 12450b4..0f244dc 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
@@ -2,11 +2,8 @@
import java.util.Iterator;
-import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.BytesWritable;
import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
-import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import edu.uci.ics.genomix.type.Kmer;
import edu.uci.ics.genomix.type.KmerUtil;
@@ -50,7 +47,9 @@
public class MergeGraphVertex extends Vertex<BytesWritable, ValueStateWritable, NullWritable, MessageWritable>{
public static final String KMER_SIZE = "MergeGraphVertex.kmerSize";
+ public static final String ITERATIONS = "MergeGraphVertex.iteration";
public static int kmerSize = -1;
+ private int maxIteration = -1;
private byte[] tmpVertexId;
private byte[] tmpDestVertexId;
@@ -63,7 +62,6 @@
* @throws Exception
* @throws
*/
-
/**
* Load KmerSize
*/
@@ -71,6 +69,8 @@
public void compute(Iterator<MessageWritable> msgIterator) {
if(kmerSize == -1)
kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+ if (maxIteration < 0)
+ maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 100);
tmpVertexId = GraphVertexOperation.generateValidDataFromBytesWritable(getVertexId());
if (getSuperstep() == 1) {
if(GraphVertexOperation.isHeadVertex(getVertexValue().getValue())){
@@ -89,8 +89,7 @@
}
//path node sends message back to head node
- else if(getSuperstep()%2 == 0){
-
+ else if(getSuperstep()%2 == 0 && getSuperstep() <= maxIteration){
if(msgIterator.hasNext()){
tmpMsg = msgIterator.next();
@@ -147,7 +146,7 @@
}
}
//head node sends message to path node
- else if(getSuperstep()%2 == 1){
+ else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
while (msgIterator.hasNext()){
tmpMsg = msgIterator.next();
if(!tmpMsg.isRear()){
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
index ab0fb57..2d70fdf 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -36,6 +36,9 @@
@Option(name = "-kmer-size", usage = "the size of kmer", required = false)
public int sizeKmer;
+
+ @Option(name = "-num-iteration", usage = "max number of iterations, for pagerank job only", required = false)
+ public long numIteration = -1;
@Option(name = "-runtime-profiling", usage = "whether to do runtime profifling", required = false)
public String profiling = "false";
@@ -59,6 +62,10 @@
FileOutputFormat.setOutputPath(job, new Path(options.outputPath));
job.getConfiguration().setInt(MergeGraphVertex.KMER_SIZE, options.sizeKmer);
job.getConfiguration().setInt(LogAlgorithmForMergeGraphVertex.KMER_SIZE, options.sizeKmer);
+ if (options.numIteration > 0){
+ job.getConfiguration().setLong(MergeGraphVertex.ITERATIONS, options.numIteration);
+ //job.getConfiguration().setLong(LogAlgorithmForMergeGraphVertex.ITERATIONS, options.numIteration);
+ }
return options;
}