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optimizations from profiling build_hyracks #68

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merged 13 commits into from
Dec 3, 2013
Merged

optimizations from profiling build_hyracks #68

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74d3449
BUILD-profile optimize: use static final EDGETYPE.values not values()
jakebiesinger Nov 21, 2013
cbfaed0
BUILD-profile optimize: only compile regex once
jakebiesinger Nov 21, 2013
6f40f96
BUILD-profile optimize: copy reference rather than deep copy in build
jakebiesinger Nov 21, 2013
d7025f3
reformat
jakebiesinger Nov 21, 2013
ea862b4
BUILD-profile optimize: remove getLengths() and return offsets from c…
jakebiesinger Nov 21, 2013
b6e4742
MERGE-profile optimize: in/out formats use tmp references
jakebiesinger Nov 22, 2013
f09b83a
MERGE-profile optimize: less reading from conf; use global debug vals
jakebiesinger Nov 22, 2013
71c5bc9
MERGE-profile optimize: random uses hash, not many calls, to break co…
jakebiesinger Nov 22, 2013
878a6b0
MERGE-profile optimize: don't send unnecessary edges in MERGE
jakebiesinger Nov 24, 2013
56e3b9b
MERGE-profile optimize: only send non-overlapping parts of kmers
jakebiesinger Nov 24, 2013
3c0a130
fix coverage bug form short kmers in MERGE messages
jakebiesinger Nov 25, 2013
f3fb261
fix bug in coverage; simplify merging with truncated kmers in messages
jakebiesinger Dec 2, 2013
17b8e0d
Merge remote-tracking branch 'origin/genomix/fullstack_genomix' into …
jakebiesinger Dec 2, 2013
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2 changes: 1 addition & 1 deletion genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenerateGraphViz.java
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Expand Up @@ -148,7 +148,7 @@ public static byte[] convertGraphToImg(JobConf conf, String srcDir, String destD

public static String convertEdgeToGraph(String outputNode, Node value, GRAPH_TYPE graphType) {
String outputEdge = "";
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
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Could you explain the different between the values() and value ?

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values() is a function that's automatically generated for all enum types and which returns a static final array including all the enum values (so FF, FR, RF and RR in this case). values as I've added here is shadowing that generated function with a public static final enum[]. I'm essentially bypassing the getter for this enum type, which was taking up to 5% of the total runtime.

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I can rename away from .values so it's not so ambiguous. In fact, it's weird that java lets me have a field called values when I can also call the function values().

for (Entry<VKmer, ReadIdSet> e : value.getEdgeMap(et).entrySet()) {
String destNode = "";
switch (graphType) {
Expand Down
4 changes: 2 additions & 2 deletions genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/DIR.java
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Expand Up @@ -44,11 +44,11 @@ public static byte fromSet(EnumSet<DIR> set) {
return b;
}

public final EnumSet<EDGETYPE> edgeTypes() {
public final EDGETYPE[] edgeTypes() {
return edgeTypesInDir(this);
}

public static final EnumSet<EDGETYPE> edgeTypesInDir(DIR direction) {
public static final EDGETYPE[] edgeTypesInDir(DIR direction) {
return direction == DIR.REVERSE ? EDGETYPE.INCOMING : EDGETYPE.OUTGOING;
}

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5 changes: 3 additions & 2 deletions genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EDGETYPE.java
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Expand Up @@ -26,8 +26,9 @@ public final byte get() {
return val;
}

public static final EnumSet<EDGETYPE> INCOMING = EnumSet.of(RF, RR);
public static final EnumSet<EDGETYPE> OUTGOING = EnumSet.of(FF, FR);
public static final EDGETYPE[] values = {FF, FR, RF, RR};
public static final EDGETYPE[] INCOMING = {RF, RR};
public static final EDGETYPE[] OUTGOING = {FF, FR};

public static EDGETYPE fromByte(short b) {
b &= MASK;
Expand Down
24 changes: 12 additions & 12 deletions genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Node.java
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Expand Up @@ -212,7 +212,7 @@ public EDGETYPE getNeighborEdgeType(DIR direction) {
if (degree(direction) != 1)
throw new IllegalArgumentException(
"getEdgetypeFromDir is used on the case, in which the vertex has and only has one EDGETYPE!");
EnumSet<EDGETYPE> ets = direction.edgeTypes();
EDGETYPE[] ets = direction.edgeTypes();
for (EDGETYPE et : ets) {
if (edges[et.get()] != null && getEdgeMap(et).size() > 0) {
return et;
Expand Down Expand Up @@ -268,7 +268,7 @@ public EdgeMap[] getEdges() {
}

public void setEdges(EdgeMap[] edges) {
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
setEdgeMap(et, edges[et.get()]);
}
}
Expand Down Expand Up @@ -343,7 +343,7 @@ public void setFlippedReadIds(ReadHeadSet flippedReadIds) {
*/
public int getSerializedLength() {
int length = Byte.SIZE / 8; // byte header
for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
if (edges[e.get()] != null && edges[e.get()].size() > 0) {
length += edges[e.get()].getLengthInBytes();
}
Expand Down Expand Up @@ -377,7 +377,7 @@ public void setAsCopy(byte[] data, int offset) {
reset();
byte activeFields = data[offset];
offset += 1;
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
// et.get() is the index of the bit; if non-zero, we this edge is present in the stream
if ((activeFields & (1 << et.get())) != 0) {
getEdgeMap(et).setAsCopy(data, offset);
Expand Down Expand Up @@ -406,7 +406,7 @@ public void setAsReference(byte[] data, int offset) {
reset();
byte activeFields = data[offset];
offset += 1;
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
// et.get() is the index of the bit; if non-zero, we this edge is present in the stream
if ((activeFields & (1 << et.get())) != 0) {
getEdgeMap(et).setAsReference(data, offset);
Expand All @@ -433,7 +433,7 @@ public void setAsReference(byte[] data, int offset) {

public static void write(Node n, DataOutput out) throws IOException {
out.writeByte(n.getActiveFields());
for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
if (n.edges[e.get()] != null && n.edges[e.get()].size() > 0) {
n.edges[e.get()].write(out);
}
Expand Down Expand Up @@ -461,7 +461,7 @@ public void write(DataOutput out) throws IOException {
public void readFields(DataInput in) throws IOException {
reset();
byte activeFields = in.readByte();
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
// et.get() is the index of the bit; if non-zero, we this edge is present in the stream
if ((activeFields & (1 << et.get())) != 0) {
getEdgeMap(et).readFields(in);
Expand Down Expand Up @@ -492,7 +492,7 @@ protected static class NODE_FIELDS {
protected byte getActiveFields() {
byte fields = 0;
// bits 0-3 are for presence of edges
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
if (edges[et.get()] != null && edges[et.get()].size() > 0) {
fields |= 1 << et.get();
}
Expand Down Expand Up @@ -530,7 +530,7 @@ public boolean equals(Object o) {
return false;

Node nw = (Node) o;
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
// If I'm null, return false if he's not null; otherwise, do a regular .equals
if (edges[et.get()] == null ? nw.edges[et.get()] != null : edges[et.get()].equals(nw.edges[et.get()])) {
return false;
Expand All @@ -550,7 +550,7 @@ public boolean equals(Object o) {
public String toString() {
StringBuilder sbuilder = new StringBuilder();
sbuilder.append('{');
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
sbuilder.append(et + ":").append(edges[et.get()] == null ? "null" : edges[et.get()].toString())
.append('\t');
}
Expand Down Expand Up @@ -740,7 +740,7 @@ public void mergeEdges(EDGETYPE edgeType, Node other) {

protected void addEdges(boolean flip, Node other) {
if (!flip) {
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
unionUpdateEdgeMap(et, et, other.edges);
}
} else {
Expand Down Expand Up @@ -848,7 +848,7 @@ protected void mergeUnflippedAndFlippedReadIDs(EDGETYPE edgeType, Node other) {
* Debug helper function to find the edge associated with the given kmer, checking all directions. If the edge doesn't exist in any direction, returns null
*/
public NeighborInfo findEdge(final VKmer kmer) {
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
if (edges[et.get()] != null && edges[et.get()].containsKey(kmer)) {
return new NeighborInfo(et, kmer, edges[et.get()].get(kmer));
}
Expand Down
13 changes: 7 additions & 6 deletions genomix/genomix-data/src/test/java/edu/uci/ics/genomix/type/NodeTest.java
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Expand Up @@ -7,6 +7,7 @@
import java.io.IOException;
import java.util.AbstractMap.SimpleEntry;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.EnumSet;
import java.util.Iterator;
import java.util.Map;
Expand Down Expand Up @@ -48,7 +49,7 @@ public static void assembleNodeRandomly(Node targetNode, int orderNum) {
ArrayList<SimpleEntry<VKmer, ReadIdSet>> sampleList;
SimpleEntry<VKmer, ReadIdSet> edgeId;
EdgeMap edge;
for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
sampleList = new ArrayList<SimpleEntry<VKmer, ReadIdSet>>();
for (int i = 0; i < min + (int) (Math.random() * ((max - min) + 1)); i++) {
String edgeStr = generateString(orderNum);
Expand Down Expand Up @@ -77,7 +78,7 @@ public static void assembleNodeRandomly(Node targetNode, int orderNum) {

public static void printSrcNodeInfo(Node srcNode) {
System.out.println("InternalKmer: " + srcNode.getInternalKmer().toString());
for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
System.out.println(e.toString());
for (Map.Entry<VKmer, ReadIdSet> iter : srcNode.getEdgeMap(e).entrySet()) {
System.out.println("edgeKmer: " + iter.getKey().toString());
Expand All @@ -101,7 +102,7 @@ public static void printSrcNodeInfo(Node srcNode) {

public static void compareTwoNodes(Node et1, Node et2) {
Assert.assertEquals(et1.getInternalKmer().toString(), et2.getInternalKmer().toString());
for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
Assert.assertEquals(et1.getEdgeMap(e).size(), et2.getEdgeMap(e).size());
for (Map.Entry<VKmer, ReadIdSet> iter1 : et1.getEdgeMap(e).entrySet()) {
Map.Entry<VKmer, ReadIdSet> iter2 = et2.getEdgeMap(e).pollFirstEntry();
Expand All @@ -127,7 +128,7 @@ public static void getEdgeMapRandomly(EdgeMap edgeMap, int orderNum) {
int max = 4;
ArrayList<SimpleEntry<VKmer, ReadIdSet>> sampleList;
SimpleEntry<VKmer, ReadIdSet> edgeId;
for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
sampleList = new ArrayList<SimpleEntry<VKmer, ReadIdSet>>();
for (int i = 0; i < min + (int) (Math.random() * ((max - min) + 1)); i++) {
String edgeStr = generateString(orderNum);
Expand Down Expand Up @@ -188,9 +189,9 @@ public void testDIR() throws IOException {
Assert.assertEquals(0b11 << 2, DIR.fromSet(EnumSet.allOf(DIR.class)));
Assert.assertEquals(0b00 << 2, DIR.fromSet(EnumSet.noneOf(DIR.class)));

EnumSet<EDGETYPE> edgeTypes1 = testDir1.edgeTypes();
EnumSet<EDGETYPE> edgeTypes1 = EnumSet.copyOf(Arrays.asList(testDir1.edgeTypes()));
EnumSet<EDGETYPE> edgeExample1 = EnumSet.noneOf(EDGETYPE.class);
EnumSet<EDGETYPE> edgeTypes2 = testDir2.edgeTypes();
EnumSet<EDGETYPE> edgeTypes2 = EnumSet.copyOf(Arrays.asList(testDir2.edgeTypes()));
EnumSet<EDGETYPE> edgeExample2 = EnumSet.noneOf(EDGETYPE.class);
edgeExample1.add(EDGETYPE.FF);
edgeExample1.add(EDGETYPE.FR);
Expand Down
2 changes: 1 addition & 1 deletion ...hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
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Expand Up @@ -37,7 +37,7 @@ public void reduce(VKmer key, Iterator<Node> values, OutputCollector<VKmer, Node
Node curNode;
while (values.hasNext()) {
curNode = values.next();
for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
outputNode.getEdgeMap(e).unionUpdate(curNode.getEdgeMap(e));
}
outputNode.getUnflippedReadIds().addAll(curNode.getUnflippedReadIds());
Expand Down
2 changes: 1 addition & 1 deletion genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GraphStatistics.java
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Expand Up @@ -72,7 +72,7 @@ public void map(VKmer key, Node value, OutputCollector<Text, LongWritable> outpu

long totalEdgeReads = 0;
long totalSelf = 0;
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
for (Entry<VKmer, ReadIdSet> e : value.getEdgeMap(et).entrySet()) {
totalEdgeReads += e.getValue().size();
if (e.getKey().equals(key)) {
Expand Down
4 changes: 2 additions & 2 deletions ...c/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/AggregateKmerAggregateFactory.java
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Expand Up @@ -106,7 +106,7 @@ public void init(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, i
// }
// }

for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
localUniNode.getEdgeMap(e).unionUpdate((readNode.getEdgeMap(e)));
}
localUniNode.getUnflippedReadIds().addAll(readNode.getUnflippedReadIds());
Expand All @@ -121,7 +121,7 @@ public void aggregate(IFrameTupleAccessor accessor, int tIndex, IFrameTupleAcces
Node localUniNode = (Node) state.state;

readNode.setAsCopy(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
for (EDGETYPE e : EDGETYPE.values()) {
for (EDGETYPE e : EDGETYPE.values) {
localUniNode.getEdgeMap(e).unionUpdate(readNode.getEdgeMap(e));
}
localUniNode.getUnflippedReadIds().addAll(readNode.getUnflippedReadIds());
Expand Down
9 changes: 5 additions & 4 deletions .../src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
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Expand Up @@ -54,6 +54,8 @@ public class ReadsKeyValueParserFactory implements IKeyValueParserFactory<LongWr
private final ConfFactory confFactory;

public static final RecordDescriptor readKmerOutputRec = new RecordDescriptor(new ISerializerDeserializer[2]);

private static final Pattern genePattern = Pattern.compile("[AGCT]+");

public ReadsKeyValueParserFactory(JobConf conf) throws HyracksDataException {
confFactory = new ConfFactory(conf);
Expand Down Expand Up @@ -131,7 +133,6 @@ public void parse(LongWritable key, Text value, IFrameWriter writer, String file
geneLine = rawLine[1];
}

Pattern genePattern = Pattern.compile("[AGCT]+");
Matcher geneMatcher = genePattern.matcher(geneLine);
if (geneMatcher.matches()) {
setReadInfo(mateId, readID, 0);
Expand Down Expand Up @@ -163,7 +164,7 @@ private void SplitReads(long readID, byte[] readLetters, IFrameWriter writer) {
DIR nextNodeDir = DIR.FORWARD;

/* middle kmer */
nextNode.reset();
nextNode = new Node();
nextNode.setAverageCoverage(1);
nextForwardKmer.setAsCopy(curForwardKmer);
for (int i = Kmer.getKmerLength(); i < readLetters.length; i++) {
Expand All @@ -176,9 +177,9 @@ private void SplitReads(long readID, byte[] readLetters, IFrameWriter writer) {

curForwardKmer.setAsCopy(nextForwardKmer);
curReverseKmer.setAsCopy(nextReverseKmer);
curNode.setAsCopy(nextNode);
curNode = nextNode;
curNodeDir = nextNodeDir;
nextNode.reset();
nextNode = new Node();
nextNode.setAverageCoverage(1);
}

Expand Down
6 changes: 3 additions & 3 deletions ...regelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/DeBruijnGraphCleanVertex.java
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Expand Up @@ -189,7 +189,7 @@ public VKmer getDestVertexId(DIR direction) {
+ getVertexValue().toString());

if (degree == 1) {
EnumSet<EDGETYPE> edgeTypes = direction.edgeTypes();
EDGETYPE[] edgeTypes = direction.edgeTypes();
for (EDGETYPE et : edgeTypes) {
if (getVertexValue().getEdgeMap(et).size() > 0)
return getVertexValue().getEdgeMap(et).firstKey();
Expand All @@ -205,7 +205,7 @@ public VKmer getDestVertexId(DIR direction) {
* check if I am a tandemRepeat
*/
public boolean isTandemRepeat(VertexValueWritable value) {
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
for (VKmer kmerToCheck : value.getEdgeMap(et).keySet()) {
if (kmerToCheck.equals(getVertexId())) {
repeatEdgetype = et;
Expand All @@ -222,7 +222,7 @@ public boolean isTandemRepeat(VertexValueWritable value) {
*/
public void broadcastKillself() {
VertexValueWritable vertex = getVertexValue();
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
for (VKmer dest : vertex.getEdgeMap(et).keySet()) {
outgoingMsg.reset();
outFlag &= EDGETYPE.CLEAR;
Expand Down
2 changes: 1 addition & 1 deletion .../main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/SimpleBubbleMergeVertex.java
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Expand Up @@ -221,7 +221,7 @@ public void receiveUpdates(Iterator<BubbleMergeMessage> msgIterator) {
deleteVertex(getVertexId());
break;
case ADD_READIDS:
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
EdgeMap edgeMap = incomingMsg.getNode().getEdgeMap(et);
if (edgeMap.size() > 0) {
getVertexValue().getEdgeMap(et).unionUpdate(edgeMap);
Expand Down
6 changes: 3 additions & 3 deletions ...x/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
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Expand Up @@ -112,10 +112,10 @@ public void updateNeighbors() {
}

DIR mergeDir = edgeType.dir();
EnumSet<EDGETYPE> mergeEdges = mergeDir.edgeTypes();
EDGETYPE[] mergeEdges = mergeDir.edgeTypes();

DIR updateDir = mergeDir.mirror();
EnumSet<EDGETYPE> updateEdges = updateDir.edgeTypes();
EDGETYPE[] updateEdges = updateDir.edgeTypes();

// prepare the update message s.t. the receiver can do a simple unionupdate
// that means we figure out any hops and place our merge-dir edges in the appropriate list of the outgoing msg
Expand Down Expand Up @@ -154,7 +154,7 @@ public void receiveUpdates(Iterator<M> msgIterator) {
// remove the edge to the node that will merge elsewhere
vertex.getEdgeMap(EDGETYPE.fromByte(incomingMsg.getFlag())).remove(incomingMsg.getSourceVertexId());
// add the node this neighbor will merge into
for (EDGETYPE edgeType : EDGETYPE.values()) {
for (EDGETYPE edgeType : EDGETYPE.values) {
vertex.getEdgeMap(edgeType).unionUpdate(incomingMsg.getEdgeList(edgeType));
}
updated = true;
Expand Down
4 changes: 2 additions & 2 deletions ...ain/java/edu/uci/ics/genomix/pregelix/operator/unrolltandemrepeat/UnrollTandemRepeat.java
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Expand Up @@ -47,7 +47,7 @@ public boolean repeatCanBeMerged() {
tmpValue.getEdgeMap(repeatEdgetype).remove(repeatKmer);
boolean hasFlip = false;
// pick one edge and flip
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
for (Entry<VKmer, ReadIdSet> edge : tmpValue.getEdgeMap(et).entrySet()) {
EDGETYPE flipEt = et.flipNeighbor();
tmpValue.getEdgeMap(flipEt).put(edge.getKey(), edge.getValue());
Expand Down Expand Up @@ -75,7 +75,7 @@ public void mergeTandemRepeat() {
getVertexValue().getEdgeMap(repeatEdgetype).remove(getVertexId());
boolean hasFlip = false;
/** pick one edge and flip **/
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
for (Entry<VKmer, ReadIdSet> edge : getVertexValue().getEdgeMap(et).entrySet()) {
EDGETYPE flipDir = et.flipNeighbor();
getVertexValue().getEdgeMap(flipDir).put(edge.getKey(), edge.getValue());
Expand Down
2 changes: 1 addition & 1 deletion ...nomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testhelper/BubbleAddVertex.java
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Expand Up @@ -123,7 +123,7 @@ public void addEdgeToInsertedBubble(EDGETYPE meToNewBubbleDir, VKmer insertedBub
}

public void setupEdgeForInsertedBubble() {
for (EDGETYPE et : EDGETYPE.values()) {
for (EDGETYPE et : EDGETYPE.values) {
edges[et.get()] = new EdgeMap();
}
edges[newBubbleToMajorEdgetype.get()].put(majorVertexId, new ReadIdSet(Arrays.asList(new Long(readId))));
Expand Down