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baunsgaard pushed a commit to branch main
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The following commit(s) were added to refs/heads/main by this push:
new a06ea0f37c [SYSTEMDS-3832] MatrixBlock Append performance
a06ea0f37c is described below
commit a06ea0f37c01c47ca4251c6f95f7b49ffe05454e
Author: Sebastian Baunsgaard <[email protected]>
AuthorDate: Fri Feb 7 17:50:00 2025 +0100
[SYSTEMDS-3832] MatrixBlock Append performance
This commit contains a new performance measuring script for appending
matrices.
See the PR for performance details
Closes #2223
---
.../java/org/apache/sysds/performance/Main.java | 4 +
.../java/org/apache/sysds/performance/README.md | 7 ++
.../org/apache/sysds/performance/TimingUtils.java | 88 +++++++++++++---------
.../sysds/performance/compression/APerfTest.java | 25 ++++--
.../sysds/performance/matrix/MatrixAppend.java | 86 +++++++++++++++++++++
src/test/scripts/performance/append.sh | 43 +++++++++++
6 files changed, 210 insertions(+), 43 deletions(-)
diff --git a/src/test/java/org/apache/sysds/performance/Main.java
b/src/test/java/org/apache/sysds/performance/Main.java
index d7f85c9b78..fc749b56df 100644
--- a/src/test/java/org/apache/sysds/performance/Main.java
+++ b/src/test/java/org/apache/sysds/performance/Main.java
@@ -31,6 +31,7 @@ import
org.apache.sysds.performance.generators.FrameTransformFile;
import org.apache.sysds.performance.generators.GenMatrices;
import org.apache.sysds.performance.generators.IGenerate;
import org.apache.sysds.performance.generators.MatrixFile;
+import org.apache.sysds.performance.matrix.MatrixAppend;
import org.apache.sysds.performance.matrix.MatrixBinaryCellPerf;
import org.apache.sysds.performance.matrix.MatrixMulPerformance;
import org.apache.sysds.performance.matrix.MatrixReplacePerf;
@@ -135,6 +136,9 @@ public class Main {
case 1007:
Transform.main(args);
break;
+ case 1008:
+ MatrixAppend.main(args);
+ break;
default:
break;
}
diff --git a/src/test/java/org/apache/sysds/performance/README.md
b/src/test/java/org/apache/sysds/performance/README.md
index 20d2757c80..4945afd9ab 100644
--- a/src/test/java/org/apache/sysds/performance/README.md
+++ b/src/test/java/org/apache/sysds/performance/README.md
@@ -89,3 +89,10 @@ transform encode
```bash
java -jar
-agentpath:$HOME/Programs/profiler/lib/libasyncProfiler.so=start,event=cpu,file=temp/log.html
-XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1007
```
+
+
+append matrix sequence
+
+```bash
+./src/test/scripts/performance/append.sh
+```
diff --git a/src/test/java/org/apache/sysds/performance/TimingUtils.java
b/src/test/java/org/apache/sysds/performance/TimingUtils.java
index 506d49cc86..e1933438f5 100644
--- a/src/test/java/org/apache/sysds/performance/TimingUtils.java
+++ b/src/test/java/org/apache/sysds/performance/TimingUtils.java
@@ -32,51 +32,26 @@ public interface TimingUtils {
/** A specification enum for the type of statistics to gather from the
time measurements */
public enum StatsType {
- MEAN_STD;
+ MEAN_STD, MEAN_STD_Q1;
}
/** The specified measurement to use in this case. Can be set from any
of the programs */
- public static StatsType st = StatsType.MEAN_STD;
-
- // /**
- // * Time the given function call
- // *
- // * @param f The function to execute
- // * @return The time it took
- // */
- // public static double time(F f) {
- // Timing time = new Timing(true);
- // f.run();
- // return time.stop();
- // }
-
- // /**
- // * Time the function and print using the string given prepended.
- // *
- // * @param f The function to time
- // * @param p The print statement
- // */
- // public static void time(F f, String p) {
- // Timing time = new Timing(true);
- // f.run();
- // System.out.print(p);
- // System.out.println(time.stop());
- // }
+ // public static StatsType st = StatsType.MEAN_STD;
-/**
+ /**
* Time the function given assuming that it should put result into the
given time array at index i.
*
- * @param f The function to time
+ * @param f The function to time
* @param rep the number of repetitions
*/
public static double[] time(F f, int rep) {
double[] times = new double[rep];
- for(int i = 0; i < rep; i ++)
+ for(int i = 0; i < rep; i++)
time(f, times, i);
-
+
return times;
}
-
+
/**
* Time the function given assuming that it should put result into the
given time array at index i.
*
@@ -116,14 +91,31 @@ public interface TimingUtils {
}
/**
- * Calculate the statistics of the times executed The default is to
calculate the mean and standard deviation and
- * return that as a string
+ * Calculate the statistics of the times executed
+ * <p>
+ * The default is to calculate the mean and standard deviation and
return that as a string
*
- * @param v The times observed
+ * @param v The times observed
+ * @param st The type of stats to print
* @return The status string.
*/
public static String stats(double[] v) {
+ return statsMeanSTD(v);
+ }
+
+ /**
+ * Calculate the statistics of the times executed, given the stats type
provided
+ * <p>
+ * The default is to calculate the mean and standard deviation and
return that as a string
+ *
+ * @param v The times observed
+ * @param st The type of stats to print
+ * @return The status string.
+ */
+ public static String stats(double[] v, StatsType st) {
switch(st) {
+ case MEAN_STD_Q1:
+ return statsMeanSTDQ1(v);
case MEAN_STD:
default:
return statsMeanSTD(v);
@@ -151,6 +143,32 @@ public interface TimingUtils {
return String.format("%8.3f+-%7.3f ms", mean, std);
}
+ private static String statsMeanSTDQ1(double[] v) {
+ final int l = v.length;
+ final int remove = (int) Math.floor(l * 0.05);
+ Arrays.sort(v);
+
+ double q1 = v[v.length - 1 - (int) (Math.floor((double)
v.length / 100))];
+ double q2p5 = v[v.length - 1 - (int) (Math.floor((double)
v.length / 40))];
+ double q5 = v[v.length - 1 - (int) (Math.floor((double)
v.length / 20))];
+ double q10 = v[v.length - 1 - (int) (Math.floor((double)
v.length / 10))];
+
+ double total = 0;
+ final int el = v.length - remove * 2;
+ for(int i = remove; i < l - remove; i++)
+ total += v[i];
+
+ double mean = total / el;
+
+ double var = 0;
+ for(int i = remove; i < l - remove; i++)
+ var += Math.pow(Math.abs(v[i] - mean), 2);
+
+ double std = Math.sqrt(var / el);
+
+ return String.format("%8.3f+-%7.3f ms [q1:%7.3f, q2.5:%7.3f,
q5:%7.3f, q10:%7.3f]", mean, std, q1, q2p5, q5, q10);
+ }
+
/**
* Interface method to enable timed calling from other Classes
*/
diff --git
a/src/test/java/org/apache/sysds/performance/compression/APerfTest.java
b/src/test/java/org/apache/sysds/performance/compression/APerfTest.java
index 2c49393384..0ac88233f5 100644
--- a/src/test/java/org/apache/sysds/performance/compression/APerfTest.java
+++ b/src/test/java/org/apache/sysds/performance/compression/APerfTest.java
@@ -23,6 +23,7 @@ import java.util.ArrayList;
import org.apache.sysds.performance.TimingUtils;
import org.apache.sysds.performance.TimingUtils.F;
+import org.apache.sysds.performance.TimingUtils.StatsType;
import org.apache.sysds.performance.generators.IGenerate;
public abstract class APerfTest<T, G> {
@@ -39,19 +40,27 @@ public abstract class APerfTest<T, G> {
/** Warmup iterations */
protected final int W;
+ /** The type of statistics to use */
+ protected final StatsType st;
+
protected APerfTest(int N, IGenerate<G> gen) {
- ret = new ArrayList<>(N);
- this.gen = gen;
- this.N = N;
- this.W = 10;
+ this(N, 10, gen, StatsType.MEAN_STD);
}
+ protected APerfTest(int N, IGenerate<G> gen, StatsType st) {
+ this(N, 10, gen, st);
+ }
protected APerfTest(int N, int W, IGenerate<G> gen) {
+ this(N, W, gen, StatsType.MEAN_STD);
+ }
+
+ protected APerfTest(int N, int W, IGenerate<G> gen, StatsType st) {
ret = new ArrayList<>(N);
this.gen = gen;
this.N = N;
- this.W = 10;
+ this.W = W;
+ this.st = st;
}
protected void execute(F f, String name) throws InterruptedException {
@@ -70,7 +79,7 @@ public abstract class APerfTest<T, G> {
ret.clear();
double[] times = TimingUtils.time(f, c, b, N, gen);
String retS = makeResString(times);
- System.out.println(String.format("%35s, %s, %10s", name,
TimingUtils.stats(times), retS));
+ System.out.println(String.format("%35s, %s, %10s", name,
TimingUtils.stats(times, st), retS));
}
protected void warmup(F f, int n) throws InterruptedException {
@@ -92,7 +101,7 @@ public abstract class APerfTest<T, G> {
ret.clear();
double[] times = TimingUtils.time(f, c, b, N, gen);
String retS = makeResString(times);
- System.out.println(String.format("%35s, %s, %10s", name,
TimingUtils.stats(times), retS));
+ System.out.println(String.format("%35s, %s, %10s", name,
TimingUtils.stats(times, st), retS));
}
protected abstract String makeResString();
@@ -106,7 +115,7 @@ public abstract class APerfTest<T, G> {
StringBuilder sb = new StringBuilder();
sb.append(String.format("%20s ",
this.getClass().getSimpleName()));
sb.append(" Repetitions: ").append(N).append("\n");
- sb.append(String.format("%20s ","Generator:"));
+ sb.append(String.format("%20s ", "Generator:"));
sb.append(gen);
sb.append("\n");
return sb.toString();
diff --git
a/src/test/java/org/apache/sysds/performance/matrix/MatrixAppend.java
b/src/test/java/org/apache/sysds/performance/matrix/MatrixAppend.java
new file mode 100644
index 0000000000..75554bb830
--- /dev/null
+++ b/src/test/java/org/apache/sysds/performance/matrix/MatrixAppend.java
@@ -0,0 +1,86 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.apache.sysds.performance.matrix;
+
+import org.apache.sysds.performance.TimingUtils.StatsType;
+import org.apache.sysds.performance.compression.APerfTest;
+import org.apache.sysds.performance.generators.ConstMatrix;
+import org.apache.sysds.performance.generators.GenMatrices;
+import org.apache.sysds.performance.generators.IGenerate;
+import org.apache.sysds.runtime.matrix.data.MatrixBlock;
+
+public class MatrixAppend extends APerfTest<Object, MatrixBlock> {
+
+ final boolean cbind;
+
+ final MatrixBlock base;
+ final MatrixBlock[] others;
+ final int n;
+
+ public MatrixAppend(int N, int n, IGenerate<MatrixBlock> gen, boolean
cbind) {
+ super(N, 0, new ConstMatrix(gen.take()), StatsType.MEAN_STD_Q1);
+ this.cbind = cbind;
+ this.n = n;
+ base = gen.take();
+
+ others = new MatrixBlock[n];
+ for(int i = 0; i < n; i++) {
+ others[i] = gen.take();
+ }
+
+ }
+
+ public void run() throws Exception {
+
+ execute(() -> append(base, others), //
+ String.format("appending: rows:%5d cols:%5d sp:%3.1f
Blocks:%4d rep:%6d ", //
+ base.getNumRows(), base.getNumColumns(),
base.getSparsity(), n, N));
+
+ }
+
+ private void append(MatrixBlock a, MatrixBlock[] others) {
+ a.append(others, null, cbind);
+ }
+
+ @Override
+ protected String makeResString() {
+ return "";
+ }
+
+ public static void main(String[] args) throws Exception {
+ IGenerate<MatrixBlock> in;
+ int nBlocks;
+ int nRepeats;
+ if(args.length == 0) {
+ in = new GenMatrices(1000, 10, 10, 1.0);
+ nBlocks = 10;
+ nRepeats = 100;
+ }
+ else {
+ in = new GenMatrices(Integer.parseInt(args[1]),
Integer.parseInt(args[2]), 10, Double.parseDouble(args[3]));
+ nBlocks = Integer.parseInt(args[4]);
+ nRepeats = Integer.parseInt(args[5]);
+ }
+ in.generate(nBlocks + 2);
+
+ new MatrixAppend(nRepeats, nBlocks, in, false).run();
+ }
+
+}
diff --git a/src/test/scripts/performance/append.sh
b/src/test/scripts/performance/append.sh
new file mode 100755
index 0000000000..d2184dd472
--- /dev/null
+++ b/src/test/scripts/performance/append.sh
@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+#-------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#-------------------------------------------------------------
+
+mvn package > /dev/null
+java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 100 100
1.0 1 30000
+java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000 100
1.0 1 3000
+java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000 1000
1.0 1 3000
+java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 100 100
0.3 1 30000
+java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000 100
0.3 1 3000
+java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000 1000
0.3 1 3000
+
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 100
100 1.0 10 30000
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000
100 1.0 10 3000
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000
1000 1.0 10 1000
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 100
100 0.3 10 30000
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000
100 0.3 10 3000
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000
1000 0.3 10 1000
+
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 100
100 1.0 100 3000
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000
100 1.0 100 300
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000
1000 1.0 100 200
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 100
100 0.3 100 3000
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000
100 0.3 100 2000
+# java -jar -XX:+UseNUMA target/systemds-3.3.0-SNAPSHOT-perf.jar 1008 1000
1000 0.3 100 1000
\ No newline at end of file
