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Performance tests #70

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Performance tests #70

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8485443
Use temporary dir and cross platform path separators
chris-allan Jul 29, 2020
fc56d17
Activate benchmark as a test
chris-allan Jul 29, 2020
b816029
Provide sufficient heap space to run the benchmark test
chris-allan Jul 29, 2020
3135da2
Don't use more threads than available processors
chris-allan Jul 30, 2020
cd1fbb9
Expand benchmark test to include read performance
chris-allan Jul 30, 2020
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7 changes: 7 additions & 0 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -204,6 +204,13 @@
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<configuration>
<argLine>-Xmx2g</argLine>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
Expand Down
171 changes: 118 additions & 53 deletions ...g/janelia/saalfeldlab/n5/N5Benchmark.java → ...nelia/saalfeldlab/n5/N5BenchmarkTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,10 +26,11 @@
import java.util.concurrent.Executors;
import java.util.concurrent.Future;

import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TemporaryFolder;

import ch.systemsx.cisd.base.mdarray.MDShortArray;
import ch.systemsx.cisd.hdf5.HDF5Factory;
Expand All @@ -51,15 +52,16 @@
*
* @author Stephan Saalfeld &lt;[email protected]&gt;
*/
public class N5Benchmark {
public class N5BenchmarkTest {

private static String testDirPath = System.getProperty("user.home") + "/tmp/n5-benchmark";
@Rule
public TemporaryFolder temp = new TemporaryFolder();

private static String datasetName = "/dataset";
private static final String datasetName = "/dataset";

private static N5Writer n5;
private N5Writer n5;

private static short[] data;
private short[] data;

private static final Compression[] compressions = {
new RawCompression(),
Expand All @@ -73,13 +75,10 @@ public class N5Benchmark {
/**
* @throws java.lang.Exception
*/
@BeforeClass
public static void setUpBeforeClass() throws Exception {
@Before
public void setUp() throws Exception {

final File testDir = new File(testDirPath);
testDir.mkdirs();
if (!(testDir.exists() && testDir.isDirectory()))
throw new IOException("Could not create benchmark directory for HDF5Utils benchmark.");
final File testDir = temp.newFolder();

data = new short[64 * 64 * 64];
final ImagePlus imp = new Opener().openURL("https://imagej.nih.gov/ij/images/t1-head-raw.zip");
Expand All @@ -88,24 +87,9 @@ public static void setUpBeforeClass() throws Exception {
for (int i = 0; i < data.length; ++i)
data[i] = (short)cursor.next().get();

n5 = new N5FSWriter(testDirPath);
n5 = new N5FSWriter(testDir.getAbsolutePath());
}

/**
* @throws java.lang.Exception
*/
@AfterClass
public static void rampDownAfterClass() throws Exception {

n5.remove("");
}

/**
* @throws java.lang.Exception
*/
@Before
public void setUp() throws Exception {}

/**
* Generates some files for documentation of the binary format. Not a test.
*/
Expand Down Expand Up @@ -153,19 +137,17 @@ public void benchmarkWritingSpeed() {

/* TIF blocks */
long t = System.currentTimeMillis();
final String compressedDatasetName = testDirPath + "/" + datasetName + ".tif";
new File(compressedDatasetName).mkdirs();
for (int z = 0; z < nBlocks; ++z)
for (int y = 0; y < nBlocks; ++y)
for (int x = 0; x < nBlocks; ++x) {
final ImagePlus impBlock = new ImagePlus("", new ShortProcessor(64, 64 * 64, data, null));
IJ.saveAsTiff(impBlock, compressedDatasetName + "/" + x + "-" + y + "-" + z + ".tif");
IJ.saveAsTiff(impBlock, temp.getRoot().toPath().resolve(x + "-" + y + "-" + z + ".tif").toString());
}
System.out.println(String.format("%d : tif : %fs", i, 0.001 * (System.currentTimeMillis() - t)));

/* HDF5 raw */
t = System.currentTimeMillis();
String hdf5Name = testDirPath + "/" + datasetName + ".h5";
String hdf5Name = temp.getRoot().toPath().resolve("dataset.h5").toString();
IHDF5Writer hdf5Writer = HDF5Factory.open(hdf5Name);
IHDF5ShortWriter uint16Writer = hdf5Writer.uint16();
uint16Writer.createMDArray(
Expand All @@ -180,11 +162,10 @@ public void benchmarkWritingSpeed() {
uint16Writer.writeMDArrayBlockWithOffset(datasetName, targetCell, new long[]{64 * z, 64 * y, 64 * x});
}
System.out.println(String.format("%d : hdf5 raw : %fs", i, 0.001 * (System.currentTimeMillis() - t)));
new File(hdf5Name).delete();

/* HDF5 gzip */
t = System.currentTimeMillis();
hdf5Name = testDirPath + "/" + datasetName + ".gz.h5";
hdf5Name = temp.getRoot().toPath().resolve("dataset.gz.h5").toString();
hdf5Writer = HDF5Factory.open(hdf5Name);
uint16Writer = hdf5Writer.uint16();
uint16Writer.createMDArray(
Expand All @@ -199,7 +180,6 @@ public void benchmarkWritingSpeed() {
uint16Writer.writeMDArrayBlockWithOffset(datasetName, targetCell, new long[]{64 * z, 64 * y, 64 * x});
}
System.out.println(String.format("%d : hdf5 gzip : %fs", i, 0.001 * (System.currentTimeMillis() - t)));
new File(hdf5Name).delete();
}
}

Expand All @@ -208,16 +188,17 @@ public void benchmarkParallelWritingSpeed() {

final int nBlocks = 5;

for (int i = 1; i <= 16; i *= 2 ) {
int maxThreads = Math.min(Runtime.getRuntime().availableProcessors(), 16);
for (int i = 1; i <= maxThreads; i *= 2 ) {

System.out.println( i + " threads.");

final ExecutorService exec = Executors.newFixedThreadPool(i);
final ArrayList<Future<Boolean>> futures = new ArrayList<>();
long t;
long start, read, write;

for (final Compression compression : compressions) {
t = System.currentTimeMillis();
start = System.currentTimeMillis();
try {
final String compressedDatasetName = datasetName + "." + compression.getType();
n5.createDataset(compressedDatasetName, new long[]{64 * nBlocks, 64 * nBlocks, 64 * nBlocks}, new int[]{64, 64, 64}, DataType.UINT16, compression);
Expand All @@ -240,19 +221,39 @@ public void benchmarkParallelWritingSpeed() {
}
for (final Future<Boolean> f : futures)
f.get();
write = System.currentTimeMillis();

for (int z = 0; z < nBlocks; ++z) {
final int fz = z;
for (int y = 0; y < nBlocks; ++y) {
final int fy = y;
for (int x = 0; x < nBlocks; ++x) {
final int fx = x;
futures.add(
exec.submit(
() -> {
final ShortArrayDataBlock dataBlock = (ShortArrayDataBlock) n5.readBlock(compressedDatasetName, attributes, new long[]{fx, fy, fz});
Assert.assertArrayEquals(new int[]{64, 64, 64}, dataBlock.size);
return true;
}));
}
}
}
for (final Future<Boolean> f : futures)
f.get();
read = System.currentTimeMillis();

System.out.println(String.format("%d : %s : %fs", i, compression.getType(), 0.001 * (System.currentTimeMillis() - t)));
System.out.println(String.format("%d : %s write : %fs", i, compression.getType(), 0.001 * (write - start)));
System.out.println(String.format("%d : %s read : %fs", i, compression.getType(), 0.001 * (read - write)));
} catch (final IOException | InterruptedException | ExecutionException e) {
fail(e.getMessage());
}
}

/* TIF blocks */
futures.clear();
t = System.currentTimeMillis();
final String compressedDatasetName = testDirPath + "/" + datasetName + ".tif";
start = System.currentTimeMillis();
try {
new File(compressedDatasetName).mkdirs();
for (int z = 0; z < nBlocks; ++z) {
final int fz = z;
for (int y = 0; y < nBlocks; ++y) {
Expand All @@ -263,25 +264,47 @@ public void benchmarkParallelWritingSpeed() {
exec.submit(
() -> {
final ImagePlus impBlock = new ImagePlus("", new ShortProcessor(64, 64 * 64, data, null));
IJ.saveAsTiff(impBlock, compressedDatasetName + "/" + fx + "-" + fy + "-" + fz + ".tif");
IJ.saveAsTiff(impBlock, temp.getRoot().toPath().resolve(fx + "-" + fy + "-" + fz + ".tif").toString());
return true;
}));
}
}
}
for (final Future<Boolean> f : futures)
f.get();
write = System.currentTimeMillis();

System.out.println(String.format("%d : tif : %fs", i, 0.001 * (System.currentTimeMillis() - t)));
for (int z = 0; z < nBlocks; ++z) {
final int fz = z;
for (int y = 0; y < nBlocks; ++y) {
final int fy = y;
for (int x = 0; x < nBlocks; ++x) {
final int fx = x;
futures.add(
exec.submit(
() -> {
final ImagePlus impBlock = new Opener().openTiff(temp.getRoot().toPath().resolve(fx + "-" + fy + "-" + fz + ".tif").toString(), 1);
Assert.assertArrayEquals(new int[]{64, 64 * 64, 1, 1, 1}, impBlock.getDimensions());
return true;
}));
}
}
}
for (final Future<Boolean> f : futures)
f.get();
read = System.currentTimeMillis();

System.out.println(String.format("%d : tif write : %fs", i, 0.001 * (write - start)));
System.out.println(String.format("%d : tif read : %fs", i, 0.001 * (read - write)));
} catch (final InterruptedException | ExecutionException e) {
fail(e.getMessage());
}

/* HDF5 raw */
futures.clear();
t = System.currentTimeMillis();
start = System.currentTimeMillis();
try {
final String hdf5Name = testDirPath + "/" + datasetName + ".h5";
final String hdf5Name = temp.getRoot().toPath().resolve("dataset.h5").toString();
final IHDF5Writer hdf5Writer = HDF5Factory.open( hdf5Name );
final IHDF5ShortWriter uint16Writer = hdf5Writer.uint16();
uint16Writer.createMDArray(
Expand All @@ -307,19 +330,40 @@ public void benchmarkParallelWritingSpeed() {
}
for (final Future<Boolean> f : futures)
f.get();
write = System.currentTimeMillis();

for (int z = 0; z < nBlocks; ++z) {
final int fz = z;
for (int y = 0; y < nBlocks; ++y) {
final int fy = y;
for (int x = 0; x < nBlocks; ++x) {
final int fx = x;
futures.add(
exec.submit(
() -> {
final MDShortArray targetCell = uint16Writer.readMDArrayBlockWithOffset(datasetName, new int[]{64, 64, 64}, new long[]{64 * fz, 64 * fy, 64 * fx});
Assert.assertArrayEquals(new int[]{64, 64, 64}, targetCell.dimensions());
return true;
}));
}
}
}
for (final Future<Boolean> f : futures)
f.get();
read = System.currentTimeMillis();

hdf5Writer.close();
System.out.println(String.format("%d : hdf5 raw : %fs", i, 0.001 * (System.currentTimeMillis() - t)));
new File(hdf5Name).delete();
System.out.println(String.format("%d : hdf5 raw write : %fs", i, 0.001 * (write - start)));
System.out.println(String.format("%d : hdf5 raw read : %fs", i, 0.001 * (read - write)));
} catch (final InterruptedException | ExecutionException e) {
fail(e.getMessage());
}

/* HDF5 gzip */
futures.clear();
t = System.currentTimeMillis();
start = System.currentTimeMillis();
try {
final String hdf5Name = testDirPath + "/" + datasetName + ".gz.h5";
final String hdf5Name = temp.getRoot().toPath().resolve("dataset.gz.h5").toString();
final IHDF5Writer hdf5Writer = HDF5Factory.open( hdf5Name );
final IHDF5ShortWriter uint16Writer = hdf5Writer.uint16();
uint16Writer.createMDArray(
Expand All @@ -345,10 +389,31 @@ public void benchmarkParallelWritingSpeed() {
}
for (final Future<Boolean> f : futures)
f.get();
write = System.currentTimeMillis();

for (int z = 0; z < nBlocks; ++z) {
final int fz = z;
for (int y = 0; y < nBlocks; ++y) {
final int fy = y;
for (int x = 0; x < nBlocks; ++x) {
final int fx = x;
futures.add(
exec.submit(
() -> {
final MDShortArray targetCell = uint16Writer.readMDArrayBlockWithOffset(datasetName, new int[]{64, 64, 64}, new long[]{64 * fz, 64 * fy, 64 * fx});
Assert.assertArrayEquals(new int[]{64, 64, 64}, targetCell.dimensions());
return true;
}));
}
}
}
for (final Future<Boolean> f : futures)
f.get();
read = System.currentTimeMillis();

hdf5Writer.close();
System.out.println(String.format("%d : hdf5 gzip : %fs", i, 0.001 * (System.currentTimeMillis() - t)));
new File(hdf5Name).delete();
System.out.println(String.format("%d : hdf5 gzip write : %fs", i, 0.001 * (write - start)));
System.out.println(String.format("%d : hdf5 gzip read : %fs", i, 0.001 * (read - write)));
} catch (final InterruptedException | ExecutionException e) {
fail(e.getMessage());
}
Expand Down