joel/largeRCRF-Java
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Fix bug where parallel forests never finish

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Add test to detect case
This commit is contained in:
Joel Therrien 2019-04-29 11:02:14 -07:00
parent de3de300cf
commit c5c74ad7e9
2 changed files with 63 additions and 20 deletions
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40
src/main/java/ca/joeltherrien/randomforest/tree/ForestTrainer.java
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@ -139,7 +139,7 @@ public class ForestTrainer<Y, TO, FO> {
int prevNumberTreesSet = -1;
while(true){
try {
if (executorService.awaitTermination(5, TimeUnit.SECONDS)) break;
if (executorService.awaitTermination(1, TimeUnit.SECONDS)) break;
} catch (InterruptedException e) {
System.err.println("There was an InterruptedException while waiting for the forest to finish training; this is unusual but on its own shouldn't be a problem.");
System.err.println("Please send a bug report about it to joelt@sfu.ca");
@ -147,21 +147,22 @@ public class ForestTrainer<Y, TO, FO> {
// do nothing; this shouldn't be an issue
}
if(displayProgress) {
int numberTreesSet = 0;
for (final Tree<TO> tree : trees) {
if (tree != null) {
numberTreesSet++;
}
int numberTreesSet = 0;
for (final Tree<TO> tree : trees) {
if (tree != null) {
numberTreesSet++;
}
}
if(displayProgress && numberTreesSet != prevNumberTreesSet) {
// Only output trees set on screen if there was a change
// In some environments where standard output is streamed to a file this method below causes frequent writes to output
if(numberTreesSet != prevNumberTreesSet){
System.out.print("\rFinished " + numberTreesSet + "/" + ntree + " trees");
prevNumberTreesSet = numberTreesSet;
}
System.out.print("\rFinished " + numberTreesSet + "/" + ntree + " trees");
prevNumberTreesSet = numberTreesSet;
}
if(numberTreesSet == ntree){
executorService.shutdown();
}
}
@ -199,26 +200,27 @@ public class ForestTrainer<Y, TO, FO> {
int prevNumberTreesSet = -1;
while(true){
try {
if (executorService.awaitTermination(5, TimeUnit.SECONDS)) break;
if (executorService.awaitTermination(1, TimeUnit.SECONDS)) break;
} catch (InterruptedException e) {
System.err.println("There was an InterruptedException while waiting for the forest to finish training; this is unusual but on its own shouldn't be a problem.");
System.err.println("Please send a bug report about it to joelt@sfu.ca");
e.printStackTrace();
// do nothing; this shouldn't be an issue
}
int numberTreesSet = treeCount.get();
if(displayProgress) {
int numberTreesSet = treeCount.get();
if(displayProgress && numberTreesSet != prevNumberTreesSet) {
// Only output trees set on screen if there was a change
// In some environments where standard output is streamed to a file this method below causes frequent writes to output
if(numberTreesSet != prevNumberTreesSet){
System.out.print("\rFinished " + numberTreesSet + "/" + ntree + " trees");
prevNumberTreesSet = numberTreesSet;
}
System.out.print("\rFinished " + numberTreesSet + "/" + ntree + " trees");
prevNumberTreesSet = numberTreesSet;
}
if(numberTreesSet == ntree){
executorService.shutdown();
}
}
if(displayProgress){

43
src/test/java/ca/joeltherrien/randomforest/TestSavingLoading.java
View file

@ -109,7 +109,7 @@ public class TestSavingLoading {
}
@Test
public void testSavingLoading() throws IOException, ClassNotFoundException {
public void testSavingLoadingSerial() throws IOException, ClassNotFoundException {
final Settings settings = getSettings();
final List<Covariate> covariates = settings.getCovariates();
final List<Row<CompetingRiskResponse>> dataset = DataUtils.loadData(covariates, settings.getResponseLoader(), settings.getTrainingDataLocation());
@ -131,6 +131,47 @@ public class TestSavingLoading {
final Forest<CompetingRiskFunctions, CompetingRiskFunctions> forest = DataUtils.loadForest(directory, new CompetingRiskFunctionCombiner(new int[]{1,2}, null));
final CovariateRow predictionRow = getPredictionRow(covariates);
final CompetingRiskFunctions functions = forest.evaluate(predictionRow);
assertNotNull(functions);
assertTrue(functions.getCumulativeIncidenceFunction(1).getX().length > 2);
assertEquals(NTREE, forest.getTrees().size());
cleanup(directory);
assertFalse(directory.exists());
}
@Test
public void testSavingLoadingParallel() throws IOException, ClassNotFoundException {
final Settings settings = getSettings();
final List<Covariate> covariates = settings.getCovariates();
final List<Row<CompetingRiskResponse>> dataset = DataUtils.loadData(covariates, settings.getResponseLoader(), settings.getTrainingDataLocation());
final File directory = new File(settings.getSaveTreeLocation());
if(directory.exists()){
cleanup(directory);
}
assertFalse(directory.exists());
directory.mkdir();
final ForestTrainer<CompetingRiskResponse, CompetingRiskFunctions, CompetingRiskFunctions> forestTrainer = new ForestTrainer<>(settings, dataset, covariates);
forestTrainer.trainParallelOnDisk(settings.getNumberOfThreads());
assertTrue(directory.exists());
assertTrue(directory.isDirectory());
assertEquals(NTREE, directory.listFiles().length);
final Forest<CompetingRiskFunctions, CompetingRiskFunctions> forest = DataUtils.loadForest(directory, new CompetingRiskFunctionCombiner(new int[]{1,2}, null));
final CovariateRow predictionRow = getPredictionRow(covariates);