From 17122798d579e593470c864868a46092f8795dfa Mon Sep 17 00:00:00 2001 From: Nicole Deflaux Date: Thu, 13 Aug 2015 11:45:25 -0700 Subject: [PATCH] Bump utils-java version. Also add more metrics for shard timings. --- pom.xml | 9 ++++++-- .../dataflow/readers/ReadStreamer.java | 9 ++++++++ .../dataflow/readers/VariantStreamer.java | 22 ++++++++++++++++--- 3 files changed, 35 insertions(+), 5 deletions(-) diff --git a/pom.xml b/pom.xml index d166644..1bb3004 100644 --- a/pom.xml +++ b/pom.xml @@ -127,7 +127,7 @@ com.google.cloud.genomics google-genomics-utils - v1beta2-0.32 + v1beta2-0.33 @@ -148,6 +148,11 @@ gov.nist.math.jama 1.1.1 + + org.apache.commons + commons-math3 + 3.2 + org.reflections reflections @@ -203,7 +208,7 @@ com.google.protobuf protobuf-java 3.0.0-alpha-3 - + diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadStreamer.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadStreamer.java index 9dc2b95..dcf3643 100644 --- a/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadStreamer.java +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/ReadStreamer.java @@ -17,9 +17,11 @@ import java.security.GeneralSecurityException; import java.util.Iterator; import java.util.List; +import java.util.concurrent.TimeUnit; import com.google.cloud.dataflow.sdk.transforms.Aggregator; import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.Max; import com.google.cloud.dataflow.sdk.transforms.PTransform; import com.google.cloud.dataflow.sdk.transforms.ParDo; import com.google.cloud.dataflow.sdk.transforms.Sum; @@ -27,6 +29,7 @@ import com.google.cloud.genomics.utils.GenomicsFactory; import com.google.cloud.genomics.utils.ShardBoundary; import com.google.cloud.genomics.utils.grpc.ReadStreamIterator; +import com.google.common.base.Stopwatch; import com.google.genomics.v1.Read; import com.google.genomics.v1.StreamReadsRequest; import com.google.genomics.v1.StreamReadsResponse; @@ -65,20 +68,26 @@ private class RetrieveReads extends DoFn> { protected Aggregator initializedShardCount; protected Aggregator finishedShardCount; + protected Aggregator shardTimeMaxSec; public RetrieveReads() { initializedShardCount = createAggregator("Initialized Shard Count", new Sum.SumIntegerFn()); finishedShardCount = createAggregator("Finished Shard Count", new Sum.SumIntegerFn()); + shardTimeMaxSec = createAggregator("Maximum Shard Processing Time (sec)", new Max.MaxLongFn()); } @Override public void processElement(ProcessContext c) throws IOException, GeneralSecurityException { initializedShardCount.addValue(1); + shardTimeMaxSec.addValue(0L); + Stopwatch stopWatch = Stopwatch.createStarted(); Iterator iter = new ReadStreamIterator(c.element(), auth, shardBoundary, fields); while (iter.hasNext()) { StreamReadsResponse readResponse = iter.next(); c.output(readResponse.getAlignmentsList()); } + stopWatch.stop(); + shardTimeMaxSec.addValue(stopWatch.elapsed(TimeUnit.SECONDS)); finishedShardCount.addValue(1); } } diff --git a/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantStreamer.java b/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantStreamer.java index fcf8ba2..94ec6fa 100644 --- a/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantStreamer.java +++ b/src/main/java/com/google/cloud/genomics/dataflow/readers/VariantStreamer.java @@ -17,9 +17,15 @@ import java.security.GeneralSecurityException; import java.util.Iterator; import java.util.List; +import java.util.concurrent.TimeUnit; + +import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import com.google.cloud.dataflow.sdk.transforms.Aggregator; import com.google.cloud.dataflow.sdk.transforms.DoFn; +import com.google.cloud.dataflow.sdk.transforms.Max; import com.google.cloud.dataflow.sdk.transforms.PTransform; import com.google.cloud.dataflow.sdk.transforms.ParDo; import com.google.cloud.dataflow.sdk.transforms.Sum; @@ -27,6 +33,7 @@ import com.google.cloud.genomics.utils.GenomicsFactory; import com.google.cloud.genomics.utils.ShardBoundary; import com.google.cloud.genomics.utils.grpc.VariantStreamIterator; +import com.google.common.base.Stopwatch; import com.google.genomics.v1.StreamVariantsRequest; import com.google.genomics.v1.StreamVariantsResponse; import com.google.genomics.v1.Variant; @@ -37,6 +44,7 @@ public class VariantStreamer extends PTransform, PCollection> { + private static final Logger LOG = LoggerFactory.getLogger(VariantStreamer.class); protected final GenomicsFactory.OfflineAuth auth; protected final ShardBoundary.Requirement shardBoundary; protected final String fields; @@ -63,25 +71,33 @@ public PCollection apply(PCollection input) { private class RetrieveVariants extends DoFn> { protected Aggregator initializedShardCount; - protected Aggregator itemCount; protected Aggregator finishedShardCount; + protected Aggregator shardTimeMaxSec; + DescriptiveStatistics stats; public RetrieveVariants() { initializedShardCount = createAggregator("Initialized Shard Count", new Sum.SumIntegerFn()); - itemCount = createAggregator("Number of variant lists", new Sum.SumLongFn()); finishedShardCount = createAggregator("Finished Shard Count", new Sum.SumIntegerFn()); + shardTimeMaxSec = createAggregator("Maximum Shard Processing Time (sec)", new Max.MaxLongFn()); + stats = new DescriptiveStatistics(500); } @Override public void processElement(ProcessContext c) throws IOException, GeneralSecurityException, InterruptedException { initializedShardCount.addValue(1); + shardTimeMaxSec.addValue(0L); + Stopwatch stopWatch = Stopwatch.createStarted(); Iterator iter = new VariantStreamIterator(c.element(), auth, shardBoundary, fields); while (iter.hasNext()) { StreamVariantsResponse variantResponse = iter.next(); c.output(variantResponse.getVariantsList()); - itemCount.addValue(1L); } + stopWatch.stop(); + shardTimeMaxSec.addValue(stopWatch.elapsed(TimeUnit.SECONDS)); + stats.addValue(stopWatch.elapsed(TimeUnit.SECONDS)); finishedShardCount.addValue(1); + LOG.info("Shard Duration in Seconds - Min: " + stats.getMin() + " Max: " + stats.getMax() + + " Avg: " + stats.getMean() + " StdDev: " + stats.getStandardDeviation()); } }