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Introduce two citation matching related fixes for issues discovered during the last provision round on BETA #1429

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merged 3 commits into from
Sep 7, 2023
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Introduce two citation matching related fixes for issues discovered during the last provision round on BETA #1429

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1bd58df
Closes #1427: Citation matching failed due to an executor exceeding m…
marekhorst Aug 17, 2023
363dfa1
Closes #1427: Citation matching failed due to an executor exceeding m…
marekhorst Aug 18, 2023
c4ff3fd
Closes #1428: Fuzzy citation matching input and output transformers d…
marekhorst Aug 18, 2023
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5 changes: 5 additions & 0 deletions ...irect/src/main/resources/eu/dnetlib/iis/wf/citationmatching/direct/oozie_app/workflow.xml
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Expand Up @@ -35,6 +35,10 @@
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>sparkExecutorOverhead</name>
<description>The amount of off heap memory (in megabytes) to be allocated for the executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
Expand Down Expand Up @@ -93,6 +97,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.yarn.executor.memoryOverhead=${sparkExecutorOverhead}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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6 changes: 5 additions & 1 deletion ...in/java/eu/dnetlib/iis/wf/citationmatching/input/CitationMatchingInputTransformerJob.java
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@@ -1,5 +1,6 @@
package eu.dnetlib.iis.wf.citationmatching.input;

import java.io.IOException;
import java.util.Collections;

import org.apache.commons.lang3.StringUtils;
Expand All @@ -17,6 +18,7 @@
import eu.dnetlib.iis.citationmatching.schemas.DocumentMetadata;
import eu.dnetlib.iis.common.WorkflowRuntimeParameters;
import eu.dnetlib.iis.common.citations.schemas.Citation;
import eu.dnetlib.iis.common.java.io.HdfsUtils;
import eu.dnetlib.iis.transformers.metadatamerger.schemas.ExtractedDocumentMetadataMergedWithOriginal;
import pl.edu.icm.sparkutils.avro.SparkAvroLoader;
import pl.edu.icm.sparkutils.avro.SparkAvroSaver;
Expand All @@ -37,7 +39,7 @@ public class CitationMatchingInputTransformerJob {

//------------------------ LOGIC --------------------------

public static void main(String[] args) throws InterruptedException {
public static void main(String[] args) throws InterruptedException, IOException {

CitationMatchingInputTransformerJobParameters params = new CitationMatchingInputTransformerJobParameters();
JCommander jcommander = new JCommander(params);
Expand All @@ -48,6 +50,8 @@ public static void main(String[] args) throws InterruptedException {
conf.set("spark.kryo.registrator", "pl.edu.icm.sparkutils.avro.AvroCompatibleKryoRegistrator");

try (JavaSparkContext sc = new JavaSparkContext(conf)) {

HdfsUtils.remove(sc.hadoopConfiguration(), params.output);

JavaRDD<ExtractedDocumentMetadataMergedWithOriginal> inputDocuments = avroLoader.loadJavaRDD(sc, params.inputMetadata, ExtractedDocumentMetadataMergedWithOriginal.class);

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7 changes: 6 additions & 1 deletion .../java/eu/dnetlib/iis/wf/citationmatching/output/CitationMatchingOutputTransformerJob.java
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@@ -1,5 +1,7 @@
package eu.dnetlib.iis.wf.citationmatching.output;

import java.io.IOException;

import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
Expand All @@ -9,6 +11,7 @@
import com.beust.jcommander.Parameters;

import eu.dnetlib.iis.citationmatching.schemas.Citation;
import eu.dnetlib.iis.common.java.io.HdfsUtils;
import pl.edu.icm.sparkutils.avro.SparkAvroLoader;
import pl.edu.icm.sparkutils.avro.SparkAvroSaver;

Expand All @@ -30,7 +33,7 @@ public class CitationMatchingOutputTransformerJob {

//------------------------ LOGIC --------------------------

public static void main(String[] args) {
public static void main(String[] args) throws IOException {

CitationMatchingOutputTransformerJobParameters params = new CitationMatchingOutputTransformerJobParameters();
JCommander jcommander = new JCommander(params);
Expand All @@ -41,6 +44,8 @@ public static void main(String[] args) {

try (JavaSparkContext sc = new JavaSparkContext(conf)) {

HdfsUtils.remove(sc.hadoopConfiguration(), params.output);

JavaRDD<Citation> inputCitations = avroLoader.loadJavaRDD(sc, params.input, Citation.class);


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1 change: 1 addition & 0 deletions ...tching/src/main/resources/eu/dnetlib/iis/wf/citationmatching/fuzzy/oozie_app/workflow.xml
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Expand Up @@ -115,6 +115,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.yarn.executor.memoryOverhead=${sparkExecutorOverhead}
--conf spark.extraListeners=${spark1ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark1SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark1YarnHistoryServerAddress}
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9 changes: 9 additions & 0 deletions ...wf-primary/src/main/resources/eu/dnetlib/iis/wf/primary/processing/oozie_app/workflow.xml
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Expand Up @@ -276,6 +276,11 @@
<value>${sparkExecutorMemory}</value>
<description>memory for individual executor</description>
</property>
<property>
<name>citationmatchingDirectSparkExecutorOverhead</name>
<value>2048</value>
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I don't understand why this value has to be specified both here and in the config-default.template. And to they have to be always kept in sync?

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This is in line with other *SparkExecutorOverhead properties defined in workflow.xml file and it does not require keeping in sync values declared in workflow.xml file with the ones from the default-config.xml files.

I think this duplication was mostly kept as safety measure: if the value is not declared in default-config.xml it will be taken from the workflow.xml as a default one. It is quite useful when performing development runs (no default-config.xml involved) but I agree it does not look well having some properties defined in two places therefore I have created a dedicated issue to consider duplicates removal: #1430.

<description>The amount of off heap memory (in megabytes) to be allocated for the executor</description>
</property>
<property>
<name>citationmatchingDirectSparkExecutorCores</name>
<value>${sparkExecutorCores}</value>
Expand Down Expand Up @@ -1657,6 +1662,10 @@
<name>sparkExecutorMemory</name>
<value>${citationmatchingDirectSparkExecutorMemory}</value>
</property>
<property>
<name>sparkExecutorOverhead</name>
<value>${citationmatchingDirectSparkExecutorOverhead}</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>${citationmatchingDirectSparkExecutorCores}</value>
Expand Down