Merge branch 'beta' into dependency-revision

dhp-common/pom.xml

@@ -63,11 +63,13 @@
 
 	<dependencies>
 		<dependency>
-			<groupId>eu.dnetlib.dhp</groupId>
+			<groupId>edu.cmu</groupId>
-			<artifactId>dhp-pace-core</artifactId>
+			<artifactId>secondstring</artifactId>
-			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>com.ibm.icu</groupId>
+			<artifactId>icu4j</artifactId>
 		</dependency>
-
 		<dependency>
 			<groupId>org.apache.hadoop</groupId>
 			<artifactId>hadoop-common</artifactId>

dhp-common/src/main/java/eu/dnetlib/pace/common/PaceCommonUtils.java

@@ -0,0 +1,100 @@
+
+package eu.dnetlib.pace.common;
+
+import com.google.common.base.Splitter;
+import com.google.common.collect.Iterables;
+import com.google.common.collect.Sets;
+import com.ibm.icu.text.Transliterator;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+
+import java.nio.charset.StandardCharsets;
+import java.text.Normalizer;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Set of common functions for the framework
+ *
+ * @author claudio
+ */
+public class PaceCommonUtils {
+
+	// transliterator
+	protected static Transliterator transliterator = Transliterator.getInstance("Any-Eng");
+
+	protected static final String aliases_from = "⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻⁼⁽⁾ⁿ₀₁₂₃₄₅₆₇₈₉₊₋₌₍₎àáâäæãåāèéêëēėęəîïíīįìôöòóœøōõûüùúūßśšłžźżçćčñń";
+	protected static final String aliases_to = "0123456789+-=()n0123456789+-=()aaaaaaaaeeeeeeeeiiiiiioooooooouuuuussslzzzcccnn";
+
+	protected static Pattern hexUnicodePattern = Pattern.compile("\\\\u(\\p{XDigit}{4})");
+
+	protected static String fixAliases(final String s) {
+		final StringBuilder sb = new StringBuilder();
+
+		s.chars().forEach(ch -> {
+			final int i = StringUtils.indexOf(aliases_from, ch);
+			sb.append(i >= 0 ? aliases_to.charAt(i) : (char) ch);
+		});
+
+		return sb.toString();
+	}
+
+	protected static String transliterate(final String s) {
+		try {
+			return transliterator.transliterate(s);
+		} catch (Exception e) {
+			return s;
+		}
+	}
+
+	public static String normalize(final String s) {
+		return fixAliases(transliterate(nfd(unicodeNormalization(s))))
+			.toLowerCase()
+			// do not compact the regexes in a single expression, would cause StackOverflowError in case of large input
+			// strings
+			.replaceAll("[^ \\w]+", "")
+			.replaceAll("(\\p{InCombiningDiacriticalMarks})+", "")
+			.replaceAll("(\\p{Punct})+", " ")
+			.replaceAll("(\\d)+", " ")
+			.replaceAll("(\\n)+", " ")
+			.trim();
+	}
+
+	public static String nfd(final String s) {
+		return Normalizer.normalize(s, Normalizer.Form.NFD);
+	}
+
+	public static String unicodeNormalization(final String s) {
+
+		Matcher m = hexUnicodePattern.matcher(s);
+		StringBuffer buf = new StringBuffer(s.length());
+		while (m.find()) {
+			String ch = String.valueOf((char) Integer.parseInt(m.group(1), 16));
+			m.appendReplacement(buf, Matcher.quoteReplacement(ch));
+		}
+		m.appendTail(buf);
+		return buf.toString();
+	}
+
+	public static Set<String> loadFromClasspath(final String classpath) {
+
+		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
+
+		final Set<String> h = Sets.newHashSet();
+		try {
+			for (final String s : IOUtils
+				.readLines(PaceCommonUtils.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
+				h.add(fixAliases(transliterator.transliterate(s))); // transliteration of the stopwords
+			}
+		} catch (final Throwable e) {
+			return Sets.newHashSet();
+		}
+		return h;
+	}
+
+	protected static Iterable<String> tokens(final String s, final int maxTokens) {
+		return Iterables.limit(Splitter.on(" ").omitEmptyStrings().trimResults().split(s), maxTokens);
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/pace/model/Person.java

@@ -1,21 +1,20 @@
 
 package eu.dnetlib.pace.model;
 
-import java.nio.charset.Charset;
-import java.text.Normalizer;
-import java.util.List;
-import java.util.Set;
-
 import com.google.common.base.Joiner;
 import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Lists;
 import com.google.common.hash.Hashing;
-
+import eu.dnetlib.pace.common.PaceCommonUtils;
-import eu.dnetlib.pace.common.AbstractPaceFunctions;
 import eu.dnetlib.pace.util.Capitalise;
 import eu.dnetlib.pace.util.DotAbbreviations;
 
+import java.nio.charset.Charset;
+import java.text.Normalizer;
+import java.util.List;
+import java.util.Set;
+
 public class Person {
 
 	private static final String UTF8 = "UTF-8";
@@ -86,7 +85,7 @@ public class Person {
 
 	private List<String> splitTerms(final String s) {
 		if (particles == null) {
-			particles = AbstractPaceFunctions.loadFromClasspath("/eu/dnetlib/pace/config/name_particles.txt");
+			particles = PaceCommonUtils.loadFromClasspath("/eu/dnetlib/pace/config/name_particles.txt");
 		}
 
 		final List<String> list = Lists.newArrayList();

dhp-common/src/main/java/eu/dnetlib/pace/util/Capitalise.java

@@ -1,9 +1,8 @@
 
 package eu.dnetlib.pace.util;
 
-import org.apache.commons.lang3.text.WordUtils;
-
 import com.google.common.base.Function;
+import org.apache.commons.lang3.text.WordUtils;
 
 public class Capitalise implements Function<String, String> {
 
@@ -15,4 +14,4 @@ public class Capitalise implements Function<String, String> {
 	public String apply(final String s) {
 		return WordUtils.capitalize(s.toLowerCase(), DELIM);
 	}
-};
+}

dhp-common/src/main/java/eu/dnetlib/pace/util/DotAbbreviations.java

@@ -8,4 +8,4 @@ public class DotAbbreviations implements Function<String, String> {
 	public String apply(String s) {
 		return s.length() == 1 ? s + "." : s;
 	}
-};
+}

dhp-pace-core/pom.xml

@@ -49,6 +49,12 @@
 	</build>
 
 	<dependencies>
+		<dependency>
+			<groupId>eu.dnetlib.dhp</groupId>
+			<artifactId>dhp-common</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+
 		<dependency>
 			<groupId>edu.cmu</groupId>
 			<artifactId>secondstring</artifactId>

dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java

@@ -1,32 +1,26 @@
 
 package eu.dnetlib.pace.common;
 
+import com.google.common.base.Joiner;
+import com.google.common.collect.Sets;
+import com.ibm.icu.text.Transliterator;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+
 import java.io.IOException;
 import java.io.StringWriter;
 import java.nio.charset.StandardCharsets;
-import java.text.Normalizer;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-
-import com.google.common.base.Joiner;
-import com.google.common.base.Splitter;
-import com.google.common.collect.Iterables;
-import com.google.common.collect.Sets;
-import com.ibm.icu.text.Transliterator;
-
-import eu.dnetlib.pace.clustering.NGramUtils;
-
 /**
  * Set of common functions for the framework
  *
  * @author claudio
  */
-public class AbstractPaceFunctions {
+public class AbstractPaceFunctions extends PaceCommonUtils {
 
 	// city map to be used when translating the city names into codes
 	private static Map<String, String> cityMap = AbstractPaceFunctions
@@ -41,9 +35,6 @@ public class AbstractPaceFunctions {
 	protected static Set<String> stopwords_it = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_it.txt");
 	protected static Set<String> stopwords_pt = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_pt.txt");
 
-	// transliterator
-	protected static Transliterator transliterator = Transliterator.getInstance("Any-Eng");
-
 	// blacklist of ngrams: to avoid generic keys
 	protected static Set<String> ngramBlacklist = loadFromClasspath("/eu/dnetlib/pace/config/ngram_blacklist.txt");
 
@@ -51,8 +42,6 @@ public class AbstractPaceFunctions {
 	public static final Pattern HTML_REGEX = Pattern.compile("<[^>]*>");
 
 	private static final String alpha = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 ";
-	private static final String aliases_from = "⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻⁼⁽⁾ⁿ₀₁₂₃₄₅₆₇₈₉₊₋₌₍₎àáâäæãåāèéêëēėęəîïíīįìôöòóœøōõûüùúūßśšłžźżçćčñń";
-	private static final String aliases_to = "0123456789+-=()n0123456789+-=()aaaaaaaaeeeeeeeeiiiiiioooooooouuuuussslzzzcccnn";
 
 	// doi prefix for normalization
 	public static final Pattern DOI_PREFIX = Pattern.compile("(https?:\\/\\/dx\\.doi\\.org\\/)|(doi:)");
@@ -129,25 +118,6 @@ public class AbstractPaceFunctions {
 		return numberPattern.matcher(strNum).matches();
 	}
 
-	protected static String fixAliases(final String s) {
-		final StringBuilder sb = new StringBuilder();
-
-		s.chars().forEach(ch -> {
-			final int i = StringUtils.indexOf(aliases_from, ch);
-			sb.append(i >= 0 ? aliases_to.charAt(i) : (char) ch);
-		});
-
-		return sb.toString();
-	}
-
-	protected static String transliterate(final String s) {
-		try {
-			return transliterator.transliterate(s);
-		} catch (Exception e) {
-			return s;
-		}
-	}
-
 	protected static String removeSymbols(final String s) {
 		final StringBuilder sb = new StringBuilder();
 
@@ -162,23 +132,6 @@ public class AbstractPaceFunctions {
 		return s != null;
 	}
 
-	public static String normalize(final String s) {
-		return fixAliases(transliterate(nfd(unicodeNormalization(s))))
-			.toLowerCase()
-			// do not compact the regexes in a single expression, would cause StackOverflowError in case of large input
-			// strings
-			.replaceAll("[^ \\w]+", "")
-			.replaceAll("(\\p{InCombiningDiacriticalMarks})+", "")
-			.replaceAll("(\\p{Punct})+", " ")
-			.replaceAll("(\\d)+", " ")
-			.replaceAll("(\\n)+", " ")
-			.trim();
-	}
-
-	public static String nfd(final String s) {
-		return Normalizer.normalize(s, Normalizer.Form.NFD);
-	}
-
 	public static String utf8(final String s) {
 		byte[] bytes = s.getBytes(StandardCharsets.UTF_8);
 		return new String(bytes, StandardCharsets.UTF_8);
@@ -233,22 +186,6 @@ public class AbstractPaceFunctions {
 		return newset;
 	}
 
-	public static Set<String> loadFromClasspath(final String classpath) {
-
-		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
-
-		final Set<String> h = Sets.newHashSet();
-		try {
-			for (final String s : IOUtils
-				.readLines(NGramUtils.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
-				h.add(fixAliases(transliterator.transliterate(s))); // transliteration of the stopwords
-			}
-		} catch (final Throwable e) {
-			return Sets.newHashSet();
-		}
-		return h;
-	}
-
 	public static Map<String, String> loadMapFromClasspath(final String classpath) {
 
 		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
@@ -303,10 +240,6 @@ public class AbstractPaceFunctions {
 		return StringUtils.substring(s, 0, 1).toLowerCase();
 	}
 
-	protected static Iterable<String> tokens(final String s, final int maxTokens) {
-		return Iterables.limit(Splitter.on(" ").omitEmptyStrings().trimResults().split(s), maxTokens);
-	}
-
 	public static String normalizePid(String pid) {
 		return DOI_PREFIX.matcher(pid.toLowerCase()).replaceAll("");
 	}

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml

@@ -102,6 +102,8 @@
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=15000
+                --conf spark.network.timeout=300s
+                --conf spark.shuffle.registration.timeout=50000
             </spark-opts>
             <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
             <arg>--graphOutputPath</arg><arg>${graphOutputPath}</arg>

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml

@@ -33,16 +33,14 @@
             <description>max number of elements in a connected component</description>
         </property>
         <property>
-            <name>sparkDriverMemory</name>
+            <name>sparkResourceOpts</name>
-            <description>memory for driver process</description>
+            <value>--executor-memory=6G --conf spark.executor.memoryOverhead=4G --executor-cores=6 --driver-memory=8G --driver-cores=4</value>
+            <description>spark resource options</description>
         </property>
         <property>
-            <name>sparkExecutorMemory</name>
+            <name>sparkResourceOptsCreateMergeRel</name>
-            <description>memory for individual executor</description>
+            <value>--executor-memory=6G --conf spark.executor.memoryOverhead=4G --executor-cores=6 --driver-memory=8G --driver-cores=4</value>
-        </property>
+            <description>spark resource options</description>
-        <property>
-            <name>sparkExecutorCores</name>
-            <description>number of cores used by single executor</description>
         </property>
         <property>
             <name>oozieActionShareLibForSpark2</name>
@@ -119,9 +117,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -146,9 +142,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkWhitelistSimRels</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -174,9 +168,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOptsCreateMergeRel}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -203,9 +195,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -230,9 +220,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCopyOpenorgsMergeRels</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -257,9 +245,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCreateOrgsDedupRecord</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -283,9 +269,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkUpdateEntity</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -309,9 +293,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCopyRelationsNoOpenorgs</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml

@@ -100,16 +100,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.sql.shuffle.partitions=8000
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
@@ -132,12 +128,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
@@ -160,12 +155,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
@@ -188,12 +182,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
@@ -218,12 +211,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${workingDir}/orcid/targetOrcidAssoc</arg>
             <arg>--outputPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
@@ -247,19 +239,14 @@
             <class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
             <jar>dhp-enrichment-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-cores=4
+                --executor-cores=${sparkExecutorCores}
-                --executor-memory=4G
+                --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=5G
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
@@ -282,15 +269,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.sql.shuffle.partitions=8000
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
             <arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
             <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
@@ -312,15 +296,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.sql.shuffle.partitions=8000
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
             <arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
             <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
@@ -342,15 +323,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.sql.shuffle.partitions=4000
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
             <arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
             <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
@@ -362,15 +340,6 @@
     </action>
     
     <join name="wait2" to="End"/>
-
-<!--    <action name="reset_workingDir">-->
-<!--        <fs>-->
-<!--            <delete path="${workingDir}"/>-->
-<!--            <mkdir path="${workingDir}"/>-->
-<!--        </fs>-->
-<!--        <ok to="End"/>-->
-<!--        <error to="Kill"/>-->
-<!--    </action>-->
     
     <end name="End"/>
     

dhp-workflows/dhp-graph-mapper/pom.xml

@@ -90,6 +90,12 @@
             <version>${project.version}</version>
         </dependency>
 
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-pace-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+
         <dependency>
             <groupId>com.jayway.jsonpath</groupId>
             <artifactId>json-path</artifactId>

dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml

@@ -71,6 +71,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkHighDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -108,6 +109,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -141,6 +143,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -176,6 +179,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -209,6 +213,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -245,6 +250,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -315,6 +321,7 @@
 				--executor-memory=${sparkNormalExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkNormalExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -361,6 +368,7 @@
 				--executor-memory=${sparkNormalExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkNormalExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -409,6 +417,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkHighDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -444,6 +453,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkHighDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -482,6 +492,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -533,6 +544,7 @@
 				--executor-memory=${sparkNormalExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkNormalExecutorMemory}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
 				--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}