SparkBlockStats allows to repartition the input rdd via the numPartitions workflow parameter
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@ -28,6 +28,8 @@ import eu.dnetlib.pace.config.DedupConfig;
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abstract class AbstractSparkAction implements Serializable {
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protected static final int NUM_PARTITIONS = 1000;
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protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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@ -2,6 +2,7 @@
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package eu.dnetlib.dhp.oa.dedup;
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import java.io.IOException;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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@ -23,49 +24,41 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.config.DedupConfig;
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import eu.dnetlib.pace.model.FieldListImpl;
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import eu.dnetlib.pace.model.FieldValueImpl;
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import eu.dnetlib.pace.model.MapDocument;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import scala.Tuple2;
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public class SparkBlockStats extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkBlockStats.class);
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private static final Logger log = LoggerFactory.getLogger(SparkBlockStats.class);
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public SparkBlockStats(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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public SparkBlockStats(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkBlockStats.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createBlockStats_parameters.json")));
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parser.parseArgument(args);
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkBlockStats.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createBlockStats_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf
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.registerKryoClasses(
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new Class[] {
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MapDocument.class, FieldListImpl.class, FieldValueImpl.class, Block.class
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});
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SparkConf conf = new SparkConf();
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new SparkBlockStats(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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new SparkBlockStats(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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public Long computeComparisons(Long blockSize, Long slidingWindowSize){
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public Long computeComparisons(Long blockSize, Long slidingWindowSize) {
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if (slidingWindowSize >= blockSize)
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return (slidingWindowSize * (slidingWindowSize - 1)) / 2;
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else {
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return (blockSize - slidingWindowSize + 1) * (slidingWindowSize * (slidingWindowSize - 1)) / 2;
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}
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}
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if (slidingWindowSize >= blockSize)
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return (slidingWindowSize * (slidingWindowSize - 1)) / 2;
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else {
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return (blockSize - slidingWindowSize + 1) * (slidingWindowSize * (slidingWindowSize - 1)) / 2;
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}
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}
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@Override
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public void run(ISLookUpService isLookUpService)
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@ -76,6 +69,10 @@ public class SparkBlockStats extends AbstractSparkAction {
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final String isLookUpUrl = parser.get("isLookUpUrl");
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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final int numPartitions = Optional
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.ofNullable(parser.get("numPartitions"))
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.map(Integer::valueOf)
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.orElse(NUM_PARTITIONS);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("isLookUpUrl: '{}'", isLookUpUrl);
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@ -95,6 +92,7 @@ public class SparkBlockStats extends AbstractSparkAction {
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JavaPairRDD<String, MapDocument> mapDocuments = sc
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.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.repartition(numPartitions)
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.mapToPair(
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(PairFunction<String, String, MapDocument>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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@ -105,6 +103,7 @@ public class SparkBlockStats extends AbstractSparkAction {
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JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf);
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JavaRDD<BlockStats> blockStats = blocks
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.repartition(numPartitions)
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.map(
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b -> new BlockStats(
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b._1(),
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@ -35,8 +35,6 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
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public static final int NUM_PARTITIONS = 1000;
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public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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@ -22,5 +22,11 @@
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"paramLongName": "workingPath",
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"paramDescription": "path of the working directory",
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"paramRequired": true
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},
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{
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"paramName": "np",
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"paramLongName": "numPartitions",
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"paramDescription": "number of partitions for the similarity relations intermediate phases",
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"paramRequired": false
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}
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]
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@ -12,6 +12,10 @@
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<name>actionSetId</name>
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<description>id of the actionSet</description>
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</property>
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<property>
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<name>numPartitions</name>
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<description>number of partitions for the similarity relations intermediate phases</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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@ -90,10 +94,11 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=3840
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</spark-opts>
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<arg>--i</arg><arg>${graphBasePath}</arg>
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<arg>--la</arg><arg>${isLookUpUrl}</arg>
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<arg>--asi</arg><arg>${actionSetId}</arg>
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<arg>--w</arg><arg>${workingDir}</arg>
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<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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<arg>--actionSetId</arg><arg>${actionSetId}</arg>
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<arg>--workingPath</arg><arg>${workingDir}</arg>
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<arg>--numPartitions</arg><arg>${numPartitions}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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