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added different limits for grouping by source and by target, incremented spark.sql.shuffle.partitions for the join operations

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Claudio Atzori 2020-07-10 19:03:33 +02:00
parent cc77446dc4
commit 06c1913062
1 changed files with 22 additions and 18 deletions
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40
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
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@ -18,8 +18,12 @@
<description>filter applied reading relations (by relClass)</description> <description>filter applied reading relations (by relClass)</description>
</property> </property>
<property> <property>
<name>maxRelations</name> <name>sourceMaxRelations</name>
<description>maximum number of relations allowed for a each entity</description> <description>maximum number of relations allowed for a each entity grouping by source</description>
</property>
<property>
<name>targetMaxRelations</name>
<description>maximum number of relations allowed for a each entity grouping by target</description>
</property> </property>
<property> <property>
<name>otherDsTypeId</name> <name>otherDsTypeId</name>
@ -133,7 +137,8 @@
</spark-opts> </spark-opts>
<arg>--inputRelationsPath</arg><arg>${inputGraphRootPath}/relation</arg> <arg>--inputRelationsPath</arg><arg>${inputGraphRootPath}/relation</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation</arg> <arg>--outputPath</arg><arg>${workingDir}/relation</arg>
<arg>--maxRelations</arg><arg>${maxRelations}</arg> <arg>--sourceMaxRelations</arg><arg>${sourceMaxRelations}</arg>
<arg>--targetMaxRelations</arg><arg>${targetMaxRelations}</arg>
<arg>--relationFilter</arg><arg>${relationFilter}</arg> <arg>--relationFilter</arg><arg>${relationFilter}</arg>
<arg>--relPartitions</arg><arg>5000</arg> <arg>--relPartitions</arg><arg>5000</arg>
</spark> </spark>
@ -166,7 +171,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680 --conf spark.sql.shuffle.partitions=15000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg> <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
@ -193,7 +198,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=15000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg> <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
@ -220,7 +225,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=10000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg> <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
@ -247,7 +252,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=5000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg> <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
@ -274,7 +279,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=5000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg> <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
@ -301,7 +306,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=5000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg> <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
@ -328,7 +333,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=5000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg> <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
@ -367,7 +372,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=15360 --conf spark.sql.shuffle.partitions=15000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/publication</arg> <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/publication</arg>
@ -395,7 +400,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680 --conf spark.sql.shuffle.partitions=10000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/dataset</arg> <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/dataset</arg>
@ -423,7 +428,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680 --conf spark.sql.shuffle.partitions=10000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/otherresearchproduct</arg> <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/otherresearchproduct</arg>
@ -451,7 +456,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=5000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/software</arg> <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/software</arg>
@ -479,7 +484,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680 --conf spark.sql.shuffle.partitions=8000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/datasource</arg> <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/datasource</arg>
@ -507,7 +512,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680 --conf spark.sql.shuffle.partitions=10000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/organization</arg> <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/organization</arg>
@ -535,7 +540,7 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840 --conf spark.sql.shuffle.partitions=5000
--conf spark.network.timeout=${sparkNetworkTimeout} --conf spark.network.timeout=${sparkNetworkTimeout}
</spark-opts> </spark-opts>
<arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/project</arg> <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/project</arg>
@ -607,5 +612,4 @@
</action> </action>
<end name="End"/> <end name="End"/>
</workflow-app> </workflow-app>