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MapReduce jobs are running infinitely during a write/read operation (Pig, Hive, Spark) #783

Closed ArcTheMaster closed 7 years ago

ArcTheMaster commented 8 years ago

Issue description

I'm facing a major issue with ES-Hadoop and more particularly when a Mapreduce job is launched. I have the same behavior with Pig, Hive and Spark.

The use case is the following (from Pig, Hive or Spark):

You can find below more information for each software.

Steps to reproduce

Pig version Code:

grunt> REGISTER /opt/application/Pig/current/lib/elasticsearch-hadoop.jar;
grunt> CSV = LOAD 'public_chicago/CSV' USING org.elasticsearch.hadoop.pig.EsStorage('es.net.ssl=true','es.net.http.auth.user=shfs3453','es.net.http.auth.pass=mypasswd!','es.nodes=es-loadbalancer.cluster.fr','es.nodes.discovery=false','es.nodes.client.only=true','es.port=9200','es.query=?q=fbicode:08B');
grunt> DUMP CSV;

Pig strack trace:

16/06/07 10:28:20 DEBUG pig.EsStorage: Using pre-defined writer serializer [org.elasticsearch.hadoop.pig.PigValueWriter] as default
16/06/07 10:28:20 DEBUG pig.EsStorage: Using pre-defined reader serializer [org.elasticsearch.hadoop.pig.PigValueReader] as default
16/06/07 10:28:20 DEBUG pig.EsStorage: Using pre-defined field extractor [org.elasticsearch.hadoop.pig.PigFieldExtractor] as default
23602 [JobControl] WARN  org.apache.hadoop.mapreduce.JobResourceUploader  - No job jar file set.  User classes may not be found. See Job or Job#setJar(String).
16/06/07 10:28:21 WARN mapreduce.JobResourceUploader: No job jar file set.  User classes may not be found. See Job or Job#setJar(String).
16/06/07 10:28:21 INFO util.Version: Elasticsearch Hadoop v2.3.2 [cae8b760fe]
16/06/07 10:28:21 DEBUG commonshttp.CommonsHttpTransport: SSL Connection enabled
16/06/07 10:28:21 INFO commonshttp.CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 10:28:22 DEBUG mr.EsInputFormat: Discovered Elasticsearch version [1.6.2]
16/06/07 10:28:22 DEBUG commonshttp.CommonsHttpTransport: SSL Connection enabled
16/06/07 10:28:22 INFO commonshttp.CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 10:28:23 DEBUG mr.EsInputFormat: Found client nodes [10.77.64.228:9200]
16/06/07 10:28:23 DEBUG mr.EsInputFormat: Filtered discovered only nodes [10.77.64.228:9200] to client-only [10.77.64.228:9200]
16/06/07 10:28:23 DEBUG commonshttp.CommonsHttpTransport: SSL Connection enabled
16/06/07 10:28:23 INFO commonshttp.CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 10:28:24 INFO mr.EsInputFormat: Reading from [public_chicago/CSV]
16/06/07 10:28:25 INFO mr.EsInputFormat: Discovered mapping {CSV=[arrest=BOOLEAN, beat=LONG, block=STRING, casenumber=STRING, communityarea=LONG, date=STRING, description=STRING, district=LONG, domestic=BOOLEAN, fbicode=STRING, geolocation=STRING, id=LONG, iucr=STRING, latitude=STRING, locationdescription=STRING, longitude=STRING, primarytype=STRING, updatedon=STRING, ward=LONG, xcoordinate=LONG, ycoordinate=LONG, year=LONG]} for [public_chicago/CSV]
16/06/07 10:28:25 DEBUG rest.RestRepository: Closing repository and connection to Elasticsearch ...
16/06/07 10:28:25 INFO mr.EsInputFormat: Created [5] shard-splits

Spark version Code:

$ spark-shell -v --name elasticsearch-hadoop --master yarn-client --conf spark.es.net.ssl=true --conf spark.es.net.http.auth.user=shfs3453 --conf spark.es.net.http.auth.pass=mypasswd! --conf spark.es.nodes=es-loadbalancer.cluster.fr --conf spark.es.port=9200 --conf spark.es.read.field.empty.as.null=true --conf spark.es.resource=public_chicago/CSV --jars /opt/application/Spark/current/lib_managed/jars/elasticsearch-hadoop.jar
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /___/ .__/\_,_/_/ /_/\_\   version 1.6.1
      /_/

Using Scala version 2.10.5 (OpenJDK 64-Bit Server VM, Java 1.7.0_101)
Type in expressions to have them evaluated.
Type :help for more information.
Spark context available as sc.
SQL context available as sqlContext.

scala> import org.elasticsearch.spark._
import org.elasticsearch.spark._

scala> val RDD1 = sc.esRDD("public_chicago/CSV", "?q=fbicode:08B")
RDD1: org.apache.spark.rdd.RDD[(String, scala.collection.Map[String,AnyRef])] = ScalaEsRDD[0] at RDD at AbstractEsRDD.scala:17

scala> RDD1.collect().foreach(println)

Spark strack trace:

16/06/07 11:01:29 DEBUG CommonsHttpTransport: SSL Connection enabled
16/06/07 11:01:29 INFO CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 11:01:30 DEBUG CommonsHttpTransport: SSL Connection enabled
16/06/07 11:01:30 INFO CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 11:01:32 DEBUG CommonsHttpTransport: SSL Connection enabled
16/06/07 11:01:32 INFO CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 11:01:32 DEBUG CommonsHttpTransport: SSL Connection enabled
16/06/07 11:01:32 INFO CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 11:01:34 DEBUG RestRepository: Closing repository and connection to Elasticsearch ...
[Stage 0:>                                                          (0 + 5) / 5]

Hive version Code:

hive (shfs3453)> add jar /opt/application/Hive/current/lib/elasticsearch-hadoop.jar;
add jar /opt/application/Hive/current/lib/elasticsearch-hadoop.jar
Added [/opt/application/Hive/current/lib/elasticsearch-hadoop.jar] to class path
Added resources: [/opt/application/Hive/current/lib/elasticsearch-hadoop.jar]
hive (shfs3453)> CREATE EXTERNAL TABLE elastic_table_1 (ID BIGINT, CaseNumber STRING, Day STRING, Block STRING, IUCR BIGINT, PrimaryType STRING, Description STRING, LocationDescription STRING, Arrest BOOLEAN, Domestic BOOLEAN, Beat BIGINT, District BIGINT, Ward BIGINT, CommunityArea BIGINT, FBICode BIGINT, XCoordinate BIGINT, YCoordinate BIGINT, Year BIGINT, UpdatedOn STRING, Latitude DOUBLE, Longitude DOUBLE, Location STRING) STORED BY 'org.elasticsearch.hadoop.hive.EsStorageHandler' TBLPROPERTIES ("es.net.ssl" = "true", "es.net.http.auth.user" = "shfs3453", "es.net.http.auth.pass" = "mypasswd!", "es.nodes" = "es-loadbalancer.cluster.fr", "es.resource" = "public_chicago/CSV");
CREATE EXTERNAL TABLE elastic_table_1 (ID BIGINT, CaseNumber STRING, Day STRING, Block STRING, IUCR BIGINT, PrimaryType STRING, Description STRING, LocationDescription STRING, Arrest BOOLEAN, Domestic BOOLEAN, Beat BIGINT, District BIGINT, Ward BIGINT, CommunityArea BIGINT, FBICode BIGINT, XCoordinate BIGINT, YCoordinate BIGINT, Year BIGINT, UpdatedOn STRING, Latitude DOUBLE, Longitude DOUBLE, Location STRING) STORED BY 'org.elasticsearch.hadoop.hive.EsStorageHandler' TBLPROPERTIES ("es.net.ssl" = "true", "es.net.http.auth.user" = "shfs3453", "es.net.http.auth.pass" = "mypasswd!", "es.nodes" = "es-loadbalancer.cluster.fr", "es.resource" = "public_chicago/CSV")
OK
Time taken: 0.518 seconds
hive (shfs3453)> SELECT * FROM elastic_table_1;

Hive strack trace:

SELECT * FROM elastic_table_1
OK

Version Info

OS: : REL 6.8 JVM : 1.7 (openJDK) Hadoop/Hive/Pig/Spark: 2.7.2/2.0.1/0.15.0/1.6.1 ES-Hadoop : 2.3.2 (stable) ES : 1.6.2

ArcTheMaster commented 8 years ago

In addition, I also have the Spark stack trace in "TRACE" below:

scala> RDD1.collect().foreach(println)
16/06/07 14:48:48 DEBUG CommonsHttpTransport: SSL Connection enabled
16/06/07 14:48:48 INFO CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 14:48:48 TRACE CommonsHttpTransport: Opening HTTP transport to 10.77.64.228:9200
16/06/07 14:48:48 TRACE CommonsHttpTransport: Tx [GET]@[10.77.64.228:9200][] w/ payload [null]
16/06/07 14:48:49 TRACE CommonsHttpTransport: Rx @[10.77.95.200] [200-OK] [{
  "status" : 200,
  "name" : "es-loadbalancer.cluster.fr",
  "cluster_name" : "ELASTIC.CLUSTER",
  "version" : {
    "number" : "1.6.2",
    "build_hash" : "622039121e53e5f520b5ff8720fdbd3d0cb5326b",
    "build_timestamp" : "2015-07-29T09:24:47Z",
    "build_snapshot" : false,
    "lucene_version" : "4.10.4"
  },
  "tagline" : "You Know, for Search"
}
]
16/06/07 14:48:49 DEBUG ScalaEsRDD: Discovered Elasticsearch version [1.6.2]
16/06/07 14:48:49 TRACE CommonsHttpTransport: Closing HTTP transport to 10.77.64.228:9200
16/06/07 14:48:49 DEBUG CommonsHttpTransport: SSL Connection enabled
16/06/07 14:48:49 INFO CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 14:48:49 TRACE CommonsHttpTransport: Opening HTTP transport to 10.77.64.228:9200
16/06/07 14:48:49 TRACE CommonsHttpTransport: Tx [GET]@[10.77.64.228:9200][_nodes/transport] w/ payload [null]
16/06/07 14:48:49 TRACE CommonsHttpTransport: Rx @[10.77.95.200] [200-OK] 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16/06/07 14:48:49 DEBUG ScalaEsRDD: Nodes discovery enabled - found [10.77.64.38:9200, 10.77.64.50:9200, 10.77.64.73:9200, 10.77.64.72:9200, 10.77.64.74:9200, 10.77.64.21:9200, 10.77.64.81:9200, 10.77.64.31:9200, 10.77.64.55:9200, 10.77.64.69:9200, 10.77.64.35:9200, 10.77.64.24:9200, 10.77.64.40:9200, 10.77.64.23:9200, 10.77.64.36:9200, 10.77.64.85:9200, 10.77.64.58:9200, 10.77.64.59:9200, 10.77.64.70:9200, 10.77.64.66:9200, 10.77.64.75:9200, 10.77.64.60:9200, 10.77.64.98:9200, 10.77.64.57:9200, 10.77.64.64:9200, 10.77.64.25:9200, 10.77.64.88:9200, 10.77.64.42:9200, 10.77.64.48:9200, 10.77.64.80:9200, 10.77.64.52:9200, 10.77.64.16:9200, 10.77.64.54:9200, 10.77.64.17:9200, 10.77.64.47:9200, 10.77.64.39:9200, 10.77.64.44:9200, 10.77.64.79:9200, 10.77.64.53:9200, 10.77.64.7:9200, 10.77.64.37:9200, 10.77.64.87:9200, 10.77.64.94:9200, 10.77.64.43:9200, 10.77.64.28:9200, 10.77.64.2:9200, 10.77.64.67:9200, 10.77.64.86:9200, 10.77.64.34:9200, 10.77.64.20:9200, 10.77.64.228:9200, 10.77.64.22:9200, 10.77.64.51:9200, 10.77.64.30:9200, 10.77.64.4:9200, 10.77.64.5:9200, 10.77.64.95:9200, 10.77.64.99:9200, 10.77.64.45:9200, 10.77.64.78:9200, 10.77.64.29:9200, 10.77.64.49:9200, 10.77.64.93:9200, 10.77.64.56:9200, 10.77.64.33:9200, 10.77.64.89:9200, 10.77.64.18:9200, 10.77.64.32:9200, 10.77.64.76:9200, 10.77.64.46:9200, 10.77.64.96:9200, 10.77.64.19:9200, 10.77.64.63:9200, 10.77.64.6:9200, 10.77.64.1:9200, 10.77.64.92:9200, 10.77.64.61:9200, 10.77.64.97:9200, 10.77.64.77:9200, 10.77.64.62:9200, 10.77.64.71:9200, 10.77.64.3:9200, 10.77.64.65:9200, 10.77.64.90:9200, 10.77.64.91:9200]
16/06/07 14:48:49 TRACE CommonsHttpTransport: Closing HTTP transport to 10.77.64.228:9200
16/06/07 14:48:49 DEBUG CommonsHttpTransport: SSL Connection enabled
16/06/07 14:48:49 INFO CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 14:48:49 TRACE CommonsHttpTransport: Opening HTTP transport to 10.77.64.63:9200
16/06/07 14:48:49 TRACE CommonsHttpTransport: Tx [GET]@[10.77.64.63:9200][_nodes/http] w/ payload [null]
16/06/07 14:48:50 TRACE CommonsHttpTransport: Rx @[10.77.95.200] [200-OK] 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16/06/07 14:48:50 DEBUG ScalaEsRDD: Found data nodes [10.77.64.38:9200, 10.77.64.50:9200, 10.77.64.73:9200, 10.77.64.72:9200, 10.77.64.74:9200, 10.77.64.21:9200, 10.77.64.81:9200, 10.77.64.31:9200, 10.77.64.55:9200, 10.77.64.69:9200, 10.77.64.35:9200, 10.77.64.24:9200, 10.77.64.40:9200, 10.77.64.23:9200, 10.77.64.36:9200, 10.77.64.85:9200, 10.77.64.58:9200, 10.77.64.59:9200, 10.77.64.70:9200, 10.77.64.66:9200, 10.77.64.75:9200, 10.77.64.60:9200, 10.77.64.98:9200, 10.77.64.57:9200, 10.77.64.64:9200, 10.77.64.25:9200, 10.77.64.88:9200, 10.77.64.42:9200, 10.77.64.48:9200, 10.77.64.80:9200, 10.77.64.52:9200, 10.77.64.16:9200, 10.77.64.54:9200, 10.77.64.17:9200, 10.77.64.47:9200, 10.77.64.39:9200, 10.77.64.44:9200, 10.77.64.79:9200, 10.77.64.53:9200, 10.77.64.7:9200, 10.77.64.37:9200, 10.77.64.87:9200, 10.77.64.94:9200, 10.77.64.43:9200, 10.77.64.28:9200, 10.77.64.2:9200, 10.77.64.67:9200, 10.77.64.86:9200, 10.77.64.34:9200, 10.77.64.20:9200, 10.77.64.22:9200, 10.77.64.51:9200, 10.77.64.30:9200, 10.77.64.4:9200, 10.77.64.5:9200, 10.77.64.95:9200, 10.77.64.99:9200, 10.77.64.45:9200, 10.77.64.78:9200, 10.77.64.29:9200, 10.77.64.49:9200, 10.77.64.93:9200, 10.77.64.56:9200, 10.77.64.33:9200, 10.77.64.89:9200, 10.77.64.18:9200, 10.77.64.32:9200, 10.77.64.76:9200, 10.77.64.46:9200, 10.77.64.96:9200, 10.77.64.19:9200, 10.77.64.63:9200, 10.77.64.6:9200, 10.77.64.1:9200, 10.77.64.92:9200, 10.77.64.61:9200, 10.77.64.97:9200, 10.77.64.77:9200, 10.77.64.62:9200, 10.77.64.71:9200, 10.77.64.3:9200, 10.77.64.65:9200, 10.77.64.90:9200, 10.77.64.91:9200]
16/06/07 14:48:50 DEBUG ScalaEsRDD: Filtered discovered only nodes [10.77.64.228:9200, 10.77.64.38:9200, 10.77.64.50:9200, 10.77.64.73:9200, 10.77.64.72:9200, 10.77.64.74:9200, 10.77.64.21:9200, 10.77.64.81:9200, 10.77.64.31:9200, 10.77.64.55:9200, 10.77.64.69:9200, 10.77.64.35:9200, 10.77.64.24:9200, 10.77.64.40:9200, 10.77.64.23:9200, 10.77.64.36:9200, 10.77.64.85:9200, 10.77.64.58:9200, 10.77.64.59:9200, 10.77.64.70:9200, 10.77.64.66:9200, 10.77.64.75:9200, 10.77.64.60:9200, 10.77.64.98:9200, 10.77.64.57:9200, 10.77.64.64:9200, 10.77.64.25:9200, 10.77.64.88:9200, 10.77.64.42:9200, 10.77.64.48:9200, 10.77.64.80:9200, 10.77.64.52:9200, 10.77.64.16:9200, 10.77.64.54:9200, 10.77.64.17:9200, 10.77.64.47:9200, 10.77.64.39:9200, 10.77.64.44:9200, 10.77.64.79:9200, 10.77.64.53:9200, 10.77.64.7:9200, 10.77.64.37:9200, 10.77.64.87:9200, 10.77.64.94:9200, 10.77.64.43:9200, 10.77.64.28:9200, 10.77.64.2:9200, 10.77.64.67:9200, 10.77.64.86:9200, 10.77.64.34:9200, 10.77.64.20:9200, 10.77.64.22:9200, 10.77.64.51:9200, 10.77.64.30:9200, 10.77.64.4:9200, 10.77.64.5:9200, 10.77.64.95:9200, 10.77.64.99:9200, 10.77.64.45:9200, 10.77.64.78:9200, 10.77.64.29:9200, 10.77.64.49:9200, 10.77.64.93:9200, 10.77.64.56:9200, 10.77.64.33:9200, 10.77.64.89:9200, 10.77.64.18:9200, 10.77.64.32:9200, 10.77.64.76:9200, 10.77.64.46:9200, 10.77.64.96:9200, 10.77.64.19:9200, 10.77.64.63:9200, 10.77.64.6:9200, 10.77.64.1:9200, 10.77.64.92:9200, 10.77.64.61:9200, 10.77.64.97:9200, 10.77.64.77:9200, 10.77.64.62:9200, 10.77.64.71:9200, 10.77.64.3:9200, 10.77.64.65:9200, 10.77.64.90:9200, 10.77.64.91:9200] to data-only [10.77.64.38:9200, 10.77.64.50:9200, 10.77.64.73:9200, 10.77.64.72:9200, 10.77.64.74:9200, 10.77.64.21:9200, 10.77.64.81:9200, 10.77.64.31:9200, 10.77.64.55:9200, 10.77.64.69:9200, 10.77.64.35:9200, 10.77.64.24:9200, 10.77.64.40:9200, 10.77.64.23:9200, 10.77.64.36:9200, 10.77.64.85:9200, 10.77.64.58:9200, 10.77.64.59:9200, 10.77.64.70:9200, 10.77.64.66:9200, 10.77.64.75:9200, 10.77.64.60:9200, 10.77.64.98:9200, 10.77.64.57:9200, 10.77.64.64:9200, 10.77.64.25:9200, 10.77.64.88:9200, 10.77.64.42:9200, 10.77.64.48:9200, 10.77.64.80:9200, 10.77.64.52:9200, 10.77.64.16:9200, 10.77.64.54:9200, 10.77.64.17:9200, 10.77.64.47:9200, 10.77.64.39:9200, 10.77.64.44:9200, 10.77.64.79:9200, 10.77.64.53:9200, 10.77.64.7:9200, 10.77.64.37:9200, 10.77.64.87:9200, 10.77.64.94:9200, 10.77.64.43:9200, 10.77.64.28:9200, 10.77.64.2:9200, 10.77.64.67:9200, 10.77.64.86:9200, 10.77.64.34:9200, 10.77.64.20:9200, 10.77.64.22:9200, 10.77.64.51:9200, 10.77.64.30:9200, 10.77.64.4:9200, 10.77.64.5:9200, 10.77.64.95:9200, 10.77.64.99:9200, 10.77.64.45:9200, 10.77.64.78:9200, 10.77.64.29:9200, 10.77.64.49:9200, 10.77.64.93:9200, 10.77.64.56:9200, 10.77.64.33:9200, 10.77.64.89:9200, 10.77.64.18:9200, 10.77.64.32:9200, 10.77.64.76:9200, 10.77.64.46:9200, 10.77.64.96:9200, 10.77.64.19:9200, 10.77.64.63:9200, 10.77.64.6:9200, 10.77.64.1:9200, 10.77.64.92:9200, 10.77.64.61:9200, 10.77.64.97:9200, 10.77.64.77:9200, 10.77.64.62:9200, 10.77.64.71:9200, 10.77.64.3:9200, 10.77.64.65:9200, 10.77.64.90:9200, 10.77.64.91:9200]
16/06/07 14:48:50 TRACE CommonsHttpTransport: Closing HTTP transport to 10.77.64.63:9200
16/06/07 14:48:50 DEBUG CommonsHttpTransport: SSL Connection enabled
16/06/07 14:48:50 INFO CommonsHttpTransport: Using detected HTTP Auth credentials...
16/06/07 14:48:50 TRACE CommonsHttpTransport: Opening HTTP transport to 10.77.64.88:9200
16/06/07 14:48:50 TRACE CommonsHttpTransport: Tx [HEAD]@[10.77.64.88:9200][public_chicago/CSV] w/ payload [null]
16/06/07 14:48:50 TRACE CommonsHttpTransport: Rx @[10.77.95.200] [200-OK] [null]
16/06/07 14:48:50 TRACE CommonsHttpTransport: Tx [GET]@[10.77.64.88:9200][public_chicago/_search_shards] w/ payload [null]
16/06/07 14:48:50 TRACE CommonsHttpTransport: Rx @[10.77.95.200] [200-OK] [{"nodes":{"aDqdFsTPTYONo9PZ_SIR3g":{"name":"elasticsearch-node57.fr","transport_address":"inet[/10.77.64.57:9300]","attributes":{"master":"false"}},"F4ZWDp29QiuwOMd6IIcdgQ":{"name":"elasticsearch-node73.fr","transport_address":"inet[/10.77.64.73:9300]","attributes":{"master":"false"}},"UMwrOxHWRU6DMac7dSv6eA":{"name":"elasticsearch-node19.fr","transport_address":"inet[/10.77.64.19:9300]","attributes":{"master":"false"}},"mLf16MJLQuSYiZMzOwefbw":{"name":"elasticsearch-node34.fr","transport_address":"inet[/10.77.64.34:9300]","attributes":{"master":"false"}},"_jiEy4H5R6ShgzdAlTwdyQ":{"name":"elasticsearch-node86.fr","transport_address":"inet[/10.77.64.86:9300]","attributes":{"master":"false"}},"o1borzldTZ6dAbWvs8Rp6Q":{"name":"elasticsearch-node06.fr","transport_address":"inet[/10.77.64.6:9300]","attributes":{"master":"false"}},"oglmjzEXRQmtTHZnyYPY1Q":{"name":"elasticsearch-node01.fr","transport_address":"inet[/10.77.64.1:9300]","attributes":{"master":"false"}},"gHVv8twTRjqlELi2f8ME8A":{"name":"elasticsearch-node52.fr","transport_address":"inet[/10.77.64.52:9300]","attributes":{"master":"false"}},"8JEVlfUDRIaHTPKTuhhl0A":{"name":"elasticsearch-node16.fr","transport_address":"inet[/10.77.64.16:9300]","attributes":{"master":"false"}},"Vv2CbP5ISiiYHyXp_nnMvw":{"name":"elasticsearch-node51.fr","transport_address":"inet[/10.77.64.51:9300]","attributes":{"master":"false"}},"Nq9MGM9DTJa6nCpwzOBcUQ":{"name":"elasticsearch-node47.fr","transport_address":"inet[/10.77.64.47:9300]","attributes":{"master":"false"}},"NzNI7nuESfmZSx5fEjiS3w":{"name":"elasticsearch-node78.fr","transport_address":"inet[/10.77.64.78:9300]","attributes":{"master":"false"}},"XR3NEzi3RUWR9dJuWKF2DA":{"name":"elasticsearch-node45.fr","transport_address":"inet[/10.77.64.45:9300]","attributes":{"master":"false"}},"NqkuQkkTQuGJtSgpcSegSg":{"name":"elasticsearch-node29.fr","transport_address":"inet[/10.77.64.29:9300]","attributes":{"master":"false"}},"v5CEI6bwTZapN7EEemDtVg":{"name":"elasticsearch-node53.fr","transport_address":"inet[/10.77.64.53:9301]","attributes":{"master":"false"}},"2ZDlxyPDSXahDmg24t2E9Q":{"name":"elasticsearch-node90.fr","transport_address":"inet[/10.77.64.90:9300]","attributes":{"master":"false"}},"hxIo-ZKuQliqvrzAAZOobQ":{"name":"elasticsearch-node70.fr","transport_address":"inet[/10.77.64.70:9300]","attributes":{"master":"false"}},"7T3MeW98SFy9QxtR2Bu5gA":{"name":"elasticsearch-node49.fr","transport_address":"inet[/10.77.64.49:9300]","attributes":{"master":"false"}},"L12cIR6QSLW-iOmm7PRX-A":{"name":"elasticsearch-node75.fr","transport_address":"inet[/10.77.64.75:9300]","attributes":{"master":"false"}},"E3PopHTCS7O3KDf_QgC4yA":{"name":"elasticsearch-node60.fr","transport_address":"inet[/10.77.64.60:9300]","attributes":{"master":"false"}}},"shards":[[{"state":"STARTED","primary":true,"node":"7T3MeW98SFy9QxtR2Bu5gA","relocating_node":null,"shard":0,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"L12cIR6QSLW-iOmm7PRX-A","relocating_node":null,"shard":0,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"v5CEI6bwTZapN7EEemDtVg","relocating_node":null,"shard":0,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"NqkuQkkTQuGJtSgpcSegSg","relocating_node":null,"shard":0,"index":"public_chicago"}],[{"state":"STARTED","primary":true,"node":"2ZDlxyPDSXahDmg24t2E9Q","relocating_node":null,"shard":1,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"hxIo-ZKuQliqvrzAAZOobQ","relocating_node":null,"shard":1,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"aDqdFsTPTYONo9PZ_SIR3g","relocating_node":null,"shard":1,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"_jiEy4H5R6ShgzdAlTwdyQ","relocating_node":null,"shard":1,"index":"public_chicago"}],[{"state":"STARTED","primary":true,"node":"Nq9MGM9DTJa6nCpwzOBcUQ","relocating_node":null,"shard":2,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"Vv2CbP5ISiiYHyXp_nnMvw","relocating_node":null,"shard":2,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"o1borzldTZ6dAbWvs8Rp6Q","relocating_node":null,"shard":2,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"F4ZWDp29QiuwOMd6IIcdgQ","relocating_node":null,"shard":2,"index":"public_chicago"}],[{"state":"STARTED","primary":false,"node":"XR3NEzi3RUWR9dJuWKF2DA","relocating_node":null,"shard":3,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"UMwrOxHWRU6DMac7dSv6eA","relocating_node":null,"shard":3,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"gHVv8twTRjqlELi2f8ME8A","relocating_node":null,"shard":3,"index":"public_chicago"},{"state":"STARTED","primary":true,"node":"mLf16MJLQuSYiZMzOwefbw","relocating_node":null,"shard":3,"index":"public_chicago"}],[{"state":"STARTED","primary":false,"node":"E3PopHTCS7O3KDf_QgC4yA","relocating_node":null,"shard":4,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"8JEVlfUDRIaHTPKTuhhl0A","relocating_node":null,"shard":4,"index":"public_chicago"},{"state":"STARTED","primary":true,"node":"NzNI7nuESfmZSx5fEjiS3w","relocating_node":null,"shard":4,"index":"public_chicago"},{"state":"STARTED","primary":false,"node":"oglmjzEXRQmtTHZnyYPY1Q","relocating_node":null,"shard":4,"index":"public_chicago"}]]}]
16/06/07 14:48:50 TRACE CommonsHttpTransport: Tx [GET]@[10.77.64.88:9200][_nodes/http] w/ payload [null]
16/06/07 14:48:51 TRACE CommonsHttpTransport: Rx @[10.77.95.200] [200-OK] 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16/06/07 14:48:51 TRACE CommonsHttpTransport: Tx [GET]@[10.77.64.88:9200][public_chicago/_aliases] w/ payload [null]
16/06/07 14:48:51 TRACE CommonsHttpTransport: Rx @[10.77.95.200] [200-OK] [{"public_chicago":{"aliases":{}}}]
16/06/07 14:48:51 TRACE ScalaEsRDD: Creating splits for shards {Shard[state=STARTED, primary=true, node=7T3MeW98SFy9QxtR2Bu5gA, name=0, index=public_chicago]=Node[id=7T3MeW98SFy9QxtR2Bu5gA, name=elasticsearch-node49.fr, ipAddress=10.77.64.49, httpPort=9200, isClient=false, isData=true], Shard[state=STARTED, primary=true, node=2ZDlxyPDSXahDmg24t2E9Q, name=1, index=public_chicago]=Node[id=2ZDlxyPDSXahDmg24t2E9Q, name=elasticsearch-node90.fr, ipAddress=10.77.64.90, httpPort=9200, isClient=false, isData=true], Shard[state=STARTED, primary=true, node=Nq9MGM9DTJa6nCpwzOBcUQ, name=2, index=public_chicago]=Node[id=Nq9MGM9DTJa6nCpwzOBcUQ, name=elasticsearch-node47.fr, ipAddress=10.77.64.47, httpPort=9200, isClient=false, isData=true], Shard[state=STARTED, primary=false, node=XR3NEzi3RUWR9dJuWKF2DA, name=3, index=public_chicago]=Node[id=XR3NEzi3RUWR9dJuWKF2DA, name=elasticsearch-node45.fr, ipAddress=10.77.64.45, httpPort=9200, isClient=false, isData=true], Shard[state=STARTED, primary=false, node=E3PopHTCS7O3KDf_QgC4yA, name=4, index=public_chicago]=Node[id=E3PopHTCS7O3KDf_QgC4yA, name=elasticsearch-node60.fr, ipAddress=10.77.64.60, httpPort=9200, isClient=false, isData=true]}
16/06/07 14:48:51 INFO ScalaEsRDD: Reading from [public_chicago/CSV]
16/06/07 14:48:51 TRACE CommonsHttpTransport: Tx [GET]@[10.77.64.88:9200][public_chicago/CSV/_mapping] w/ payload [null]
16/06/07 14:48:52 TRACE CommonsHttpTransport: Rx @[10.77.95.200] [200-OK] [{"public_chicago":{"mappings":{"CSV":{"properties":{"arrest":{"type":"boolean"},"beat":{"type":"long"},"block":{"type":"string"},"casenumber":{"type":"string"},"communityarea":{"type":"long"},"date":{"type":"string"},"description":{"type":"string"},"district":{"type":"long"},"domestic":{"type":"boolean"},"fbicode":{"type":"string"},"geolocation":{"type":"string"},"id":{"type":"long"},"iucr":{"type":"string"},"latitude":{"type":"string"},"locationdescription":{"type":"string"},"longitude":{"type":"string"},"primarytype":{"type":"string"},"updatedon":{"type":"string"},"ward":{"type":"long"},"xcoordinate":{"type":"long"},"ycoordinate":{"type":"long"},"year":{"type":"long"}}}}}}]
16/06/07 14:48:52 INFO ScalaEsRDD: Discovered mapping {CSV=[arrest=BOOLEAN, beat=LONG, block=STRING, casenumber=STRING, communityarea=LONG, date=STRING, description=STRING, district=LONG, domestic=BOOLEAN, fbicode=STRING, geolocation=STRING, id=LONG, iucr=STRING, latitude=STRING, locationdescription=STRING, longitude=STRING, primarytype=STRING, updatedon=STRING, ward=LONG, xcoordinate=LONG, ycoordinate=LONG, year=LONG]} for [public_chicago/CSV]
16/06/07 14:48:52 DEBUG RestRepository: Closing repository and connection to Elasticsearch ...
16/06/07 14:48:52 TRACE CommonsHttpTransport: Closing HTTP transport to 10.77.64.88:9200
[Stage 0:>                                                          (0 + 5) / 5]
jbaiera commented 8 years ago

I'm assuming that you're running the tasks on a cluster and not locally. Could you post the same level of logging for some of the worker processes? Also, could you run jstack a few times for a thread dump on the executing worker processes to see if they're hung up on something? Thanks

ArcTheMaster commented 8 years ago

Hi @jbaiera, thank you for your reply. You're right, I'm working on a cluster (with more than 50 datanodes).

You can find below the logs of a Spark executor during a collect: 16/06/23 15:24:14 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 4 16/06/23 15:24:14 INFO executor.Executor: Running task 0.0 in stage 4.0 (TID 4) 16/06/23 15:24:14 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 8 16/06/23 15:24:14 INFO executor.Executor: Running task 4.0 in stage 4.0 (TID 8) 16/06/23 15:24:14 INFO broadcast.TorrentBroadcast: Started reading broadcast variable 4 16/06/23 15:24:14 INFO storage.MemoryStore: Block broadcast_4_piece0 stored as bytes in memory (estimated size 1007.0 B, free 1007.0 B) 16/06/23 15:24:14 INFO broadcast.TorrentBroadcast: Reading broadcast variable 4 took 30 ms 16/06/23 15:24:14 INFO storage.MemoryStore: Block broadcast_4 stored as values in memory (estimated size 1528.0 B, free 2.5 KB) 16/06/23 15:38:48 ERROR executor.Executor: Exception in task 4.0 in stage 4.0 (TID 8) org.elasticsearch.hadoop.rest.EsHadoopInvalidRequest: AuthException[org.apache.directory.api.ldap.model.exception.LdapException: The response queue has been emptied, no response was found.]; nested: LdapException[The response queue has been emptied, no response was found.]; nested: LdapException[TimeOut occurred]; at org.elasticsearch.hadoop.rest.RestClient.checkResponse(RestClient.java:478) at org.elasticsearch.hadoop.rest.RestClient.execute(RestClient.java:436) at org.elasticsearch.hadoop.rest.RestClient.execute(RestClient.java:426) at org.elasticsearch.hadoop.rest.RestClient.scroll(RestClient.java:496) at org.elasticsearch.hadoop.rest.RestRepository.scroll(RestRepository.java:454) at org.elasticsearch.hadoop.rest.ScrollQuery.hasNext(ScrollQuery.java:86) at org.elasticsearch.spark.rdd.AbstractEsRDDIterator.hasNext(AbstractEsRDDIterator.scala:43) at scala.collection.Iterator$class.foreach(Iterator.scala:727) at org.elasticsearch.spark.rdd.AbstractEsRDDIterator.foreach(AbstractEsRDDIterator.scala:10) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273) at org.elasticsearch.spark.rdd.AbstractEsRDDIterator.to(AbstractEsRDDIterator.scala:10) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265) at org.elasticsearch.spark.rdd.AbstractEsRDDIterator.toBuffer(AbstractEsRDDIterator.scala:10) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252) at org.elasticsearch.spark.rdd.AbstractEsRDDIterator.toArray(AbstractEsRDDIterator.scala:10) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$12.apply(RDD.scala:927) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$12.apply(RDD.scala:927) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) at org.apache.spark.scheduler.Task.run(Task.scala:89) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) 16/06/23 15:38:54 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 11 16/06/23 15:38:54 INFO executor.Executor: Running task 1.1 in stage 4.0 (TID 11)

The AuthException is very strange because a curl like the following will work: curl -XGET "http://datanode81.domain.fr:9200/public_chicago/CSV/_search?q=*&pretty" -u shfs3453

This is also the same if I restrict the number of documents returned by Spark, through a take for example (I give the example on Spark but it's the same behavior with the others): RDD1.take(10000).foreach(println)

The take produces a strack trace like this one: 16/06/23 14:58:06 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 1 16/06/23 14:58:06 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1) 16/06/23 14:58:06 INFO executor.Executor: Fetching http://10.77.95.201:55596/jars/elasticsearch-hadoop.jar with timestamp 1466686424868 16/06/23 14:58:06 INFO util.Utils: Fetching http://10.77.95.201:55596/jars/elasticsearch-hadoop.jar to /mnt/hd6/hadoop/yarn/local/usercache/shfs3453/appcache/application_1461692698792_81063/spark-88497755-37b1-4b4c-bda2-63076e6b99e6/fetchFileTemp3865958073615203249.tmp 16/06/23 14:58:06 INFO util.Utils: Copying /mnt/hd6/hadoop/yarn/local/usercache/shfs3453/appcache/application_1461692698792_81063/spark-88497755-37b1-4b4c-bda2-63076e6b99e6/-17184871161466686424868_cache to /mnt/hd1/hadoop/yarn/local/usercache/shfs3453/appcache/application_1461692698792_81063/container_1461692698792_81063_01_000003/./elasticsearch-hadoop.jar 16/06/23 14:58:06 INFO executor.Executor: Adding file:/mnt/hd1/hadoop/yarn/local/usercache/shfs3453/appcache/application_1461692698792_81063/container_1461692698792_81063_01_000003/./elasticsearch-hadoop.jar to class loader 16/06/23 14:58:06 INFO broadcast.TorrentBroadcast: Started reading broadcast variable 1 16/06/23 14:58:06 INFO storage.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 1057.0 B, free 1057.0 B) 16/06/23 14:58:06 INFO broadcast.TorrentBroadcast: Reading broadcast variable 1 took 116 ms 16/06/23 14:58:07 INFO storage.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 1560.0 B, free 2.6 KB) 16/06/23 14:58:28 INFO executor.Executor: Finished task 0.0 in stage 1.0 (TID 1). 459989 bytes result sent to driver

jbaiera commented 7 years ago

This is a fairly old ticket and the conversation has seemed to trail off. Based on previous discussion it seems that there's a problem in communication between ES and LDAP that is causing the requests to hang for long periods. If this is still an issue we can start up the conversation again. Closing this until then.