GC overhead limit exceeded

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tiny657

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Aug 31, 2020, 9:09:51 PM8/31/20
to Druid User
Hi,
Got out of memory even though my data volume is not that big compared to the server.

Error Message: Terminating due to java.lang.OutOfMemoryError: GC overhead limit exceeded


Installed druid on a single machine for i3.4xlarge and launched by bin/start-medium
-----
Medium: 16 CPU, 128GB RAM (~i3.4xlarge)
  • Launch command: bin/start-medium
  • Configuration directory: conf/druid/single-server/medium


Here is the default jvm config for medium I used.
- broker: -Xms8g -Xmx8g -XX:MaxDirectMemorySize=5g
- coordinator-overlord: -Xms9g -Xmx9g
- historical: -Xms8g -Xmx8g -XX:MaxDirectMemorySize=13g
- middleManager: -Xms256m -Xmx256m
- router: -Xms512m -Xmx512, -XX:MaxDirectMemorySize=128m


Also, I tried to increase the memory in jvm config.  But got the same Out of Memory error.
- broker: -Xms32g -Xmx32g -XX:MaxDirectMemorySize=20g
- coordinator-overlord: -Xms36g -Xmx 36g
- historical: -Xms32g -Xmx32g -XX:MaxDirectMemorySize=52g
- middleManager: -Xms10g -Xmx10g
- router: -Xms2g -Xmx2g -XX:MaxDirectMemorySize=512m


Here is the data example I used.
Tried to ingest 1.5G bytes (25M rows)
Screen Shot 2020-08-31 at 2.55.37 PM.png

Ingestion spec:

{

  "type": "index_parallel",

  "spec": {

    "dataSchema": {

      "dataSource": “table_name”,

      "dimensionsSpec" : {

        "dimensions" : ["test_option", "abtest_metric_id", "dimension_name", "dimension_value", "event_value", "user_id"]

      },

      "timestampSpec": {

        "column": "dt",

        "format": "yyyyMMdd",

        "missingValue": "20200822"

      },

"metricsSpec": [ { "type": "count", "name": "count" } ],

      "granularitySpec": {

        "segmentGranularity": "day",

        "queryGranularity": "none"

      }

    },

    "ioConfig": {

      "type": "index_parallel",

      "inputSource": {

        "type": "s3",

        "prefixes": ["s3://buckets/"]

      },

      "inputFormat": {

        "type": "parquet"

      }

    },

    "tuningConfig": {

        "type": "index_parallel",

        "maxNumConcurrentSubTasks": 20

    }

  }

}



Full Error Log:

2020-09-01T00:51:14,974 INFO [main] org.apache.zookeeper.ZooKeeper - Initiating client connection, connectString=localhost sessionTimeout=30000 watcher=org.apache.curator.ConnectionState@55d99dc3
2020-09-01T00:51:15,035 INFO [main] org.apache.curator.framework.imps.CuratorFrameworkImpl - Default schema
2020-09-01T00:51:15,045 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Opening socket connection to server localhost/127.0.0.1:2181. Will not attempt to authenticate using SASL (unknown error)
2020-09-01T00:51:15,054 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Socket connection established to localhost/127.0.0.1:2181, initiating session
2020-09-01T00:51:15,077 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Session establishment complete on server localhost/127.0.0.1:2181, sessionid = 0x1000f97e8a80014, negotiated timeout = 30000
2020-09-01T00:51:15,083 INFO [main-EventThread] org.apache.curator.framework.state.ConnectionStateManager - State change: CONNECTED
2020-09-01T00:51:15,206 INFO [NodeRoleWatcher[COORDINATOR]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Node[http://localhost:8081] of role[coordinator] detected.
2020-09-01T00:51:15,206 INFO [NodeRoleWatcher[OVERLORD]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Node[http://localhost:8081] of role[overlord] detected.
2020-09-01T00:51:15,206 INFO [NodeRoleWatcher[COORDINATOR]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Node watcher of role[coordinator] is now initialized.
2020-09-01T00:51:15,206 INFO [NodeRoleWatcher[OVERLORD]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Node watcher of role[overlord] is now initialized.
2020-09-01T00:51:15,378 INFO [main] org.apache.druid.indexing.worker.executor.ExecutorLifecycle - Running with task: {
  "type" : "single_phase_sub_task",
  "id" : "single_phase_sub_task_maxRetry3_biinapgd_2020-09-01T00:49:33.063Z",
  "groupId" : "index_parallel_maxRetry3_pgibohji_2020-09-01T00:45:45.039Z",
  "resource" : {
    "availabilityGroup" : "single_phase_sub_task_maxRetry3_biinapgd_2020-09-01T00:49:33.063Z",
    "requiredCapacity" : 1
  },
  "supervisorTaskId" : "index_parallel_maxRetry3_pgibohji_2020-09-01T00:45:45.039Z",
  "numAttempts" : 2,
  "spec" : {
    "dataSchema" : {
      "dataSource" : "maxRetry3",
      "timestampSpec" : {
        "column" : "dt",
        "format" : "yyyyMMdd",
        "missingValue" : "20200822-01-01T00:00:00.000Z"
      },
      "dimensionsSpec" : {
        "dimensions" : [ {
          "type" : "string",
          "name" : "test_option",
          "multiValueHandling" : "SORTED_ARRAY",
          "createBitmapIndex" : true
        }, {
          "type" : "string",
          "name" : "abtest_metric_id",
          "multiValueHandling" : "SORTED_ARRAY",
          "createBitmapIndex" : true
        }, {
          "type" : "string",
          "name" : "dimension_name",
          "multiValueHandling" : "SORTED_ARRAY",
          "createBitmapIndex" : true
        }, {
          "type" : "string",
          "name" : "dimension_value",
          "multiValueHandling" : "SORTED_ARRAY",
          "createBitmapIndex" : true
        }, {
          "type" : "string",
          "name" : "event_value",
          "multiValueHandling" : "SORTED_ARRAY",
          "createBitmapIndex" : true
        }, {
          "type" : "string",
          "name" : "user_id",
          "multiValueHandling" : "SORTED_ARRAY",
          "createBitmapIndex" : true
        } ],
        "dimensionExclusions" : [ "dt", "count" ]
      },
      "metricsSpec" : [ {
        "type" : "count",
        "name" : "count"
      } ],
      "granularitySpec" : {
        "type" : "uniform",
        "segmentGranularity" : "DAY",
        "queryGranularity" : {
          "type" : "none"
        },
        "rollup" : true,
        "intervals" : null
      },
      "transformSpec" : {
        "filter" : null,
        "transforms" : [ ]
      }
    },
    "ioConfig" : {
      "type" : "index_parallel",
      "inputSource" : {
        "type" : "s3",
        "uris" : null,
        "prefixes" : null,
        "objects" : [ {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00006-ef28c0f9-f2d4-4f7a-84a9-1e36aea39816-c000.snappy.parquet"
        }, {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00006-ef28c0f9-f2d4-4f7a-84a9-1e36aea39816-c001.snappy.parquet"
        }, {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00007-eccc7759-c75a-43c8-817b-2fa2076967d8-c000.snappy.parquet"
        }, {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00007-ef28c0f9-f2d4-4f7a-84a9-1e36aea39816-c000.snappy.parquet"
        }, {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00007-ef28c0f9-f2d4-4f7a-84a9-1e36aea39816-c001.snappy.parquet"
        }, {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00008-eccc7759-c75a-43c8-817b-2fa2076967d8-c000.snappy.parquet"
        }, {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00008-ef28c0f9-f2d4-4f7a-84a9-1e36aea39816-c000.snappy.parquet"
        }, {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00008-ef28c0f9-f2d4-4f7a-84a9-1e36aea39816-c001.snappy.parquet"
        }, {
          "bucket" : "s3-abtest-prod",
          "path" : "xpe/daily_unique/area_metric_type=Search/abtest_instance_id=34554/dt=20200822/part-00009-eccc7759-c75a-43c8-817b-2fa2076967d8-c000.snappy.parquet"
        } ],
        "properties" : null
      },
      "inputFormat" : {
        "type" : "parquet",
        "flattenSpec" : {
          "useFieldDiscovery" : true,
          "fields" : [ ]
        },
        "binaryAsString" : false
      },
      "appendToExisting" : false
    },
    "tuningConfig" : {
      "type" : "index_parallel",
      "maxRowsPerSegment" : null,
      "maxRowsInMemory" : 1000000,
      "maxBytesInMemory" : 0,
      "maxTotalRows" : null,
      "numShards" : null,
      "splitHintSpec" : null,
      "partitionsSpec" : null,
      "indexSpec" : {
        "bitmap" : {
          "type" : "roaring",
          "compressRunOnSerialization" : true
        },
        "dimensionCompression" : "lz4",
        "metricCompression" : "lz4",
        "longEncoding" : "longs",
        "segmentLoader" : null
      },
      "indexSpecForIntermediatePersists" : {
        "bitmap" : {
          "type" : "roaring",
          "compressRunOnSerialization" : true
        },
        "dimensionCompression" : "lz4",
        "metricCompression" : "lz4",
        "longEncoding" : "longs",
        "segmentLoader" : null
      },
      "maxPendingPersists" : 0,
      "forceGuaranteedRollup" : false,
      "reportParseExceptions" : false,
      "pushTimeout" : 0,
      "segmentWriteOutMediumFactory" : null,
      "maxNumConcurrentSubTasks" : 20,
      "maxRetry" : 3,
      "taskStatusCheckPeriodMs" : 1000,
      "chatHandlerTimeout" : "PT10S",
      "chatHandlerNumRetries" : 5,
      "maxNumSegmentsToMerge" : 100,
      "totalNumMergeTasks" : 10,
      "logParseExceptions" : false,
      "maxParseExceptions" : 2147483647,
      "maxSavedParseExceptions" : 0,
      "buildV9Directly" : true,
      "partitionDimensions" : [ ]
    }
  },
  "context" : {
    "forceTimeChunkLock" : true
  },
  "dataSource" : "maxRetry3"
}
2020-09-01T00:51:15,380 INFO [main] org.apache.druid.indexing.worker.executor.ExecutorLifecycle - Attempting to lock file[var/druid/task/single_phase_sub_task_maxRetry3_biinapgd_2020-09-01T00:49:33.063Z/lock].
2020-09-01T00:51:15,387 INFO [main] org.apache.druid.indexing.worker.executor.ExecutorLifecycle - Acquired lock file[var/druid/task/single_phase_sub_task_maxRetry3_biinapgd_2020-09-01T00:49:33.063Z/lock] in 2ms.
2020-09-01T00:51:15,394 INFO [main] org.apache.druid.indexing.common.task.AbstractBatchIndexTask - [forceTimeChunkLock] is set to true in task context. Use timeChunk lock
2020-09-01T00:51:15,415 INFO [task-runner-0-priority-0] org.apache.druid.indexing.overlord.SingleTaskBackgroundRunner - Running task: single_phase_sub_task_maxRetry3_biinapgd_2020-09-01T00:49:33.063Z
2020-09-01T00:51:15,418 WARN [task-runner-0-priority-0] org.apache.druid.indexing.common.task.batch.parallel.SinglePhaseSubTask - Intervals are missing in granularitySpec while this task is potentially overwriting existing segments. Forced to use timeChunk lock.
2020-09-01T00:51:15,421 INFO [main] org.apache.druid.java.util.common.lifecycle.Lifecycle - Starting lifecycle [module] stage [SERVER]
2020-09-01T00:51:15,425 INFO [main] org.eclipse.jetty.server.Server - jetty-9.4.12.v20180830; built: 2018-08-30T13:59:14.071Z; git: 27208684755d94a92186989f695db2d7b21ebc51; jvm 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01
2020-09-01T00:51:15,740 INFO [main] org.eclipse.jetty.server.session - DefaultSessionIdManager workerName=node0
2020-09-01T00:51:15,740 INFO [main] org.eclipse.jetty.server.session - No SessionScavenger set, using defaults
2020-09-01T00:51:15,742 INFO [main] org.eclipse.jetty.server.session - node0 Scavenging every 600000ms
2020-09-01T00:51:16,086 INFO [main] com.sun.jersey.server.impl.application.WebApplicationImpl - Initiating Jersey application, version 'Jersey: 1.19.3 10/24/2016 03:43 PM'
2020-09-01T00:51:18,040 INFO [main] org.eclipse.jetty.server.handler.ContextHandler - Started o.e.j.s.ServletContextHandler@2bf4fa1{/,null,AVAILABLE}
2020-09-01T00:51:18,111 INFO [main] org.eclipse.jetty.server.AbstractConnector - Started ServerConnector@40aad17d{HTTP/1.1,[http/1.1]}{0.0.0.0:8101}
2020-09-01T00:51:18,112 INFO [main] org.eclipse.jetty.server.Server - Started @16126ms
2020-09-01T00:51:18,115 INFO [main] org.apache.druid.java.util.common.lifecycle.Lifecycle - Starting lifecycle [module] stage [ANNOUNCEMENTS]
2020-09-01T00:51:18,115 INFO [main] org.apache.druid.java.util.common.lifecycle.Lifecycle - Successfully started lifecycle [module]
2020-09-01T00:51:21,011 INFO [task-runner-0-priority-0] org.apache.parquet.hadoop.InternalParquetRecordReader - RecordReader initialized will read a total of 2000000 records.
2020-09-01T00:51:21,011 INFO [task-runner-0-priority-0] org.apache.parquet.hadoop.InternalParquetRecordReader - at row 0. reading next block
2020-09-01T00:51:21,134 INFO [task-runner-0-priority-0] org.apache.hadoop.io.compress.CodecPool - Got brand-new decompressor [.snappy]
2020-09-01T00:51:21,150 INFO [task-runner-0-priority-0] org.apache.parquet.hadoop.InternalParquetRecordReader - block read in memory in 139 ms. row count = 2000000
2020-09-01T00:51:21,779 INFO [task-runner-0-priority-0] org.apache.druid.segment.realtime.appenderator.BaseAppenderatorDriver - New segment[maxRetry3_20200822-01-01T00:00:00.000Z_20200822-01-02T00:00:00.000Z_2020-09-01T00:46:01.484Z_8] for sequenceName[single_phase_sub_task_maxRetry3_biinapgd_2020-09-01T00:49:33.063Z].
2020-09-01T00:51:39,503 INFO [task-runner-0-priority-0] org.apache.druid.segment.realtime.appenderator.AppenderatorImpl - Flushing in-memory data to disk because No more rows can be appended to sink,bytesCurrentlyInMemory[171529596] is greater than maxBytesInMemory[171529557].
2020-09-01T00:52:24,863 WARN [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Client session timed out, have not heard from server in 26076ms for sessionid 0x1000f97e8a80014
2020-09-01T00:52:24,864 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Client session timed out, have not heard from server in 26076ms for sessionid 0x1000f97e8a80014, closing socket connection and attempting reconnect
2020-09-01T00:52:29,704 INFO [main-EventThread] org.apache.curator.framework.state.ConnectionStateManager - State change: SUSPENDED
2020-09-01T00:52:29,705 WARN [NodeRoleWatcher[OVERLORD]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Ignored event type[CONNECTION_SUSPENDED] for node watcher of role[overlord].
2020-09-01T00:52:29,706 WARN [NodeRoleWatcher[COORDINATOR]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Ignored event type[CONNECTION_SUSPENDED] for node watcher of role[coordinator].
2020-09-01T00:52:31,883 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Opening socket connection to server localhost/127.0.0.1:2181. Will not attempt to authenticate using SASL (unknown error)
2020-09-01T00:52:31,884 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Socket connection established to localhost/127.0.0.1:2181, initiating session
2020-09-01T00:52:31,886 WARN [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Unable to reconnect to ZooKeeper service, session 0x1000f97e8a80014 has expired
2020-09-01T00:52:31,886 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Unable to reconnect to ZooKeeper service, session 0x1000f97e8a80014 has expired, closing socket connection
2020-09-01T00:52:31,886 WARN [main-EventThread] org.apache.curator.ConnectionState - Session expired event received
2020-09-01T00:52:31,887 INFO [main-EventThread] org.apache.zookeeper.ZooKeeper - Initiating client connection, connectString=localhost sessionTimeout=30000 watcher=org.apache.curator.ConnectionState@55d99dc3
2020-09-01T00:52:34,162 INFO [main-EventThread] org.apache.curator.framework.state.ConnectionStateManager - State change: LOST
2020-09-01T00:52:34,162 INFO [main-EventThread] org.apache.zookeeper.ClientCnxn - EventThread shut down for session: 0x1000f97e8a80014
2020-09-01T00:52:34,164 WARN [NodeRoleWatcher[OVERLORD]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Ignored event type[CONNECTION_LOST] for node watcher of role[overlord].
2020-09-01T00:52:34,164 WARN [NodeRoleWatcher[COORDINATOR]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Ignored event type[CONNECTION_LOST] for node watcher of role[coordinator].
2020-09-01T00:52:36,705 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Opening socket connection to server localhost/127.0.0.1:2181. Will not attempt to authenticate using SASL (unknown error)
2020-09-01T00:52:36,705 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Socket connection established to localhost/127.0.0.1:2181, initiating session
2020-09-01T00:52:36,709 INFO [main-SendThread(localhost:2181)] org.apache.zookeeper.ClientCnxn - Session establishment complete on server localhost/127.0.0.1:2181, sessionid = 0x1000f97e8a80017, negotiated timeout = 30000
2020-09-01T00:52:36,709 INFO [main-EventThread] org.apache.curator.framework.state.ConnectionStateManager - State change: RECONNECTED
2020-09-01T00:52:36,712 WARN [NodeRoleWatcher[OVERLORD]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Ignored event type[CONNECTION_RECONNECTED] for node watcher of role[overlord].
2020-09-01T00:52:36,716 WARN [NodeRoleWatcher[COORDINATOR]] org.apache.druid.curator.discovery.CuratorDruidNodeDiscoveryProvider$NodeRoleWatcher - Ignored event type[CONNECTION_RECONNECTED] for node watcher of role[coordinator].
Terminating due to java.lang.OutOfMemoryError: GC overhead limit exceeded

tiny657

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Aug 31, 2020, 9:22:17 PM8/31/20
to Druid User
And while ingesting data from S3, CPU usage is 99%.
Is it normal?

Screen Shot 2020-08-31 at 5.52.41 PM.png


2020년 8월 31일 월요일 오후 6시 9분 51초 UTC-7에 tiny657님이 작성:

Rachel Pedreschi

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Aug 31, 2020, 9:30:53 PM8/31/20
to druid...@googlegroups.com
This doc may help:   https://druid.apache.org/docs/latest/ingestion/native-batch.html#parallel-task

I'd start with a config that uses less resources, and make sure that can run, then start to step up to utilize more of the resources.  Also, what version of Druid are you using?

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Rachel Pedreschi
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youngwan lim

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Aug 31, 2020, 9:33:21 PM8/31/20
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I am using the latest version.

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Jay R

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Sep 1, 2020, 12:52:59 AM9/1/20
to Druid User
@tiny657

Did you change the runtime.properties too?.
while ingestion in progress, ssh to middle manager node and check exactly how much Xms/Xmx the sessions is using.(It may be using default Xms1g). 

ps -ef| grep Xmas
ps -ef| grep druid

after changing the config files, apply the changes to the system before ingestion.

systemctl daemon-reload  (cent os)

Regards,
Jay R

youngwan lim

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Sep 1, 2020, 1:00:07 AM9/1/20
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Hi Jay,
Thanks for your reply.
I did not touch runtime.properties.
So middleManager is using ` -Xms1g -Xmx1g` while ingesting.

Do you have any recommend heap size?

Regards,

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Jay R

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Sep 1, 2020, 1:13:05 AM9/1/20
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  1. How many tasks spawned?. If its n,  then each task can have Xmx = memory allocated for middle manager/n. Try increasing the Xmx in run time properties.
  2. Since the machine you used as only 16CPUs, decrease the maxNumConcurrentSubTasks to 8 (after exlcuding other processes needs).

youngwan lim

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Sep 1, 2020, 1:25:41 AM9/1/20
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Thanks.
After replacing runtime.config with -Xms5g -Xmx5g, there is no more OOM.

I am using `druid.worker.capacity=4`

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youngwan lim

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Sep 1, 2020, 1:34:12 AM9/1/20
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One more quick question:
- After changing druid.worker.capacity from 4 to 8, 4 workers are still running in parallel for ingestion.

Should I change the other config to increase the worker size?

Jay R

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Sep 2, 2020, 10:22:55 AM9/2/20
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Since it is single node, there will be few cores availble for middle manager,after excluding cores for other processes.
Then maxNumConcurrentSubTasks drives it with the above availble CPU cores.
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