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output_makedb_4
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Using properties file: null
Parsed arguments:
master spark://inf040:7077
deployMode null
executorMemory 192g
executorCores 1
totalExecutorCores null
propertiesFile null
driverMemory 192g
driverCores null
driverExtraClassPath null
driverExtraLibraryPath null
driverExtraJavaOptions -XX:MaxHeapSize=220g
supervise false
queue null
numExecutors null
files null
pyFiles null
archives null
mainClass SparkLeMakeDB
primaryResource file:/projects/synergy_lab/ritvik/Voltron/SparkLeBLAST/target/scala-2.11/simple-project_2.11-1.0.jar
name SparkLeMakeDB
childArgs [4 /fastscratch/karimy/blastDB/uniprot_sprot.fasta /projects/synergy_lab/ritvik/Voltron/SparkLeBLAST/formatdbScript /localscratch/uniprot_sprot_formatted prot]
jars null
packages null
packagesExclusions null
repositories null
verbose true
Spark properties used, including those specified through
--conf and those from the properties file null:
(spark.local.dir,/home/ritvikp/tmpSpark)
(spark.network.timeout,3600)
(spark.driver.memory,192g)
(spark.executor.memory,192g)
(spark.driver.extraJavaOptions,-XX:MaxHeapSize=220g)
(spark.worker.extraJavaOptions,-XX:MaxHeapSize=220g)
Main class:
SparkLeMakeDB
Arguments:
4
/fastscratch/karimy/blastDB/uniprot_sprot.fasta
/projects/synergy_lab/ritvik/Voltron/SparkLeBLAST/formatdbScript
/localscratch/uniprot_sprot_formatted
prot
System properties:
(spark.local.dir,/home/ritvikp/tmpSpark)
(spark.network.timeout,3600)
(spark.executor.memory,192g)
(spark.driver.memory,192g)
(SPARK_SUBMIT,true)
(spark.app.name,SparkLeMakeDB)
(spark.driver.extraJavaOptions,-XX:MaxHeapSize=220g)
(spark.jars,file:/projects/synergy_lab/ritvik/Voltron/SparkLeBLAST/target/scala-2.11/simple-project_2.11-1.0.jar)
(spark.submit.deployMode,client)
(spark.worker.extraJavaOptions,-XX:MaxHeapSize=220g)
(spark.master,spark://inf040:7077)
(spark.executor.cores,1)
Classpath elements:
file:/projects/synergy_lab/ritvik/Voltron/SparkLeBLAST/target/scala-2.11/simple-project_2.11-1.0.jar
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
24/02/19 17:55:25 INFO SparkContext: Running Spark version 2.2.0
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.hadoop.security.authentication.util.KerberosUtil (file:/projects/synergy_lab/ritvik/Voltron/Dependencies/spark-2.2.0-bin-hadoop2.6/jars/hadoop-auth-2.6.5.jar) to method sun.security.krb5.Config.getInstance()
WARNING: Please consider reporting this to the maintainers of org.apache.hadoop.security.authentication.util.KerberosUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
24/02/19 17:55:26 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
24/02/19 17:55:26 WARN SparkConf: In Spark 1.0 and later spark.local.dir will be overridden by the value set by the cluster manager (via SPARK_LOCAL_DIRS in mesos/standalone and LOCAL_DIRS in YARN).
24/02/19 17:55:26 INFO SparkContext: Submitted application: SparkLeMakeDB
24/02/19 17:55:26 INFO SecurityManager: Changing view acls to: ritvikp
24/02/19 17:55:26 INFO SecurityManager: Changing modify acls to: ritvikp
24/02/19 17:55:26 INFO SecurityManager: Changing view acls groups to:
24/02/19 17:55:26 INFO SecurityManager: Changing modify acls groups to:
24/02/19 17:55:26 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(ritvikp); groups with view permissions: Set(); users with modify permissions: Set(ritvikp); groups with modify permissions: Set()
24/02/19 17:55:26 INFO Utils: Successfully started service 'sparkDriver' on port 41362.
24/02/19 17:55:26 INFO SparkEnv: Registering MapOutputTracker
24/02/19 17:55:26 INFO SparkEnv: Registering BlockManagerMaster
24/02/19 17:55:26 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
24/02/19 17:55:26 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
24/02/19 17:55:26 INFO DiskBlockManager: Created local directory at /home/ritvikp/tmpSpark/blockmgr-dc26dbe7-d804-43bf-9c75-403fff82e467
24/02/19 17:55:26 INFO MemoryStore: MemoryStore started with capacity 131.8 GB
24/02/19 17:55:26 INFO SparkEnv: Registering OutputCommitCoordinator
24/02/19 17:55:27 INFO Utils: Successfully started service 'SparkUI' on port 4040.
24/02/19 17:55:27 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://10.91.254.241:4040
24/02/19 17:55:27 INFO SparkContext: Added JAR file:/projects/synergy_lab/ritvik/Voltron/SparkLeBLAST/target/scala-2.11/simple-project_2.11-1.0.jar at spark://10.91.254.241:41362/jars/simple-project_2.11-1.0.jar with timestamp 1708383327215
24/02/19 17:55:27 INFO StandaloneAppClient$ClientEndpoint: Connecting to master spark://inf040:7077...
24/02/19 17:55:27 WARN StandaloneAppClient$ClientEndpoint: Failed to connect to master inf040:7077
org.apache.spark.SparkException: Exception thrown in awaitResult:
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:205)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
at org.apache.spark.rpc.RpcEnv.setupEndpointRefByURI(RpcEnv.scala:100)
at org.apache.spark.rpc.RpcEnv.setupEndpointRef(RpcEnv.scala:108)
at org.apache.spark.deploy.client.StandaloneAppClient$ClientEndpoint$$anonfun$tryRegisterAllMasters$1$$anon$1.run(StandaloneAppClient.scala:106)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.io.IOException: Failed to connect to inf040/10.91.0.40:7077
at org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:232)
at org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:182)
at org.apache.spark.rpc.netty.NettyRpcEnv.createClient(NettyRpcEnv.scala:197)
at org.apache.spark.rpc.netty.Outbox$$anon$1.call(Outbox.scala:194)
at org.apache.spark.rpc.netty.Outbox$$anon$1.call(Outbox.scala:190)
... 4 more
Caused by: io.netty.channel.AbstractChannel$AnnotatedConnectException: Connection refused: inf040/10.91.0.40:7077
at java.base/sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)
at java.base/sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:779)
at io.netty.channel.socket.nio.NioSocketChannel.doFinishConnect(NioSocketChannel.java:257)
at io.netty.channel.nio.AbstractNioChannel$AbstractNioUnsafe.finishConnect(AbstractNioChannel.java:291)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:631)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
... 1 more
24/02/19 17:55:47 INFO StandaloneAppClient$ClientEndpoint: Connecting to master spark://inf040:7077...
24/02/19 17:55:47 WARN StandaloneAppClient$ClientEndpoint: Failed to connect to master inf040:7077
org.apache.spark.SparkException: Exception thrown in awaitResult:
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:205)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
at org.apache.spark.rpc.RpcEnv.setupEndpointRefByURI(RpcEnv.scala:100)
at org.apache.spark.rpc.RpcEnv.setupEndpointRef(RpcEnv.scala:108)
at org.apache.spark.deploy.client.StandaloneAppClient$ClientEndpoint$$anonfun$tryRegisterAllMasters$1$$anon$1.run(StandaloneAppClient.scala:106)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.io.IOException: Failed to connect to inf040/10.91.0.40:7077
at org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:232)
at org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:182)
at org.apache.spark.rpc.netty.NettyRpcEnv.createClient(NettyRpcEnv.scala:197)
at org.apache.spark.rpc.netty.Outbox$$anon$1.call(Outbox.scala:194)
at org.apache.spark.rpc.netty.Outbox$$anon$1.call(Outbox.scala:190)
... 4 more
Caused by: io.netty.channel.AbstractChannel$AnnotatedConnectException: Connection refused: inf040/10.91.0.40:7077
at java.base/sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)
at java.base/sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:779)
at io.netty.channel.socket.nio.NioSocketChannel.doFinishConnect(NioSocketChannel.java:257)
at io.netty.channel.nio.AbstractNioChannel$AbstractNioUnsafe.finishConnect(AbstractNioChannel.java:291)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:631)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
... 1 more
24/02/19 17:56:07 INFO StandaloneAppClient$ClientEndpoint: Connecting to master spark://inf040:7077...
24/02/19 17:56:07 WARN StandaloneAppClient$ClientEndpoint: Failed to connect to master inf040:7077
org.apache.spark.SparkException: Exception thrown in awaitResult:
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:205)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
at org.apache.spark.rpc.RpcEnv.setupEndpointRefByURI(RpcEnv.scala:100)
at org.apache.spark.rpc.RpcEnv.setupEndpointRef(RpcEnv.scala:108)
at org.apache.spark.deploy.client.StandaloneAppClient$ClientEndpoint$$anonfun$tryRegisterAllMasters$1$$anon$1.run(StandaloneAppClient.scala:106)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.io.IOException: Failed to connect to inf040/10.91.0.40:7077
at org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:232)
at org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:182)
at org.apache.spark.rpc.netty.NettyRpcEnv.createClient(NettyRpcEnv.scala:197)
at org.apache.spark.rpc.netty.Outbox$$anon$1.call(Outbox.scala:194)
at org.apache.spark.rpc.netty.Outbox$$anon$1.call(Outbox.scala:190)
... 4 more
Caused by: io.netty.channel.AbstractChannel$AnnotatedConnectException: Connection refused: inf040/10.91.0.40:7077
at java.base/sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)
at java.base/sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:779)
at io.netty.channel.socket.nio.NioSocketChannel.doFinishConnect(NioSocketChannel.java:257)
at io.netty.channel.nio.AbstractNioChannel$AbstractNioUnsafe.finishConnect(AbstractNioChannel.java:291)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:631)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
... 1 more
24/02/19 17:56:27 ERROR StandaloneSchedulerBackend: Application has been killed. Reason: All masters are unresponsive! Giving up.
24/02/19 17:56:27 WARN StandaloneSchedulerBackend: Application ID is not initialized yet.
24/02/19 17:56:27 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 43079.
24/02/19 17:56:27 INFO NettyBlockTransferService: Server created on 10.91.254.241:43079
24/02/19 17:56:27 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
24/02/19 17:56:27 INFO SparkUI: Stopped Spark web UI at http://10.91.254.241:4040
24/02/19 17:56:27 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.91.254.241, 43079, None)
24/02/19 17:56:27 INFO BlockManagerMasterEndpoint: Registering block manager 10.91.254.241:43079 with 131.8 GB RAM, BlockManagerId(driver, 10.91.254.241, 43079, None)
24/02/19 17:56:27 INFO StandaloneSchedulerBackend: Shutting down all executors
24/02/19 17:56:27 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.91.254.241, 43079, None)
24/02/19 17:56:27 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.91.254.241, 43079, None)
24/02/19 17:56:27 INFO CoarseGrainedSchedulerBackend$DriverEndpoint: Asking each executor to shut down
24/02/19 17:56:27 WARN StandaloneAppClient$ClientEndpoint: Drop UnregisterApplication(null) because has not yet connected to master
24/02/19 17:56:27 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
24/02/19 17:56:27 INFO MemoryStore: MemoryStore cleared
24/02/19 17:56:27 INFO BlockManager: BlockManager stopped
24/02/19 17:56:27 INFO BlockManagerMaster: BlockManagerMaster stopped
24/02/19 17:56:27 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
24/02/19 17:56:27 INFO SparkContext: Successfully stopped SparkContext
24/02/19 17:56:27 ERROR SparkContext: Error initializing SparkContext.
java.lang.IllegalArgumentException: requirement failed: Can only call getServletHandlers on a running MetricsSystem
at scala.Predef$.require(Predef.scala:224)
at org.apache.spark.metrics.MetricsSystem.getServletHandlers(MetricsSystem.scala:91)
at org.apache.spark.SparkContext.<init>(SparkContext.scala:524)
at SparkLeMakeDB$.main(SparkLeMakeDB.scala:21)
at SparkLeMakeDB.main(SparkLeMakeDB.scala)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:755)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:119)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
24/02/19 17:56:27 INFO SparkContext: SparkContext already stopped.
Exception in thread "main" java.lang.IllegalArgumentException: requirement failed: Can only call getServletHandlers on a running MetricsSystem
at scala.Predef$.require(Predef.scala:224)
at org.apache.spark.metrics.MetricsSystem.getServletHandlers(MetricsSystem.scala:91)
at org.apache.spark.SparkContext.<init>(SparkContext.scala:524)
at SparkLeMakeDB$.main(SparkLeMakeDB.scala:21)
at SparkLeMakeDB.main(SparkLeMakeDB.scala)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:755)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:119)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
24/02/19 17:56:27 INFO ShutdownHookManager: Shutdown hook called
24/02/19 17:56:27 INFO ShutdownHookManager: Deleting directory /home/ritvikp/tmpSpark/spark-cec24184-0931-4041-94c3-d8468c365c4b