[
https://issues.apache.org/jira/browse/SPARK-16819?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Asmaa Ali updated SPARK-16819:
-------------------------------
Description:
What is the reason of this exception ?!
cancerdetector@cluster-cancerdetector-m:~/SparkBWA/build$ spark-submit --class
SparkBWA --master yarn-cluster --deploy-mode cluster --conf
spark.yarn.jar=hdfs:///user/spark/spark-assembly.jar --driver-memory 1500m
--executor-memory 1500m --executor-cores 1 --archives ./bwa.zip --verbose
./SparkBWA.jar -algorithm mem -reads paired -index /Data/HumanBase/hg38
-partitions 32 ERR000589_1.filt.fastq ERR000589_2.filt.fastqhb Output_ERR000589
Using properties file: /usr/lib/spark/conf/spark-defaults.conf
Adding default property:
spark.executor.extraJavaOptions=-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
Adding default property:
spark.history.fs.logDirectory=hdfs://cluster-cancerdetector-m/user/spark/eventlog
Adding default property: spark.eventLog.enabled=true
Adding default property: spark.driver.maxResultSize=1920m
Adding default property: spark.shuffle.service.enabled=true
Adding default property:
spark.yarn.historyServer.address=cluster-cancerdetector-m:18080
Adding default property: spark.sql.parquet.cacheMetadata=false
Adding default property: spark.driver.memory=3840m
Adding default property: spark.dynamicAllocation.maxExecutors=10000
Adding default property: spark.scheduler.minRegisteredResourcesRatio=0.0
Adding default property: spark.yarn.am.memoryOverhead=558
Adding default property: spark.yarn.am.memory=5586m
Adding default property:
spark.driver.extraJavaOptions=-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
Adding default property: spark.master=yarn-client
Adding default property: spark.executor.memory=5586m
Adding default property:
spark.eventLog.dir=hdfs://cluster-cancerdetector-m/user/spark/eventlog
Adding default property: spark.dynamicAllocation.enabled=true
Adding default property: spark.executor.cores=2
Adding default property: spark.yarn.executor.memoryOverhead=558
Adding default property: spark.dynamicAllocation.minExecutors=1
Adding default property: spark.dynamicAllocation.initialExecutors=10000
Adding default property: spark.akka.frameSize=512
Parsed arguments:
master yarn-cluster
deployMode cluster
executorMemory 1500m
executorCores 1
totalExecutorCores null
propertiesFile /usr/lib/spark/conf/spark-defaults.conf
driverMemory 1500m
driverCores null
driverExtraClassPath null
driverExtraLibraryPath null
driverExtraJavaOptions
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
supervise false
queue null
numExecutors null
files null
pyFiles null
archives file:/home/cancerdetector/SparkBWA/build/./bwa.zip
mainClass SparkBWA
primaryResource
file:/home/cancerdetector/SparkBWA/build/./SparkBWA.jar
name SparkBWA
childArgs [-algorithm mem -reads paired -index
/Data/HumanBase/hg38 -partitions 32 ERR000589_1.filt.fastq
ERR000589_2.filt.fastqhb Output_ERR000589]
jars null
packages null
packagesExclusions null
repositories null
verbose true
Spark properties used, including those specified through
--conf and those from the properties file
/usr/lib/spark/conf/spark-defaults.conf:
spark.yarn.am.memoryOverhead -> 558
spark.driver.memory -> 1500m
spark.yarn.jar -> hdfs:///user/spark/spark-assembly.jar
spark.executor.memory -> 5586m
spark.yarn.historyServer.address -> cluster-cancerdetector-m:18080
spark.eventLog.enabled -> true
spark.scheduler.minRegisteredResourcesRatio -> 0.0
spark.dynamicAllocation.maxExecutors -> 10000
spark.akka.frameSize -> 512
spark.executor.extraJavaOptions ->
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
spark.sql.parquet.cacheMetadata -> false
spark.shuffle.service.enabled -> true
spark.history.fs.logDirectory ->
hdfs://cluster-cancerdetector-m/user/spark/eventlog
spark.dynamicAllocation.initialExecutors -> 10000
spark.dynamicAllocation.minExecutors -> 1
spark.yarn.executor.memoryOverhead -> 558
spark.driver.extraJavaOptions ->
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
spark.eventLog.dir -> hdfs://cluster-cancerdetector-m/user/spark/eventlog
spark.yarn.am.memory -> 5586m
spark.driver.maxResultSize -> 1920m
spark.master -> yarn-client
spark.dynamicAllocation.enabled -> true
spark.executor.cores -> 2
Main class:
org.apache.spark.deploy.yarn.Client
Arguments:
--name
SparkBWA
--driver-memory
1500m
--executor-memory
1500m
--executor-cores
1
--archives
file:/home/cancerdetector/SparkBWA/build/./bwa.zip
--jar
file:/home/cancerdetector/SparkBWA/build/./SparkBWA.jar
--class
SparkBWA
--arg
-algorithm
--arg
mem
--arg
-reads
--arg
paired
--arg
-index
--arg
/Data/HumanBase/hg38
--arg
-partitions
--arg
32
--arg
ERR000589_1.filt.fastq
--arg
ERR000589_2.filt.fastqhb
--arg
Output_ERR000589
System properties:
spark.yarn.am.memoryOverhead -> 558
spark.driver.memory -> 1500m
spark.yarn.jar -> hdfs:///user/spark/spark-assembly.jar
spark.executor.memory -> 1500m
spark.yarn.historyServer.address -> cluster-cancerdetector-m:18080
spark.eventLog.enabled -> true
spark.scheduler.minRegisteredResourcesRatio -> 0.0
SPARK_SUBMIT -> true
spark.dynamicAllocation.maxExecutors -> 10000
spark.akka.frameSize -> 512
spark.sql.parquet.cacheMetadata -> false
spark.executor.extraJavaOptions ->
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
spark.app.name -> SparkBWA
spark.shuffle.service.enabled -> true
spark.history.fs.logDirectory ->
hdfs://cluster-cancerdetector-m/user/spark/eventlog
spark.dynamicAllocation.initialExecutors -> 10000
spark.dynamicAllocation.minExecutors -> 1
spark.yarn.executor.memoryOverhead -> 558
spark.driver.extraJavaOptions ->
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
spark.submit.deployMode -> cluster
spark.eventLog.dir -> hdfs://cluster-cancerdetector-m/user/spark/eventlog
spark.yarn.am.memory -> 5586m
spark.driver.maxResultSize -> 1920m
spark.master -> yarn-cluster
spark.dynamicAllocation.enabled -> true
spark.executor.cores -> 1
Classpath elements:
spark.yarn.am.memory is set but does not apply in cluster mode.
spark.yarn.am.memoryOverhead is set but does not apply in cluster mode.
16/07/31 01:12:39 INFO org.apache.hadoop.yarn.client.RMProxy: Connecting to
ResourceManager at cluster-cancerdet
ector-m/10.132.0.2:8032
16/07/31 01:12:40 INFO org.apache.hadoop.yarn.client.api.impl.YarnClientImpl:
Submitted application application_
1467990031555_0106
Exception in thread "main" org.apache.spark.SparkException: Application
application_1467990031555_0106 finished
with failed status
at org.apache.spark.deploy.yarn.Client.run(Client.scala:1034)
at org.apache.spark.deploy.yarn.Client$.main(Client.scala:1081)
at org.apache.spark.deploy.yarn.Client.main(Client.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:7
31)
at
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
When I tried to check the AM and executor logs. the command didn't work (I have
set the yarn.log-aggregation-enable to true), So I tried to manually access
into NM's log dir to see the detailed application logs. Here are the
application logs from the NM's log file:
2016-07-31 01:12:40,387 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.4:50010 is added to
blk_1073742335_1511{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-31 01:12:40,387 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.3:50010 is added to
blk_1073742335_1511{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-31 01:12:40,391 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile:
/user/cancerdetector/.sparkStaging/application_1467990031555_0106/SparkBWA.jar
is closed by DFSClient_NONMAPREDUCE_-762268348_1
2016-07-31 01:12:40,419 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
allocate blk_1073742336_1512{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
for /user/cancerdetector/.sparkStaging/application_1467990031555_0106/bwa.zip
2016-07-31 01:12:40,445 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.4:50010 is added to
blk_1073742336_1512{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-31 01:12:40,446 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.3:50010 is added to
blk_1073742336_1512{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-31 01:12:40,448 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile:
/user/cancerdetector/.sparkStaging/application_1467990031555_0106/bwa.zip is
closed by DFSClient_NONMAPREDUCE_-762268348_1
2016-07-31 01:12:40,495 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
allocate blk_1073742337_1513{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
for
/user/cancerdetector/.sparkStaging/application_1467990031555_0106/__spark_conf__2552000168715758347.zip
2016-07-31 01:12:40,506 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.4:50010 is added to
blk_1073742337_1513{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-31 01:12:40,506 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.3:50010 is added to
blk_1073742337_1513{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-31 01:12:40,509 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile:
/user/cancerdetector/.sparkStaging/application_1467990031555_0106/__spark_conf__2552000168715758347.zip
is closed by DFSClient_NONMAPREDUCE_-762268348_1
2016-07-31 01:12:44,720 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
allocate blk_1073742338_1514{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
for /user/spark/eventlog/application_1467990031555_0106_1.inprogress
2016-07-31 01:12:44,877 INFO org.apache.hadoop.hdfs.StateChange: BLOCK* fsync:
/user/spark/eventlog/application_1467990031555_0106_1.inprogress for
DFSClient_NONMAPREDUCE_-1111833453_14
2016-07-31 01:12:45,373 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.4:50010 is added to
blk_1073742338_1514{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 231
2016-07-31 01:12:45,375 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.3:50010 is added to
blk_1073742338_1514{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 231
2016-07-31 01:12:45,379 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/application_1467990031555_0106_1.inprogress
is closed by DFSClient_NONMAPREDUCE_-1111833453_14
2016-07-31 01:12:45,843 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.b7989393-f278-477c-8e83-ff5da9079e8a is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:12:49,914 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
allocate blk_1073742339_1515{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
for /user/spark/eventlog/application_1467990031555_0106_2.inprogress
2016-07-31 01:12:50,100 INFO org.apache.hadoop.hdfs.StateChange: BLOCK* fsync:
/user/spark/eventlog/application_1467990031555_0106_2.inprogress for
DFSClient_NONMAPREDUCE_378341726_14
2016-07-31 01:12:50,737 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.4:50010 is added to
blk_1073742339_1515{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 231
2016-07-31 01:12:50,738 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.3:50010 is added to
blk_1073742339_1515{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 231
2016-07-31 01:12:50,742 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/application_1467990031555_0106_2.inprogress
is closed by DFSClient_NONMAPREDUCE_378341726_14
2016-07-31 01:12:50,892 INFO BlockStateChange: BLOCK* addToInvalidates:
blk_1073742335_1511 10.132.0.3:50010 10.132.0.4:50010
2016-07-31 01:12:50,892 INFO BlockStateChange: BLOCK* addToInvalidates:
blk_1073742337_1513 10.132.0.3:50010 10.132.0.4:50010
2016-07-31 01:12:50,892 INFO BlockStateChange: BLOCK* addToInvalidates:
blk_1073742336_1512 10.132.0.3:50010 10.132.0.4:50010
2016-07-31 01:12:51,804 INFO BlockStateChange: BLOCK* BlockManager: ask
10.132.0.3:50010 to delete [blk_1073742336_1512, blk_1073742337_1513,
blk_1073742335_1511]
2016-07-31 01:12:54,804 INFO BlockStateChange: BLOCK* BlockManager: ask
10.132.0.4:50010 to delete [blk_1073742336_1512, blk_1073742337_1513,
blk_1073742335_1511]
2016-07-31 01:12:55,868 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.46380a1f-b5fd-4924-96aa-f59dcae0cbec is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:13:05,882 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 244 Total time for transactions(ms): 5 Number of
transactions batched in Syncs: 0 Number of syncs: 234 SyncTimes(ms): 221
2016-07-31 01:13:05,885 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.7273ee28-eb1c-4fe2-98d2-c5a20ebe4ffa is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:13:15,892 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.0f640743-d06c-4583-ac95-9d520dc8f301 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:13:25,902 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.bc63864c-0267-47b5-bcc1-96ba81d6c9a5 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:13:35,910 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.93557793-2ba2-47e8-b54c-234c861b6e6c is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:13:45,918 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.0fdf083c-3c53-4051-af16-d579f700962e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:13:55,927 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.834632f1-d9c6-4e14-9354-72f8c18f66d0 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:14:05,933 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 262 Total time for transactions(ms): 5 Number of
transactions batched in Syncs: 0 Number of syncs: 252 SyncTimes(ms): 236
2016-07-31 01:14:05,936 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.d06ef3b4-873f-464d-9cd0-e360da48e194 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:14:15,944 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.32ccba74-5f6c-45fc-b5db-26efb1b840e2 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:14:25,952 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.fef919cd-9952-4af8-a49a-e6dd2aa032f1 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:14:35,961 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.77ffdf36-8e42-43d8-9c1f-df6f3d11700d is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:14:45,968 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.c31cfcbb-b47c-4169-ab0f-7ae87d4f815d is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:14:55,976 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.6429570d-fb0a-4117-bb12-127a67e0a0b7 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:15:05,981 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 280 Total time for transactions(ms): 6 Number of
transactions batched in Syncs: 0 Number of syncs: 270 SyncTimes(ms): 253
2016-07-31 01:15:05,984 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.8030b18d-05f2-4520-b5c4-2fe42338b92b is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:15:15,991 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.f608a0f4-e730-43cd-a19d-da57caac346e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:15:25,999 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.9d5a1f80-2f2a-43a7-84f1-b26a8c90a98f is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:15:36,007 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.279e96fc-180c-47a5-a3ba-cfda581eedad is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:15:46,015 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.a85bbf52-61f4-4899-98b1-23615a549774 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:15:56,023 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.80613e8e-7015-4aeb-81df-49884bd0eb5e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:16:06,028 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 298 Total time for transactions(ms): 6 Number of
transactions batched in Syncs: 0 Number of syncs: 288 SyncTimes(ms): 267
2016-07-31 01:16:06,031 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.2be7fc48-bd1c-4042-88e4-239b1c630458 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:16:16,038 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.40fc68a6-f003-4e35-b4b3-50bd3c4a0c82 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:16:26,045 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.97e7d15c-4d28-4089-b4a5-9f0935a72589 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:16:36,052 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.84d8e78d-90fd-419f-9000-fa04ab56955e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:16:46,059 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.6691cc3e-6969-4a8f-938f-272d1c96701d is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:16:56,066 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.077143b6-281a-468c-8b2c-bcb6cd3bc27a is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:17:06,070 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 316 Total time for transactions(ms): 6 Number of
transactions batched in Syncs: 0 Number of syncs: 306 SyncTimes(ms): 284
2016-07-31 01:17:06,073 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.817d1886-aea2-450a-a586-08677dc18d60 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:17:16,080 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.abd46886-1359-4c5e-8276-ea4f2969411f is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:17:26,087 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.24625260-59be-4a9b-b47b-b8d5b76cb789 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:17:36,096 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.11630782-e50e-4260-a0da-99845bc3f1db is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:17:46,103 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.16cdd027-f1b8-4cbf-a30c-2f1712f4abb5 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:17:56,111 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.93fb2e86-2fec-4069-b73b-632750fda603 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:18:06,116 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 334 Total time for transactions(ms): 6 Number of
transactions batched in Syncs: 0 Number of syncs: 324 SyncTimes(ms): 300
2016-07-31 01:18:06,119 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.b19fddda-ea90-49ab-b44d-434cce28cb67 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:18:16,127 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.d81ab189-bde5-4878-b82b-903983466f86 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:18:26,135 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.e5b51632-f714-4814-b896-59bba137b42d is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:18:36,144 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.39791121-9399-4a22-a50c-90eaddf31ffb is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:18:46,153 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.861c269b-5466-4855-84fd-587ed3306012 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:18:56,162 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.8a9ff721-bd56-4bea-b399-31bfaabe8c7c is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:19:06,168 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 352 Total time for transactions(ms): 7 Number of
transactions batched in Syncs: 0 Number of syncs: 342 SyncTimes(ms): 313
2016-07-31 01:19:06,170 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.492bf987-4991-4533-80e2-678efa843cb9 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:19:16,178 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.9294c0c6-43db-4f6d-9d31-f493143b6baf is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:19:26,187 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.341dd131-c14c-4147-bcbc-849d1d6bba8c is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:19:36,196 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.56f92e8e-ef93-4279-a57f-472dd5d8f399 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:19:46,204 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5ddcda82-b501-4043-bb54-a29902d9d234 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:19:56,212 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.31e7517b-2ef3-458c-9979-324d7a96302f is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:20:06,218 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 370 Total time for transactions(ms): 7 Number of
transactions batched in Syncs: 0 Number of syncs: 360 SyncTimes(ms): 329
2016-07-31 01:20:06,220 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5251f5df-0957-4008-b664-8d82eaa9789e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:20:16,229 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.3320b948-2478-4807-9ab3-d23e4945765e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:20:26,237 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.0928c940-e57d-4a34-a7dc-53dade7ff909 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:20:36,246 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.6240fcdf-696e-49c4-a883-3eda5ab89b4d is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:20:46,254 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5622850e-b7b0-458a-9ffa-89e134fa3fda is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:20:56,262 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.faa076e8-490c-489f-8183-778325e0b144 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:21:06,268 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 388 Total time for transactions(ms): 7 Number of
transactions batched in Syncs: 0 Number of syncs: 378 SyncTimes(ms): 347
2016-07-31 01:21:06,270 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.18b2464e-9d14-4bae-95d9-f261edbdee1b is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:21:16,278 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.6c53dd52-3996-4541-b368-e8406f99f68e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:21:26,287 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.8b5ac93c-b268-432d-9236-48c004c33743 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:21:36,303 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.22a03e6f-4531-466c-af28-e0797d6b803e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:21:46,311 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.1df0d173-6432-481f-af97-6632660700b0 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:21:56,319 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.4095d5a1-ba2d-4966-ad13-99843c51ee91 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:22:06,325 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 406 Total time for transactions(ms): 8 Number of
transactions batched in Syncs: 0 Number of syncs: 396 SyncTimes(ms): 362
2016-07-31 01:22:06,328 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.f35e73f9-842d-4fc2-96b3-9b70df17e7e3 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:22:16,337 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.fdfa32ef-5c3c-48a3-9d15-0edc1b9d5072 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:22:26,345 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.0315d9f7-ea5c-4a58-ad68-3f942d97676a is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:22:36,353 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.eecbddee-6bfb-44b6-97ef-1b5eece8a982 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:22:46,362 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.2c363a5b-bd43-47c5-9050-b15f1f6ade77 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-31 01:22:56,449 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.6f4e8030-39a7-4fc8-b551-5b1d88e0885e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
was:
What is the reason of this exception ?!
cancerdetector@cluster-cancerdetector-m:~/SparkBWA/build$ spark-submit --class
SparkBWA --master yarn-cluster --deploy-mode cluster --conf
spark.yarn.jar=hdfs:///user/spark/spark-assembly.jar --driver-memory 1500m
--executor-memory 1500m --executor-cores 1 --archives ./bwa.zip --verbose
./SparkBWA.jar -algorithm mem -reads paired -index /Data/HumanBase/hg38
-partitions 32 ERR000589_1.filt.fastq ERR000589_2.filt.fastqhb Output_ERR000589
Using properties file: /usr/lib/spark/conf/spark-defaults.conf
Adding default property:
spark.executor.extraJavaOptions=-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
Adding default property:
spark.history.fs.logDirectory=hdfs://cluster-cancerdetector-m/user/spark/eventlog
Adding default property: spark.eventLog.enabled=true
Adding default property: spark.driver.maxResultSize=1920m
Adding default property: spark.shuffle.service.enabled=true
Adding default property:
spark.yarn.historyServer.address=cluster-cancerdetector-m:18080
Adding default property: spark.sql.parquet.cacheMetadata=false
Adding default property: spark.driver.memory=3840m
Adding default property: spark.dynamicAllocation.maxExecutors=10000
Adding default property: spark.scheduler.minRegisteredResourcesRatio=0.0
Adding default property: spark.yarn.am.memoryOverhead=558
Adding default property: spark.yarn.am.memory=5586m
Adding default property:
spark.driver.extraJavaOptions=-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
Adding default property: spark.master=yarn-client
Adding default property: spark.executor.memory=5586m
Adding default property:
spark.eventLog.dir=hdfs://cluster-cancerdetector-m/user/spark/eventlog
Adding default property: spark.dynamicAllocation.enabled=true
Adding default property: spark.executor.cores=2
Adding default property: spark.yarn.executor.memoryOverhead=558
Adding default property: spark.dynamicAllocation.minExecutors=1
Adding default property: spark.dynamicAllocation.initialExecutors=10000
Adding default property: spark.akka.frameSize=512
Parsed arguments:
master yarn-cluster
deployMode cluster
executorMemory 1500m
executorCores 1
totalExecutorCores null
propertiesFile /usr/lib/spark/conf/spark-defaults.conf
driverMemory 1500m
driverCores null
driverExtraClassPath null
driverExtraLibraryPath null
driverExtraJavaOptions
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
supervise false
queue null
numExecutors null
files null
pyFiles null
archives file:/home/cancerdetector/SparkBWA/build/./bwa.zip
mainClass SparkBWA
primaryResource
file:/home/cancerdetector/SparkBWA/build/./SparkBWA.jar
name SparkBWA
childArgs [-algorithm mem -reads paired -index
/Data/HumanBase/hg38 -partitions 32 ERR000589_1.filt.fastq
ERR000589_2.filt.fastqhb Output_ERR000589]
jars null
packages null
packagesExclusions null
repositories null
verbose true
Spark properties used, including those specified through
--conf and those from the properties file
/usr/lib/spark/conf/spark-defaults.conf:
spark.yarn.am.memoryOverhead -> 558
spark.driver.memory -> 1500m
spark.yarn.jar -> hdfs:///user/spark/spark-assembly.jar
spark.executor.memory -> 5586m
spark.yarn.historyServer.address -> cluster-cancerdetector-m:18080
spark.eventLog.enabled -> true
spark.scheduler.minRegisteredResourcesRatio -> 0.0
spark.dynamicAllocation.maxExecutors -> 10000
spark.akka.frameSize -> 512
spark.executor.extraJavaOptions ->
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
spark.sql.parquet.cacheMetadata -> false
spark.shuffle.service.enabled -> true
spark.history.fs.logDirectory ->
hdfs://cluster-cancerdetector-m/user/spark/eventlog
spark.dynamicAllocation.initialExecutors -> 10000
spark.dynamicAllocation.minExecutors -> 1
spark.yarn.executor.memoryOverhead -> 558
spark.driver.extraJavaOptions ->
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
spark.eventLog.dir -> hdfs://cluster-cancerdetector-m/user/spark/eventlog
spark.yarn.am.memory -> 5586m
spark.driver.maxResultSize -> 1920m
spark.master -> yarn-client
spark.dynamicAllocation.enabled -> true
spark.executor.cores -> 2
Main class:
org.apache.spark.deploy.yarn.Client
Arguments:
--name
SparkBWA
--driver-memory
1500m
--executor-memory
1500m
--executor-cores
1
--archives
file:/home/cancerdetector/SparkBWA/build/./bwa.zip
--jar
file:/home/cancerdetector/SparkBWA/build/./SparkBWA.jar
--class
SparkBWA
--arg
-algorithm
--arg
mem
--arg
-reads
--arg
paired
--arg
-index
--arg
/Data/HumanBase/hg38
--arg
-partitions
--arg
32
--arg
ERR000589_1.filt.fastq
--arg
ERR000589_2.filt.fastqhb
--arg
Output_ERR000589
System properties:
spark.yarn.am.memoryOverhead -> 558
spark.driver.memory -> 1500m
spark.yarn.jar -> hdfs:///user/spark/spark-assembly.jar
spark.executor.memory -> 1500m
spark.yarn.historyServer.address -> cluster-cancerdetector-m:18080
spark.eventLog.enabled -> true
spark.scheduler.minRegisteredResourcesRatio -> 0.0
SPARK_SUBMIT -> true
spark.dynamicAllocation.maxExecutors -> 10000
spark.akka.frameSize -> 512
spark.sql.parquet.cacheMetadata -> false
spark.executor.extraJavaOptions ->
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
spark.app.name -> SparkBWA
spark.shuffle.service.enabled -> true
spark.history.fs.logDirectory ->
hdfs://cluster-cancerdetector-m/user/spark/eventlog
spark.dynamicAllocation.initialExecutors -> 10000
spark.dynamicAllocation.minExecutors -> 1
spark.yarn.executor.memoryOverhead -> 558
spark.driver.extraJavaOptions ->
-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
spark.submit.deployMode -> cluster
spark.eventLog.dir -> hdfs://cluster-cancerdetector-m/user/spark/eventlog
spark.yarn.am.memory -> 5586m
spark.driver.maxResultSize -> 1920m
spark.master -> yarn-cluster
spark.dynamicAllocation.enabled -> true
spark.executor.cores -> 1
Classpath elements:
spark.yarn.am.memory is set but does not apply in cluster mode.
spark.yarn.am.memoryOverhead is set but does not apply in cluster mode.
16/07/31 01:12:39 INFO org.apache.hadoop.yarn.client.RMProxy: Connecting to
ResourceManager at cluster-cancerdet
ector-m/10.132.0.2:8032
16/07/31 01:12:40 INFO org.apache.hadoop.yarn.client.api.impl.YarnClientImpl:
Submitted application application_
1467990031555_0106
Exception in thread "main" org.apache.spark.SparkException: Application
application_1467990031555_0106 finished
with failed status
at org.apache.spark.deploy.yarn.Client.run(Client.scala:1034)
at org.apache.spark.deploy.yarn.Client$.main(Client.scala:1081)
at org.apache.spark.deploy.yarn.Client.main(Client.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:7
31)
at
org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
When I tried to check the AM and executor logs. the command didn't work (I have
set the yarn.log-aggregation-enable to true), So I tried to manually access
into NM's log dir to see the detailed application logs. Here are the
application logs from the NM's log file:
2016-07-30 19:37:23,620 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
allocate blk_1073742332_1508{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW],
ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW]]}
for
/user/cancerdetector/.sparkStaging/application_1467990031555_0105/SparkBWA.jar
2016-07-30 19:37:23,807 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.4:50010 is added to
blk_1073742332_1508{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW],
ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW]]}
size 0
2016-07-30 19:37:23,807 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.3:50010 is added to
blk_1073742332_1508{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW],
ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW]]}
size 0
2016-07-30 19:37:23,812 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile:
/user/cancerdetector/.sparkStaging/application_1467990031555_0105/SparkBWA.jar
is closed by DFSClient_NONMAPREDUCE_606595546_1
2016-07-30 19:37:23,843 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
allocate blk_1073742333_1509{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
for /user/cancerdetector/.sparkStaging/application_1467990031555_0105/bwa.zip
2016-07-30 19:37:23,862 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.4:50010 is added to
blk_1073742333_1509{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-30 19:37:23,862 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.3:50010 is added to
blk_1073742333_1509{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-30 19:37:23,864 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile:
/user/cancerdetector/.sparkStaging/application_1467990031555_0105/bwa.zip is
closed by DFSClient_NONMAPREDUCE_606595546_1
2016-07-30 19:37:23,911 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
allocate blk_1073742334_1510{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
for
/user/cancerdetector/.sparkStaging/application_1467990031555_0105/__spark_conf__3335387778472809466.zip
2016-07-30 19:37:23,922 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.4:50010 is added to
blk_1073742334_1510{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-30 19:37:23,922 INFO BlockStateChange: BLOCK* addStoredBlock: blockMap
updated: 10.132.0.3:50010 is added to
blk_1073742334_1510{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
primaryNodeIndex=-1,
replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
size 0
2016-07-30 19:37:23,925 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile:
/user/cancerdetector/.sparkStaging/application_1467990031555_0105/__spark_conf__3335387778472809466.zip
is closed by DFSClient_NONMAPREDUCE_606595546_1
2016-07-30 19:37:26,235 INFO BlockStateChange: BLOCK* addToInvalidates:
blk_1073742332_1508 10.132.0.3:50010 10.132.0.4:50010
2016-07-30 19:37:26,236 INFO BlockStateChange: BLOCK* addToInvalidates:
blk_1073742334_1510 10.132.0.3:50010 10.132.0.4:50010
2016-07-30 19:37:26,236 INFO BlockStateChange: BLOCK* addToInvalidates:
blk_1073742333_1509 10.132.0.3:50010 10.132.0.4:50010
2016-07-30 19:37:26,961 INFO BlockStateChange: BLOCK* BlockManager: ask
10.132.0.3:50010 to delete [blk_1073742332_1508, blk_1073742333_1509,
blk_1073742334_1510]
2016-07-30 19:37:28,791 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.1b2f4ed4-0992-4bf3-a453-4c02e9ce00fe is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:37:29,961 INFO BlockStateChange: BLOCK* BlockManager: ask
10.132.0.4:50010 to delete [blk_1073742332_1508, blk_1073742333_1509,
blk_1073742334_1510]
2016-07-30 19:37:38,799 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.a0ca1b29-3022-4d1c-a868-4710d56903f9 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:37:48,806 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.fa70676f-ce52-4ddf-8fb6-1649284f5da0 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:37:58,814 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.7550f1fe-81e1-4a4f-9a72-5210dbae1a31 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:38:08,819 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 674 Total time for transactions(ms): 12 Number of
transactions batched in Syncs: 0 Number of syncs: 668 SyncTimes(ms): 628
2016-07-30 19:38:08,822 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.f6d27b3c-f60d-4c70-b9eb-9a682c783cf9 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:38:18,830 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.33f22e09-343f-4192-b194-a4617ba6fde5 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:38:28,838 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.9a90102c-bb41-42e8-ab5f-285e74f14388 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:38:38,846 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.f9a82533-de04-4da8-9054-f7f74f781351 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:38:48,854 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.96d8dfad-bcfa-4116-b159-62caa493208d is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:38:58,862 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.2c24d60a-c76e-4c6e-a6f2-868b6f7d746b is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:39:08,867 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 692 Total time for transactions(ms): 14 Number of
transactions batched in Syncs: 0 Number of syncs: 686 SyncTimes(ms): 643
2016-07-30 19:39:08,870 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.200cfa9e-9429-4c9f-9227-aad743d833d7 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:39:18,878 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.b2c007fb-0334-4539-b83f-152069a0cde9 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:39:28,885 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.c5cc9039-11de-4a18-aa1d-95d16db8dcf9 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:39:38,893 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5b18a8cc-18d2-404e-aed4-799257e460d2 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:39:48,901 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.82de795e-9c85-4b03-b596-d6dcdee6eaa3 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:39:58,909 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.c724a7b0-722b-4207-b946-f859fe2f10cc is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:40:08,914 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 710 Total time for transactions(ms): 14 Number of
transactions batched in Syncs: 0 Number of syncs: 704 SyncTimes(ms): 659
2016-07-30 19:40:08,917 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.46ce84b2-885c-497a-8b9f-8f3202a317c2 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:40:18,925 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5fa59a96-cda0-4820-b1ec-38d120ff5dca is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:40:29,006 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.0f45738e-9626-4713-b39d-3883f0408146 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:40:39,014 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.005ce47c-ef57-4d4c-9a2f-57c32927aca1 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:40:49,023 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.1f889794-c1e6-4054-a533-7f43ee06966b is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:40:59,029 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.bc953f0d-287e-4745-b862-cfdd713e3777 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:41:09,034 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 728 Total time for transactions(ms): 14 Number of
transactions batched in Syncs: 0 Number of syncs: 722 SyncTimes(ms): 675
2016-07-30 19:41:09,038 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5129bf62-08d3-4171-9591-57a5b004bb34 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:41:19,045 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.2f78852f-309c-45ef-ae9e-38b46c705e98 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:41:29,052 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.b0dc7906-651d-4b26-b683-1799b325ba8d is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:41:39,059 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.cbcca99f-bedc-43d8-a890-a69c18b29b43 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:41:49,067 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.7ea8f3d6-dfd8-4080-8a45-a42419303fa0 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:41:59,074 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.1f22a8fd-ccb7-4138-b9f9-ab1ff1963b02 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:42:09,078 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 746 Total time for transactions(ms): 14 Number of
transactions batched in Syncs: 0 Number of syncs: 740 SyncTimes(ms): 691
2016-07-30 19:42:09,081 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.6b4b0b45-00bf-47d6-bc2b-9dc149e10f01 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:42:19,089 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.2a1a8c1e-1b8b-485d-a108-41ea8087bafe is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:42:29,096 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.8c1b7511-83b2-4584-ab14-408a9e85d0c4 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:42:39,103 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.216d4363-b070-47c3-97ac-f0eac64ed411 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:42:49,110 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5d5cbb0a-8cad-41be-ba17-388b9fc955c4 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:42:59,117 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.c805224b-1833-4dba-8cf5-80164b3ecd7b is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:43:09,121 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 764 Total time for transactions(ms): 14 Number of
transactions batched in Syncs: 0 Number of syncs: 758 SyncTimes(ms): 707
2016-07-30 19:43:09,125 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.51715f99-5d67-4fa7-907b-7522fcca03c2 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:43:19,132 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.95920ee2-d9e2-41f4-a9f6-a495560af73f is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:43:29,141 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.0d4d5099-21d1-4e3f-84e0-7623511c542c is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:43:39,148 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.b6c93d4f-040c-4b9e-a89e-15313efd13ce is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:43:49,157 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.35ed35e6-2c7d-4a45-ae4f-afaf538afc78 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:43:59,164 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.49c44bf3-ea11-4df1-ac71-a26203e9abba is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:44:09,170 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 782 Total time for transactions(ms): 14 Number of
transactions batched in Syncs: 0 Number of syncs: 776 SyncTimes(ms): 725
2016-07-30 19:44:09,173 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.060f7d11-d341-4cab-8925-9b6203316744 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:44:19,181 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.666c8d61-405e-49bd-b2d0-939c920b6cd2 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:44:29,188 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.433f0daa-3386-44a6-b6b1-0285e9f5b176 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:44:39,197 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.1e840f6a-999b-4e1d-8eda-a95c409e351c is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:44:49,206 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.c0df4079-d352-4aae-8392-9596f355c408 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:44:59,215 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.df28952f-5a2a-411b-b72d-49380b1ac88e is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:45:09,221 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 800 Total time for transactions(ms): 14 Number of
transactions batched in Syncs: 0 Number of syncs: 794 SyncTimes(ms): 743
2016-07-30 19:45:09,224 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5515b3ca-de5d-46df-a49c-c07d5c09969d is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:45:19,234 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.3991cd72-3fb2-48a4-8083-5327d82be73b is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:45:29,243 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.5233a5f3-e15a-4bae-9baa-5d81b5da0459 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:45:39,252 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.6097d0dd-d3c4-482e-8fb7-baa22602fb53 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:45:49,261 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.f94ba7f7-313b-4387-a447-59214ddf6ecc is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:45:59,269 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.864e23f9-2b2a-44f4-b11d-e4d48249c7f3 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:46:09,275 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 818 Total time for transactions(ms): 14 Number of
transactions batched in Syncs: 0 Number of syncs: 812 SyncTimes(ms): 761
2016-07-30 19:46:09,278 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.96da4a90-afeb-4fe9-84eb-2d759785d428 is
closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:46:19,288 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.a50035
66-95ab-4a4b-a1f3-7de6302d26a0 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:46:29,296 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.65acb8
c8-9f16-49cc-951c-01dadd298e86 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:46:39,306 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.a3281e
71-6713-422e-b43f-5cd9500f8dd2 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:46:49,314 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.343366
ba-49fc-4b9a-b4d8-7a6b6c8683e0 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:46:59,323 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.88395b
cf-4668-4a9e-8586-69de43e7e0b9 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:47:09,328 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 836 Total
time for transactions(ms): 14 Number of transactions batched in Syncs: 0
Number of syncs: 830 SyncTimes(ms): 77
9
2016-07-30 19:47:09,331 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.c3c519
04-dda5-4e25-af9c-6188615063d5 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:47:19,338 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.163b09
48-28a7-4a1e-9a09-a8de560d0200 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:47:29,346 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.b726de
12-176b-47c0-964c-0fa5196f626f is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:47:39,354 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.8eddb5
b2-746c-4852-8b15-f15c7a7068f0 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:47:49,364 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.0f467a
89-42d3-4b2e-ae9e-36714bd417f3 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:47:59,374 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.074a81
30-f4ba-4be6-a614-e39a252cd57b is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:48:09,380 INFO org.apache.hadoop.hdfs.server.namenode.FSEditLog:
Number of transactions: 854 Total
time for transactions(ms): 14 Number of transactions batched in Syncs: 0
Number of syncs: 848 SyncTimes(ms): 79
7
2016-07-30 19:48:09,383 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.b7e19c
12-827d-4ca7-87e9-1e3b8ab01c01 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:48:19,391 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.a06d3b
48-6a08-4294-9b6a-7c8ffcebef52 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
2016-07-30 19:48:29,401 INFO org.apache.hadoop.hdfs.StateChange: DIR*
completeFile: /user/spark/eventlog/.89fc29
55-136b-400f-a78c-c439726e4964 is closed by DFSClient_NONMAPREDUCE_-1615501432_1
> Exception in thread “main” org.apache.spark.SparkException: Application
> application finished with failed status
> ---------------------------------------------------------------------------------------------------------------
>
> Key: SPARK-16819
> URL: https://issues.apache.org/jira/browse/SPARK-16819
> Project: Spark
> Issue Type: Question
> Components: Streaming, YARN
> Reporter: Asmaa Ali
> Labels: beginner
> Original Estimate: 24h
> Remaining Estimate: 24h
>
> What is the reason of this exception ?!
> cancerdetector@cluster-cancerdetector-m:~/SparkBWA/build$ spark-submit
> --class SparkBWA --master yarn-cluster --deploy-mode cluster --conf
> spark.yarn.jar=hdfs:///user/spark/spark-assembly.jar --driver-memory 1500m
> --executor-memory 1500m --executor-cores 1 --archives ./bwa.zip --verbose
> ./SparkBWA.jar -algorithm mem -reads paired -index /Data/HumanBase/hg38
> -partitions 32 ERR000589_1.filt.fastq ERR000589_2.filt.fastqhb
> Output_ERR000589
> Using properties file: /usr/lib/spark/conf/spark-defaults.conf
> Adding default property:
> spark.executor.extraJavaOptions=-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
> Adding default property:
> spark.history.fs.logDirectory=hdfs://cluster-cancerdetector-m/user/spark/eventlog
> Adding default property: spark.eventLog.enabled=true
> Adding default property: spark.driver.maxResultSize=1920m
> Adding default property: spark.shuffle.service.enabled=true
> Adding default property:
> spark.yarn.historyServer.address=cluster-cancerdetector-m:18080
> Adding default property: spark.sql.parquet.cacheMetadata=false
> Adding default property: spark.driver.memory=3840m
> Adding default property: spark.dynamicAllocation.maxExecutors=10000
> Adding default property: spark.scheduler.minRegisteredResourcesRatio=0.0
> Adding default property: spark.yarn.am.memoryOverhead=558
> Adding default property: spark.yarn.am.memory=5586m
> Adding default property:
> spark.driver.extraJavaOptions=-Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
> Adding default property: spark.master=yarn-client
> Adding default property: spark.executor.memory=5586m
> Adding default property:
> spark.eventLog.dir=hdfs://cluster-cancerdetector-m/user/spark/eventlog
> Adding default property: spark.dynamicAllocation.enabled=true
> Adding default property: spark.executor.cores=2
> Adding default property: spark.yarn.executor.memoryOverhead=558
> Adding default property: spark.dynamicAllocation.minExecutors=1
> Adding default property: spark.dynamicAllocation.initialExecutors=10000
> Adding default property: spark.akka.frameSize=512
> Parsed arguments:
> master yarn-cluster
> deployMode cluster
> executorMemory 1500m
> executorCores 1
> totalExecutorCores null
> propertiesFile /usr/lib/spark/conf/spark-defaults.conf
> driverMemory 1500m
> driverCores null
> driverExtraClassPath null
> driverExtraLibraryPath null
> driverExtraJavaOptions
> -Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
> supervise false
> queue null
> numExecutors null
> files null
> pyFiles null
> archives file:/home/cancerdetector/SparkBWA/build/./bwa.zip
> mainClass SparkBWA
> primaryResource
> file:/home/cancerdetector/SparkBWA/build/./SparkBWA.jar
> name SparkBWA
> childArgs [-algorithm mem -reads paired -index
> /Data/HumanBase/hg38 -partitions 32 ERR000589_1.filt.fastq
> ERR000589_2.filt.fastqhb Output_ERR000589]
> jars null
> packages null
> packagesExclusions null
> repositories null
> verbose true
> Spark properties used, including those specified through
> --conf and those from the properties file
> /usr/lib/spark/conf/spark-defaults.conf:
> spark.yarn.am.memoryOverhead -> 558
> spark.driver.memory -> 1500m
> spark.yarn.jar -> hdfs:///user/spark/spark-assembly.jar
> spark.executor.memory -> 5586m
> spark.yarn.historyServer.address -> cluster-cancerdetector-m:18080
> spark.eventLog.enabled -> true
> spark.scheduler.minRegisteredResourcesRatio -> 0.0
> spark.dynamicAllocation.maxExecutors -> 10000
> spark.akka.frameSize -> 512
> spark.executor.extraJavaOptions ->
> -Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
> spark.sql.parquet.cacheMetadata -> false
> spark.shuffle.service.enabled -> true
> spark.history.fs.logDirectory ->
> hdfs://cluster-cancerdetector-m/user/spark/eventlog
> spark.dynamicAllocation.initialExecutors -> 10000
> spark.dynamicAllocation.minExecutors -> 1
> spark.yarn.executor.memoryOverhead -> 558
> spark.driver.extraJavaOptions ->
> -Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
> spark.eventLog.dir -> hdfs://cluster-cancerdetector-m/user/spark/eventlog
> spark.yarn.am.memory -> 5586m
> spark.driver.maxResultSize -> 1920m
> spark.master -> yarn-client
> spark.dynamicAllocation.enabled -> true
> spark.executor.cores -> 2
>
> Main class:
> org.apache.spark.deploy.yarn.Client
> Arguments:
> --name
> SparkBWA
> --driver-memory
> 1500m
> --executor-memory
> 1500m
> --executor-cores
> 1
> --archives
> file:/home/cancerdetector/SparkBWA/build/./bwa.zip
> --jar
> file:/home/cancerdetector/SparkBWA/build/./SparkBWA.jar
> --class
> SparkBWA
> --arg
> -algorithm
> --arg
> mem
> --arg
> -reads
> --arg
> paired
> --arg
> -index
> --arg
> /Data/HumanBase/hg38
> --arg
> -partitions
> --arg
> 32
> --arg
> ERR000589_1.filt.fastq
> --arg
> ERR000589_2.filt.fastqhb
> --arg
> Output_ERR000589
> System properties:
> spark.yarn.am.memoryOverhead -> 558
> spark.driver.memory -> 1500m
> spark.yarn.jar -> hdfs:///user/spark/spark-assembly.jar
> spark.executor.memory -> 1500m
> spark.yarn.historyServer.address -> cluster-cancerdetector-m:18080
> spark.eventLog.enabled -> true
> spark.scheduler.minRegisteredResourcesRatio -> 0.0
> SPARK_SUBMIT -> true
> spark.dynamicAllocation.maxExecutors -> 10000
> spark.akka.frameSize -> 512
> spark.sql.parquet.cacheMetadata -> false
> spark.executor.extraJavaOptions ->
> -Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
> spark.app.name -> SparkBWA
> spark.shuffle.service.enabled -> true
> spark.history.fs.logDirectory ->
> hdfs://cluster-cancerdetector-m/user/spark/eventlog
> spark.dynamicAllocation.initialExecutors -> 10000
> spark.dynamicAllocation.minExecutors -> 1
> spark.yarn.executor.memoryOverhead -> 558
> spark.driver.extraJavaOptions ->
> -Xbootclasspath/p:/usr/local/share/google/alpn/alpn-boot-8.1.7.v20160121.jar
> spark.submit.deployMode -> cluster
> spark.eventLog.dir -> hdfs://cluster-cancerdetector-m/user/spark/eventlog
> spark.yarn.am.memory -> 5586m
> spark.driver.maxResultSize -> 1920m
> spark.master -> yarn-cluster
> spark.dynamicAllocation.enabled -> true
> spark.executor.cores -> 1
> Classpath elements:
> spark.yarn.am.memory is set but does not apply in cluster mode.
> spark.yarn.am.memoryOverhead is set but does not apply in cluster mode.
> 16/07/31 01:12:39 INFO org.apache.hadoop.yarn.client.RMProxy: Connecting to
> ResourceManager at cluster-cancerdet
> ector-m/10.132.0.2:8032
> 16/07/31 01:12:40 INFO org.apache.hadoop.yarn.client.api.impl.YarnClientImpl:
> Submitted application application_
> 1467990031555_0106
> Exception in thread "main" org.apache.spark.SparkException: Application
> application_1467990031555_0106 finished
> with failed status
> at org.apache.spark.deploy.yarn.Client.run(Client.scala:1034)
> at org.apache.spark.deploy.yarn.Client$.main(Client.scala:1081)
> at org.apache.spark.deploy.yarn.Client.main(Client.scala)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at
> org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:7
> 31)
> at
> org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
> at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
> at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
> at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
> When I tried to check the AM and executor logs. the command didn't work (I
> have set the yarn.log-aggregation-enable to true), So I tried to manually
> access into NM's log dir to see the detailed application logs. Here are the
> application logs from the NM's log file:
> 2016-07-31 01:12:40,387 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.4:50010 is added to
> blk_1073742335_1511{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 0
> 2016-07-31 01:12:40,387 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.3:50010 is added to
> blk_1073742335_1511{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 0
> 2016-07-31 01:12:40,391 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile:
> /user/cancerdetector/.sparkStaging/application_1467990031555_0106/SparkBWA.jar
> is closed by DFSClient_NONMAPREDUCE_-762268348_1
> 2016-07-31 01:12:40,419 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
> allocate blk_1073742336_1512{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> for /user/cancerdetector/.sparkStaging/application_1467990031555_0106/bwa.zip
> 2016-07-31 01:12:40,445 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.4:50010 is added to
> blk_1073742336_1512{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 0
> 2016-07-31 01:12:40,446 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.3:50010 is added to
> blk_1073742336_1512{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 0
> 2016-07-31 01:12:40,448 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile:
> /user/cancerdetector/.sparkStaging/application_1467990031555_0106/bwa.zip is
> closed by DFSClient_NONMAPREDUCE_-762268348_1
> 2016-07-31 01:12:40,495 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
> allocate blk_1073742337_1513{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> for
> /user/cancerdetector/.sparkStaging/application_1467990031555_0106/__spark_conf__2552000168715758347.zip
> 2016-07-31 01:12:40,506 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.4:50010 is added to
> blk_1073742337_1513{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 0
> 2016-07-31 01:12:40,506 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.3:50010 is added to
> blk_1073742337_1513{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 0
> 2016-07-31 01:12:40,509 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile:
> /user/cancerdetector/.sparkStaging/application_1467990031555_0106/__spark_conf__2552000168715758347.zip
> is closed by DFSClient_NONMAPREDUCE_-762268348_1
> 2016-07-31 01:12:44,720 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
> allocate blk_1073742338_1514{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> for /user/spark/eventlog/application_1467990031555_0106_1.inprogress
> 2016-07-31 01:12:44,877 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
> fsync: /user/spark/eventlog/application_1467990031555_0106_1.inprogress for
> DFSClient_NONMAPREDUCE_-1111833453_14
> 2016-07-31 01:12:45,373 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.4:50010 is added to
> blk_1073742338_1514{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 231
> 2016-07-31 01:12:45,375 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.3:50010 is added to
> blk_1073742338_1514{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 231
> 2016-07-31 01:12:45,379 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile:
> /user/spark/eventlog/application_1467990031555_0106_1.inprogress is closed by
> DFSClient_NONMAPREDUCE_-1111833453_14
> 2016-07-31 01:12:45,843 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.b7989393-f278-477c-8e83-ff5da9079e8a is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:12:49,914 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
> allocate blk_1073742339_1515{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> for /user/spark/eventlog/application_1467990031555_0106_2.inprogress
> 2016-07-31 01:12:50,100 INFO org.apache.hadoop.hdfs.StateChange: BLOCK*
> fsync: /user/spark/eventlog/application_1467990031555_0106_2.inprogress for
> DFSClient_NONMAPREDUCE_378341726_14
> 2016-07-31 01:12:50,737 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.4:50010 is added to
> blk_1073742339_1515{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 231
> 2016-07-31 01:12:50,738 INFO BlockStateChange: BLOCK* addStoredBlock:
> blockMap updated: 10.132.0.3:50010 is added to
> blk_1073742339_1515{UCState=UNDER_CONSTRUCTION, truncateBlock=null,
> primaryNodeIndex=-1,
> replicas=[ReplicaUC[[DISK]DS-19f52f20-0053-443d-bf33-dd636d8b2d07:NORMAL:10.132.0.3:50010|RBW],
>
> ReplicaUC[[DISK]DS-6b7272d9-24d2-4d77-85e2-49c492bd12a4:NORMAL:10.132.0.4:50010|RBW]]}
> size 231
> 2016-07-31 01:12:50,742 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile:
> /user/spark/eventlog/application_1467990031555_0106_2.inprogress is closed by
> DFSClient_NONMAPREDUCE_378341726_14
> 2016-07-31 01:12:50,892 INFO BlockStateChange: BLOCK* addToInvalidates:
> blk_1073742335_1511 10.132.0.3:50010 10.132.0.4:50010
> 2016-07-31 01:12:50,892 INFO BlockStateChange: BLOCK* addToInvalidates:
> blk_1073742337_1513 10.132.0.3:50010 10.132.0.4:50010
> 2016-07-31 01:12:50,892 INFO BlockStateChange: BLOCK* addToInvalidates:
> blk_1073742336_1512 10.132.0.3:50010 10.132.0.4:50010
> 2016-07-31 01:12:51,804 INFO BlockStateChange: BLOCK* BlockManager: ask
> 10.132.0.3:50010 to delete [blk_1073742336_1512, blk_1073742337_1513,
> blk_1073742335_1511]
> 2016-07-31 01:12:54,804 INFO BlockStateChange: BLOCK* BlockManager: ask
> 10.132.0.4:50010 to delete [blk_1073742336_1512, blk_1073742337_1513,
> blk_1073742335_1511]
> 2016-07-31 01:12:55,868 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.46380a1f-b5fd-4924-96aa-f59dcae0cbec is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:13:05,882 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 244
> Total time for transactions(ms): 5 Number of transactions batched in Syncs: 0
> Number of syncs: 234 SyncTimes(ms): 221
> 2016-07-31 01:13:05,885 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.7273ee28-eb1c-4fe2-98d2-c5a20ebe4ffa is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:13:15,892 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.0f640743-d06c-4583-ac95-9d520dc8f301 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:13:25,902 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.bc63864c-0267-47b5-bcc1-96ba81d6c9a5 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:13:35,910 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.93557793-2ba2-47e8-b54c-234c861b6e6c is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:13:45,918 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.0fdf083c-3c53-4051-af16-d579f700962e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:13:55,927 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.834632f1-d9c6-4e14-9354-72f8c18f66d0 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:14:05,933 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 262
> Total time for transactions(ms): 5 Number of transactions batched in Syncs: 0
> Number of syncs: 252 SyncTimes(ms): 236
> 2016-07-31 01:14:05,936 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.d06ef3b4-873f-464d-9cd0-e360da48e194 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:14:15,944 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.32ccba74-5f6c-45fc-b5db-26efb1b840e2 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:14:25,952 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.fef919cd-9952-4af8-a49a-e6dd2aa032f1 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:14:35,961 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.77ffdf36-8e42-43d8-9c1f-df6f3d11700d is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:14:45,968 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.c31cfcbb-b47c-4169-ab0f-7ae87d4f815d is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:14:55,976 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.6429570d-fb0a-4117-bb12-127a67e0a0b7 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:15:05,981 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 280
> Total time for transactions(ms): 6 Number of transactions batched in Syncs: 0
> Number of syncs: 270 SyncTimes(ms): 253
> 2016-07-31 01:15:05,984 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.8030b18d-05f2-4520-b5c4-2fe42338b92b is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:15:15,991 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.f608a0f4-e730-43cd-a19d-da57caac346e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:15:25,999 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.9d5a1f80-2f2a-43a7-84f1-b26a8c90a98f is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:15:36,007 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.279e96fc-180c-47a5-a3ba-cfda581eedad is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:15:46,015 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.a85bbf52-61f4-4899-98b1-23615a549774 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:15:56,023 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.80613e8e-7015-4aeb-81df-49884bd0eb5e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:16:06,028 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 298
> Total time for transactions(ms): 6 Number of transactions batched in Syncs: 0
> Number of syncs: 288 SyncTimes(ms): 267
> 2016-07-31 01:16:06,031 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.2be7fc48-bd1c-4042-88e4-239b1c630458 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:16:16,038 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.40fc68a6-f003-4e35-b4b3-50bd3c4a0c82 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:16:26,045 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.97e7d15c-4d28-4089-b4a5-9f0935a72589 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:16:36,052 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.84d8e78d-90fd-419f-9000-fa04ab56955e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:16:46,059 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.6691cc3e-6969-4a8f-938f-272d1c96701d is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:16:56,066 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.077143b6-281a-468c-8b2c-bcb6cd3bc27a is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:17:06,070 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 316
> Total time for transactions(ms): 6 Number of transactions batched in Syncs: 0
> Number of syncs: 306 SyncTimes(ms): 284
> 2016-07-31 01:17:06,073 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.817d1886-aea2-450a-a586-08677dc18d60 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:17:16,080 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.abd46886-1359-4c5e-8276-ea4f2969411f is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:17:26,087 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.24625260-59be-4a9b-b47b-b8d5b76cb789 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:17:36,096 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.11630782-e50e-4260-a0da-99845bc3f1db is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:17:46,103 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.16cdd027-f1b8-4cbf-a30c-2f1712f4abb5 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:17:56,111 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.93fb2e86-2fec-4069-b73b-632750fda603 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:18:06,116 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 334
> Total time for transactions(ms): 6 Number of transactions batched in Syncs: 0
> Number of syncs: 324 SyncTimes(ms): 300
> 2016-07-31 01:18:06,119 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.b19fddda-ea90-49ab-b44d-434cce28cb67 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:18:16,127 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.d81ab189-bde5-4878-b82b-903983466f86 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:18:26,135 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.e5b51632-f714-4814-b896-59bba137b42d is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:18:36,144 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.39791121-9399-4a22-a50c-90eaddf31ffb is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:18:46,153 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.861c269b-5466-4855-84fd-587ed3306012 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:18:56,162 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.8a9ff721-bd56-4bea-b399-31bfaabe8c7c is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:19:06,168 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 352
> Total time for transactions(ms): 7 Number of transactions batched in Syncs: 0
> Number of syncs: 342 SyncTimes(ms): 313
> 2016-07-31 01:19:06,170 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.492bf987-4991-4533-80e2-678efa843cb9 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:19:16,178 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.9294c0c6-43db-4f6d-9d31-f493143b6baf is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:19:26,187 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.341dd131-c14c-4147-bcbc-849d1d6bba8c is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:19:36,196 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.56f92e8e-ef93-4279-a57f-472dd5d8f399 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:19:46,204 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.5ddcda82-b501-4043-bb54-a29902d9d234 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:19:56,212 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.31e7517b-2ef3-458c-9979-324d7a96302f is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:20:06,218 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 370
> Total time for transactions(ms): 7 Number of transactions batched in Syncs: 0
> Number of syncs: 360 SyncTimes(ms): 329
> 2016-07-31 01:20:06,220 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.5251f5df-0957-4008-b664-8d82eaa9789e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:20:16,229 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.3320b948-2478-4807-9ab3-d23e4945765e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:20:26,237 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.0928c940-e57d-4a34-a7dc-53dade7ff909 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:20:36,246 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.6240fcdf-696e-49c4-a883-3eda5ab89b4d is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:20:46,254 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.5622850e-b7b0-458a-9ffa-89e134fa3fda is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:20:56,262 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.faa076e8-490c-489f-8183-778325e0b144 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:21:06,268 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 388
> Total time for transactions(ms): 7 Number of transactions batched in Syncs: 0
> Number of syncs: 378 SyncTimes(ms): 347
> 2016-07-31 01:21:06,270 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.18b2464e-9d14-4bae-95d9-f261edbdee1b is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:21:16,278 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.6c53dd52-3996-4541-b368-e8406f99f68e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:21:26,287 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.8b5ac93c-b268-432d-9236-48c004c33743 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:21:36,303 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.22a03e6f-4531-466c-af28-e0797d6b803e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:21:46,311 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.1df0d173-6432-481f-af97-6632660700b0 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:21:56,319 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.4095d5a1-ba2d-4966-ad13-99843c51ee91 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:22:06,325 INFO
> org.apache.hadoop.hdfs.server.namenode.FSEditLog: Number of transactions: 406
> Total time for transactions(ms): 8 Number of transactions batched in Syncs: 0
> Number of syncs: 396 SyncTimes(ms): 362
> 2016-07-31 01:22:06,328 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.f35e73f9-842d-4fc2-96b3-9b70df17e7e3 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:22:16,337 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.fdfa32ef-5c3c-48a3-9d15-0edc1b9d5072 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:22:26,345 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.0315d9f7-ea5c-4a58-ad68-3f942d97676a is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:22:36,353 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.eecbddee-6bfb-44b6-97ef-1b5eece8a982 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:22:46,362 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.2c363a5b-bd43-47c5-9050-b15f1f6ade77 is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
> 2016-07-31 01:22:56,449 INFO org.apache.hadoop.hdfs.StateChange: DIR*
> completeFile: /user/spark/eventlog/.6f4e8030-39a7-4fc8-b551-5b1d88e0885e is
> closed by DFSClient_NONMAPREDUCE_-1615501432_1
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