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Python script has been killed due to timeout after waiting 300 secs in service check

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Python script has been killed due to timeout after waiting 300 secs in service check

New Contributor

2017-10-06 05:17:44,162 - Using hadoop conf dir: /usr/hdp/current/hadoop-client/conf

2017-10-06 05:17:44,170 - HdfsResource['/user/ambari-qa'] {'security_enabled': False, 'hadoop_bin_dir': '/usr/hdp/current/hadoop-client/bin', 'keytab': [EMPTY], 'dfs_type': '', 'default_fs': 'hdfs://ip-172-31-12-191.us-east-2.compute.internal:8020', 'hdfs_resource_ignore_file': '/var/lib/ambari-agent/data/.hdfs_resource_ignore', 'hdfs_site': ..., 'kinit_path_local': 'kinit', 'principal_name': [EMPTY], 'user': 'hdfs', 'owner': 'ambari-qa', 'hadoop_conf_dir': '/usr/hdp/current/hadoop-client/conf', 'type': 'directory', 'action': ['create_on_execute'], 'immutable_paths': [u'/apps/hive/warehouse', u'/mr-history/done', u'/app-logs', u'/tmp'], 'mode': 0770}
2017-10-06 05:17:44,173 - call['ambari-sudo.sh su hdfs -l -s /bin/bash -c 'curl -sS -L -w '"'"'%{http_code}'"'"' -X GET '"'"'http://ip-172-31-12-191.us-east-2.compute.internal:50070/webhdfs/v1/user/ambari-qa?op=GETFILESTATUS&user.name=hdfs'"'"' 1>/tmp/tmpzOeEsr 2>/tmp/tmp7BuJX3''] {'logoutput': None, 'quiet': False}
2017-10-06 05:17:44,218 - call returned (0, '')
2017-10-06 05:17:44,219 - HdfsResource['/user/ambari-qa/pigsmoke.out'] {'security_enabled': False, 'hadoop_bin_dir': '/usr/hdp/current/hadoop-client/bin', 'keytab': [EMPTY], 'dfs_type': '', 'default_fs': 'hdfs://ip-172-31-12-191.us-east-2.compute.internal:8020', 'hdfs_resource_ignore_file': '/var/lib/ambari-agent/data/.hdfs_resource_ignore', 'hdfs_site': ..., 'kinit_path_local': 'kinit', 'principal_name': [EMPTY], 'user': 'hdfs', 'owner': 'ambari-qa', 'hadoop_conf_dir': '/usr/hdp/current/hadoop-client/conf', 'type': 'directory', 'action': ['delete_on_execute'], 'immutable_paths': [u'/apps/hive/warehouse', u'/mr-history/done', u'/app-logs', u'/tmp']}
2017-10-06 05:17:44,220 - call['ambari-sudo.sh su hdfs -l -s /bin/bash -c 'curl -sS -L -w '"'"'%{http_code}'"'"' -X GET '"'"'http://ip-172-31-12-191.us-east-2.compute.internal:50070/webhdfs/v1/user/ambari-qa/pigsmoke.out?op=GETFILESTATUS&user.name=hdfs'"'"' 1>/tmp/tmpwdjQAo 2>/tmp/tmp4k4Dme''] {'logoutput': None, 'quiet': False}
2017-10-06 05:17:44,265 - call returned (0, '')
2017-10-06 05:17:44,267 - call['ambari-sudo.sh su hdfs -l -s /bin/bash -c 'curl -sS -L -w '"'"'%{http_code}'"'"' -X DELETE '"'"'http://ip-172-31-12-191.us-east-2.compute.internal:50070/webhdfs/v1/user/ambari-qa/pigsmoke.out?op=DELETE&recursive=True&user.name=hdfs'"'"' 1>/tmp/tmpecNoes 2>/tmp/tmpxvvwEZ''] {'logoutput': None, 'quiet': False}
2017-10-06 05:17:44,312 - call returned (0, '')
2017-10-06 05:17:44,313 - HdfsResource['/user/ambari-qa/passwd'] {'security_enabled': False, 'hadoop_bin_dir': '/usr/hdp/current/hadoop-client/bin', 'keytab': [EMPTY], 'source': '/etc/passwd', 'dfs_type': '', 'default_fs': 'hdfs://ip-172-31-12-191.us-east-2.compute.internal:8020', 'hdfs_resource_ignore_file': '/var/lib/ambari-agent/data/.hdfs_resource_ignore', 'hdfs_site': ..., 'kinit_path_local': 'kinit', 'principal_name': [EMPTY], 'user': 'hdfs', 'owner': 'ambari-qa', 'hadoop_conf_dir': '/usr/hdp/current/hadoop-client/conf', 'type': 'file', 'action': ['create_on_execute'], 'immutable_paths': [u'/apps/hive/warehouse', u'/mr-history/done', u'/app-logs', u'/tmp']}
2017-10-06 05:17:44,314 - call['ambari-sudo.sh su hdfs -l -s /bin/bash -c 'curl -sS -L -w '"'"'%{http_code}'"'"' -X GET '"'"'http://ip-172-31-12-191.us-east-2.compute.internal:50070/webhdfs/v1/user/ambari-qa/passwd?op=GETFILESTATUS&user.name=hdfs'"'"' 1>/tmp/tmpriVL9x 2>/tmp/tmp7s8cyv''] {'logoutput': None, 'quiet': False}
2017-10-06 05:17:44,358 - call returned (0, '')
2017-10-06 05:17:44,359 - Creating new file /user/ambari-qa/passwd in DFS
2017-10-06 05:17:44,359 - call['ambari-sudo.sh su hdfs -l -s /bin/bash -c 'curl -sS -L -w '"'"'%{http_code}'"'"' -X PUT --data-binary @/etc/passwd -H '"'"'Content-Type: application/octet-stream'"'"' '"'"'http://ip-172-31-12-191.us-east-2.compute.internal:50070/webhdfs/v1/user/ambari-qa/passwd?op=CREATE&user.name=hdfs&overwrite=True'"'"' 1>/tmp/tmpbHi8Ml 2>/tmp/tmpmAOKuW''] {'logoutput': None, 'quiet': False}
2017-10-06 05:17:44,432 - call returned (0, '')
2017-10-06 05:17:44,433 - HdfsResource[None] {'security_enabled': False, 'hadoop_bin_dir': '/usr/hdp/current/hadoop-client/bin', 'keytab': [EMPTY], 'dfs_type': '', 'default_fs': 'hdfs://ip-172-31-12-191.us-east-2.compute.internal:8020', 'hdfs_resource_ignore_file': '/var/lib/ambari-agent/data/.hdfs_resource_ignore', 'hdfs_site': ..., 'kinit_path_local': 'kinit', 'principal_name': [EMPTY], 'user': 'hdfs', 'action': ['execute'], 'hadoop_conf_dir': '/usr/hdp/current/hadoop-client/conf', 'immutable_paths': [u'/apps/hive/warehouse', u'/mr-history/done', u'/app-logs', u'/tmp']}
2017-10-06 05:17:44,433 - File['/var/lib/ambari-agent/tmp/pigSmoke.sh'] {'content': StaticFile('pigSmoke.sh'), 'mode': 0755}
2017-10-06 05:17:44,435 - Writing File['/var/lib/ambari-agent/tmp/pigSmoke.sh'] because it doesn't exist
2017-10-06 05:17:44,435 - Changing permission for /var/lib/ambari-agent/tmp/pigSmoke.sh from 644 to 755
2017-10-06 05:17:44,435 - Execute['pig /var/lib/ambari-agent/tmp/pigSmoke.sh'] {'logoutput': True, 'path': [u'/usr/hdp/current/pig-client/bin:/usr/sbin:/sbin:/usr/local/bin:/bin:/usr/bin'], 'tries': 3, 'user': 'ambari-qa', 'try_sleep': 5}
17/10/06 05:17:45 INFO pig.ExecTypeProvider: Trying ExecType : LOCAL
17/10/06 05:17:45 INFO pig.ExecTypeProvider: Trying ExecType : MAPREDUCE
17/10/06 05:17:45 INFO pig.ExecTypeProvider: Picked MAPREDUCE as the ExecType
2017-10-06 05:17:45,556 [main] INFO  org.apache.pig.Main - Apache Pig version 0.16.0.2.5.3.0-37 (rexported) compiled Nov 30 2016, 02:28:11
2017-10-06 05:17:45,556 [main] INFO  org.apache.pig.Main - Logging error messages to: /home/ambari-qa/pig_1507267065554.log
2017-10-06 05:17:46,241 [main] INFO  org.apache.pig.impl.util.Utils - Default bootup file /home/ambari-qa/.pigbootup not found
2017-10-06 05:17:46,355 [main] INFO  org.apache.pig.backend.hadoop.executionengine.HExecutionEngine - Connecting to hadoop file system at: hdfs://ip-172-31-12-191.us-east-2.compute.internal:8020
2017-10-06 05:17:46,812 [main] INFO  org.apache.pig.PigServer - Pig Script ID for the session: PIG-pigSmoke.sh-77b352b2-4ead-4b2a-9d1b-c4e92ec93769
2017-10-06 05:17:47,169 [main] INFO  org.apache.hadoop.yarn.client.api.impl.TimelineClientImpl - Timeline service address: http://ip-172-31-3-20.us-east-2.compute.internal:8188/ws/v1/timeline/
2017-10-06 05:17:47,261 [main] INFO  org.apache.pig.backend.hadoop.PigATSClient - Created ATS Hook
2017-10-06 05:17:48,005 [main] INFO  org.apache.pig.tools.pigstats.ScriptState - Pig features used in the script: UNKNOWN
2017-10-06 05:17:48,051 [main] INFO  org.apache.pig.data.SchemaTupleBackend - Key [pig.schematuple] was not set... will not generate code.
2017-10-06 05:17:48,088 [main] INFO  org.apache.pig.newplan.logical.optimizer.LogicalPlanOptimizer - {RULES_ENABLED=[AddForEach, ColumnMapKeyPrune, ConstantCalculator, GroupByConstParallelSetter, LimitOptimizer, LoadTypeCastInserter, MergeFilter, MergeForEach, PartitionFilterOptimizer, PredicatePushdownOptimizer, PushDownForEachFlatten, PushUpFilter, SplitFilter, StreamTypeCastInserter]}
2017-10-06 05:17:48,153 [main] INFO  org.apache.pig.impl.util.SpillableMemoryManager - Selected heap (PS Old Gen) of size 699400192 to monitor. collectionUsageThreshold = 489580128, usageThreshold = 489580128
2017-10-06 05:17:48,201 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MRCompiler - File concatenation threshold: 100 optimistic? false
2017-10-06 05:17:48,235 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MultiQueryOptimizer - MR plan size before optimization: 1
2017-10-06 05:17:48,236 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MultiQueryOptimizer - MR plan size after optimization: 1
2017-10-06 05:17:48,407 [main] INFO  org.apache.hadoop.yarn.client.api.impl.TimelineClientImpl - Timeline service address: http://ip-172-31-3-20.us-east-2.compute.internal:8188/ws/v1/timeline/
2017-10-06 05:17:48,414 [main] INFO  org.apache.hadoop.yarn.client.RMProxy - Connecting to ResourceManager at ip-172-31-3-20.us-east-2.compute.internal/172.31.3.20:8050
2017-10-06 05:17:48,562 [main] INFO  org.apache.hadoop.yarn.client.AHSProxy - Connecting to Application History server at ip-172-31-3-20.us-east-2.compute.internal/172.31.3.20:10200
2017-10-06 05:17:48,640 [main] INFO  org.apache.pig.tools.pigstats.mapreduce.MRScriptState - Pig script settings are added to the job
2017-10-06 05:17:48,646 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.JobControlCompiler - mapred.job.reduce.markreset.buffer.percent is not set, set to default 0.3
2017-10-06 05:17:48,648 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.JobControlCompiler - This job cannot be converted run in-process
2017-10-06 05:17:48,970 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.JobControlCompiler - Added jar file:/usr/hdp/2.5.3.0-37/pig/pig-0.16.0.2.5.3.0-37-core-h2.jar to DistributedCache through /tmp/temp-620740268/tmp-1469178571/pig-0.16.0.2.5.3.0-37-core-h2.jar
2017-10-06 05:17:48,990 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.JobControlCompiler - Added jar file:/usr/hdp/2.5.3.0-37/pig/lib/automaton-1.11-8.jar to DistributedCache through /tmp/temp-620740268/tmp1280680167/automaton-1.11-8.jar
2017-10-06 05:17:49,008 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.JobControlCompiler - Added jar file:/usr/hdp/2.5.3.0-37/pig/lib/antlr-runtime-3.4.jar to DistributedCache through /tmp/temp-620740268/tmp-245846803/antlr-runtime-3.4.jar
2017-10-06 05:17:49,037 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.JobControlCompiler - Added jar file:/usr/hdp/2.5.3.0-37/hadoop/lib/joda-time-2.8.1.jar to DistributedCache through /tmp/temp-620740268/tmp1888445821/joda-time-2.8.1.jar
2017-10-06 05:17:49,046 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.JobControlCompiler - Setting up single store job
2017-10-06 05:17:49,053 [main] INFO  org.apache.pig.data.SchemaTupleFrontend - Key [pig.schematuple] is false, will not generate code.
2017-10-06 05:17:49,053 [main] INFO  org.apache.pig.data.SchemaTupleFrontend - Starting process to move generated code to distributed cacche
2017-10-06 05:17:49,053 [main] INFO  org.apache.pig.data.SchemaTupleFrontend - Setting key [pig.schematuple.classes] with classes to deserialize []
2017-10-06 05:17:49,093 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MapReduceLauncher - 1 map-reduce job(s) waiting for submission.
2017-10-06 05:17:49,178 [JobControl] INFO  org.apache.hadoop.yarn.client.api.impl.TimelineClientImpl - Timeline service address: http://ip-172-31-3-20.us-east-2.compute.internal:8188/ws/v1/timeline/
2017-10-06 05:17:49,179 [JobControl] INFO  org.apache.hadoop.yarn.client.RMProxy - Connecting to ResourceManager at ip-172-31-3-20.us-east-2.compute.internal/172.31.3.20:8050
2017-10-06 05:17:49,179 [JobControl] INFO  org.apache.hadoop.yarn.client.AHSProxy - Connecting to Application History server at ip-172-31-3-20.us-east-2.compute.internal/172.31.3.20:10200
2017-10-06 05:17:49,406 [JobControl] WARN  org.apache.hadoop.mapreduce.JobResourceUploader - No job jar file set.  User classes may not be found. See Job or Job#setJar(String).
2017-10-06 05:17:49,471 [JobControl] INFO  org.apache.pig.builtin.PigStorage - Using PigTextInputFormat
2017-10-06 05:17:49,480 [JobControl] INFO  org.apache.hadoop.mapreduce.lib.input.FileInputFormat - Total input paths to process : 1
2017-10-06 05:17:49,480 [JobControl] INFO  org.apache.pig.backend.hadoop.executionengine.util.MapRedUtil - Total input paths to process : 1
2017-10-06 05:17:49,505 [JobControl] INFO  org.apache.pig.backend.hadoop.executionengine.util.MapRedUtil - Total input paths (combined) to process : 1
2017-10-06 05:17:49,982 [JobControl] INFO  org.apache.hadoop.mapreduce.JobSubmitter - number of splits:1
2017-10-06 05:17:50,126 [JobControl] INFO  org.apache.hadoop.mapreduce.JobSubmitter - Submitting tokens for job: job_1507266152786_0006
2017-10-06 05:17:50,243 [JobControl] INFO  org.apache.hadoop.mapred.YARNRunner - Job jar is not present. Not adding any jar to the list of resources.
2017-10-06 05:17:50,519 [JobControl] INFO  org.apache.hadoop.yarn.client.api.impl.YarnClientImpl - Submitted application application_1507266152786_0006
2017-10-06 05:17:50,553 [JobControl] INFO  org.apache.hadoop.mapreduce.Job - The url to track the job: http://ip-172-31-3-20.us-east-2.compute.internal:8088/proxy/application_1507266152786_0006/
2017-10-06 05:17:50,553 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MapReduceLauncher - HadoopJobId: job_1507266152786_0006
2017-10-06 05:17:50,553 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MapReduceLauncher - Processing aliases A,B
2017-10-06 05:17:50,553 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MapReduceLauncher - detailed locations: M: A[16,4],B[17,4] C:  R: 
2017-10-06 05:17:50,562 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MapReduceLauncher - 0% complete
2017-10-06 05:17:50,562 [main] INFO  org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.MapReduceLauncher - Running jobs are [job_1507266152786_0006]

Command failed after 1 tries

40713-pig.png

4 REPLIES 4
Highlighted

Re: Python script has been killed due to timeout after waiting 300 secs in service check

New Contributor

I am also having same problem with Check Habse Operation,

Python script has been killed due to timeout after waiting 300 secs


2017-10-11 01:53:22,752 - Stack Feature Version Info: Cluster Stack=2.6, Cluster Current Version=2.6.2.0-205, Command Stack=None, Command Version=2.6.2.0-205 -> 2.6.2.0-205
2017-10-11 01:53:22,764 - Using hadoop conf dir: /usr/hdp/current/hadoop-client/conf
2017-10-11 01:53:22,769 - checked_call['hostid'] {}
2017-10-11 01:53:22,774 - checked_call returned (0, '1c09eea3')
2017-10-11 01:53:22,780 - File['/var/lib/ambari-agent/tmp/hbaseSmokeVerify.sh'] {'content': StaticFile('hbaseSmokeVerify.sh'), 'mode': 0755}
2017-10-11 01:53:22,812 - File['/var/lib/ambari-agent/tmp/hbase-smoke-cleanup.sh'] {'content': StaticFile('hbase-smoke-cleanup.sh'), 'mode': 0755}
2017-10-11 01:53:22,839 - File['/var/lib/ambari-agent/tmp/hbase-smoke.sh'] {'content': Template('hbase-smoke.sh.j2'), 'mode': 0755}
2017-10-11 01:53:22,887 - Writing File['/var/lib/ambari-agent/tmp/hbase-smoke.sh'] because contents don't match
2017-10-11 01:53:22,888 - Execute[' /usr/hdp/current/hbase-client/bin/hbase --config /usr/hdp/current/hbase-client/conf shell /var/lib/ambari-agent/tmp/hbase-smoke.sh && /var/lib/ambari-agent/tmp/hbaseSmokeVerify.sh /usr/hdp/current/hbase-client/conf id1c09eea3_date531117 /usr/hdp/current/hbase-client/bin/hbase &&  /usr/hdp/current/hbase-client/bin/hbase --config /usr/hdp/current/hbase-client/conf shell /var/lib/ambari-agent/tmp/hbase-smoke-cleanup.sh'] {'logoutput': True, 'tries': 6, 'user': 'ambari-qa', 'try_sleep': 5}

ERROR: Can't get the location for replica 0

Here is some help for this command:
Start disable of named table:
  hbase> disable 't1'
  hbase> disable 'ns1:t1'



ERROR: Can't get the location for replica 0

Here is some help for this command:
Drop the named table. Table must first be disabled:
  hbase> drop 't1'
  hbase> drop 'ns1:t1'



ERROR: org.apache.hadoop.hbase.PleaseHoldException: Master is initializing
 at org.apache.hadoop.hbase.master.HMaster.checkInitialized(HMaster.java:2672)
 at org.apache.hadoop.hbase.master.HMaster.checkNamespaceManagerReady(HMaster.java:2677)
 at org.apache.hadoop.hbase.master.HMaster.ensureNamespaceExists(HMaster.java:2915)
 at org.apache.hadoop.hbase.master.HMaster.createTable(HMaster.java:1686)
 at org.apache.hadoop.hbase.master.MasterRpcServices.createTable(MasterRpcServices.java:483)
 at org.apache.hadoop.hbase.protobuf.generated.MasterProtos$MasterService$2.callBlockingMethod(MasterProtos.java:59846)
 at org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java:2150)
 at org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner.java:112)
 at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run(RpcExecutor.java:187)
 at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run(RpcExecutor.java:167)

Here is some help for this command:
Creates a table. Pass a table name, and a set of column family
specifications (at least one), and, optionally, table configuration.
Column specification can be a simple string (name), or a dictionary
(dictionaries are described below in main help output), necessarily 
including NAME attribute. 
Examples:

Create a table with namespace=ns1 and table qualifier=t1
  hbase> create 'ns1:t1', {NAME => 'f1', VERSIONS => 5}

Create a table with namespace=default and table qualifier=t1
  hbase> create 't1', {NAME => 'f1'}, {NAME => 'f2'}, {NAME => 'f3'}
  hbase> # The above in shorthand would be the following:
  hbase> create 't1', 'f1', 'f2', 'f3'
  hbase> create 't1', {NAME => 'f1', VERSIONS => 1, TTL => 2592000, BLOCKCACHE => true}
  hbase> create 't1', {NAME => 'f1', CONFIGURATION => {'hbase.hstore.blockingStoreFiles' => '10'}}
  
Table configuration options can be put at the end.
Examples:

  hbase> create 'ns1:t1', 'f1', SPLITS => ['10', '20', '30', '40']
  hbase> create 't1', 'f1', SPLITS => ['10', '20', '30', '40']
  hbase> create 't1', 'f1', SPLITS_FILE => 'splits.txt', OWNER => 'johndoe'
  hbase> create 't1', {NAME => 'f1', VERSIONS => 5}, METADATA => { 'mykey' => 'myvalue' }
  hbase> # Optionally pre-split the table into NUMREGIONS, using
  hbase> # SPLITALGO ("HexStringSplit", "UniformSplit" or classname)
  hbase> create 't1', 'f1', {NUMREGIONS => 15, SPLITALGO => 'HexStringSplit'}
  hbase> create 't1', 'f1', {NUMREGIONS => 15, SPLITALGO => 'HexStringSplit', REGION_REPLICATION => 2, CONFIGURATION => {'hbase.hregion.scan.loadColumnFamiliesOnDemand' => 'true'}}

You can also keep around a reference to the created table:

  hbase> t1 = create 't1', 'f1'

Which gives you a reference to the table named 't1', on which you can then
call methods.

Command failed after 1 tries







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Highlighted

Re: Python script has been killed due to timeout after waiting 300 secs in service check

Rising Star

@azhar shaikh

Timeout is coming from the finite timeout that Ambari has put for Service Check python scripts in order to bail out, rather than running forever.

The point to note here is that there may be a problem in terms of HBase health in general, which is either making HBase service check to not finish within 300 secs (performance) or HBase process is not responding at all.

Can you check the logs for HBase and the the services it depends on to verify their workable state ?

CC @Chinmay Das

Highlighted

Re: Python script has been killed due to timeout after waiting 300 secs in service check

I have the same problem , What can I do now ?

Highlighted

Re: Python script has been killed due to timeout after waiting 300 secs in service check

Edit /var/lib/ambari-server/resources/common-services/OOZIE/your_version_number/metainfo.xml <time_out>300<time_out>

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