Re: HDFS HA issue in Flink 1.4 caused by failing to use fs.hdfs.hadoopconf in Flink conf

[Aljoscha Krettek]

Thanks for figuring this out, Shuyi!

> On 9. Oct 2018, at 09:09, Shuyi Chen  wrote:
> 
> I think the bug is introduced in FLINK-7643 (Rework FileSystem loading to use 
> factories). In YarnApplicationMasterRunner, after the JIRA, FileSystem was 
> not properly initialized with the correct flink configuration before calling 
> runApplicationMaster(). W/o the initialization, a call of 
> FileSystem.get("hdfs://nameservice0/") will cause the HadoopFsFactory to be 
> initialized with an empty Flink Configuration, thus not able to recognize 
> nameservice0.
> 
> I've composed unittests in YarnApplicationMasterRunner, 
> YarnTaskManagerRunnerFactory and YarnTaskExecutorRunner, and verify that 
> YarnApplicationMasterRunner fail to initialize the FileSystem properly, and  
> YarnTaskManagerRunnerFactory does the right thing, so does 
> YarnTaskExecutorRunner.
> 
> I'll create a JIRA to track the fix.
> 
> 
> On Thu, Oct 4, 2018 at 11:23 AM Yan Yan  > wrote:
> Hi Aljoscha,
> 
> Thanks for looking into this! Yes, we toggled Flink 1.4 back to Flink 1.3.2 
> and it works. So seems truly a feature disparity between 1.3.2 and 1.4.
> 
> Best,
> Yan
> 
> 
> On Thu, Oct 4, 2018 at 6:36 AM Aljoscha Krettek  > wrote:
> Another thing: when you retry this again with Flink 1.3.2 it works? I'm 
> trying to rule out another problem in the setup.
> 
> 
>> On 4. Oct 2018, at 15:17, Aljoscha Krettek > > wrote:
>> 
>> Hi Yan,
>> 
>> This seems to be a bug in the FileSystems and how they're initialized. I'm 
>> looking into this myself but I'm also looping in Stephan and Stefan how have 
>> worked on this the most in the past. Maybe they have some valuable input.
>> 
>> Best,
>> Aljoscha
>> 
>> 
>>> On 4. Oct 2018, at 01:18, Yan Yan >> > wrote:
>>> 
>>> Hi,
>>> 
>>> We recently bumped to Flink 1.4 from 1.3.2, and found out an issue on HDFS 
>>> configuration.
>>> 
>>> We are using FlinkYarnSessionCli to start the cluster and submit job.
>>> 
>>> In 1.3.2, we set below Flink properties when using checkpoints:
>>> state.backend.fs.checkpointdir = hdfs://nameservice0/ <>.../..
>>> state.checkpoints.dir = hdfs://nameservice0/ <>../..
>>> 
>>> The mapping between logical nameservice (nameservice0) and actual namenodes 
>>> hostports are passed to Flink via yarnship/core-site.xml (by providing the 
>>> -yt option), and set fs.hdfs.hadoopconf=yarnship/
>>> 
>>> However, we encountered below error after bumping to 1.4, which caused the 
>>> checkpointing to fail.
>>> 
>>> 2018-09-20 01:01:00.041 [yarn-jobmanager-io-thread-18] WARN  
>>> org.apache.flink.runtime.checkpoint.OperatorSubtaskState  - Error while 
>>> discarding operator states.
>>> java.io.IOException: Cannot instantiate file system for URI: 
>>> hdfs://nameservice0/app/athena_checkpoint/rt_data/gairos-athena-flink-demand-processor-opticclient-flink-job/flink/checkpoints/ckpt_1537402213581/data/ebb30a2d3b26e4d63682538a9bcdc752/chk-3204/da1d44d3-d3eb-4e57-9145-bdf30c96993a
>>>  <>
>>> at 
>>> org.apache.flink.runtime.fs.hdfs.HadoopFsFactory.create(HadoopFsFactory.java:187)
>>> at 
>>> org.apache.flink.core.fs.FileSystem.getUnguardedFileSystem(FileSystem.java:401)
>>> at org.apache.flink.core.fs.FileSystem.get(FileSystem.java:320)
>>> at 
>>> org.apache.flink.runtime.state.filesystem.FileStateHandle.getFileSystem(FileStateHandle.java:109)
>>> at 
>>> org.apache.flink.runtime.state.filesystem.FileStateHandle.discardState(FileStateHandle.java:81)
>>> at 
>>> org.apache.flink.runtime.state.OperatorStateHandle.discardState(OperatorStateHandle.java:65)
>>> at 
>>> org.apache.flink.util.LambdaUtil.applyToAllWhileSuppressingExceptions(LambdaUtil.java:51)
>>> at 
>>> org.apache.flink.runtime.state.StateUtil.bestEffortDiscardAllStateObjects(StateUtil.java:53)
>>> at 
>>> org.apache.flink.runtime.checkpoint.OperatorSubtaskState.discardState(OperatorSubtaskState.java:207)
>>> at 
>>> org.apache.flink.runtime.checkpoint.OperatorState.discardState(OperatorState.java:108)
>>> at 
>>> org.apache.flink.util.LambdaUtil.applyToAllWhileSuppressingExceptions(LambdaUtil.java:51)
>>> at 
>>> org.apache.flink.runtime.state.StateUtil.bestEffortDiscardAllStateObjects(StateUtil.java:53)
>>> at 
>>> org.apache.flink.runtime.checkpoint.PendingCheckpoint$1.run(PendingCheckpoint.java:530)
>>> at 
>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>> at 
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>> at java.lang.Thread.run(Thread.java:748)
>>> Caused by: java.lang.IllegalArgumentException: 
>>> java.net.UnknownHostException: nameservice0
>>> at 
>>> org.apache.hadoop.security.SecurityUtil.buildTokenService(SecurityUtil.java:378)
>>> at 
>>> org.apache.hadoop.hdfs.NameNodeProxies.createNonHAProxy(NameNodeProxies.java:310)
>>> at 
>>> 

Re: HDFS HA issue in Flink 1.4 caused by failing to use fs.hdfs.hadoopconf in Flink conf

[Shuyi Chen]

I think the bug is introduced in FLINK-7643 (Rework FileSystem loading to
use factories). In YarnApplicationMasterRunner, after the JIRA, FileSystem
was not properly initialized with the correct flink configuration before
calling runApplicationMaster(). W/o the initialization, a call of
FileSystem.get("hdfs://nameservice0/") will cause the HadoopFsFactory to be
initialized with an empty Flink Configuration, thus not able to
recognize nameservice0.

I've composed unittests in YarnApplicationMasterRunner,
YarnTaskManagerRunnerFactory and YarnTaskExecutorRunner, and verify
that YarnApplicationMasterRunner fail to initialize the FileSystem
properly, and  YarnTaskManagerRunnerFactory does the right thing, so does
YarnTaskExecutorRunner.

I'll create a JIRA to track the fix.


On Thu, Oct 4, 2018 at 11:23 AM Yan Yan  wrote:

> Hi Aljoscha,
>
> Thanks for looking into this! Yes, we toggled Flink 1.4 back to Flink
> 1.3.2 and it works. So seems truly a feature disparity between 1.3.2 and
> 1.4.
>
> Best,
> Yan
>
>
> On Thu, Oct 4, 2018 at 6:36 AM Aljoscha Krettek 
> wrote:
>
>> Another thing: when you retry this again with Flink 1.3.2 it works? I'm
>> trying to rule out another problem in the setup.
>>
>>
>> On 4. Oct 2018, at 15:17, Aljoscha Krettek  wrote:
>>
>> Hi Yan,
>>
>> This seems to be a bug in the FileSystems and how they're initialized.
>> I'm looking into this myself but I'm also looping in Stephan and Stefan how
>> have worked on this the most in the past. Maybe they have some valuable
>> input.
>>
>> Best,
>> Aljoscha
>>
>>
>> On 4. Oct 2018, at 01:18, Yan Yan  wrote:
>>
>> Hi,
>>
>> We recently bumped to Flink 1.4 from 1.3.2, and found out an issue on
>> HDFS configuration.
>>
>> We are using *FlinkYarnSessionCli* to start the cluster and submit job.
>>
>> In 1.3.2, we set below Flink properties when using checkpoints:
>> state.backend.fs.checkpointdir = hdfs://nameservice0/.../..
>> state.checkpoints.dir = hdfs://nameservice0/../..
>>
>> The mapping between logical nameservice (nameservice0) and actual
>> namenodes hostports are passed to Flink via *yarnship/core-site.xml *(by
>> providing the -yt option), and set fs.hdfs.hadoopconf=yarnship/
>>
>> However, we encountered below error after bumping to 1.4, which caused
>> the checkpointing to fail.
>>
>> 2018-09-20 01:01:00.041 [yarn-jobmanager-io-thread-18] WARN  
>> org.apache.flink.runtime.checkpoint.OperatorSubtaskState  - Error while 
>> discarding operator states.
>> java.io.IOException: Cannot instantiate file system for URI: 
>> hdfs://nameservice0/app/athena_checkpoint/rt_data/gairos-athena-flink-demand-processor-opticclient-flink-job/flink/checkpoints/ckpt_1537402213581/data/ebb30a2d3b26e4d63682538a9bcdc752/chk-3204/da1d44d3-d3eb-4e57-9145-bdf30c96993a
>> at 
>> org.apache.flink.runtime.fs.hdfs.HadoopFsFactory.create(HadoopFsFactory.java:187)
>> at 
>> org.apache.flink.core.fs.FileSystem.getUnguardedFileSystem(FileSystem.java:401)
>> at org.apache.flink.core.fs.FileSystem.get(FileSystem.java:320)
>> at 
>> org.apache.flink.runtime.state.filesystem.FileStateHandle.getFileSystem(FileStateHandle.java:109)
>> at 
>> org.apache.flink.runtime.state.filesystem.FileStateHandle.discardState(FileStateHandle.java:81)
>> at 
>> org.apache.flink.runtime.state.OperatorStateHandle.discardState(OperatorStateHandle.java:65)
>> at 
>> org.apache.flink.util.LambdaUtil.applyToAllWhileSuppressingExceptions(LambdaUtil.java:51)
>> at 
>> org.apache.flink.runtime.state.StateUtil.bestEffortDiscardAllStateObjects(StateUtil.java:53)
>> at 
>> org.apache.flink.runtime.checkpoint.OperatorSubtaskState.discardState(OperatorSubtaskState.java:207)
>> at 
>> org.apache.flink.runtime.checkpoint.OperatorState.discardState(OperatorState.java:108)
>> at 
>> org.apache.flink.util.LambdaUtil.applyToAllWhileSuppressingExceptions(LambdaUtil.java:51)
>> at 
>> org.apache.flink.runtime.state.StateUtil.bestEffortDiscardAllStateObjects(StateUtil.java:53)
>> at 
>> org.apache.flink.runtime.checkpoint.PendingCheckpoint$1.run(PendingCheckpoint.java:530)
>> at 
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>> at 
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>> at java.lang.Thread.run(Thread.java:748)
>> Caused by: java.lang.IllegalArgumentException: 
>> java.net.UnknownHostException: nameservice0
>> at 
>> org.apache.hadoop.security.SecurityUtil.buildTokenService(SecurityUtil.java:378)
>> at 
>> org.apache.hadoop.hdfs.NameNodeProxies.createNonHAProxy(NameNodeProxies.java:310)
>> at 
>> org.apache.hadoop.hdfs.NameNodeProxies.createProxy(NameNodeProxies.java:176)
>> at org.apache.hadoop.hdfs.DFSClient.(DFSClient.java:678)
>> at org.apache.hadoop.hdfs.DFSClient.(DFSClient.java:619)
>> at 
>> org.apache.hadoop.hdfs.DistributedFileSystem.initialize(DistributedFileSystem.java:149)
>> at 
>> 

Re: HDFS HA issue in Flink 1.4 caused by failing to use fs.hdfs.hadoopconf in Flink conf

[Yan Yan]

Hi Aljoscha,

Thanks for looking into this! Yes, we toggled Flink 1.4 back to Flink 1.3.2
and it works. So seems truly a feature disparity between 1.3.2 and 1.4.

Best,
Yan


On Thu, Oct 4, 2018 at 6:36 AM Aljoscha Krettek  wrote:

> Another thing: when you retry this again with Flink 1.3.2 it works? I'm
> trying to rule out another problem in the setup.
>
>
> On 4. Oct 2018, at 15:17, Aljoscha Krettek  wrote:
>
> Hi Yan,
>
> This seems to be a bug in the FileSystems and how they're initialized. I'm
> looking into this myself but I'm also looping in Stephan and Stefan how
> have worked on this the most in the past. Maybe they have some valuable
> input.
>
> Best,
> Aljoscha
>
>
> On 4. Oct 2018, at 01:18, Yan Yan  wrote:
>
> Hi,
>
> We recently bumped to Flink 1.4 from 1.3.2, and found out an issue on HDFS
> configuration.
>
> We are using *FlinkYarnSessionCli* to start the cluster and submit job.
>
> In 1.3.2, we set below Flink properties when using checkpoints:
> state.backend.fs.checkpointdir = hdfs://nameservice0/.../..
> state.checkpoints.dir = hdfs://nameservice0/../..
>
> The mapping between logical nameservice (nameservice0) and actual
> namenodes hostports are passed to Flink via *yarnship/core-site.xml *(by
> providing the -yt option), and set fs.hdfs.hadoopconf=yarnship/
>
> However, we encountered below error after bumping to 1.4, which caused the
> checkpointing to fail.
>
> 2018-09-20 01:01:00.041 [yarn-jobmanager-io-thread-18] WARN  
> org.apache.flink.runtime.checkpoint.OperatorSubtaskState  - Error while 
> discarding operator states.
> java.io.IOException: Cannot instantiate file system for URI: 
> hdfs://nameservice0/app/athena_checkpoint/rt_data/gairos-athena-flink-demand-processor-opticclient-flink-job/flink/checkpoints/ckpt_1537402213581/data/ebb30a2d3b26e4d63682538a9bcdc752/chk-3204/da1d44d3-d3eb-4e57-9145-bdf30c96993a
> at 
> org.apache.flink.runtime.fs.hdfs.HadoopFsFactory.create(HadoopFsFactory.java:187)
> at 
> org.apache.flink.core.fs.FileSystem.getUnguardedFileSystem(FileSystem.java:401)
> at org.apache.flink.core.fs.FileSystem.get(FileSystem.java:320)
> at 
> org.apache.flink.runtime.state.filesystem.FileStateHandle.getFileSystem(FileStateHandle.java:109)
> at 
> org.apache.flink.runtime.state.filesystem.FileStateHandle.discardState(FileStateHandle.java:81)
> at 
> org.apache.flink.runtime.state.OperatorStateHandle.discardState(OperatorStateHandle.java:65)
> at 
> org.apache.flink.util.LambdaUtil.applyToAllWhileSuppressingExceptions(LambdaUtil.java:51)
> at 
> org.apache.flink.runtime.state.StateUtil.bestEffortDiscardAllStateObjects(StateUtil.java:53)
> at 
> org.apache.flink.runtime.checkpoint.OperatorSubtaskState.discardState(OperatorSubtaskState.java:207)
> at 
> org.apache.flink.runtime.checkpoint.OperatorState.discardState(OperatorState.java:108)
> at 
> org.apache.flink.util.LambdaUtil.applyToAllWhileSuppressingExceptions(LambdaUtil.java:51)
> at 
> org.apache.flink.runtime.state.StateUtil.bestEffortDiscardAllStateObjects(StateUtil.java:53)
> at 
> org.apache.flink.runtime.checkpoint.PendingCheckpoint$1.run(PendingCheckpoint.java:530)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.lang.IllegalArgumentException: java.net.UnknownHostException: 
> nameservice0
> at 
> org.apache.hadoop.security.SecurityUtil.buildTokenService(SecurityUtil.java:378)
> at 
> org.apache.hadoop.hdfs.NameNodeProxies.createNonHAProxy(NameNodeProxies.java:310)
> at 
> org.apache.hadoop.hdfs.NameNodeProxies.createProxy(NameNodeProxies.java:176)
> at org.apache.hadoop.hdfs.DFSClient.(DFSClient.java:678)
> at org.apache.hadoop.hdfs.DFSClient.(DFSClient.java:619)
> at 
> org.apache.hadoop.hdfs.DistributedFileSystem.initialize(DistributedFileSystem.java:149)
> at 
> org.apache.flink.runtime.fs.hdfs.HadoopFsFactory.create(HadoopFsFactory.java:159)
> ... 15 common frames omitted
> Caused by: java.net.UnknownHostException: nameservice0
> ... 22 common frames omitted
>
>
> It does not recognize nameservice0 because the *core-site.xml *on the
> actual machine (read in by Flink via $HADOOP_CONF_DIR) does not use
> nameservice0 but something else for the *fs.defaultFs*
>
> Digging a little bit, I found that the *hadoopConfig* (code
> )
>  does
> not have the properties we set via *yarnship/core-site.xml*. Especially,
> I suspect it is due to the cached *HadoopFsFactory* is initialized with
> an dummy Configuration (code
> ),
> which prevents future 

Re: HDFS HA issue in Flink 1.4 caused by failing to use fs.hdfs.hadoopconf in Flink conf

[Aljoscha Krettek]

Another thing: when you retry this again with Flink 1.3.2 it works? I'm trying 
to rule out another problem in the setup.

> On 4. Oct 2018, at 15:17, Aljoscha Krettek  wrote:
> 
> Hi Yan,
> 
> This seems to be a bug in the FileSystems and how they're initialized. I'm 
> looking into this myself but I'm also looping in Stephan and Stefan how have 
> worked on this the most in the past. Maybe they have some valuable input.
> 
> Best,
> Aljoscha
> 
> 
>> On 4. Oct 2018, at 01:18, Yan Yan > > wrote:
>> 
>> Hi,
>> 
>> We recently bumped to Flink 1.4 from 1.3.2, and found out an issue on HDFS 
>> configuration.
>> 
>> We are using FlinkYarnSessionCli to start the cluster and submit job.
>> 
>> In 1.3.2, we set below Flink properties when using checkpoints:
>> state.backend.fs.checkpointdir = hdfs://nameservice0/ 
>> .../..
>> state.checkpoints.dir = hdfs://nameservice0/ ../..
>> 
>> The mapping between logical nameservice (nameservice0) and actual namenodes 
>> hostports are passed to Flink via yarnship/core-site.xml (by providing the 
>> -yt option), and set fs.hdfs.hadoopconf=yarnship/
>> 
>> However, we encountered below error after bumping to 1.4, which caused the 
>> checkpointing to fail.
>> 
>> 2018-09-20 01:01:00.041 [yarn-jobmanager-io-thread-18] WARN  
>> org.apache.flink.runtime.checkpoint.OperatorSubtaskState  - Error while 
>> discarding operator states.
>> java.io.IOException: Cannot instantiate file system for URI: 
>> hdfs://nameservice0/app/athena_checkpoint/rt_data/gairos-athena-flink-demand-processor-opticclient-flink-job/flink/checkpoints/ckpt_1537402213581/data/ebb30a2d3b26e4d63682538a9bcdc752/chk-3204/da1d44d3-d3eb-4e57-9145-bdf30c96993a
>>  
>> 
>> at 
>> org.apache.flink.runtime.fs.hdfs.HadoopFsFactory.create(HadoopFsFactory.java:187)
>> at 
>> org.apache.flink.core.fs.FileSystem.getUnguardedFileSystem(FileSystem.java:401)
>> at org.apache.flink.core.fs.FileSystem.get(FileSystem.java:320)
>> at 
>> org.apache.flink.runtime.state.filesystem.FileStateHandle.getFileSystem(FileStateHandle.java:109)
>> at 
>> org.apache.flink.runtime.state.filesystem.FileStateHandle.discardState(FileStateHandle.java:81)
>> at 
>> org.apache.flink.runtime.state.OperatorStateHandle.discardState(OperatorStateHandle.java:65)
>> at 
>> org.apache.flink.util.LambdaUtil.applyToAllWhileSuppressingExceptions(LambdaUtil.java:51)
>> at 
>> org.apache.flink.runtime.state.StateUtil.bestEffortDiscardAllStateObjects(StateUtil.java:53)
>> at 
>> org.apache.flink.runtime.checkpoint.OperatorSubtaskState.discardState(OperatorSubtaskState.java:207)
>> at 
>> org.apache.flink.runtime.checkpoint.OperatorState.discardState(OperatorState.java:108)
>> at 
>> org.apache.flink.util.LambdaUtil.applyToAllWhileSuppressingExceptions(LambdaUtil.java:51)
>> at 
>> org.apache.flink.runtime.state.StateUtil.bestEffortDiscardAllStateObjects(StateUtil.java:53)
>> at 
>> org.apache.flink.runtime.checkpoint.PendingCheckpoint$1.run(PendingCheckpoint.java:530)
>> at 
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>> at 
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>> at java.lang.Thread.run(Thread.java:748)
>> Caused by: java.lang.IllegalArgumentException: 
>> java.net.UnknownHostException: nameservice0
>> at 
>> org.apache.hadoop.security.SecurityUtil.buildTokenService(SecurityUtil.java:378)
>> at 
>> org.apache.hadoop.hdfs.NameNodeProxies.createNonHAProxy(NameNodeProxies.java:310)
>> at 
>> org.apache.hadoop.hdfs.NameNodeProxies.createProxy(NameNodeProxies.java:176)
>> at org.apache.hadoop.hdfs.DFSClient.(DFSClient.java:678)
>> at org.apache.hadoop.hdfs.DFSClient.(DFSClient.java:619)
>> at 
>> org.apache.hadoop.hdfs.DistributedFileSystem.initialize(DistributedFileSystem.java:149)
>> at 
>> org.apache.flink.runtime.fs.hdfs.HadoopFsFactory.create(HadoopFsFactory.java:159)
>> ... 15 common frames omitted
>> Caused by: java.net.UnknownHostException: nameservice0
>> ... 22 common frames omitted
>> 
>> It does not recognize nameservice0 because the core-site.xml on the actual 
>> machine (read in by Flink via $HADOOP_CONF_DIR) does not use nameservice0 
>> but something else for the fs.defaultFs
>> 
>> Digging a little bit, I found that the hadoopConfig (code 
>> )
>>  does not have the properties we set via yarnship/core-site.xml. Especially, 
>> I suspect it is due to the cached HadoopFsFactory is initialized with an 
>> dummy Configuration (code 
>> ),
>>  which prevents future flinkConfig getting passed in (code 
>>