Hi Ufuk,
One more update: I tried copying all the hadoop native `.so` files (mainly
`libhadoop.so`) into `/lib` and am I still experiencing the issue I
reported. I also tried naively adding the `.so` files to the jar with the
flink application and am still experiencing the issue I reported (however,
I'm going to investigate this further as I might not have done it
correctly).
Best,
Aaron Levin
On Wed, Jan 23, 2019 at 3:18 PM Aaron Levin <aaronle...@stripe.com> wrote:
> Hi Ufuk,
>
> Two updates:
>
> 1. As suggested in the ticket, I naively copied the every `.so` in
> `hadoop-3.0.0/lib/native/` into `/lib/` and this did not seem to help. My
> knowledge of how shared libs get picked up is hazy, so I'm not sure if
> blindly copying them like that should work. I did check what
> `System.getProperty("java.library.path")` returns at the call-site and
> it's:
> java.library.path=/usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
> 2. The exception I see comes from
> `hadoop.util.NativeCodeLoader.buildSupportsSnappy` (stack-trace below).
> This uses `System.loadLibrary("hadoop")`.
>
> [2019-01-23 19:52:33.081216] java.lang.UnsatisfiedLinkError:
> org.apache.hadoop.util.NativeCodeLoader.buildSupportsSnappy()Z
> [2019-01-23 19:52:33.081376] at
> org.apache.hadoop.util.NativeCodeLoader.buildSupportsSnappy(Native Method)
> [2019-01-23 19:52:33.081406] at
> org.apache.hadoop.io.compress.SnappyCodec.checkNativeCodeLoaded(SnappyCodec.java:63)
> [2019-01-23 19:52:33.081429] at
> org.apache.hadoop.io.compress.SnappyCodec.getDecompressorType(SnappyCodec.java:195)
> [2019-01-23 19:52:33.081457] at
> org.apache.hadoop.io.compress.CodecPool.getDecompressor(CodecPool.java:181)
> [2019-01-23 19:52:33.081494] at
> org.apache.hadoop.io.SequenceFile$Reader.init(SequenceFile.java:2037)
> [2019-01-23 19:52:33.081517] at
> org.apache.hadoop.io.SequenceFile$Reader.initialize(SequenceFile.java:1923)
> [2019-01-23 19:52:33.081549] at
> org.apache.hadoop.io.SequenceFile$Reader.<init>(SequenceFile.java:1872)
> ... (redacted) ...
> [2019-01-23 19:52:33.081728] at
> scala.collection.immutable.List.foreach(List.scala:392)
> ... (redacted) ...
> [2019-01-23 19:52:33.081832] at
> org.apache.flink.streaming.api.operators.StreamSource.run(StreamSource.java:94)
> [2019-01-23 19:52:33.081854] at
> org.apache.flink.streaming.api.operators.StreamSource.run(StreamSource.java:58)
> [2019-01-23 19:52:33.081882] at
> org.apache.flink.streaming.runtime.tasks.SourceStreamTask.run(SourceStreamTask.java:99)
> [2019-01-23 19:52:33.081904] at
> org.apache.flink.streaming.runtime.tasks.StreamTask.invoke(StreamTask.java:300)
> [2019-01-23 19:52:33.081946] at
> org.apache.flink.runtime.taskmanager.Task.run(Task.java:704)
> [2019-01-23 19:52:33.081967] at java.lang.Thread.run(Thread.java:748)
>
> On Tue, Jan 22, 2019 at 2:31 PM Aaron Levin <aaronle...@stripe.com> wrote:
>
>> Hey Ufuk,
>>
>> So, I looked into this a little bit:
>>
>> 1. clarification: my issues are with the hadoop-related snappy libraries
>> and not libsnappy itself (this is my bad for not being clearer, sorry!). I
>> already have `libsnappy` on my classpath, but I am looking into including
>> the hadoop snappy libraries.
>> 2. exception: I don't see the class loading error. I'm going to try to
>> put some more instrumentation and see if I can get a clearer stacktrace
>> (right now I get an NPE on closing a sequence file in a finalizer - when I
>> last logged the exception it was something deep in hadoop's snappy libs -
>> I'll get clarification soon).
>> 3. I'm looking into including hadoop's snappy libs in my jar and we'll
>> see if that resolves the problem.
>>
>> Thanks again for your help!
>>
>> Best,
>>
>> Aaron Levin
>>
>> On Tue, Jan 22, 2019 at 10:47 AM Aaron Levin <aaronle...@stripe.com>
>> wrote:
>>
>>> Hey,
>>>
>>> Thanks so much for the help! This is awesome. I'll start looking into
>>> all of this right away and report back.
>>>
>>> Best,
>>>
>>> Aaron Levin
>>>
>>> On Mon, Jan 21, 2019 at 5:16 PM Ufuk Celebi <u...@apache.org> wrote:
>>>
>>>> Hey Aaron,
>>>>
>>>> sorry for the late reply.
>>>>
>>>> (1) I think I was able to reproduce this issue using snappy-java. I've
>>>> filed a ticket here:
>>>> https://issues.apache.org/jira/browse/FLINK-11402. Can you check the
>>>> ticket description whether it's in line with what you are
>>>> experiencing? Most importantly, do you see the same Exception being
>>>> reported after cancelling and re-starting the job?
>>>>
>>>> (2) I don't think it's caused by the environment options not being
>>>> picked up. You can check the head of the log files of the JobManager
>>>> or TaskManager to verify that your provided option is picked up as
>>>> expected. You should see something similar to this:
>>>>
>>>> 2019-01-21 22:53:49,863 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>>
>>>> --------------------------------------------------------------------------------
>>>> 2019-01-21 22:53:49,864 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> Starting StandaloneSessionClusterEntrypoint (Version: 1.7.0,
>>>> Rev:49da9f9, Date:28.11.2018 @ 17:59:06 UTC)
>>>> ...
>>>> 2019-01-21 22:53:49,865 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint - JVM
>>>> Options:
>>>> 2019-01-21 22:53:49,865 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> -Xms1024m
>>>> 2019-01-21 22:53:49,865 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> -Xmx1024m
>>>> You are looking for this line ----> 2019-01-21 22:53:49,865 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> -Djava.library.path=/.../org/xerial/snappy/native/Mac/x86_64/ <----
>>>> 2019-01-21 22:53:49,865 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> -Dlog.file=/.../flink-1.7.0/log/flink-standalonesession-0.local.log
>>>> ...
>>>> 2019-01-21 22:53:49,866 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> Program Arguments:
>>>> 2019-01-21 22:53:49,866 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> --configDir
>>>> 2019-01-21 22:53:49,866 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> /.../flink-1.7.0/conf
>>>> 2019-01-21 22:53:49,866 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> --executionMode
>>>> 2019-01-21 22:53:49,866 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>> cluster
>>>> ...
>>>> 2019-01-21 22:53:49,866 INFO
>>>> org.apache.flink.runtime.entrypoint.ClusterEntrypoint -
>>>>
>>>> --------------------------------------------------------------------------------
>>>>
>>>> Can you verify that you see the log messages as expected?
>>>>
>>>> (3) As noted FLINK-11402, is it possible to package the snappy library
>>>> as part of your user code instead of loading the library via
>>>> java.library.path? In my example, that seems to work fine.
>>>>
>>>> – Ufuk
>>>>
>>>> On Thu, Jan 17, 2019 at 5:53 PM Aaron Levin <aaronle...@stripe.com>
>>>> wrote:
>>>> >
>>>> > Hello!
>>>> >
>>>> > *tl;dr*: settings in `env.java.opts` seem to stop having impact when
>>>> a job is canceled or fails and then is restarted (with or without
>>>> savepoint/checkpoints). If I restart the task-managers, the `env.java.opts`
>>>> seem to start having impact again and our job will run without failure.
>>>> More below.
>>>> >
>>>> > We use consume Snappy-compressed sequence files in our flink job.
>>>> This requires access to the hadoop native libraries. In our
>>>> `flink-conf.yaml` for both the task manager and the job manager, we put:
>>>> >
>>>> > ```
>>>> > env.java.opts: -Djava.library.path=/usr/local/hadoop/lib/native
>>>> > ```
>>>> >
>>>> > If I launch our job on freshly-restarted task managers, the job
>>>> operates fine. If at some point I cancel the job or if the job restarts for
>>>> some other reason, the job will begin to crashloop because it tries to open
>>>> a Snappy-compressed file but doesn't have access to the codec from the
>>>> native hadoop libraries in `/usr/local/hadoop/lib/native`. If I then
>>>> restart the task manager while the job is crashlooping, the job is start
>>>> running without any codec failures.
>>>> >
>>>> > The only reason I can conjure that would cause the Snappy compression
>>>> to fail is if the `env.java.opts` were not being passed through to the job
>>>> on restart for some reason.
>>>> >
>>>> > Does anyone know what's going on? Am I missing some additional
>>>> configuration? I really appreciate any help!
>>>> >
>>>> > About our setup:
>>>> >
>>>> > - Flink Version: 1.7.0
>>>> > - Deployment: Standalone in HA
>>>> > - Hadoop/S3 setup: we do *not* set `HADOOP_CLASSPATH`. We use Flink’s
>>>> shaded jars to access our files in S3. We do not use the
>>>> `bundled-with-hadoop` distribution of Flink.
>>>> >
>>>> > Best,
>>>> >
>>>> > Aaron Levin
>>>>
>>>
