(DEPRECATED) Apache Flink User Mailing List archive.

Re: HBase config settings go missing within Yarn.

Posted by Niels Basjes on
URL: http://deprecated-apache-flink-user-mailing-list-archive.369.s1.nabble.com/HBase-config-settings-go-missing-within-Yarn-tp16304p16377.html

I did some more digging.

I added extra code to print both the environment variables and the classpath that is used by the HBaseConfiguration to load the resource files.

I call this both locally and during startup of the job (i.e. these logs arrive in the jobmanager.log on the cluster)

Summary of that I found locally:

Environment

2017-10-24 08:50:15,612 INFO com.bol.bugreports.Main - HADOOP_CONF_DIR = /etc/hadoop/conf/

2017-10-24 08:50:15,613 INFO com.bol.bugreports.Main - HBASE_CONF_DIR = /etc/hbase/conf/

2017-10-24 08:50:15,613 INFO com.bol.bugreports.Main - FLINK_CONF_DIR = /usr/local/flink-1.3.2/conf

2017-10-24 08:50:15,613 INFO com.bol.bugreports.Main - HIVE_CONF_DIR = /etc/hive/conf/

2017-10-24 08:50:15,613 INFO com.bol.bugreports.Main - YARN_CONF_DIR = /etc/hadoop/conf/

ClassPath

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - --> HBaseConfiguration: URLClassLoader = sun.misc.Launcher$AppClassLoader@1b6d3586

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/local/flink-1.3.2/lib/flink-python_2.11-1.3.2.jar

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/local/flink-1.3.2/lib/flink-shaded-hadoop2-uber-1.3.2.jar

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/local/flink-1.3.2/lib/joda-time-2.9.1.jar

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/local/flink-1.3.2/lib/log4j-1.2.17.jar

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/local/flink-1.3.2/lib/slf4j-log4j12-1.7.7.jar

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/local/flink-1.3.2/lib/flink-dist_2.11-1.3.2.jar

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - ----> ClassPath = file:/home/nbasjes/FlinkHBaseConnect/

2017-10-24 08:50:15,614 INFO com.bol.bugreports.Main - ----> ClassPath = file:/etc/hadoop/conf/

2017-10-24 08:50:15,615 INFO com.bol.bugreports.Main - ----> ClassPath = file:/etc/hbase/conf/

2017-10-24 08:50:15,615 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.141-2.b16.el6_9.x86_64/lib/tools.jar

2017-10-24 08:50:15,615 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hbase/

2017-10-24 08:50:15,615 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hbase/lib/activation-1.1.jar

2017-10-24 08:50:15,615 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hbase/lib/aopalliance-1.0.jar

2017-10-24 08:50:15,615 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hbase/lib/apacheds-i18n-2.0.0-M15.jar

2017-10-24 08:50:15,615 INFO com.bol.bugreports.Main - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hbase/lib/apacheds-kerberos-codec-2.0.0-M

...

On the cluster node in the jobmanager.log:

ENVIRONMENT
2017-10-24 10:50:19,971 INFO  com.bol.bugreports.Main                                       - HADOOP_CONF_DIR = /usr/hdp/current/hadoop-yarn-nodemanager/../hadoop/conf
2017-10-24 10:50:19,971 INFO  com.bol.bugreports.Main                                       - TEZ_CONF_DIR = /etc/tez/conf
2017-10-24 10:50:19,973 INFO  com.bol.bugreports.Main                                       - YARN_CONF_DIR = /usr/hdp/current/hadoop-yarn-nodemanager/../hadoop/conf
2017-10-24 10:50:19,973 INFO  com.bol.bugreports.Main                                       - LOG_DIRS = /var/log/hadoop-yarn/containers/application_1503304315746_0062/container_1503304315746_0062_01_000001
2017-10-24 10:50:19,973 INFO  com.bol.bugreports.Main                                       - HADOOP_YARN_HOME = /usr/hdp/2.3.4.0-3485/hadoop-yarn
2017-10-24 10:50:19,974 INFO  com.bol.bugreports.Main                                       - HADOOP_HOME = /usr/hdp/2.3.4.0-3485/hadoop
2017-10-24 10:50:19,975 INFO  com.bol.bugreports.Main                                       - HDP_VERSION = 2.3.4.0-3485

And the classpath:

2017-10-24 10:50:19,977 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/15/flink-hbase-connect-1.0-SNAPSHOT.jar
2017-10-24 10:50:19,977 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/13/lib/flink-dist_2.11-1.3.2.jar
2017-10-24 10:50:19,977 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/13/lib/flink-python_2.11-1.3.2.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/13/lib/flink-shaded-hadoop2-uber-1.3.2.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/13/lib/joda-time-2.9.1.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/13/lib/log4j-1.2.17.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/13/lib/slf4j-log4j12-1.7.7.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/14/log4j.properties
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/11/logback.xml
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/16/flink-dist_2.11-1.3.2.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/filecache/10/flink-conf.yaml
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/var/lib/hadoop-yarn/cache/yarn/nm-local-dir/usercache/nbasjes/appcache/application_1503304315746_0062/container_1503304315746_0062_01_000001/
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/etc/hadoop/conf/
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hadoop/hadoop-nfs-2.7.1.2.3.4.0-3485.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hadoop/hadoop-common-2.7.1.2.3.4.0-3485-tests.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hadoop/hadoop-common-2.7.1.2.3.4.0-3485.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hadoop/hadoop-annotations-2.7.1.2.3.4.0-3485.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hadoop/hadoop-auth-2.7.1.2.3.4.0-3485.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hadoop/hadoop-azure-2.7.1.2.3.4.0-3485.jar
2017-10-24 10:50:19,978 INFO  com.bol.bugreports.Main                                       - ----> ClassPath = file:/usr/hdp/2.3.4.0-3485/hadoop/hadoop-aws-2.7.1.2.3.4.0-3485.jar

So apparently everything HBase that was specified clientside is missing when the task is running on my cluster.

The thing is that when running for example a Pig script I get everything perfectly fine on this cluster as it is configured right now.

Also the config 'shouldn't' (I think) need anything different because this application only needs the HBase client (Jar, packaged into application) and the HBase zookeeper settings (present on the machine where it is started).

Niels Basjes

On Mon, Oct 23, 2017 at 10:23 AM, Piotr Nowojski <[hidden email]> wrote:

Till do you have some idea what is going on? I do not see any meaningful difference between Niels code and HBaseWriteStreamExample.java. There is also a very similar issue on mailing list as well: “Flink can't read hdfs namenode logical url”

Piotrek
On 22 Oct 2017, at 12:56, Niels Basjes <[hidden email]> wrote:
HI,

Yes, on all nodes the the same /etc/hbase/conf/hbase-site.xml that contains the correct settings for hbase to find zookeeper.
That is why adding that files as an additional resource to the configuration works.
I have created a very simple project that reproduces the problem on my setup:
https://github.com/nielsbasjes/FlinkHBaseConnectProblem

Niels Basjes
On Fri, Oct 20, 2017 at 6:54 PM, Piotr Nowojski <[hidden email]> wrote:
Is this /etc/hbase/conf/hbase-site.xml file is present on all of the machines? If yes, could you share your code?
On 20 Oct 2017, at 16:29, Niels Basjes <[hidden email]> wrote:
I look at the logfiles from the Hadoop Yarn webinterface. I.e. actually looking in the jobmanager.log of the container running the Flink task.
That is where I was able to find these messages .

I do the
hbaseConfig.addResource(new Path("file:/etc/hbase/conf/hbase-site.xml"));
in all places directly after the HBaseConfiguration.create();
That way I simply force the task to look on the actual Hadoop node for the same file it already loaded locally.

The reason I'm suspecting Flink is because the clientside part of the Flink application does have the right setting and the task/job actually running in the cluster does not have the same settings.
So it seems in the transition into the cluster the application does not copy everything it has available locally for some reason.

There is a very high probability I did something wrong, I'm just not seeing it at this moment.

Niels
On Fri, Oct 20, 2017 at 2:53 PM, Piotr Nowojski <[hidden email]> wrote:
Hi,

What do you mean by saying:

When I open the logfiles on the Hadoop cluster I see this:

The error doesn’t come from Flink? Where do you execute

hbaseConfig.addResource(new Path("file:/etc/hbase/conf/hbase-site.xml"));

?

To me it seems like it is a problem with misconfigured HBase and not something related to Flink.

Piotrek
On 20 Oct 2017, at 13:44, Niels Basjes <[hidden email]> wrote:
To facilitate you guys helping me I put this test project on github:
https://github.com/nielsbasjes/FlinkHBaseConnectProblem

Niels Basjes
On Fri, Oct 20, 2017 at 1:32 PM, Niels Basjes <[hidden email]> wrote:
Hi,

Ik have a Flink 1.3.2 application that I want to run on a Hadoop yarn cluster where I need to connect to HBase.

What I have:

In my environment:
HADOOP_CONF_DIR=/etc/hadoop/conf/
HBASE_CONF_DIR=/etc/hbase/conf/
HIVE_CONF_DIR=/etc/hive/conf/
YARN_CONF_DIR=/etc/hadoop/conf/

In /etc/hbase/conf/hbase-site.xml I have correctly defined the zookeeper hosts for HBase.

My test code is this:
public class Main {
private static final Logger LOG = LoggerFactory.getLogger(Main.class);

public static void main(String[] args) throws Exception {
printZookeeperConfig();
final StreamExecutionEnvironment env = StreamExecutionEnvironment.getExecutionEnvironment().setParallelism(1);
env.createInput(new HBaseSource()).print();
env.execute("HBase config problem");
}

public static void printZookeeperConfig() {
String zookeeper = HBaseConfiguration.create().get("hbase.zookeeper.quorum");
LOG.info("----> Loading HBaseConfiguration: Zookeeper = {}", zookeeper);
}

public static class HBaseSource extends AbstractTableInputFormat<String> {
@Override
public void configure(org.apache.flink.configuration.Configuration parameters) {
table = createTable();
if (table != null) {
scan = getScanner();
}
}

private HTable createTable() {
LOG.info("Initializing HBaseConfiguration");
// Uses files found in the classpath
org.apache.hadoop.conf.Configuration hConf = HBaseConfiguration.create();
printZookeeperConfig();

try {
return new HTable(hConf, getTableName());
} catch (Exception e) {
LOG.error("Error instantiating a new HTable instance", e);
}
return null;
}

@Override
public String getTableName() {
return "bugs:flink";
}

@Override
protected String mapResultToOutType(Result result) {
return new String(result.getFamilyMap("v".getBytes(UTF_8)).get("column".getBytes(UTF_8)));
}

@Override
protected Scan getScanner() {
return new Scan();
}
}

}

I run this application with this command on my Yarn cluster (note: first starting a yarn-cluster and then submitting the job yields the same result).

flink \
run \
-m yarn-cluster \
--yarncontainer 1 \
--yarnname "Flink on Yarn HBase problem" \
--yarnslots 1 \
--yarnjobManagerMemory 4000 \
--yarntaskManagerMemory 4000 \
--yarnstreaming \
target/flink-hbase-connect-1.0-SNAPSHOT.jar

Now in the client side logfile /usr/local/flink-1.3.2/log/flink--client-80d2d21b10e0.log I see
1) Classpath actually contains /etc/hbase/conf/ both near the start and at the end.
2) The zookeeper settings of my experimental environent have been picked up by the software
2017-10-20 11:17:23,973 INFO com.bol.bugreports.Main - ----> Loading HBaseConfiguration: Zookeeper = node1.kluster.local.nl.bol.com:2181,node2.kluster.local.nl.bol.com:2181,node3.kluster.local.nl.bol.com:2181
When I open the logfiles on the Hadoop cluster I see this:
2017-10-20 13:17:33,250 INFO com.bol.bugreports.Main - ----> Loading HBaseConfiguration: Zookeeper = localhost
and as a consequence
2017-10-20 13:17:33,368 INFO org.apache.zookeeper.ClientCnxn - Opening socket connection to server localhost.localdomain/127.0.0.1:2181
2017-10-20 13:17:33,369 WARN org.apache.zookeeper.ClientCnxn - Session 0x0 for server null, unexpected error, closing socket connection and attempting reconnect
java.net.ConnectException: Connection refused
at sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)
at sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:717)
at org.apache.zookeeper.ClientCnxnSocketNIO.doTransport(ClientCnxnSocketNIO.java:361)
at org.apache.zookeeper.ClientCnxn$SendThread.run(ClientCnxn.java:1081)
2017-10-20 13:17:33,475 WARN org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper - Possibly transient ZooKeeper, quorum=localhost:2181, exception=org.apache.zookeeper.KeeperException$ConnectionLossException: KeeperErrorCode = ConnectionLoss for /hbase/hbaseid
The value 'localhost:2181' has been defined within the HBase jar in the hbase-default.xml as the default value for the zookeeper nodes.

As a workaround I currently put this extra line in my code which I know is nasty but "works on my cluster"
hbaseConfig.addResource(new Path("file:/etc/hbase/conf/hbase-site.xml"));

What am I doing wrong?

What is the right way to fix this?
--
Best regards / Met vriendelijke groeten,

Niels Basjes
--
Best regards / Met vriendelijke groeten,

Niels Basjes
--
Best regards / Met vriendelijke groeten,

Niels Basjes
--
Best regards / Met vriendelijke groeten,

Niels Basjes

Best regards / Met vriendelijke groeten,

Niels Basjes