Hello folks,
We've just installed Hbase 0.89 on a 24-node cluster running Hadoop 0.20.2 here
at our government lab.
Got a problem. The Hbase interactive shell works fine. I can create a table
with a column family, add a couple rows, get the rows back out. Also, the
Hbase web site on our cluster at
http://h01.emsl.pnl.gov:60010/master.jsp
doesn't appear (to our untrained eyes) to show anything going wrong
However, the Hbase programs that I used on another cluster that ran an earlier
version of Hbase no longer run. I altered such a program to use the new API,
and it compiles fine. However, when I try to run it, I get the error msgs seen
below.
So - I downloaded the sample 0.89 Hbase program from the Hbase web site and tried that, simply altering the
table name used to "peptideTable", column family to "f1", and column to "name".
The interactive shell shows that the table and data are there . But the
slightly altered program from the Hbase web site, while compiling fine, again
shows the same errors as I got using my own Hbase program. I've tried running
the programs in both my own 'rtaylor' account, and in the 'hbase' account - I
get the same errors.
So my colleague Tim and I think we missed something in the install.
I have appended the test program in full below, followed by the error msgs that
it generated. Lastly, I have appended a screen dump of the contents of the web
page at
http://h01.emsl.pnl.gov:60010/master.jsp
on our cluster.
We would very much appreciate some guidance.
Cheers,
Ron Taylor
___________________________________________
Ronald Taylor, Ph.D.
Computational Biology& Bioinformatics Group
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, Mail Stop J4-33
Richland, WA 99352 USA
Office: 509-372-6568
Email: ronald.tay...@pnl.gov
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Contents of MyLittleHBaseClient.java:
import java.io.IOException;
// javac MyLittleHBaseClient.java
// javac -Xlint MyLittleHBaseClient.java
// java MyLittleHBaseClient
import org.apache.hadoop.hbase.HBaseConfiguration;
import org.apache.hadoop.hbase.client.Get;
import org.apache.hadoop.hbase.client.HTable;
import org.apache.hadoop.hbase.client.Put;
import org.apache.hadoop.hbase.client.Result;
import org.apache.hadoop.hbase.client.ResultScanner;
import org.apache.hadoop.hbase.client.Scan;
import org.apache.hadoop.hbase.util.Bytes;
// Class that has nothing but a main.
// Does a Put, Get and a Scan against an hbase table.
public class MyLittleHBaseClient {
public static void main(String[] args) throws IOException {
// You need a configuration object to tell the client where to connect.
// When you create a HBaseConfiguration, it reads in whatever you've
set
// into your hbase-site.xml and in hbase-default.xml, as long as these
can
// be found on the CLASSPATH
HBaseConfiguration config = new HBaseConfiguration();
// This instantiates an HTable object that connects you to
// the "myLittleHBaseTable" table.
HTable table = new HTable(config, "peptideTable");
// To add to a row, use Put. A Put constructor takes the name of the
row
// you want to insert into as a byte array. In HBase, the Bytes class
has
// utility for converting all kinds of java types to byte arrays. In
the
// below, we are converting the String "myLittleRow" into a byte array
to
// use as a row key for our update. Once you have a Put instance, you
can
// adorn it by setting the names of columns you want to update on the
row,
// the timestamp to use in your update, etc.If no timestamp, the server
// applies current time to the edits.
//
Put p = new Put(Bytes.toBytes("2001"));
// To set the value you'd like to update in the row 'myLittleRow',
specify
// the column family, column qualifier, and value of the table cell
you'd
// like to update. The column family must already exist in your table
// schema. The qualifier can be anything. All must be specified as
byte
// arrays as hbase is all about byte arrays. Lets pretend the table
// 'myLittleHBaseTable' was created with a family 'myLittleFamily'.
//
p.add(Bytes.toBytes("f1"), Bytes.toBytes("name"),
Bytes.toBytes("p2001"));
// Once you've adorned your Put instance with all the updates you want
to
// make, to commit it do the following (The HTable#put method takes the
// Put instance you've been building and pushes the changes you made
into
// hbase)
//
table.put(p);
// Now, to retrieve the data we just wrote. The values that come back
are
// Result instances. Generally, a Result is an object that will
package up
// the hbase return into the form you find most palatable.
//
Get g = new Get(Bytes.toBytes("2001"));
Result r = table.get(g);
byte [] value = r.getValue(Bytes.toBytes("f1"),
Bytes.toBytes("name"));
// If we convert the value bytes, we should get back 'Some Value', the
// value we inserted at this location.
//
String valueStr = Bytes.toString(value);
System.out.println("GET: " + valueStr);
// Sometimes, you won't know the row you're looking for. In this case,
you
// use a Scanner. This will give you cursor-like interface to the
contents
// of the table. To set up a Scanner, do like you did above making a
Put
// and a Get, create a Scan. Adorn it with column names, etc.
//
Scan s = new Scan();
s.addColumn(Bytes.toBytes("f1"), Bytes.toBytes("name"));
ResultScanner scanner = table.getScanner(s);
try {
// Scanners return Result instances.
// Now, for the actual iteration. One way is to use a while loop
like so:
for (Result rr = scanner.next(); rr != null; rr = scanner.next()) {
// print out the row we found and the columns we were looking
for
System.out.println("Found row: " + rr);
}
// The other approach is to use a foreach loop. Scanners are
iterable!
// for (Result rr : scanner) {
// System.out.println("Found row: " + rr);
// }
} finally {
// Make sure you close your scanners when you are done!
// Thats why we have it inside a try/finally clause
scanner.close();
}
}
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error msgs seen:
[rtay...@h01 Sid]$ java MyLittleHBaseClient
10/09/07 14:09:51 WARN hbase.HBaseConfiguration: instantiating
HBaseConfiguration() is deprecated. Please use HBaseConfiguration#create() to
construct a plain Configura\
tion
10/09/07 14:09:51 INFO zookeeper.ZooKeeperWrapper: Reconnecting to zookeeper
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:zookeeper.version=3.3.1-942149, built on 05/07/2010 17:14 GMT
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:host.name=h01.emsl.pnl.gov
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:java.version=1.6.0_21
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client environment:java.vendor=Sun
Microsystems Inc.
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:java.home=/usr/java/jdk1.6.0_21/jre
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:java.class.path=/home/hadoop/hadoop/lib/commons-logging-api-1.0.4.jar:/home/hadoop/hadoop/lib/commons-log\
ging-1.0.4.jar:/home/hadoop/hadoop/lib/commons-net-1.4.1.jar:/home/hadoop/hadoop/lib/commons-httpclient-3.0.1.jar:/home/hadoop/hadoop/lib/commons-el-1.0.jar:/home/hadoo\
p/hadoop/lib/commons-codec-1.3.jar:/home/hadoop/hadoop/lib/commons-cli-1.2.jar:/home/hbase/hbase/hbase-0.89.20100726.jar:/home/rtaylor/HadoopWork/log4j-1.2.16.jar:/home\
/rtaylor/HadoopWork/zookeeper-3.3.1.jar:/home/hadoop/hadoop/hadoop-0.20.2-tools.jar:/home/hadoop/hadoop/hadoop-0.20.2-test.jar:/home/hadoop/hadoop/hadoop-0.20.2-example\
s.jar:/home/hadoop/hadoop/hadoop-0.20.2-ant.jar:/home/hadoop/hadoop/hadoop-0.20.2-core.jar:.
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:java.library.path=/usr/java/jdk1.6.0_21/jre/lib/i386/server:/usr/java/jdk1.6.0_21/jre/lib/i386:/usr/java/\
jdk1.6.0_21/jre/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:java.io.tmpdir=/tmp
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:java.compiler=<NA>
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client environment:os.name=Linux
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client environment:os.arch=i386
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:os.version=2.6.18-194.11.1.el5
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client environment:user.name=rtaylor
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:user.home=/home/rtaylor
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Client
environment:user.dir=/home/rtaylor/HadoopWork/Sid
10/09/07 14:09:52 INFO zookeeper.ZooKeeper: Initiating client connection,
connectString=localhost:2181 sessionTimeout=60000
watcher=org.apache.hadoop.hbase.zookeeper.Zo\
okeeperwrap...@1c86be5
10/09/07 14:09:52 INFO zookeeper.ClientCnxn: Opening socket connection to
server localhost/127.0.0.1:2181
10/09/07 14:09:52 WARN 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:574)
at org.apache.zookeeper.ClientCnxn$SendThread.run(ClientCnxn.java:1078)
10/09/07 14:09:53 INFO zookeeper.ClientCnxn: Opening socket connection to
server localhost/127.0.0.1:2181
10/09/07 14:09:53 WARN zookeeper.ClientCnxn: Session 0x0 for server null,
unexpected error, closing socket connection and attempting reconnect
java.net.ConnectException: Connection refused
.... (long section skiipped - just the same msgs as seen above and below)
10/09/07 14:38:31 WARN zookeeper.ClientCnxn: Session 0x0 for server null,
unexpected error, closing socket connection and attempting reconnect
java.net.ConnectException: Connection refused
at sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)
at
sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:574)
at org.apache.zookeeper.ClientCnxn$SendThread.run(ClientCnxn.java:1078)
10/09/07 14:38:32 INFO zookeeper.ClientCnxn: Opening socket connection to
server localhost/127.0.0.1:2181
10/09/07 14:38:32 WARN 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:574)
at org.apache.zookeeper.ClientCnxn$SendThread.run(ClientCnxn.java:1078)
10/09/07 14:38:34 INFO zookeeper.ClientCnxn: Opening socket connection to
server localhost/127.0.0.1:2181
10/09/07 14:38:34 WARN zookeeper.ClientCnxn: Session 0x0 for server null,
unexpected error, closing socket connection and attempting reconnect
java.net.ConnectException: Connection refused
at sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)
at
sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:574)
at org.apache.zookeeper.ClientCnxn$SendThread.run(ClientCnxn.java:1078)
10/09/07 14:38:36 INFO zookeeper.ClientCnxn: Opening socket connection to
server localhost/127.0.0.1:2181
10/09/07 14:38:36 WARN 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:574)
at org.apache.zookeeper.ClientCnxn$SendThread.run(ClientCnxn.java:1078)
10/09/07 14:38:36 INFO zookeeper.ZooKeeper: Session: 0x0 closed
[rtay...@h01 Sid]$
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Screen dump from
http://h01.emsl.pnl.gov:60010/master.jsp
Master Attributes
Attribute Name Value Description
HBase Version 0.89.20100726, r979826 HBase version and svn revision
HBase Compiled Sat Jul 31 02:01:58 PDT 2010, stack When HBase version was
compiled and by whom
Hadoop Version 0.20.3-append-r964955-1240, r960957 Hadoop version and svn
revision
Hadoop Compiled Fri Jul 16 14:34:43 PDT 2010, Stack When Hadoop version was
compiled and by whom
HBase Root Directory hdfs://h01.emsl.pnl.gov:9000/scratch/hbase
Location of HBase home directory
Load average 0.20833333333333334 Average number of regions per
regionserver. Naive computation.
Regions On FS 5 Number of regions on FileSystem. Rough count.
Zookeeper Quorum
h05:2182,h04:2182,h03:2182,h02:2182,h10:2182,h09:2182,h08:2182,h07:2182,h06:2182
Addresses of all registered ZK servers. For more, see zk dump</zk.jsp>.
Catalog Tables
Table Description
-ROOT-<table.jsp?name=-ROOT-> The -ROOT- table holds references to all
.META. regions.
.META.<table.jsp?name=.META.> The .META. table holds references to all User
Table regions
User Tables
Table Description
fulltable<table.jsp?name=fulltable> {NAME => 'fulltable', FAMILIES => [{NAME =>
'fullcolumnfamily', BLOOMFILTER => 'NONE', REPLICATION_SCOPE => '0', COMPRESSION => 'NONE', VERSIONS =>
'3', TTL => '2147483647', BLOCKSIZE => '65536', IN_MEMORY => 'false', BLOCKCACHE => 'true'}]}
peptideTable<table.jsp?name=peptideTable> {NAME => 'peptideTable', FAMILIES => [{NAME =>
'f1', BLOOMFILTER => 'NONE', REPLICATION_SCOPE => '0', COMPRESSION => 'NONE', VERSIONS => '3', TTL
=> '2147483647', BLOCKSIZE => '65536', IN_MEMORY => 'false', BLOCKCACHE => 'true'}]}
pseudoetable<table.jsp?name=pseudoetable> {NAME => 'pseudoetable', FAMILIES => [{NAME =>
'pseudoecolumnfamily', BLOOMFILTER => 'NONE', REPLICATION_SCOPE => '0', COMPRESSION => 'NONE', VERSIONS
=> '3', TTL => '2147483647', BLOCKSIZE => '65536', IN_MEMORY => 'false', BLOCKCACHE => 'true'}]}
3 table(s) in set.
Region Servers
Address Start Code Load
h02.emsl.pnl.gov:60030<http://h02.emsl.pnl.gov:60030/> 1282848897506
requests=0, regions=0, usedHeap=24, maxHeap=996
h03.emsl.pnl.gov:60030<http://h03.emsl.pnl.gov:60030/> 1282848897225
requests=0, regions=0, usedHeap=22, maxHeap=996
h04.emsl.pnl.gov:60030<http://h04.emsl.pnl.gov:60030/> 1282848897511
requests=0, regions=0, usedHeap=33, maxHeap=996
h05.emsl.pnl.gov:60030<http://h05.emsl.pnl.gov:60030/> 1282848897452
requests=0, regions=1, usedHeap=32, maxHeap=996
h06.emsl.pnl.gov:60030<http://h06.emsl.pnl.gov:60030/> 1282848897259
requests=0, regions=0, usedHeap=32, maxHeap=996
h07.emsl.pnl.gov:60030<http://h07.emsl.pnl.gov:60030/> 1282848897274
requests=0, regions=0, usedHeap=23, maxHeap=996
h08.emsl.pnl.gov:60030<http://h08.emsl.pnl.gov:60030/> 1282848897531
requests=0, regions=0, usedHeap=25, maxHeap=996
h09.emsl.pnl.gov:60030<http://h09.emsl.pnl.gov:60030/> 1282848897283
requests=0, regions=0, usedHeap=32, maxHeap=996
h10.emsl.pnl.gov:60030<http://h10.emsl.pnl.gov:60030/> 1282848897520
requests=0, regions=1, usedHeap=25, maxHeap=996
h11.emsl.pnl.gov:60030<http://h11.emsl.pnl.gov:60030/> 1282848897521
requests=0, regions=0, usedHeap=29, maxHeap=996
h12.emsl.pnl.gov:60030<http://h12.emsl.pnl.gov:60030/> 1282848897310
requests=0, regions=1, usedHeap=25, maxHeap=996
h13.emsl.pnl.gov:60030<http://h13.emsl.pnl.gov:60030/> 1282848897367
requests=0, regions=1, usedHeap=25, maxHeap=996
h14.emsl.pnl.gov:60030<http://h14.emsl.pnl.gov:60030/> 1282848897365
requests=0, regions=0, usedHeap=30, maxHeap=996
h15.emsl.pnl.gov:60030<http://h15.emsl.pnl.gov:60030/> 1282848897379
requests=0, regions=0, usedHeap=23, maxHeap=996
h16.emsl.pnl.gov:60030<http://h16.emsl.pnl.gov:60030/> 1282848897434
requests=0, regions=0, usedHeap=32, maxHeap=996
h17.emsl.pnl.gov:60030<http://h17.emsl.pnl.gov:60030/> 1282848897507
requests=0, regions=0, usedHeap=31, maxHeap=996
h18.emsl.pnl.gov:60030<http://h18.emsl.pnl.gov:60030/> 1282848897413
requests=0, regions=0, usedHeap=30, maxHeap=996
h19.emsl.pnl.gov:60030<http://h19.emsl.pnl.gov:60030/> 1282848897412
requests=0, regions=0, usedHeap=29, maxHeap=996
h20.emsl.pnl.gov:60030<http://h20.emsl.pnl.gov:60030/> 1282848897394
requests=0, regions=0, usedHeap=30, maxHeap=996
h22.emsl.pnl.gov:60030<http://h22.emsl.pnl.gov:60030/> 1282848897415
requests=0, regions=0, usedHeap=30, maxHeap=996
h23.emsl.pnl.gov:60030<http://h23.emsl.pnl.gov:60030/> 1282848897397
requests=0, regions=1, usedHeap=28, maxHeap=996
h24.emsl.pnl.gov:60030<http://h24.emsl.pnl.gov:60030/> 1282848897475
requests=0, regions=0, usedHeap=23, maxHeap=996
h25.emsl.pnl.gov:60030<http://h25.emsl.pnl.gov:60030/> 1282848897466
requests=0, regions=0, usedHeap=31, maxHeap=996
h26.emsl.pnl.gov:60030<http://h26.emsl.pnl.gov:60030/> 1282848897469
requests=0, regions=0, usedHeap=30, maxHeap=996
Total:
servers: 24 requests=0, regions=5
Load is requests per second and count of regions loaded
