Re: [joshua-support] NO space left on device Error while running thrax.

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Phu Le

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Mar 8, 2013, 4:32:48 AM3/8/13
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Hi,

Please follow this guide https://github.com/jweese/thrax/wiki/Standalone-hadoop , section 2: Configuration
and change your hadoop config file $HADOOP/conf/mapred-site.xml .

By default, Hadoop writes tmp files to /tmp/hadoop-<user> folder, which eats up the disk space in that partition. You can change to another folder on another partition that has sufficient amount of free disk space.

LTVP 

On Mar 8, 2013, at 5:16 PM, bibek....@gmail.com wrote:


While trying to run Joshua on the server i used up the entire disk space. 
org.apache.hadoop.fs.FSError: java.io.IOException: No space left on device
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:192)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
at java.io.FilterOutputStream.close(FilterOutputStream.java:157)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:61)
at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:86)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1298)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1129)
at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:549)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:623)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:305)
at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:177)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:297)
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:190)
... 11 more
13/03/08 18:33:32 WARN mapred.LocalJobRunner: job_local_0007
org.apache.hadoop.fs.FSError: java.io.IOException: No space left on device
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:192)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.write(FSDataOutputStream.java:49)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at org.apache.hadoop.mapred.IFileOutputStream.write(IFileOutputStream.java:84)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.write(FSDataOutputStream.java:49)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at org.apache.hadoop.mapred.IFile$Writer.append(IFile.java:217)
at org.apache.hadoop.mapred.Merger.writeFile(Merger.java:157)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.mergeParts(MapTask.java:1535)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1154)
at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:549)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:623)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:305)
at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:177)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:297)
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:190)
... 15 more

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Luke Orland

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Mar 8, 2013, 2:37:50 PM3/8/13
to joshua_...@googlegroups.com
bibek, you should add this property to your core-sites.xml, and between the <value></value> tags specify a path to a directory on a device with a lot of storage.

     <property>
         <name>hadoop.tmp.dir</name>
         <value>custom-hadoop-directory</value>
     </property>


On Fri, Mar 8, 2013 at 2:01 PM, <bibek....@gmail.com> wrote:
This is config file
-----------------------------------------------------------------
<?xml version="1.0"?>
<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>

<!-- Put site-specific property overrides in this file. -->

<configuration>

<property>
<name>mapred.job.tracker</name>
<value>kunti:9001</value>
</property>
<property>
<name>mapred.map.tasks</name>
<value>20</value>
</property>
<property>
<name>mapred.reduce.tasks</name>
<value>10</value>
</property>
<property>
<name>mapred.system.dir</name>
<value>/data1/hadoop-0.20.2_filesystem/mapreduce/system</value>
</property>
<property>
<name>mapred.local.dir</name>
<value>/data1/hadoop-0.20.2_filesystem/mapreduce/local</value>
</property>
----------------------------------------------------------------------------------
Which line should i change or insert?

Matt Post

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Apr 1, 2013, 10:40:25 AM4/1/13
to joshua_...@googlegroups.com, bibek....@gmail.com
It seems your job does require more. Was this with the new thrax?


On Mar 30, 2013, at 2:21 PM, bibek....@gmail.com wrote:

I am still getting the error. This disk has about 250 GB .
org.apache.hadoop.fs.FSError: java.io.IOException: No space left on device
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:192)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
at java.io.FilterOutputStream.close(FilterOutputStream.java:157)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:61)
at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:86)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1298)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1129)
at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:549)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:623)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:305)
at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:177)

Does hadoop require more than that?

Matt Post

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Apr 1, 2013, 2:22:36 PM4/1/13
to joshua_...@googlegroups.com, bibek....@gmail.com
You should. If you pull the latest changes on our development branch, you will have it.


On Apr 1, 2013, at 2:21 PM, bibek....@gmail.com wrote:

no i havent tried the latest thrax


On Friday, 8 March 2013 14:46:31 UTC+5:30, bibek....@gmail.com wrote:

While trying to run Joshua on the server i used up the entire disk space. 
org.apache.hadoop.fs.FSError: java.io.IOException: No space left on device
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:192)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
at java.io.FilterOutputStream.close(FilterOutputStream.java:157)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:61)
at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:86)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1298)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1129)
at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:549)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:623)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:305)
at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:177)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:297)
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:190)
... 11 more
13/03/08 18:33:32 WARN mapred.LocalJobRunner: job_local_0007
org.apache.hadoop.fs.FSError: java.io.IOException: No space left on device
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:192)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.write(FSDataOutputStream.java:49)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at org.apache.hadoop.mapred.IFileOutputStream.write(IFileOutputStream.java:84)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.write(FSDataOutputStream.java:49)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at org.apache.hadoop.mapred.IFile$Writer.append(IFile.java:217)
at org.apache.hadoop.mapred.Merger.writeFile(Merger.java:157)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.mergeParts(MapTask.java:1535)
at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1154)
at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:549)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:623)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:305)
at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:177)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:297)
at org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileOutputStream.write(RawLocalFileSystem.java:190)
... 15 more

Luke Orland

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Apr 1, 2013, 2:26:06 PM4/1/13
to joshua_...@googlegroups.com, Bibek Behera
After pulling the latest changes, update submodules with the command:

git submodule update

Luke Orland

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Apr 1, 2013, 2:46:01 PM4/1/13
to joshua_...@googlegroups.com
Bibek,

That command will only clone Thrax. Thrax is a submodule in Joshua, and that is you probably want to get the latest version of Thrax.

If you already have a local clone of Joshua, then you should cd into that directory where you clone it and type

git checkout devel
git pull
git submodule update
ant

If your copy of Joshua came from a tarball and you don't have a clone yet, then go to a directory where you want to create the clone and type

git clone g...@github.com:joshua-decoder/joshua.git
git submodule update --init
ant

Thanks,
--Luke


On Mon, Apr 1, 2013 at 2:34 PM, Bibek Behera <bibek....@gmail.com> wrote:
git clone g...@github.com:joshua-decoder/thrax.git


On Tue, Apr 2, 2013 at 12:04 AM, Bibek Behera <bibek....@gmail.com> wrote:
i shud use this command right
--
Regards,
Bibek behera
IIT Bombay


Ph no.- 8879005749



--
Regards,
Bibek behera
IIT Bombay


Ph no.- 8879005749

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