Can't get apache nutch to crawl - permissions

Question

I am trying to run a basic crawl as per the NutchTutorial:

bin/nutch crawl urls -dir crawl -depth 3 -topN 5

So I have Nutch all installed and set up with Solr. I set my $JAVA_HOME in my .bashrc to /usr/lib/jvm/java-1.6.0-openjdk-amd64.

I don't see any problems when I run bin/nutch from the nutch home directory, but when I try to run the crawl as above I get the following error:

log4j:ERROR setFile(null,true) call failed.
java.io.FileNotFoundException: /usr/share/nutch/logs/hadoop.log (Permission denied)
        at java.io.FileOutputStream.openAppend(Native Method)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:207)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:131)
        at org.apache.log4j.FileAppender.setFile(FileAppender.java:290)
        at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:164)
        at org.apache.log4j.DailyRollingFileAppender.activateOptions(DailyRollingFileAppender.java:216)
        at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:257)
        at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:133)
        at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:97)
        at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:689)
        at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:647)
        at org.apache.log4j.PropertyConfigurator.configureRootCategory(PropertyConfigurator.java:544)
        at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:440)
        at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:476)
        at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:471)
        at org.apache.log4j.LogManager.<clinit>(LogManager.java:125)
        at org.slf4j.impl.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:73)
        at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:270)
        at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:281)
        at org.apache.nutch.crawl.Crawl.<clinit>(Crawl.java:43)
log4j:ERROR Either File or DatePattern options are not set for appender [DRFA].
solrUrl is not set, indexing will be skipped...
crawl started in: crawl
rootUrlDir = urls
threads = 10
depth = 3
solrUrl=null
topN = 5
Injector: starting at 2013-06-28 16:24:53
Injector: crawlDb: crawl/crawldb
Injector: urlDir: urls
Injector: Converting injected urls to crawl db entries.
Injector: total number of urls rejected by filters: 0
Injector: total number of urls injected after normalization and filtering: 1
Injector: Merging injected urls into crawl db.
Exception in thread "main" java.io.IOException: Job failed!
        at org.apache.hadoop.mapred.JobClient.runJob(JobClient.java:1357)
        at org.apache.nutch.crawl.Injector.inject(Injector.java:296)
        at org.apache.nutch.crawl.Crawl.run(Crawl.java:132)
        at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:65)
        at org.apache.nutch.crawl.Crawl.main(Crawl.java:55)

I suspect it might have something to do with file permissions as I have to run sudo on almost everything on this server, but if I run the same crawl command with sudo I get:

Error: JAVA_HOME is not set.

So I feel like I've got a catch-22 situation going on here. Should I be able to run this command with sudo, or is there something else I need to do such that I don't have to run it with sudo and it will work, or is there something else entirely going on here?

Answer 1

The key to solving this issue is to add the JAVA_HOME variable to your sudo environment. For example, type env and sudo env and you will see that JAVA_HOME is not set for sudo. To remedy this, you will need to add the path.

1. Run sudo visudo to edit your /etc/sudoers file. (Do not use a standard text editor. This special vi text editor that will validate syntax before allowing you to save it.)

2. Add this line:

   Defaults env_keep+="JAVA_HOME"
   

   at the end of the Defaults env_keep section.

3. Reboot

Answer 2

It seems that, as a normal user, you don't have permission to write to /usr/share/nutch/logs/hadoop.log, which makes sense as security feature.

To get around this, create a simple bash script:

#!/bin/sh
export JAVA_HOME=/usr/lib/jvm/java-1.6.0-openjdk-amd64
bin/nutch crawl urls -dir crawl -depth 3 -topN 5

Save it as nutch.sh, then run it with sudo:

sudo sh nutch.sh