Getting elasticsearch "can not run as root" error after upgrading from SonarQube 6.5 to 6.6. Nothing else changed

Question

Getting elasticsearch "can not run as root" error after upgrading from SonarQube 6.5 to 6.6. Nothing else changed.

CentOS release 6.8 (Final) Java(TM) SE Runtime Environment (build 1.8.0_101-b13)

java.lang.RuntimeException: can not run elasticsearch as root
        at org.elasticsearch.bootstrap.Bootstrap.initializeNatives(Bootstrap.java:106) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:195) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:342) [elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:132) [elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Elasticsearch.execute(Elasticsearch.java:123) [elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:67) [elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:134) [elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.cli.Command.main(Command.java:90) [elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:91) [elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:84) [elasticsearch-5.6.2.jar:5.6.2]
2017.10.20 11:59:14 WARN  es[][o.e.b.ElasticsearchUncaughtExceptionHandler] uncaught exception in thread [main]
org.elasticsearch.bootstrap.StartupException: java.lang.RuntimeException: can not run elasticsearch as root
        at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:136) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Elasticsearch.execute(Elasticsearch.java:123) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:67) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:134) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.cli.Command.main(Command.java:90) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:91) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:84) ~[elasticsearch-5.6.2.jar:5.6.2]
Caused by: java.lang.RuntimeException: can not run elasticsearch as root
        at org.elasticsearch.bootstrap.Bootstrap.initializeNatives(Bootstrap.java:106) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:195) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:342) ~[elasticsearch-5.6.2.jar:5.6.2]
        at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:132) ~[elasticsearch-5.6.2.jar:5.6.2]
        ... 6 more

Answer 1

I also experienced this problem, running SonarQube, as root, on Centos 7, not inside docker. As mentioned in previous comments, the problem comes from SonarQube upgrading ElasticSearch, and the new version no longer allows itself to be run as root.

In my environment the fix was easy enough: I had already created a user ("sonar") and group ("sonar") to "own" the sonarqube files. Since my SonarQube process had been running as root, it had left the logs and temp files owned by root.
1. I stopped the service.
2. Reassigned all the ownserships ("chown -R sonar:sonar /opt/sonarqube-6.6")
3. Changed #RUN_AS_USER= in /opt/sonarqube-6.6/bin/linux-x86-64/sonar.sh line 48 to RUN_AS_USER=sonar and both the sonarqube service and its elasticsearch service restarted without further problems. I was left having to go to http://<sonarhost:port>/setup to upgrade the database and from there everything worked fine.