Troubleshooting lengthy Java analysis

SonarQube Server / Community Build
7
  1. around 3m lines of code
  2. it consist ~30k+ files
  3. the analysis takes around 62h and failing at the end.
    Between the 10 seconds info report we are receiving multiple "Warn: Too many duplication references on file myFile.java for block at line x. Keep only the first 100 references."

The longer the analysis takes the more warn messages appears. Could this appears due to a wrong configuration?

We are using the following Configuration:
sonar.projectKey=MyProject
sonar.projectName=MyProject
sonar.projectVersion=1.0

sonar.sources=.
sonar.java.binaries=**bin
java.libraries=D:/jdk/lib/*.jar,D:/jdk/jre/lib**.jar,**_if.jar
sonar.showProfiling=true
sonar.sourceEncoding=UTF-8

  1. Processor: Intel Xeon CPU @ 3.60Ghz
    RAM: 64 GB

  2. We didn’t set any performance tuning related paramters for the analysis.

Version
Sonar Plugin api 6.7
Sonar Java Plugin 5.1.0.13090
Sonar Scanner 3.2.0.1227