When you run Oak Run tool to clean up the checkpoint, it throws OutOfMemory.
The logs show the following exception:
Apache Jackrabbit Oak 1.0.6
Checkpoints /wcm/cq-author/crx-quickstart/repository/segmentstore
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at org.apache.jackrabbit.oak.plugins.segment.file.TarReader.loadGraph(TarReader.java:453)
at org.apache.jackrabbit.oak.plugins.segment.file.TarReader.(TarReader.java:481)
at org.apache.jackrabbit.oak.plugins.segment.file.TarReader.openFirstFileWithValidIndex(TarReader.java:230)
at org.apache.jackrabbit.oak.plugins.segment.file.TarReader.open(TarReader.java:107)
at org.apache.jackrabbit.oak.plugins.segment.file.FileStore.(FileStore.java:191)
at org.apache.jackrabbit.oak.plugins.segment.file.FileStore.(FileStore.java:149)
at org.apache.jackrabbit.oak.plugins.segment.file.FileStore.(FileStore.java:154)
at org.apache.jackrabbit.oak.run.Main.checkpoints(Main.java:223)
at org.apache.jackrabbit.oak.run.Main.main(Main.java:121)
Make sure that you have 64-bit JVM installed. Then rerun the Oak Run tool with the following parameter.
java -Dtar.memoryMapped=true -Xmx8g -jar oak-run-1.0.7-SNAPSHOT.jar checkpoint
The parameter -Dtar.memoryMapped=true tells the tool to load the segments memory mapped, which means that it's not using the JVM memory but the available native memory.