Install environment: Ubuntu 12.04 with Alfresco 4.0.d stand install on AWS ec2, data size about 100G. The system run about more than about a year without issues. Did a system update and reboot few days ado, now we got in trouble, as far as the system init finished, the java still using about 100%CPU(2 core, init stage 120~199% usage), and the system become slow then no respond. The CPU usage on AWS like a flat line, even the tomcat page can't load.
Have you checked the logs that are located in <ALFRESCO_HOME>/tomcat/logs for any errors during startup? It could be that your repository is re-indexing, which can take a long time and is very CPU intensive. Please post any errors that you're seeing in the logs.