Log processing was one of the original purposes of MapReduce. Unfortunately, using Apache Hadoop MapReduce to monitor Apache Hadoop can be inefficient. Batch processing nature of Apache Hadoop MapReduce prevents the system to provide real time status of the cluster.
We started this journey at beginning of 2008, and a lot of Apache Hadoop components have been built to improve overall reliability of the system and improve realtimeness of monitoring. We have adopted HBase to facilitate lower latency of random reads and using in memory updates and write ahead logs to improve the reliability for root cause analysis.
Logs are generated incrementally across many machines, but Apache Hadoop MapReduce works best on a small number of large files. Merging the reduced output of multiple runs may require additional mapreduce jobs. This creates some overhead for data management on Apache Hadoop.
Apache Chukwa is a Apache Hadoop subproject devoted to bridging that gap between logs processing and Hadoop ecosystem. Apache Chukwa is a scalable distributed monitoring and analysis system, particularly logs from Apache Hadoop and other distributed systems.
Apache Chukwa Documentation provides the information you need to get started using Apache Chukwa. Architecture and Design document provides high level view of Apache Chukwa design.
If you're trying to set up a Apache Chukwa cluster from scratch, User Guide describes the setup and deploy procedure.
If you want to configure Apache Chukwa agent process, to control what's collected, you should read the Agent Guide. There is also a Pipeline Guide describing configuration parameters for ETL processes for the data pipeline.
And if you want to develop Apache Chukwa to monitor other data source, Programming Guide maybe handy to learn about Apache Chukwa programming API.
If you have more questions, you can ask on the Apache Chukwa mailing lists