I am working on my module. I create a store , website and other related information programatically. It is successfully created. But when i reindex data from admin panel my mysql stop working. I don't know what is problem. Let me know how can i solve this problem.
You have to increase your MySQL performances especially if you are working on a development machine.
You can follow websites as it http://astrio.net/blog/magento-performance-optimize-mysql/ to optimize your MySQL config for Magento.
For reindexation prefer with command line : https://www.branded3.com/blog/re-indexing-magento-command-line/