Sometimes using SSH to re-index Magento data is the best way to avoid the connection timed out problems in stores which have a big database. To avoid this you can run the re-index PHP code under SSH instead of web browser! to do it simply enter your Magento root folder in your SSH client and run following command:
# php shell/indexer.php reindexall
Make sure that you are in your Magento root folder!
You can use “php shell/indexer.php reindexall” as a cronjob command as well and run the re-index script based on a cycle you like.
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