If you have SSH access to your Linux (or Unix) server you can easy re-index Magento database from Linux command shell.
You can use such re-index method to decrease load on your server. The PHP shell commands will be executed directly, without Apache overloading.
Here is an instruction on how to use default Magento indexer via SSH console:
1 - Go to "shell" folder in your Magento installation:
cd shell
2 - Execute the re-index process using this command:
php -f indexer.php reindexall
It is possible to get full list of Magento indexer commands using this command:
php -f indexer.php help
To get a list of all available indexes, execute this command:
php -f indexer.php info
By default there are 8 indexes in Magento:
catalog_product_attribute Product Attributes catalog_product_price Product Prices catalog_url Catalog Url Rewrites catalog_product_flat Product Flat Data catalog_category_flat Category Flat Data catalog_category_product Category Products catalogsearch_fulltext Catalog Search Index cataloginventory_stock Stock status