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In .htaccess under public_html, add the following: 

suPHP_ConfigPath /home/user/public_html 
<Files php.ini> 
order allow,deny 
deny from all 
</Files>

In php.ini under public_html add the following, or any other settings that you want to use: 

register_globals = On 
allow_url_fopen = On
upload_max_filesize = 80M 
post_max_size = 80M 
memory_limit = 80M 
upload_tmp_dir = 80M 
max_execution_time = 20000

[Zend] 
zend_extension=/usr/local/ioncube/ioncube_loader_lin_4.4.so 
zend_optimizer.optimization_level=15 
zend_extension_manager.optimizer=/usr/local/Zend/lib/Optimizer-3.2.6 
zend_extension_manager.optimizer_ts=/usr/local/Zend/lib/Optimizer_TS-3.2.6 
zend_extension=/usr/local/Zend/lib/ZendExtensionManager.so 
zend_extension_ts=/usr/local/Zend/lib/ZendExtensionManager_TS.so

The zend and ioncube lines are added because a custom php.ini will disable those for your account if they are not contained within it. You can also just copy over /usr/local/lib/php.ini and make any changes that you want.

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