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We have a new linux server CentOS 6.5 with Plesk. Default PHP is 5.3.3, I have installed PHP5.4 & 5.5 on the server.

I have to install PHP by using this guide

PHP installed successfully but some functions do not work, such as mysqli.

Default PHP 5.3.3 configure command is:

--with-mysql=shared,/usr --with-mysqli=shared,/usr/lib64/mysql/mysql_config

but my installed PHP 5.4 configure command is:

--with-mysql=/usr --with-mysqli

I think something is missing.

I want to know how to restore mysqli features?

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You can get PHP 5.3, 5.4 and 5.5 from IUS repos: https://iuscommunity.org/

There are detailed instructions on how to set this up here: Difficulty installing PHP from source to CentOS 6.4

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