We have a 4.1 installation with PHP 5.3. The current PHP install uses MySQL, not MySQLi. I need to enable MySQLi to support a new application. Our hosting company says this will entail recompiling PHP and Apache to enable this.

Will this completely break our CiviCRM install?

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In my case it did not break CiviCRM (4.6.9 at the time). In fact, CiviCRM recently made a blog post suggesting the same upgrade in preparation for future versions.

Edit: a link to said blog post: https://civicrm.org/blog/totten/psa-please-verify-php-extension-mysqli

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