I have a machine running Ubuntu 14.04.3 LTS that is deployed via Ansible. I've got PHP 7 installed using Ondřej Surý's PPA for PHP.
$ dpkg -l | grep -i php
ii libapache2-mod-php7.0 7.0.3-2+deb.sury.org~trusty+1 amd64 server-side, HTML-embedded scripting language (Apache 2 module)
ii php-common 1:36+deb.sury.org~trusty+1 all Common files for PHP packages
ii php7.0 7.0.4-6+deb.sury.org~trusty+1 all server-side, HTML-embedded scripting language (metapackage)
ii php7.0-cli 7.0.0-5+deb.sury.org~trusty+1 amd64 command-line interpreter for the PHP scripting language
ii php7.0-common 7.0.4-6+deb.sury.org~trusty+1 amd64 documentation, examples and common module for PHP
ii php7.0-fpm 7.0.4-6+deb.sury.org~trusty+1 amd64 server-side, HTML-embedded scripting language (FPM-CGI binary)
ii php7.0-json 7.0.0-5+deb.sury.org~trusty+1 amd64 JSON module for PHP
ii php7.0-opcache 7.0.0-5+deb.sury.org~trusty+1 amd64 Zend OpCache module for PHP
ii php7.0-pgsql 7.0.4-6+deb.sury.org~trusty+1 amd64 PostgreSQL module for PHP
The warnings
When cron runs /usr/lib/php/sessionclean, I get the following warnings:
PHP Warning: Module 'PDO' already loaded in Unknown on line 0
PHP Warning: Module 'calendar' already loaded in Unknown on line 0
PHP Warning: Module 'ctype' already loaded in Unknown on line 0
PHP Warning: Module 'exif' already loaded in Unknown on line 0
PHP Warning: Module 'fileinfo' already loaded in Unknown on line 0
PHP Warning: Module 'ftp' already loaded in Unknown on line 0
PHP Warning: Module 'gettext' already loaded in Unknown on line 0
PHP Warning: Module 'iconv' already loaded in Unknown on line 0
PHP Warning: Module 'Phar' already loaded in Unknown on line 0
PHP Warning: Module 'posix' already loaded in Unknown on line 0
PHP Warning: Module 'sockets' already loaded in Unknown on line 0
PHP Warning: Module 'sysvmsg' already loaded in Unknown on line 0
PHP Warning: Module 'sysvsem' already loaded in Unknown on line 0
PHP Warning: Module 'sysvshm' already loaded in Unknown on line 0
PHP Warning: Module 'tokenizer' already loaded in Unknown on line 0
PHP Warning: Module 'PDO' already loaded in Unknown on line 0
PHP Warning: Module 'calendar' already loaded in Unknown on line 0
PHP Warning: Module 'ctype' already loaded in Unknown on line 0
PHP Warning: Module 'exif' already loaded in Unknown on line 0
PHP Warning: Module 'fileinfo' already loaded in Unknown on line 0
PHP Warning: Module 'ftp' already loaded in Unknown on line 0
PHP Warning: Module 'gettext' already loaded in Unknown on line 0
PHP Warning: Module 'iconv' already loaded in Unknown on line 0
PHP Warning: Module 'Phar' already loaded in Unknown on line 0
PHP Warning: Module 'posix' already loaded in Unknown on line 0
PHP Warning: Module 'sockets' already loaded in Unknown on line 0
PHP Warning: Module 'sysvmsg' already loaded in Unknown on line 0
PHP Warning: Module 'sysvsem' already loaded in Unknown on line 0
PHP Warning: Module 'sysvshm' already loaded in Unknown on line 0
PHP Warning: Module 'tokenizer' already loaded in Unknown on line 0
PHP Warning: Module 'PDO' already loaded in Unknown on line 0
PHP Warning: Module 'calendar' already loaded in Unknown on line 0
When running php -v I get a subset of those warnings:
PHP Warning: Module 'PDO' already loaded in Unknown on line 0
PHP Warning: Module 'calendar' already loaded in Unknown on line 0
PHP Warning: Module 'ctype' already loaded in Unknown on line 0
PHP Warning: Module 'exif' already loaded in Unknown on line 0
PHP Warning: Module 'fileinfo' already loaded in Unknown on line 0
PHP Warning: Module 'ftp' already loaded in Unknown on line 0
PHP Warning: Module 'gettext' already loaded in Unknown on line 0
PHP Warning: Module 'iconv' already loaded in Unknown on line 0
PHP Warning: Module 'Phar' already loaded in Unknown on line 0
PHP Warning: Module 'posix' already loaded in Unknown on line 0
PHP Warning: Module 'sockets' already loaded in Unknown on line 0
PHP Warning: Module 'sysvmsg' already loaded in Unknown on line 0
PHP Warning: Module 'sysvsem' already loaded in Unknown on line 0
PHP Warning: Module 'sysvshm' already loaded in Unknown on line 0
PHP Warning: Module 'tokenizer' already loaded in Unknown on line 0
And occasionally in the logs for CodeIgniter I get the line:
Severity: Core Warning --> Module 'tokenizer' already loaded Unknown 0
The config files
This error is not a new one so I've had plenty of other questions to look at, but the solution they suggest is to make sure there aren't any duplicate extension=... lines in my php.ini but there aren't any.
Here are all the files in /etc/php. There are a bunch of ini files for individual modules linked to in multiple places that are likely causing the issue.
/etc/php/mods-available/json.ini
/etc/php/mods-available/opcache.ini
/etc/php/7.0/fpm/php-fpm.conf
/etc/php/7.0/fpm/conf.d/* -> /etc/php/7.0/mods-available/*
/etc/php/7.0/fpm/pool.d
/etc/php/7.0/fpm/pool.d/www.conf
/etc/php/7.0/fpm/php.ini
/etc/php/7.0/cli/conf.d/* -> /etc/php/7.0/mods-available/*
/etc/php/7.0/cli/php.ini
/etc/php/7.0/apache2/php.ini.ucf-dist
/etc/php/7.0/apache2/conf.d/* -> /etc/php/7.0/mods-available/*
/etc/php/7.0/apache2/php.ini
/etc/php/7.0/mods-available/fileinfo.ini
/etc/php/7.0/mods-available/pdo_pgsql.ini
/etc/php/7.0/mods-available/sockets.ini
/etc/php/7.0/mods-available/exif.ini
/etc/php/7.0/mods-available/shmop.ini
/etc/php/7.0/mods-available/ctype.ini
/etc/php/7.0/mods-available/sysvshm.ini
/etc/php/7.0/mods-available/gettext.ini
/etc/php/7.0/mods-available/ftp.ini
/etc/php/7.0/mods-available/sysvmsg.ini
/etc/php/7.0/mods-available/calendar.ini
/etc/php/7.0/mods-available/iconv.ini
/etc/php/7.0/mods-available/pdo.ini
/etc/php/7.0/mods-available/phar.ini
/etc/php/7.0/mods-available/posix.ini
/etc/php/7.0/mods-available/tokenizer.ini
/etc/php/7.0/mods-available/pgsql.ini
/etc/php/7.0/mods-available/sysvsem.ini
Which of these files do I need to delete to stop the warnings without stopping PHP working (via web and CLI)? (bonus points if this is easily done via Ansible)
Try renaming the .ini files in /etc/php/7.0/mods-available/ to nameofthemodule.ini.back
Per example: sudo mv tokenizer.ini tokenizer.ini.back
Restart php, then check php -m and check if the warning for that module is gone.
It seems that when installing an extension the php-common is installed too, this install then makes new .ini files for the extensions included. But those extensions are already compiled in the php binary.
Process with caution, the above paragraph is just a guess.