PHP7 CLI attempts to load xdebug twice - "Cannot load Xdebug - it was already loaded"

Question

After upgrading Ubuntu from 14.04 to 16.04, PHP CLI started complaining about xdebug:

$ php -v
Cannot load Xdebug - it was already loaded
PHP 7.0.13-0ubuntu0.16.04.1 (cli) ( NTS )
Copyright (c) 1997-2016 The PHP Group
Zend Engine v3.0.0, Copyright (c) 1998-2016 Zend Technologies
    with Zend OPcache v7.0.13-0ubuntu0.16.04.1, Copyright (c) 1999-2016, by Zend Technologies
    with Xdebug v2.4.0, Copyright (c) 2002-2016, by Derick Rethans

There is only one .ini file:

$ ls -la /etc/php/7.0/cli/conf.d/ | grep xdebug
lrwxrwxrwx 1 root root   38 Jan 19 11:41 20-xdebug.ini -> /etc/php/7.0/mods-available/xdebug.ini

And it's only referenced once in this output from php -i:

$ php -i | grep -i configuration
Cannot load Xdebug - it was already loaded
Configuration File (php.ini) Path => /etc/php/7.0/cli
Loaded Configuration File => /etc/php/7.0/cli/php.ini
Configuration

And there's only one reference to xdebug in the entire directory (so it's not being included twice):

/etc/php/7.0$ grep -r xdebug *
mods-available/xdebug.ini:zend_extension=xdebug.so
mods-available/xdebug.ini:[xdebug]
mods-available/xdebug.ini:xdebug.remote_enable=1
mods-available/xdebug.ini:xdebug.remote_autostart=1
mods-available/xdebug.ini:xdebug.remote_port=9000
mods-available/xdebug.ini:xdebug.idekey=PHPSTORM

If I do $ phpdismod xdebug I get the following output, suggesting that it still has xdebug loaded:

$ php -v
PHP 7.0.13-0ubuntu0.16.04.1 (cli) ( NTS )
Copyright (c) 1997-2016 The PHP Group
Zend Engine v3.0.0, Copyright (c) 1998-2016 Zend Technologies
    with Zend OPcache v7.0.13-0ubuntu0.16.04.1, Copyright (c) 1999-2016, by Zend Technologies
    with Xdebug v2.4.0, Copyright (c) 2002-2016, by Derick Rethans

Having done that it is no longer present in the apache config as shown by phpinfo().

How do I fix this?

---

Edit: Additional output as requested:

$ php --ini
Cannot load Xdebug - it was already loaded
Configuration File (php.ini) Path: /etc/php/7.0/cli
Loaded Configuration File:         /etc/php/7.0/cli/php.ini
Scan for additional .ini files in: /etc/php/7.0/cli/conf.d
Additional .ini files parsed:      /etc/php/7.0/cli/conf.d/10-mysqlnd.ini,
/etc/php/7.0/cli/conf.d/10-opcache.ini,
/etc/php/7.0/cli/conf.d/10-pdo.ini,
/etc/php/7.0/cli/conf.d/15-xml.ini,
/etc/php/7.0/cli/conf.d/20-bcmath.ini,
/etc/php/7.0/cli/conf.d/20-calendar.ini,
/etc/php/7.0/cli/conf.d/20-ctype.ini,
/etc/php/7.0/cli/conf.d/20-curl.ini,
/etc/php/7.0/cli/conf.d/20-dom.ini,
/etc/php/7.0/cli/conf.d/20-exif.ini,
/etc/php/7.0/cli/conf.d/20-fileinfo.ini,
/etc/php/7.0/cli/conf.d/20-ftp.ini,
/etc/php/7.0/cli/conf.d/20-gd.ini,
/etc/php/7.0/cli/conf.d/20-gettext.ini,
/etc/php/7.0/cli/conf.d/20-iconv.ini,
/etc/php/7.0/cli/conf.d/20-json.ini,
/etc/php/7.0/cli/conf.d/20-mbstring.ini,
/etc/php/7.0/cli/conf.d/20-mcrypt.ini,
/etc/php/7.0/cli/conf.d/20-mysqli.ini,
/etc/php/7.0/cli/conf.d/20-pdo_mysql.ini,
/etc/php/7.0/cli/conf.d/20-pdo_sqlite.ini,
/etc/php/7.0/cli/conf.d/20-phar.ini,
/etc/php/7.0/cli/conf.d/20-posix.ini,
/etc/php/7.0/cli/conf.d/20-readline.ini,
/etc/php/7.0/cli/conf.d/20-shmop.ini,
/etc/php/7.0/cli/conf.d/20-simplexml.ini,
/etc/php/7.0/cli/conf.d/20-sockets.ini,
/etc/php/7.0/cli/conf.d/20-sqlite3.ini,
/etc/php/7.0/cli/conf.d/20-sysvmsg.ini,
/etc/php/7.0/cli/conf.d/20-sysvsem.ini,
/etc/php/7.0/cli/conf.d/20-sysvshm.ini,
/etc/php/7.0/cli/conf.d/20-tokenizer.ini,
/etc/php/7.0/cli/conf.d/20-wddx.ini,
/etc/php/7.0/cli/conf.d/20-xdebug.ini,
/etc/php/7.0/cli/conf.d/20-xmlreader.ini,
/etc/php/7.0/cli/conf.d/20-xmlwriter.ini,
/etc/php/7.0/cli/conf.d/20-xsl.ini

---

$ cat /etc/php/7.0/mods-available/xdebug.ini 
zend_extension=xdebug.so
[xdebug]
xdebug.remote_enable=1
xdebug.remote_autostart=1
xdebug.remote_port=9000
xdebug.idekey=PHPSTORM

---

As this is still an issue I have found some further detail:

Paths:

$ ls -la /usr/bin/php
lrwxrwxrwx 1 root root 21 Apr 18  2017 /usr/bin/php -> /etc/alternatives/php
$ ls -la /etc/alternatives/php
lrwxrwxrwx 1 root root 15 Feb 12 15:43 /etc/alternatives/php -> /usr/bin/php7.1

php:

$ php -v
Cannot load Xdebug - it was already loaded
PHP 7.1.15-1+ubuntu16.04.1+deb.sury.org+2 (cli) (built: Mar  6 2018 11:10:13) ( NTS )
Copyright (c) 1997-2018 The PHP Group
Zend Engine v3.1.0, Copyright (c) 1998-2018 Zend Technologies
    with Zend OPcache v7.1.15-1+ubuntu16.04.1+deb.sury.org+2, Copyright (c) 1999-2018, by Zend Technologies
    with Xdebug v2.6.0, Copyright (c) 2002-2018, by Derick Rethans

php7.1:

$ php7.1 -v
PHP 7.1.15-1+ubuntu16.04.1+deb.sury.org+2 (cli) (built: Mar  6 2018 11:10:13) ( NTS )
Copyright (c) 1997-2018 The PHP Group
Zend Engine v3.1.0, Copyright (c) 1998-2018 Zend Technologies
    with Zend OPcache v7.1.15-1+ubuntu16.04.1+deb.sury.org+2, Copyright (c) 1999-2018, by Zend Technologies
    with Xdebug v2.6.0, Copyright (c) 2002-2018, by Derick Rethans

The interesting thing there is that the php binary is identical to php7.1 but when called as the specific it doesn't show the already loaded message.

---

Edit, 20181006:

I still have this issue. The image below is a diff of the output of the two php --ini calls. As you can see, the sets of ini files loaded are the same.

They are also the same symlinked binaries:

ben@ben-work:~$ which php
/usr/bin/php
ben@ben-work:~$ ls -la /usr/bin/php
lrwxrwxrwx 1 root root 21 May 15 16:07 /usr/bin/php -> /etc/alternatives/php
ben@ben-work:~$ ls -la /etc/alternatives/php
lrwxrwxrwx 1 root root 15 May 30 10:13 /etc/alternatives/php -> /usr/bin/php7.1
ben@ben-work:~$ which php7.1 
/usr/bin/php7.1

Answer 1

I've fixed this by removing zend_extension=xdebug.so as I already enabled it in my docker container with docker-php-ext-enable xdebug. It might be that it's enabled for you as well.

Answer 2

In Arch Linux the package xdebug generates the following configuration:

/etc/php/conf.d/xdebug.ini
----------
zend_extension=xdebug.so
xdebug.remote_enable=on
xdebug.remote_host=127.0.0.1
xdebug.remote_port=9000
xdebug.remote_handler=dbgp
#xdebug.max_nesting_level=300

This loads twice the same zend_extension=xdebug.so located in /etc/php/php.ini

Answer 3

You need serch the zend_extension declaration in your PHP config dir, for example

grep -Hnir zend_extension /etc/php/7.2/

The command will tell you where you the files:line where is defined the extension, in my case:

/etc/php/7.2/mods-available/xdebug.ini:2:zend_extension=/usr/lib/php/20170718/xdebug.so
/etc/php/7.2/cli/php.ini:1938:; zend_extension = /usr/lib/php/20170718/xdebug.so
/etc/php/7.2/apache2/php.ini:368:zend_extension = /usr/lib/php/20170718/xdebug.so

Here, both cli/php.ini and apache2/php.ini are the same config file but mods-available/xdebug.ini is another file with only xdebug info.

You can comment out or move the lines about xdebug in your php.ini to xdebug.ini and create a joined config under [xdebug] section.

Example:

#xdebug.ini
[xdebug]
zend_extension=/usr/lib/php/20170718/xdebug.so
xdebug.collect_params=4
xdebug.collect_vars=on
xdebug.remote_autostart=on

xdebug.var_display_max_children=128
xdebug.var_display_max_data=4086
xdebug.var_display_max_depth=10

Answer 4

Debian and derivate:

I fixed it locating my php.ini, changing the zend_extension=xdebug.so to the old (so I guess the same would happend commenting the line) zend_extension_ts=zdebug.so.

Then with: php -i | grep xdebug there should be only one conf.d with the zend_extension=xdebug.so. If there were more than one delete the rest of entries.

Answer 5

I had the same issue and solved it by removing extra line of code zend_extension="xdebug.so" inside php.ini file in the php folder that php --version showing, usually inside /usr/local/etc/php/ for mac users.

Answer 6

The cause may indeed be duplicate config files. In my case 15-xdebug.ini had been added by dnf install php-pecl-xdebug3-3.0.4-1.el8.remi.8.0.x86_64. Listing the INI files shows this:

ls /etc/php*/*xdebug.ini

/etc/php-cli.d/99-xdebug.ini  /etc/php.d/15-xdebug.ini  /etc/php.d/99-xdebug.ini  /etc/php-zts.d/15-xdebug.ini

Answer 7

For users who face the same problem.

In my scenario, it was problem with php cli so every time I tried to get to php in the console, I was getting notice: Cannot load the ionCube PHP Loader - extension already loaded

I guess it will be similar to other extensions.

What I have finally done is:

cd /opt/cpanel/ea-php56/root/etc
grep -r "cube" .
# now I saw two files loading the .so files:
# ./php.d/01-ioncube.ini:zend_extension="/opt/cpanel/ea-php56/root/usr/lib64/php/modules/ioncube_loader_lin_5.6.so"
# ./php.d/pecl.ini:zend_extension="/opt/cpanel/ea-php56/root/usr/lib64/php/modules/ioncube_loader_lin_5.6.so"
mv php.d/pecl.ini .

That was it.

Answer 8

this is just what i faced tried to solve this , this might help someone to figure it out .

obviously, its declared in two places, but no harm in that . the case for me is that it is declared in the /etc/php/8.1/cli/conf.d/99-xdebug.ini ( this is the default for some reason )

and here /etc/php/8.1/cli/php.ini

by executing php -i | grep php.ini

you ll find that it mentions the second location only ( my assumption thatit ovverides the firt loading location )

? php -i | grep php.ini
Configuration File (php.ini) Path => /etc/php/8.1/cli
Loaded Configuration File => /etc/php/8.1/cli/php.ini

so i commented out the zend_extension line from the second ini file .