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I've read numerous posts on this problem and none of them matches my problem exactly. I have a WordPress site (currently 3.5) on a GoDaddy virtual host. In November I opted to upgrade the O/S from CentOS 5 to CentOS 6.3, which involved a full O/S reinstall over which I had no control and about which I had no information. Following the O/S reinstall I rebuilt the site from a backup I had taken just before starting.

After the rebuild, a WordPress plugin we've been using for years, WP-DBManager, suddenly stopped backing up our mysql database. The backup fails because the backup panel claims "MYSQL path does NOT exist." Annoyingly, when you go to the DB Options page and tell it to auto-detect the mysql path, the options page produces /usr/bin/mysql, which is correct. I can log into the site with SSH and there it is. The permissions are:

-rwxr-xr-x 1 root root 338184 Jun 22 05:58 /usr/bin/mysql

This SHOULD work. SOMETHING in my site permissions changed with this rebuild and I don't know what; so far I've only documented WordPress configurations. The research I've done suggests it may be something to do with PHP safe mode. We run PHP 5.3.3, and the configuration list from phpinfo() does not show 

--enable-safe-mode

which means safe mode should be OFF. The safe mode settings in php.ini when this started were:

safe_mode_allowed_env_vars = PHP_
safe_mode_protected_env_vars = LD_LIBRARY_PATH
safe_mode_exec_dir = 
safe_mode_include_dir = 
safe_mode = off
safe_mode_gid = off

I have since changed safe_mode_gid to ON, with no effect. I have a test site built from the production site, where safe_mode_include_dir = ~ so I tried that, with no effect. The test site runs PHP 5.3.14 and the safe mode settings above were identical except for safe_mode_include_dir. I checked the ENV variable and /usr/bin is included in the PATH:

PATH=/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/lrservice/bin

I don't know if this is an environment variable problem, here are the safe mode entries for that:

safe_mode_allowed_env_vars = PHP_
safe_mode_protected_env_vars = LD_LIBRARY_PATH

These settings are not all the same on the working test site, one reads:

safe_mode_allowed_env_vars = PHP_ LANG LANG_

Since the site is fully functional except for this, I know that mysql's permissions are generally correct. Does this ring any bell for anyone?? Why am I getting all this if safe mode is officially turned off? I have a feeling there's something obvious and stupid that I'm missing.

hedera
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1 Answers1

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You have access to the mysql binary from an ssh session in the /usr/bin directory, but php is unable to find it at that same location. I am assuming that your system is using the apache2 webserver.

Is the ChrootDir directive present in the apache configuration file (usually located at /etc/httpd/conf/httpd.conf)?

If that's the case, you can check in the directory pointed by this directive if there is a link to the mysql binary. If not, simply add it by executing the following command (assuming you have the priviledges to do so) in your ssh session:

$ ln /usr/bin/mysql /chroot/path/usr/bin/mysql

with /chroot/path replaced by the ChrootDir directive path.

One of the comments mentions the open_basedir PHP setting, which can be configured either in php.ini, httpd.conf, or .htaccess files.

This setting limits access to certain directory of the filesystem available to PHP. A possible fix is to remove this restriction for the scripts executed by the plugin you are using, if that setting is not protected:

  • locate the scripts installed by the plugin in your wordpress directory,

  • create a .htaccess file lifting the restriction in the directory containing the scripts with the following commands:

    $ echo 'php_value open_basedir none' >> .htaccess

The above will add the text between simple quote at the end of the .htaccess file, creating it if necessary. This solution is probably the safest, as it reduces the security relaxing to only these scripts. You should be wary that you are going to let these scripts potentially have access to much more than they really need to operate.

If the above does not work, it means that the setting is protected, and must be changed in either httpd.conf or php.ini which should be both located within the /etc directory. See this SO question for details.

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didierc
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    Also the php.ini [`open_basedir`](http://php.net/manual/en/ini.core.php#ini.open-basedir) directive may be set – dualed Dec 19 '12 at 02:01
  • To answer a couple of questions, here are the permissions for /usr and /usr/bin: drwxr-xr-x 13 root root 4096 Sep 28 2011 usr – hedera Dec 19 '12 at 22:26
  • To answer @cryptic's question, here are the permissions for /usr and /usr/bin:
    drwxr-xr-x 13 root root 4096 Sep 28 2011 usr drwxr-xr-x 2 root root 20480 Nov 11 15:21 bin I'll check out the stream_resolve_include_path command. The ChrootDir directive is not present in httpd.conf and when I try to cd to /usr/bin/mysql bash tells me it is not a directory. (Oh. That's why it's bolded in ExtraPutty. It's a symlink.) I'm running Apache 2.2.15. The php open_basedir directive is set, it is open_basedir = "/var/www/vhosts/lifering.org/:/tmp/"     – hedera Dec 19 '12 at 22:35
  • @hedera dualed found the reason, the remedy is the same as mine, make a link, or copy the file. – didierc Dec 19 '12 at 23:13
  • I thought that might be it. So I need a symlink to /usr/bin/mysql in the /tmp directory? Copying the file seems risky. – hedera Dec 19 '12 at 23:18
  • Actually I realized a hard link would do so I did that. Let's see if it worked. – hedera Dec 19 '12 at 23:22
  • indeed, just a symlink should be enough. – didierc Dec 19 '12 at 23:22
  • The hard link worked! I realized I also had to go to my Options page and change the path statement to /tmp/mysql. Yowza! This has been driving me nuts for about 3 weeks. THANK YOU ALL! – hedera Dec 19 '12 at 23:27
  • I wanted to report on this. Unfortunately, although I eliminated the error on the WP-DBManager backup page, the backup still doesn't run, and the only error I get is: Database Failed To Backup On 'January 6, 2013 @ 5:22 pm'. Backup File Size Is 0KB. So I still don't have a backup. I'm using an XML backup function in the Plesk management panel, but I think that means I have to use Plesk to restore anything. Sigh. – hedera Jan 16 '13 at 19:13
  • I updated my answer with details regarding the `open_basedir` problem. You should remove the hardlink you created, since it doesn't fix the issue you have, it is unrelated to the new fix I detailed, and it could turn into a security issue. – didierc Jan 17 '13 at 02:32