File "something.php" is writeable by group on cPanel

On a cPanel system, if your php files are group writable, then you'll get HTTP 500 Internal Server Errors, and the following in /usr/local/apache/logs/error_log (not in the error_log in the documentroot):

SoftException in Application.cpp:256: File "/home/netfecom/subdomains/store/index.php" is writeable by group
Premature end of script headers: index.php

This check is silly, as cPanel uses user private groups. All the resources on google will tell you something like do a chmod g-w or change umask to 022. But the whole point of user private groups is to have the files group writable by default. So we need to change suphp behaviour. But unfortunately the config file is not anywhere where you would look for it, and searching for "configure suphp cpanel" leads to nothing. So the key information is that it can be found at /opt/suphp/etc/suphp.conf. These changes will do:

--- /opt/suphp/etc/suphp.conf.orig 2014-01-13 15:21:07.000000000 -0500
+++ /opt/suphp/etc/suphp.conf 2014-01-13 15:22:04.000000000 -0500
@@ -28,9 +28,9 @@
 
 
 ; Security options
-allow_file_group_writeable=false
+allow_file_group_writeable=true
 allow_file_others_writeable=false
-allow_directory_group_writeable=false
+allow_directory_group_writeable=true
 allow_directory_others_writeable=false
 
 

Correctly install xdebug on cPanel

There is a lot of conflicting and incomplete information about this around so let me write how to correctly install xdebug on a cPanel system.

First we need to actually install the xdebug php extension. This will of course not work with yum because cPanel replaces the distro php with it's own source-compiled one. So we'll need to install it through cPanel. Go to WHM -> Software -> Module Installers -> PHP Pecl -> Manage. In the search box type "xdebug", for me it currently shows version 2.2.3. Click install. It looks that it actually configures php.ini correctly and if you verify it with phpinfo(), then it actually works.

But in reality it doesn't work properly. You'll get the following messages in the error_log:

PHP Warning:  Xdebug MUST be loaded as a Zend extension in Unknown on line 0

This is annoying and fills up the logs fast. So go to WHM -> Service Configuration -> PHP Configuration Editor -> Advanced Mode. Look for "extension", you'll find that the value is "xdebug.so", delete it.

The above will take care of the warning in the error_log, but xdebug will stop working. For it to work again look for "zend_extension", you'll see "xdebug.so" as a value there, so everything looks fine. But the trick is, that you need to use the full path here. You can find it on the install screen, for me it is /usr/local/lib/php/extensions/no-debug-non-zts-20100525/xdebug.so. Save the configuration and voila, xdebug works and there is no warning in the error_log.

PS: If you know how to do these from the command line, I'd appreciate it.

Installing sysbench on cPanel

I'm making a note of it because it was non-trivial and no google search led me to the solution.

The problem is that the sysbench package won't install on cPanel infested CentOS:

# yum install sysbench
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
epel/metalink                                                                                                                                                                                            |  24 kB     00:00     
 * base: ftp.nluug.nl
 * epel: ftp.nluug.nl
 * extras: ftp.nluug.nl
 * updates: ftp.nluug.nl
base                                                                                                                                                                                                     | 3.7 kB     00:00     
epel                                                                                                                                                                                                     | 4.2 kB     00:00     
epel/primary_db                                                                                                                                                                                          | 5.8 MB     00:00     
extras                                                                                                                                                                                                   | 3.4 kB     00:00     
updates                                                                                                                                                                                                  | 3.4 kB     00:00     
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package sysbench.x86_64 0:0.4.12-5.el6 will be installed
--> Processing Dependency: libmysqlclient_r.so.16(libmysqlclient_16)(64bit) for package: sysbench-0.4.12-5.el6.x86_64
--> Processing Dependency: libpq.so.5()(64bit) for package: sysbench-0.4.12-5.el6.x86_64
--> Processing Dependency: libmysqlclient_r.so.16()(64bit) for package: sysbench-0.4.12-5.el6.x86_64
--> Running transaction check
---> Package postgresql-libs.x86_64 0:8.4.18-1.el6_4 will be installed
---> Package sysbench.x86_64 0:0.4.12-5.el6 will be installed
--> Processing Dependency: libmysqlclient_r.so.16(libmysqlclient_16)(64bit) for package: sysbench-0.4.12-5.el6.x86_64
--> Processing Dependency: libmysqlclient_r.so.16()(64bit) for package: sysbench-0.4.12-5.el6.x86_64
--> Finished Dependency Resolution
Error: Package: sysbench-0.4.12-5.el6.x86_64 (epel)
           Requires: libmysqlclient_r.so.16()(64bit)
Error: Package: sysbench-0.4.12-5.el6.x86_64 (epel)
           Requires: libmysqlclient_r.so.16(libmysqlclient_16)(64bit)
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest

The problem is that cPanel adds exclude=mysql* to /etc/yum.conf. But even when ignoring the excludes, installing sysbench won't work:

# yum install --disableexcludes=all sysbench
Loaded plugins: downloadonly, fastestmirror
Loading mirror speeds from cached hostfile
 * base: ftp.nluug.nl
 * epel: ftp.nluug.nl
 * extras: ftp.nluug.nl
 * updates: ftp.nluug.nl
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package sysbench.x86_64 0:0.4.12-5.el6 will be installed
--> Processing Dependency: libmysqlclient_r.so.16(libmysqlclient_16)(64bit) for package: sysbench-0.4.12-5.el6.x86_64
--> Processing Dependency: libpq.so.5()(64bit) for package: sysbench-0.4.12-5.el6.x86_64
--> Processing Dependency: libmysqlclient_r.so.16()(64bit) for package: sysbench-0.4.12-5.el6.x86_64
--> Running transaction check
---> Package mysql-libs.x86_64 0:5.1.71-1.el6 will be installed
---> Package postgresql-libs.x86_64 0:8.4.18-1.el6_4 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================================================================================================================================================================
 Package                                                    Arch                                              Version                                                     Repository                                       Size
================================================================================================================================================================================================================================
Installing:
 sysbench                                                   x86_64                                            0.4.12-5.el6                                                epel                                             74 k
Installing for dependencies:
 mysql-libs                                                 x86_64                                            5.1.71-1.el6                                                base                                            1.2 M
 postgresql-libs                                            x86_64                                            8.4.18-1.el6_4                                              base                                            201 k

Transaction Summary
================================================================================================================================================================================================================================
Install       3 Package(s)

Total download size: 1.5 M
Installed size: 4.8 M
Is this ok [y/N]: y
Downloading Packages:
(1/3): mysql-libs-5.1.71-1.el6.x86_64.rpm                                                                                                                                                                | 1.2 MB     00:00     
(2/3): postgresql-libs-8.4.18-1.el6_4.x86_64.rpm                                                                                                                                                         | 201 kB     00:00     
(3/3): sysbench-0.4.12-5.el6.x86_64.rpm                                                                                                                                                                  |  74 kB     00:00     
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                                                                                                           9.4 MB/s | 1.5 MB     00:00     
warning: rpmts_HdrFromFdno: Header V3 RSA/SHA256 Signature, key ID 0608b895: NOKEY
Retrieving key from file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6
Importing GPG key 0x0608B895:
 Userid : EPEL (6) 
 Package: epel-release-6-8.noarch (@epel/6.5)
 From   : /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6
Is this ok [y/N]: y
Running rpm_check_debug
Running Transaction Test


Transaction Check Error:
  file /usr/share/mysql/charsets/README from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/Index.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/armscii8.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/ascii.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/cp1250.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/cp1251.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/cp1256.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/cp1257.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/cp850.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/cp852.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/cp866.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/dec8.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/geostd8.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/greek.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/hebrew.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/hp8.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/keybcs2.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/koi8r.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/koi8u.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/latin1.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/latin2.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/latin5.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/latin7.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/macce.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/macroman.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/charsets/swe7.xml from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/czech/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/danish/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/dutch/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/english/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/estonian/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/french/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/german/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/greek/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/hungarian/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/italian/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/japanese/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/korean/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/norwegian-ny/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/norwegian/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/polish/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/portuguese/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/romanian/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/russian/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/serbian/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/slovak/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/spanish/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/swedish/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64
  file /usr/share/mysql/ukrainian/errmsg.sys from install of mysql-libs-5.1.71-1.el6.x86_64 conflicts with file from package MySQL55-server-5.5.34-2.cp1136.x86_64

Error Summary
-------------

Ok, let's try to install without dependencies:

# yumdownloader sysbench
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: ftp.nluug.nl
 * epel: ftp.nluug.nl
 * extras: ftp.nluug.nl
 * updates: ftp.nluug.nl
sysbench-0.4.12-5.el6.x86_64.rpm                                                                                                                                                                         |  74 kB     00:00     

# rpm -ivh sysbench-0.4.12-5.el6.x86_64.rpm 
warning: sysbench-0.4.12-5.el6.x86_64.rpm: Header V3 RSA/SHA256 Signature, key ID 0608b895: NOKEY
error: Failed dependencies:
 libmysqlclient_r.so.16()(64bit) is needed by sysbench-0.4.12-5.el6.x86_64
 libmysqlclient_r.so.16(libmysqlclient_16)(64bit) is needed by sysbench-0.4.12-5.el6.x86_64
 libpq.so.5()(64bit) is needed by sysbench-0.4.12-5.el6.x86_64

# rpm -ivh --nodeps sysbench-0.4.12-5.el6.x86_64.rpm 
warning: sysbench-0.4.12-5.el6.x86_64.rpm: Header V3 RSA/SHA256 Signature, key ID 0608b895: NOKEY
Preparing...                ########################################### [100%]
   1:sysbench               ########################################### [100%]

Great, we have sysbench installed now, but it doesn't work:

# sysbench
sysbench: error while loading shared libraries: libmysqlclient_r.so.16: cannot open shared object file: No such file or directory

And here comes the trick, quoting cPanel support:

I can't guarantee that this will work, however the file you need is located at /usr/lib64/libmysqlclient_r.so. You may try creating a symlink from the missing file to this file to see if that resolves this issue.

# ln -s /usr/lib64/libmysqlclient_r.so /usr/lib64/libmysqlclient_r.so.16

Please note that the version installed is /usr/lib64/libmysqlclient_r.so.18 while you need /usr/lib64/libmysqlclient_r.so.16 so there is a chance that this may not work with this library, however if it will work the above should do it.

We are not done yet though, because after symlinking it still doesn't work:

# ln -s /usr/lib64/libmysqlclient_r.so /usr/lib64/libmysqlclient_r.so.16
# sysbench
sysbench: error while loading shared libraries: libpq.so.5: cannot open shared object file: No such file or directory

But that's easy to solve:

root@three [~]# yum whatprovides libpq.so.5
Loaded plugins: downloadonly, fastestmirror
Loading mirror speeds from cached hostfile
 * base: ftp.nluug.nl
 * epel: ftp.nluug.nl
 * extras: ftp.nluug.nl
 * updates: ftp.nluug.nl
postgresql-libs-8.4.18-1.el6_4.i686 : The shared libraries required for any PostgreSQL clients
Repo        : base
Matched from:
Other       : libpq.so.5



root@three [~]# yum install postgresql-libs
Loaded plugins: downloadonly, fastestmirror
Loading mirror speeds from cached hostfile
 * base: ftp.nluug.nl
 * epel: ftp.nluug.nl
 * extras: ftp.nluug.nl
 * updates: ftp.nluug.nl
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package postgresql-libs.x86_64 0:8.4.18-1.el6_4 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================================================================================================================================================================
 Package                                                    Arch                                              Version                                                     Repository                                       Size
================================================================================================================================================================================================================================
Installing:
 postgresql-libs                                            x86_64                                            8.4.18-1.el6_4                                              base                                            201 k

Transaction Summary
================================================================================================================================================================================================================================
Install       1 Package(s)

Total size: 201 k
Installed size: 624 k
Is this ok [y/N]: y
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : postgresql-libs-8.4.18-1.el6_4.x86_64                                                                                                                                                                        1/1 
  Verifying  : postgresql-libs-8.4.18-1.el6_4.x86_64                                                                                                                                                                        1/1 

Installed:
  postgresql-libs.x86_64 0:8.4.18-1.el6_4                                                                                                                                                                                       

Complete!

And now we are finally happy. There is still a warning on stderr, but seems to work fine (I didn't test the mysql benchmarks):

# sysbench --version
sysbench: /usr/lib64/libmysqlclient_r.so.16: no version information available (required by sysbench)
sysbench 0.4.12