SystemError: dynamic module not initialized properly in Centos 6.5

[Helio Gutierrez]

Hi 

I've downloaded Python 2.7.7 and compiled mod_wsgi3.5 with that Python version on Centos 6.5 (Parallel Desktop 11) with Django 1.6.2, but i have an error in my server. 

I have the next configuration, maybe someone can help me:

Apache/2.2.15 (Unix) DAV/2 mod_fcgid/2.3.6 mod_python/3.3.1 Python/2.6.6 mod_ssl/2.2.15 OpenSSL/1.0.1e-fips mod_wsgi/3.5 Python/2.7.7 mod_perl/2.0.4 Perl/v5.10.1 configured -- resuming normal operations

[root@u16844278 mod_wsgi-3.5]# ldd /usr/lib64/httpd/modules/mod_wsgi.so

linux-vdso.so.1 =>  (0x00007fff15fff000)

libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007fd1eb3ee000)

libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fd1eb1d1000)

libdl.so.2 => /lib64/libdl.so.2 (0x00007fd1eafcc000)

libutil.so.1 => /lib64/libutil.so.1 (0x00007fd1eadc9000)

libm.so.6 => /lib64/libm.so.6 (0x00007fd1eab45000)

libc.so.6 => /lib64/libc.so.6 (0x00007fd1ea7b0000)

/lib64/ld-linux-x86-64.so.2 (0x00007fd1eba07000)

vhost.conf:

WSGIDaemonProcess holding python-path=/var/www/html/holding/src:/usr/local/lib/python2.7/site-packages

WSGIProcessGroup holding

WSGIScriptAlias / /var/www/html/holding/src/wsgi.py

<Location "/">  

Order Allow,Deny

Allow from all

</Location>

Alias /static/admin/ /usr/local/lib/python2.7/site-packages/django/contrib/admin/static/admin

 

<Location "/static">

SetHandler None

</Location>

 

Alias /static/ /var/www/vhosts/mysite.com/holding/static

 

<Location "/media">

SetHandler None

</Location>

 

Alias /media /var/www/vhosts/mysite.com/holding/media

 

<LocationMatch "\.(jpg|gif|png|css|js)$">

SetHandler None

</LocationMatch>

wsgi.py

import os, sys

sys.path.append('/usr/local/lib/python2.7')

sys.path.append('/usr/local/lib/python2.7/site-packages')

sys.path.append('/var/www/html/holding')

sys.path.append('/var/www/html/holding/src')

prev_sys_path = list(sys.path)

 

# reorder sys.path so new directories from the addsitedir show up first

new_sys_path = [p for p in sys.path if p not in prev_sys_path]

for item in new_sys_path:

    sys.path.remove(item)

sys.path[:0] = new_sys_path

os.environ['DJANGO_SETTINGS_MODULE'] = 'src.settings'

from django.core.wsgi import get_wsgi_application

application = get_wsgi_application()

error_log

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94] mod_wsgi (pid=12642): Target WSGI script '/var/www/html/holding/src/wsgi.py' cannot be loaded as Python module.

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94] mod_wsgi (pid=12642): Exception occurred processing WSGI script '/var/www/html/holding/src/wsgi.py'.

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94] Traceback (most recent call last):

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94]   File "/var/www/html/holding/src/wsgi.py", line 38, in <module>

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94]     from django.core.wsgi import get_wsgi_application

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/wsgi.py", line 1, in <module>

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94]     from django.core.handlers.wsgi import WSGIHandler

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/handlers/wsgi.py", line 4, in <module>

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94]     import logging

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/logging/__init__.py", line 26, in <module>

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94]     import sys, os, time, cStringIO, traceback, warnings, weakref, collections

[Mon Jun 09 12:49:45 2014] [error] [client 189.219.102.94] SystemError: dynamic module not initialized properly

[Graham Dumpleton]

First up, stop loading mod_python into Apache. It is using a different Python version and is likely the cause of all the problems as you cannot use both mod_python and mod_wsgi together when they are using different Python versions.

Second, if you mean you installed Python 2.7.7 from source code and at the same time you still had a system Python 2.7 of a different patch level revision, then mod_wsgi.so is linked against the shared library from the wrong Python installation>

Your mod_wsgi.so should be loading libpython2.7.so from /usr/local/lib.

You should go back into mod_wsgi source code and do:

make distclean

./configure --with-python=/usr/local/bin/python

LD_RUN_PATH=/usr/local/lib make

sudo make install

Check again whether ldd is picking up the wrong library.

There also should be no need to list /usr/local/lib/python2.7/site-packages in python-path.

When using an alternate Python installation under /usr/local and a global one is being picked up instead, use:

WSGIPythonHome /usr/local

Albeit that this will not work if mod_python is also loaded even if using the same Python version. Another reason why you shouldn't use mod_python at same time.

Also, if you are using a Python virtual environment as well, which is correctly built from the Python 2.7.7 under /usr/local, then you can drop the sys.path fixes up in your WSGI script file for having it be used and instead simply use:

WSGIDaemonProcess holding python-home=/var/www/html/holding

where python-home is set to the value of sys.prefix for that Python virtual environment.

Graham

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[Helio Gutierrez]

Thank you Graham!

Its correct, my problem was that i had loaded mod_python and i have already commented this function in /etc/httpd/conf.d/python.conf:

#LoadModule python_module modules/mod_python.so

I did your next recomendations:

- reinstall mod_wsgi with your instructions

- block mod_python

- remove in the pythonpath the text ":/usr/local/lib/python2.7/site-packages"

- WSGIPythonHome /usr/local: did'nt work because my vhost.conf is into virtual host and i have only one version 2.7.7 (compiled from sources) under /usr/local/lib.

Now my error was gone, but i have another different error: (this is for a bad path?)

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94] mod_wsgi (pid=31984): Exception occurred processing WSGI script '/var/www/html/holding/src/wsgi.py'.

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94] Traceback (most recent call last):

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/handlers/wsgi.py", line 187, in __call__

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     self.load_middleware()

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/handlers/base.py", line 47, in load_middleware

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     mw_instance = mw_class()

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/middleware/locale.py", line 24, in __init__

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     for url_pattern in get_resolver(None).url_patterns:

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/urlresolvers.py", line 365, in url_patterns

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     patterns = getattr(self.urlconf_module, "urlpatterns", self.urlconf_module)

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/urlresolvers.py", line 360, in urlconf_module

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     self._urlconf_module = import_module(self.urlconf_name)

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/utils/importlib.py", line 40, in import_module

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     __import__(name)

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/var/www/html/holding/src/urls.py", line 18, in <module>

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     from django.contrib import admin

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/contrib/admin/__init__.py", line 6, in <module>

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     from django.contrib.admin.sites import AdminSite, site

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/contrib/admin/sites.py", line 3, in <module>

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     from django.contrib.admin import ModelAdmin, actions

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94] ImportError: cannot import name actions

etc/profile

unset i

unset -f pathmunge

export LD_LIBRARY_PATH=/opt/PostgreSQL/9.2/lib:/usr/local/lib

[Graham Dumpleton]

On 11/06/2014, at 1:53 AM, Helio Gutierrez <helio.g...@gmail.com> wrote:

Thank you Graham!

Its correct, my problem was that i had loaded mod_python and i have already commented this function in /etc/httpd/conf.d/python.conf:

#LoadModule python_module modules/mod_python.so

I did your next recomendations:

- reinstall mod_wsgi with your instructions

- block mod_python

- remove in the pythonpath the text ":/usr/local/lib/python2.7/site-packages"

- WSGIPythonHome /usr/local: did'nt work because my vhost.conf is into virtual host and i have only one version 2.7.7 (compiled from sources) under /usr/local/lib.

The reason for suggesting that was that you showed:

[root@u16844278 mod_wsgi-3.5]# ldd /usr/lib64/httpd/modules/mod_wsgi.so
linux-vdso.so.1 =>  (0x00007fff15fff000)
libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007fd1eb3ee000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fd1eb1d1000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fd1eafcc000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007fd1eadc9000)
libm.so.6 => /lib64/libm.so.6 (0x00007fd1eab45000)
libc.so.6 => /lib64/libc.so.6 (0x00007fd1ea7b0000)
/lib64/ld-linux-x86-64.so.2 (0x00007fd1eba07000)

This indicates that libpython2.7.so was being picked up from /usr/lib64.

If you had installed Python 2.7.7 under /usr/local, then the shared library would not normally have been installed in /usr/lib64 but /usr/local/lib.

Thus having it find that that other library suggests that you have a separate Python 2.7 installation, not necessarily the same patch revision.

If there is a separate Python 2.7 installation, it is quite important the both the correct shared library is found at runtime, as well as the correct Pythin installation itself.

For the library, the LD_RUN_PATH fix was needed and to find the right Python installation WSGIPythonHome is necessary.

If you do have a separate Python 2.7 installation installed system wide, even if the correct libpython2.7.so is found in /usr/local/lib, the way the embedded Python finds the Python installation means that it would still use the system wide one, which could cause issues.

Either way, just make sure you can check. You can do:

http://code.google.com/p/modwsgi/wiki/CheckingYourInstallation#Python_Installation_In_Use

The value of sys.prefix should match that for the Python installation you want it to use.

Now my error was gone, but i have another different error: (this is for a bad path?)

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94] mod_wsgi (pid=31984): Exception occurred processing WSGI script '/var/www/html/holding/src/wsgi.py'.

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94] Traceback (most recent call last):

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/handlers/wsgi.py", line 187, in __call__

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     self.load_middleware()

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/handlers/base.py", line 47, in load_middleware

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     mw_instance = mw_class()

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/middleware/locale.py", line 24, in __init__

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     for url_pattern in get_resolver(None).url_patterns:

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/urlresolvers.py", line 365, in url_patterns

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     patterns = getattr(self.urlconf_module, "urlpatterns", self.urlconf_module)

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/core/urlresolvers.py", line 360, in urlconf_module

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     self._urlconf_module = import_module(self.urlconf_name)

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/utils/importlib.py", line 40, in import_module

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     __import__(name)

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/var/www/html/holding/src/urls.py", line 18, in <module>

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     from django.contrib import admin

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/contrib/admin/__init__.py", line 6, in <module>

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     from django.contrib.admin.sites import AdminSite, site

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]   File "/usr/local/lib/python2.7/site-packages/django/contrib/admin/sites.py", line 3, in <module>

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94]     from django.contrib.admin import ModelAdmin, actions

[Mon Jun 09 21:19:14 2014] [error] [client 189.219.102.94] ImportError: cannot import name actions

I am entirely sure that this point. It could be caused by a mixup with different Python installations. Only other cause could be not all directories/files being readable to user your code runs under as Apache, but that seems unlikely given it got as far as it did.

etc/profile

unset i

unset -f pathmunge

export LD_LIBRARY_PATH=/opt/PostgreSQL/9.2/lib:/usr/local/lib

To avoid the need for that system wide LD_LIBRARY_PATH, when installing psycopg2, if that is what you are using, you should use LD_RUN_PATH again.

  LD_RUN_PATH=/opt/PostgreSQL/9.2/lib pip install psycopg2

I have never seen people having psycopg2 use the wrong libpq though, which leads me to think that the setup.py for psycopg2 handles that mixup automatically somehow.

Graham

[Helio Gutierrez]

Ok..

I searched the file "/usr/lib64/libpython2.7.so.1.0" and i found that is a link to "/usr/local/lib/libpython2.7.so.1.0", but i don't know how it happen that in the instalation.

This is my history:

First i had python2.7.6 (compiled from sources) and i only remove /usr/local/lib/python2.7 folder and installed the new version 2.7.7 in the same location (compiled from sources too).

There are some way to remove a Python instalation compiled from sources?

I will try uninstall python and mod_wsgi and install it again.

[Graham Dumpleton]

On 13/06/2014, at 9:07 AM, Helio Gutierrez <helio.g...@gmail.com> wrote:

Ok..

I searched the file "/usr/lib64/libpython2.7.so.1.0" and i found that is a link to "/usr/local/lib/libpython2.7.so.1.0", but i don't know how it happen that in the installation.

Even if the Python shared library is linked into /usr/lib64, it is still advisable to ensure you are setting WSGIPythonHome to /usr/local.

This is because the way an embedded Python interpreter finds the appropriate .../lib/pythonX.Y, is by looking for the 'python' executable in PATH.

If there is one in /usr/bin, it will find that and set up sys.prefix as /usr and use the lib directory under /usr/lib/pythonX.Y.

The WSGIPythonHome must be outside of any VirtualHost.

If you are even getting as far as you are, I am worried about what it may be find in /usr/lib then.

Do either of these exist and what do they refer to:

/usr/lib/python2.7

/usr/lib64/python2.7

As far as removing a Python installation, it will have installed things under:

/usr/local/bin/{various executables}

/usr/local/lib/python2.7

/usr/local/include/python2.7

For a patch level update only, it generally should have been safe to simple install over the top of the existing versions.

Anyway, as per:

http://code.google.com/p/modwsgi/wiki/CheckingYourInstallation#Python_Installation_In_Use

I would be double checking where Python is getting stuff from with a hello world.

Add to then printing out of sys.path and provide the results.

As to the original error, one final possibility may be that it is failing because you have SELinux extensions enabled.

Try disabling them temporarily and try again.

http://www.crypt.gen.nz/selinux/disable_selinux.html

If reinstalling Python, make sure you are using '--enable-shared' to configure for Python. Ensure you did a 'make distclean' in Pythin before running configure again to rebuild it.

Graham

[Helio Gutierrez]

Thank you Graham

My problem is solved, 

I've uninstalled the old psycopg2 and installed again with your recommendation:

LD_RUN_PATH=/opt/PostgreSQL/9.2/lib pip install psycopg2

and with this my problem was gone!

I guess my old psycopg2 aren't the adecuate version for Python2.7.7

Regards!