Passenger always shows "Index of" - ruby-on-rails

Question

I've been sticking with this problem for a week. I cannot get my Rails application running via passenger module of Apache2. I use Ubuntu 12.04 64-bit with Rails 3.2.8 Ruby 1.9.3 Passenger 4.0.5.
My Rails apps is at /home/sarunint/cafe_grader/web
This is my /etc/apache2/sites-available/default
<VirtualHost *:80>
ServerAdmin webmaster#localhost
DocumentRoot /var/www
RailsBaseURI /grader
<Directory />
Options FollowSymLinks
AllowOverride None
</Directory>
<Directory /var/www/>
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
allow from all
</Directory>
ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
<Directory "/usr/lib/cgi-bin">
AllowOverride None
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
Order allow,deny
Allow from all
</Directory>
ErrorLog ${APACHE_LOG_DIR}/error.log
# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
LogLevel warn
CustomLog ${APACHE_LOG_DIR}/access.log combined
Alias /doc/ "/usr/share/doc/"
<Directory "/usr/share/doc/">
Options Indexes MultiViews FollowSymLinks
AllowOverride None
Order deny,allow
Deny from all
Allow from 127.0.0.0/255.0.0.0 ::1/128
</Directory>
</VirtualHost>
And this is my /etc/apache2/httpd.conf
LoadModule passenger_module /home/sarunint/.rvm/gems/ruby-1.9.3-p392/gems/passenger-4.0.5/libout/apache2/mod_passenger.so
PassengerRoot /home/sarunint/.rvm/gems/ruby-1.9.3-p392/gems/passenger-4.0.5
PassengerRuby /home/sarunint/.rvm/wrappers/ruby-1.9.3-p392/ruby
PS. If this is a duplicated topic, feel free to tell me :)
Thanks
Update
I've just noticed that when I restart Apache2 I got this :
sarunint#server1:~$ sudo /etc/init.d/apache2 restart
* Restarting web server apache2
[Tue Jun 18 23:05:56 2013] [warn] module passenger_module is already loaded, skipping
... waiting [Tue Jun 18 23:05:57 2013] [warn] module passenger_module is already loaded, skipping
Update 2
After doing some grep's by #mohamed-abshir, I got these lines :
sarunint#server1:/etc/apache2$ grep -irl "LoadModule passenger_module" .
./mods-available/passenger.load
./mods-enabled/passenger.load
./httpd.conf
Thanks.
Update 3
which ruby prints this :
/home/sarunint/.rvm/rubies/ruby-1.9.3-p392/bin/ruby
cat /etc/apache2/mods-enabled/passenger.load prints this :
LoadModule passenger_module /usr/lib/apache2/modules/mod_passenger.so
and this is the file you want :
<VirtualHost *:80>
ServerName sarunint.uni.me
ServerAdmin webmaster#localhost
DocumentRoot /var/www
RailsBaseURI /grader
<Directory />
Options FollowSymLinks
AllowOverride None
</Directory>
<Directory /var/www/>
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
allow from all
</Directory>
ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
<Directory "/usr/lib/cgi-bin">
AllowOverride None
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
Order allow,deny
Allow from all
</Directory>
ErrorLog ${APACHE_LOG_DIR}/error.log
# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
LogLevel warn
CustomLog ${APACHE_LOG_DIR}/access.log combined
Alias /doc/ "/usr/share/doc/"
<Directory "/usr/share/doc/">
Options Indexes MultiViews FollowSymLinks
AllowOverride None
Order deny,allow
Deny from all
Allow from 127.0.0.0/255.0.0.0 ::1/128
</Directory>
<Directory /home/sarunint/cafe_grader/web/public>
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
allow from all
</Directory>
</VirtualHost>

Answer 1

Since passenger 2.0 it's not following symlinks for DocumentRoot, the way passenger detects if its a ruby on rails application is looking for a config.ru one level behind the DocumentRoot directory. Suppose DocumentRoot is /var/www/public, it will search in /var/www for a config.ru file. But if www is a symlink to another location, let's say /var/www -> /home/ruby/my_app/public it will not follow the sym links so wouldn't be able to find the file and will not process the request.
To fix this, you can add to the httpd.conf:
PassengerResolveSymlinksInDocumentRoot on

Answer 2

If your sitename is "example.com" then under ServerAdmin webmaster#localhost line, you need:
ServerName example.com
ServerAlias www.example.com #not necessary
DocumentRoot should point to your site files and become:
DocumentRoot home/sarunint/cafe_grader/web/public
Your Directory block should be:
<Directory /home/sarunint/cafe_grader/web/public>
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
allow from all
</Directory>
Then restart apache and go to your site url.
I haven't checked your Ruby pointers, but basically on commandline when do "which ruby" the location that gets printed out, should match your what you posted above as your ruby interpreter.
Update
The op posted a note about passenger module being loaded again.
When Passenger is installed normally via rvm, it tells you what commands to run and where to put the 3 lines of code that you posted above(they normally go under conf.d/passenger.conf). It appears there is "Passenger module is loaded twice" so go to your Apache directory search for it like:
cd /etc/apache2/
grep -irl "LoadModule passenger_module" . # this searchs those words in current dir(don't remove the dot = current dir"

Answer 3

<VirtualHost *:80>
#this isn't working, it's running under drew
PassengerDefaultUser www-data
ServerAdmin youremail#mail.com
ServerName mysite.localhost.com
Options ExecCGI -MultiViews +SymLinksIfOwnerMatch
DocumentRoot /var/www/rails/ridcyDevelopment/public
RailsEnv development
#RailsBaseURI /
<Directory /var/www/rails>
Options Indexes FollowSymLinks -MultiViews +ExecCGI
AllowOverride all
Allow from All
</Directory>