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Start with existing CentOS installation » History » Revision 66

Revision 65 (Amber Herold, 03/25/2010 03:18 PM) → Revision 66/80 (Amber Herold, 04/06/2010 12:43 PM)

h1. Start with existing CentOS 5.3 64-bit installation 

 {{>toc}} 

 h2. 3 Download additional software  

 [[Download additional Software]] 

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 h2. 4 MRC PHP Extension Installation and Testing 

 [[MRC PHP Extension Installation and Testing]] 

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 h2. 5 Setup MySQL (appiondata) databases  

 [[Setup MySQL database]] 

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 h2. 6 Compile and setup Appion python programs  

 [[Setup Appion programs]] 

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 h2. 7 Install webpages (myamiweb) 


 Refer to [[Web Server Installation]] 


 *TODO:* The next steps have already been completed, grab any extra info from here and move to other location. 

 h3. Install MRC Tools  

 h4. Compile MRC tools  

 * Go to your php devel directory and untar the archive 
 * If unsure where it is, use info.php to find it under *extension_dir* 

 <pre> 
 $ cd /usr/include/php/ext/ 
 $ sudo mkdir mrc 
 $ sudo chmod 777 mrc 
 $ sudo chown $USER mrc 
 </pre> 

 * Unpackage MRC Tools from http://emg.nysbc.org/software/mrctools/ 

 <pre> 
 $ tar zxvf ~/php_mrc.tgz 
 $ cd mrc/ 
 </pre> 

 * Compile and install the MRC module 

 <pre> 
 $ phpize 
 $ ./configure  
 $ make 
 $ sudo make install 
 </pre> 

 h4. Configure PHP for MRC Tools  

 * Confirm the location of "additional .ini files parsed" from info.php web page (/etc/php.d in this example) 

 * Create a file called    "mrc.ini" in this directory. 

 <pre> 
 $ sudo nano /etc/php.d/mrc.ini 
 </pre> 

 * Add these lines in the file "mrc.ini" to make mrc.so an extension 

 <pre> 
 ; Enable mrc extension module 
 extension=mrc.so 
 </pre> 

 * To test MRC tools, go to this website: 
 http://emg.nysbc.org/software/mrctools/mrc_so.php 


 

 h3. Configure PHP  

 * increase the memory limit, EM images are big 64MB: 

 <pre> 
 memory_limit = 256M; Maximum amount of memory 
 </pre> 

 * Turn error display on: 

 <pre> 
 display_errors = On 
 </pre> 

 <pre> 
 error_reporting = E_ALL & ~E_NOTICE & ~E_WARNING 
 </pre> 

 * restart the webserver 

 <pre> 
 $ sudo /sbin/service httpd restart 
 </pre> 

 h3. Install DBEM and project php source  

 Please consult the other [[Start_with_existing_ANY_Linux_flavor_OS#3-Web-server-side-installation|Install guide]] 

 h3. Configuration  

 h4. configure apache  

 * allow REMOTE_HOST lookups in apache 

 <pre> 
 $ sudo nano /etc/httpd/conf/httpd.conf 
 </pre> 

 * turn _HostnameLookups_ to On 

 <pre> 
 HostnameLookups On 
 </pre> 

 * restart the webserver 

 <pre> 
 $ sudo /sbin/service httpd restart 
 </pre> 

 h4. configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing  

 Please consult the other [[Start_with_existing_ANY_Linux_flavor_OS#3-Web-server-side-installation|Install guide]] 

 h3. Initialize database tables from the web tools  

 Please consult [[Start_with_existing_ANY_Linux_flavor_OS#4-Create-a-test-project-and-processing-database|Create a test project and processing database]] 

 h3. Potential problems  

 h4. Firewall settings  

 You may need to configure your firewall to allow incoming HTTP (port 80) and MySQL (port 3306) traffic: 

 <pre> 
 $ system-config-securitylevel 
 </pre> 

 h4. Security-enhanced linux  

 "Security-enhanced linux (SELinux)":http://en.wikipedia.org/wiki/Security-Enhanced_Linux    may be preventing your files from loading. To fix this run the following command: 

 <pre> 
 $ sudo /usr/bin/chcon -R -t httpd_sys_content_t /var/www/html/ 
 </pre> 

 see "this website":http://docs.fedoraproject.org/selinux-apache-fc3/sn-simple-setup.html    for more details on SELinux 

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 h2. 8 Install external packages  

 *Please follow individual package installation instruction provided with them* 

 h3. Compile Xmipp for OpenMPI  

 [[Install Xmipp]] 

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 h2. 9 Install a PBS job submission system 

 [[Install PBS]] 

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 h2. 10 Do testing (Start at 4 of any flavor) 

 [[Start_with_existing_ANY_Linux_flavor_OS#4-Create-a-test-project-and-processing-database|Get started with a project]] 
 This has some repeated information. 
 Basically need to do the following: 

 # Add a group 
 # Add a user 
 # Add instruments 
 # Create a project 
 # Create the project database 
 # Upload images to a new session 
 # View the images 
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