Start with existing CentOS installation » History » Revision 65
Revision 64 (Amber Herold, 03/25/2010 12:40 PM) → Revision 65/80 (Amber Herold, 03/25/2010 03:18 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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