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Start with existing CentOS installation » History » Revision 62

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Anchi Cheng, 03/23/2010 01:47 PM


Start with existing CentOS 5.3 64-bit installation

3 Download additional software

Download additional Software


4 MRC PHP Extension Installation and Testing

MRC PHP Extension Installation and Testing


5 Setup MySQL (appiondata) databases

Setup MySQL database


6 Compile and setup Appion python programs

Setup Appion programs


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.

Install MRC Tools

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
$ cd /usr/include/php/ext/
$ sudo mkdir mrc
$ sudo chmod 777 mrc
$ sudo chown $USER mrc
$ tar zxvf ~/php_mrc.tgz
$ cd mrc/
  • Compile and install the MRC module
$ phpize
$ ./configure 
$ make
$ sudo make install

Configure PHP for MRC Tools

  • Find the location of "additional .ini files parsed" from info.php web page, and create a file called "mrc.ini" in this directory.
$ sudo nano /etc/php.d/mrc.ini
  • Add these lines in the file "mrc.ini" to make mrc.so an extension
; Enable mrc extension module
extension=mrc.so

Configure PHP

  • increase the memory limit, EM images are big 64MB:
memory_limit = 256M; Maximum amount of memory
  • Turn error display on:
display_errors = On
error_reporting = E_ALL & ~E_NOTICE
  • restart the webserver
$ sudo /sbin/service httpd restart

Install DBEM and project php source

Please consult the other Install guide

Configuration

configure apache

  • allow REMOTE_HOST lookups in apache
$ sudo nano /etc/httpd/conf/httpd.conf
  • turn HostnameLookups to On
HostnameLookups On
  • restart the webserver
$ sudo /sbin/service httpd restart

configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing

Please consult the other Install guide

Initialize database tables from the web tools

Please consult Create a test project and processing database

Potential problems

Firewall settings

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

$ system-config-securitylevel

Security-enhanced linux

Security-enhanced linux may be preventing your files from loading. To fix this run the following command:

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

see this website for more details on SELinux


8 Install external packages

Please follow individual package installation instruction provided with them

Compile Xmipp for OpenMPI

Install Xmipp


9 Install a PBS job submission system

Install PBS


10 Do testing (Start at 4 of any flavor)


Updated by Anchi Cheng over 14 years ago · 62 revisions