Start with existing CentOS 5.3 64-bit installation¶

• Table of contents
• Start with existing CentOS 5.3 64-bit installation
  • 3 Download additional software
  • 4 MRC PHP Extension Installation and Testing
  • 5 Setup MySQL (appiondata) databases
  • 6 Compile and setup Appion python programs
  • 7 Install webpages (myamiweb)
    • Install MRC Tools
      • Compile MRC tools
      • Configure PHP for MRC Tools
    • Configure PHP
    • Install DBEM and project php source
    • Configuration
      • configure apache
      • configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing
    • Initialize database tables from the web tools
    • Potential problems
      • Firewall settings
      • Security-enhanced linux
  • 8 Install external packages
    • Compile Xmipp for OpenMPI
  • 9 Install a PBS job submission system
  • 10 Do testing (Start at 4 of any flavor)

3 Download additional software¶

Download additional Software

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4 MRC PHP Extension Installation and Testing¶

MRC PHP Extension Installation and Testing

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5 Setup MySQL (appiondata) databases¶

Setup MySQL database

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6 Compile and setup Appion python programs¶

Setup Appion programs

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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

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

$ tar zxvf ~/php_mrc.tgz
$ cd mrc/

• Compile and install the MRC module

$ phpize
$ ./configure 
$ make
$ sudo make install

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.

$ 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

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

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 & ~E_WARNING

• 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

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8 Install external packages¶

Please follow individual package installation instruction provided with them

Compile Xmipp for OpenMPI¶

Install Xmipp

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9 Install a PBS job submission system¶

Install PBS

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10 Do testing (Start at 4 of any flavor)¶

Get started with a project
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