Appion

h1. Install the Web Interface Advanced

h3. Manual configuration instructions (Advanced User)

*Note:* You may skip this section if you configured your installation with the setup wizard at http://localhost/myamiweb/setup.

Copy config.php.template to config.php and edit the latter by adding these parameters:

"config.php" should be located in /var/www/html/myamiweb/ on CentOS and /srv/www/htdocs/myamiweb/ on SuSE.

# define site base path

This should be changed if the myamiweb directory is located

in a sub-directory of the Apache web directory.

ex. myamiweb is in /var/www/html/applications/myamiweb/ then

change to  define('BASE_PATH',"applications/myamiweb");

 

<pre>

define('BASE_PATH',"myamiweb"); 

</pre>

 

# myamiweb login system

<pre>

// Browse to the administration tools in myamiweb prior to 

// changing this to true to populate DB tables correctly.

define('ENABLE_LOGIN', false);	

</pre>

 

# Administrator email title and email address

<pre>

define('EMAIL_TITLE', 'The name of your institute');

define('ADMIN_EMAIL', "example@institute.edu");

</pre>

 

# SMTP Server setup (not required but recommended):

<pre>

define('ENABLE_SMTP', false);

define('SMTP_HOST', 'mail.institute.edu');	//your smtp host

</pre>

 

## When SMTP server requires authentication

<pre>

// --- Check this with your email administrator -- //

// --- Set it to true if your SMTP server requires authentication -- //

define('SMTP_AUTH', false);

// --- If SMTP_AUTH is not required(SMTP_AUTH set to false, -- //

// --- no need to fill in 'SMTP_USERNAME' & SMTP_PASSWORD -- //

define('SMTP_USERNAME', "");

define('SMTP_PASSWORD', "");

</pre>

 

# Setup your MySQL database server parameters:

<pre>

define('DB_HOST', "");		// DB Host name

define('DB_USER', "");		// DB User name

define('DB_PASS', "");		// DB Password

define('DB_LEGINON', "");	// Leginon database name

define('DB_PROJECT', "");	// Project database name

</pre>

 

# Enable Image Cache

If you want to use caching function for faster image loading time in image viewer, change 'ENABLE_CACHE' to true.

You can change the 'CACHE_PATH' to other location, but make sure the apache user has write access to this folder.

<pre>

// --- Enable Image Cache --- //

define('ENABLE_CACHE', true);

// --- caching location --- //

// --- please make sure the apache user has write access to this folder --- //

define('CACHE_PATH', '/srv/www/cache/');

define('CACHE_SCRIPT', WEB_ROOT.'/makejpg.php');

</pre>

h3. Additional parameters needed for Appion Installations only:

# Enable the processing plug-in by uncommenting out the following line in the file`myamiweb/config.php`

<pre>

addplugin("processing");

</pre>

 

# IMAGIC and Other features:

<pre>

// Check if IMAGIC is installed and running, otherwise hide all functions

define('HIDE_IMAGIC', false);

// hide processing tools still under development.

define('HIDE_FEATURE', true);

</pre>

 

# Add processing host information

 

*Appion version 2.2 and later:*

The following code should be added and modified for each processing host available. 

<pre>

$PROCESSING_HOSTS[] = array(

'host' => 'myhost.inst.edu',	

'nproc' => 32,  // number of processors available on the host, not used

'nodesdef' => '4', // default number of nodes used by a refinement job

'nodesmax' => '280', // maximum number of nodes a user may request for a refinement job

'ppndef' => '32', // default number of processors per node used for a refinement job

'ppnmax' => '32', // maximum number of processors per node a user may request for a refinement job

'reconpn' => '16', // recons per node, not used 

'walltimedef' => '48', // default wall time in hours that a job is allowed to run

'walltimemax' => '240', // maximum hours in wall time a user may request for a job

'cputimedef' => '1536', // default cpu time in hours a job is allowed to run (wall time x number of cpu's) 

'cputimemax' => '10000', // maximum cpu time in hours a user may request for a job

'memorymax' => '', // the maximum memory a job may use

'appionbin' => 'bin/', // the path to the myami/appion/bin directory on this host

'appionlibdir' => 'appion/', // the path to the myami/appion/appionlib directory on this host

'baseoutdir' => 'appion', // the directory that processing output should be stored in

'localhelperhost' => '', // a machine that has access to both the web server and the processing host file systems to copy data between the systems

'dirsep' => '/', // the directory separator used by this host

'wrapperpath' => '', // advanced option that enables more than one Appion installation on a single machine, contact us for info 

'loginmethod' => 'SHAREDKEY', // Appion currently supports 'SHAREDKEY' or 'USERPASSWORD' 

'loginusername' => '', // if this is not set, Appion uses the username provided by the user in the Appion Processing GUI

'passphrase' => '', // if this is not set, Appion uses the password provided by the user in the Appion Processing GUI

'publickey' => 'rsa.pub', // set this if using 'SHAREDKEY'

'privatekey' => 'rsa'	  // set this if using 'SHAREDKEY'

);

</pre>

 

*Appion version 2.1 and prior:*

<pre>

// --- Please enter your processing host information associate with -- //

// --- Maximum number of the processing nodes									-- //

// --- $PROCESSING_HOSTS[] = array('host' => 'host1.school.edu', 'nproc' => 4); -- //

// --- $PROCESSING_HOSTS[] = array('host' => 'host2.school.edu', 'nproc' => 8); -- //

// $PROCESSING_HOSTS[] = array('host' => '', 'nproc' => );

</pre>

 

# Microscope spherical aberration constant

 

Not needed for Appion version 2.2 and later. Version 2.1 and earlier only:

<pre>

$DEFAULTCS = "2.0";

</pre>

We will not include the cluster registration now. It is covered in the last part of this document.

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