Appion

# 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' => 'LOCAL_CLUSTER_HEADNODE.INSTITUTE.EDU', // for a single computer installation, this can be 'localhost'	

'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>