Configure web server to submit job to local cluster¶

Option 1: Use the setup wizard and add the local cluster headnode¶

1. Go the setup wizard: http://localhost/myamiweb/setup or http://HOST.INSTITUTE.EDU/myamiweb/setup

Option 2: Manually edit the config.php and add the local cluster headnode to the config.php¶

Edit the file /var/www/html/myamiweb/config.php and ensure the following changes are made:

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

   addplugin("processing");
   

   
    
2. IMAGIC and Other features:
   

   // 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);
   

   
    
3. Add processing host information
   processing host is the computer with pbs server running (i.e. the head node of a computer cluster if applicable)
    
   Appion version 2.2 and later:
   The following code should be added and modified for each processing host available.
   

   $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' => 'USERPASSWORD', // Appion currently supports 'USERPASSWORD'.  'SHAREKEY' is possible, but not preferable. 
   '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' (not supported 
   'privatekey' => 'rsa'      // set this if using 'SHAREDKEY'
   );
   

   
    
   Appion version 2.1 and prior:
   

   // --- 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' => );
   

   
    
4. Microscope spherical aberration constant
    
   Not needed for Appion version 2.2 and later. Version 2.1 and earlier only:
   

   $DEFAULTCS = "2.0";
   

   
    
5. Redux server information
    
   This is a very new feature, post Appion 2.2, so you only need this if you are running the trunk or 2.2-redux.
   The Redux server replaces the old mrc_php module and will be released in Appion version 3.0.
   Information on redux parameters to add to the config.php

< Install SSH module for PHP | Testing job submission >