Appion

h1. Example config file

*The example config file below may be out of date.*

<pre>

<?php

/**

* The Leginon software is Copyright 2010

* The Scripps Research Institute, La Jolla, CA

* For terms of the license agreement

* see http://emg.nysbc.org/software/leginon-license

*

*/

/**

* Please visit http://yourhost/myamiwebfolder/setup

* for automatically setup this config file for the

* first time.

*/

require_once 'inc/config.inc';

define('WEB_ROOT',dirname(__FILE__));

// --- define myamiweb tools base --- //

define('PROJECT_NAME',"myamiweb");

define('PROJECT_TITLE',"Ambers Trunk Appion and Leginon Tools");

// --- 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 "myamiweb to "applications/myamiweb" -- //

define('BASE_PATH',"~amber/myamiweb");

define('BASE_URL',"/~amber/myamiweb/");

define('PROJECT_URL',"/~amber/myamiweb/project/");

// --- myamiweb login --- //

// Browse to the administration tools in myamiweb prior to

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

define('ENABLE_LOGIN', true);

// --- Administrator email title and email address -- //

define('EMAIL_TITLE',"asdfasf");

define('ADMIN_EMAIL',"amber@scripps.edu");

// --- When 'ENABLE_SMTP set to true, email will send out -- //

// --- via ADMIN_EMIL's SMTP server. --//

define('ENABLE_SMTP', false);

define('SMTP_HOST',"");

// --- 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',"");

// --- Set your MySQL database server parameters -- //

define('DB_HOST',"cronus4.scripps.edu");

define('DB_USER',ask someone);

define('DB_PASS',ask someone);

define('DB_LEGINON',"dbemdata");

define('DB_PROJECT',"project");

// --- default URL for project section --- //

define('VIEWER_URL', BASE_URL."3wviewer.php?expId=");

define('SUMMARY_URL', BASE_URL."summary.php?expId=");

define('UPLOAD_URL', BASE_URL."processing/uploadimage.php");

// --- Set cookie session time -- //

define('COOKIE_TIME', 0); //0 is never expire.

// --- defaut user group -- //

define('GP_USER', 'users');

// --- XML test dataset -- //

$XML_DATA = "test/viewerdata.xml";

// --- Set Default table definition -- //

define('DEF_PROCESSING_TABLES_FILE', "defaultprocessingtables.xml");

define('DEF_PROCESSING_PREFIX',"ap");

// --- Set External SQL server here (use for import/export application) -- //

// --- You can add as many as you want, just copy and paste the block -- //

// --- to a new one and update the connection parameters -- //

// --- $SQL_HOSTS['example_host_name']['db_host'] = 'example_host_name'; -- //

// --- $SQL_HOSTS['example_host_name']['db_user'] = 'usr_object'; -- //

// --- $SQL_HOSTS['example_host_name']['db_pass'] = ''; -- //

// --- $SQL_HOSTS['example_host_name']['db'] = 'legniondb'; -- //

$SQL_HOSTS[DB_HOST]['db_host'] = DB_HOST;

$SQL_HOSTS[DB_HOST]['db_user'] = DB_USER;

$SQL_HOSTS[DB_HOST]['db_pass'] = DB_PASS;

$SQL_HOSTS[DB_HOST]['db'] = DB_LEGINON;

// --- path to main --- //

set_include_path(dirname(__FILE__).PATH_SEPARATOR

.dirname(__FILE__)."/project".PATH_SEPARATOR

.dirname(__FILE__)."/lib".PATH_SEPARATOR

.dirname(__FILE__)."/lib/PEAR");

// --- add plugins --- //

// --- uncomment to enable processing web pages -- //

addplugin("processing");

define('DEFAULT_APPION_PATH',"/ami/data00/appion/");

// --- Add as many processing hosts as you like -- //

// --- 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' => 'guppy.scripps.edu',

							'nproc' => 8,

							'nodesdef' => '2',

							'nodesmax' => '8',

							'ppndef' => '8',

							'ppnmax' => '8',

							'reconpn' => '8',

							'walltimedef' => '2',

							'walltimemax' => '2',

							'cputimedef' => '2',

							'cputimemax' => '2',

							'memorymax' => '30',

							'appionbin' => '/opt/myamisnap/bin/appion/',

							'baseoutdir' => DEFAULT_APPION_PATH,

							'localhelperhost' => 'guppy.scripps.edu',

							'dirsep' => '/' );

$PROCESSING_HOSTS[] = array('host' => 'garibaldi.scripps.edu', 

							'nproc' => 8,

							'nodesdef' => '16',

							'nodesmax' => '280',

							'ppndef' => '4',

							'ppnmax' => '8',

							'reconpn' => '4',

							'walltimedef' => '240',

							'walltimemax' => '240',

							'cputimedef' => '240',

							'cputimemax' => '240',

							'memorymax' => '30',

							'appionbin' => '~bcarr/appionbin/',

							'baseoutdir' => '', //sends appion procession output to a location under the users home directory on the remote host

							'localhelperhost' => 'amibox03.scripps.edu',

							'dirsep' => '/' );

// --- register your cluster configure file below i.e (default_cluster) --- //

// --- $CLUSTER_CONFIGS[] = 'cluster1'; -- //

// --- $CLUSTER_CONFIGS[] = 'cluster2'; -- //

//$CLUSTER_CONFIGS[] = 'guppy_cluster';

//$CLUSTER_CONFIGS[] = 'garibaldi';

//$CLUSTER_CONFIGS[] = 'test1_cluster';

//$CLUSTER_CONFIGS[] = 'test2_cluster';

// --- Microscope spherical aberration constant

// --- Example : 2.0 --- //

define('DEFAULTCS',"2.0");

// --- Restrict file server if you want --- //

// --- Add your allowed processing directory as string in the array

$DATA_DIRS = array();

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

define('ENABLE_CACHE', false);

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

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

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

define('CACHE_PATH',"");

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

// --- define Flash player base url --- //

define('FLASHPLAYER_URL', "/flashplayer/");

// --- define python commands - path --- //

// to download images as TIFF or JPEG

// $pythonpath="/your/site-packages";

// putenv("PYTHONPATH=$pythonpath");

// To use mrc2any, you need to install the pyami package which is part

// of myami. See installation documentation for help.

// --- define('MRC2ANY', "/usr/bin/mrc2any" --- //

define('MRC2ANY',"/usr/bin/mrc2any");

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

define('HIDE_IMAGIC', false);

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

define('HIDE_MATLAB', false);

// --- hide processing tools still under development. --- //

define('HIDE_FEATURE', false);

// --- temporary images upload directory --- //

define('TEMP_IMAGES_DIR',"/tmp");

// --- use appion warpper --- //

define('USE_APPION_WRAPPER', true);

// --- define('APPION_WRAPPER_PATH', ""); --- //

define('APPION_WRAPPER_PATH',"/opt/myamisnap/bin/appion");

// --- sample tracking ---//

define('SAMPLE_TRACK', false);

// --- exclude projects in statistics. give a string with numbers separated by ',' ---//

// --- for example, "1,2" ---//

define('EXCLUDED_PROJECTS',"");

// --- hide processing tools still under development. --- //

define('HIDE_TEST_TOOLS', false);

$TEST_SESSIONS = array(

		'zz07jul25b'

		,'zz06apr27c'

		,'zz09feb12b'

		,'zz09apr14b'

		,'zz09feb18c'

	);

?>

</pre>