Configure web server to submit jobs¶

Remote Appion Processing through ssh¶

A more advanced way to run appion script is done through an ssh session. This is equivalent of having you ssh into a computer and starting the appion processes.

There are two kinds of appion processes:

• The first is a single-node process that can be run on a stand-alone workstation or the head-node of a computer cluster without PBS.
• The second is a multiple-node process that requires PBS to run on the cluster.

When you use "Just Show Command" option, it is always a single-node process, but if you run through ssh it could be either, depending on the demand of the process. For example, imageuploader.py is typically always run as single-node process while maxlikeAlignment.py is either run on single-node with "Just Show Command" or as a PBS job submission when you run through ssh.

Install the php-ssh2 extension¶

For newer systems the extension is available through the repository, e.g., on Fedora 12 type "sudo yum install php-pecl-ssh2"

This enables an ssh session initialized from appionweb

1. Download and install the ssh2 extension for php as instructed at its download site:
• http://www.php.net/manual/en/ssh2.installation.php
  Install openssl and compile libssh first before compiling php-ssh2 extension. Once you get the final ssh2.so, add it in your php.ini

The extension module is added to php in the same way as does the php-mrc module we distribute for the viewing mrc images through php. To check whether it worked and for alternative way to make php recognize the module used in newer php, see http://emg.nysbc.org/documentation/leginon/bk02ch04s07.php under the section Check php information and Alternative approach if mrc module does not show up in info.php output

configuration at web server side¶

IMPORTANT: What we refer here as your_cluster.php should not be taken literally. For example, if you access your cluster through network with a name "bestclusterever", you should name your cluster configuration php file bestclusterever.php, not your_cluster.php.

1. Go to your_dbem_1_5_1/processing directory
2. Copy default_cluster.php to your_cluster.php
3. Edit your_cluster.php to correspond to your cluster configuration.
4. Edit config_processing.php to add your cluster and, if desired, a stand-alone workstation as processing_host and register the your_cluster.php you just created.

$PROCESSING_HOSTS[]="your_stand-alone_processing_workstation";
$PROCESSING_HOSTS[]="your_cluster";
$CLUSTER_CONFIGS= array (
  'your_cluster'
);

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