Pirana and Clusters

Pirana supports interaction with Linux-based clusters on which NONMEM and/or PsN are installed. The Job-schedulers Sun Grid Engine (SGE), Torque, and Condor are supported along with SSI-type cluster managers such as MOSIX. Connecting to a cluster is established using the SSH protocol or any method that can be invoked from the command line. Two methods are available for using Pirana with a grid/cluster system, which involve installation of Pirana either on the local system or directly on the cluster server. The following paragraphs discuss these two separate methods.

Note:Single-system image clusters such as MOSIX, openMOSIX, and Kerrighed distribute processes automatically across nodes, and therefore no alternative setup is required in Pirana.

Additional information is available on the following topics:

Method 1: Server-based installation
Method 2: Local installation
Installing public and private authentication keys
Setting up and working with a cluster over SSH on Windows

–Monitoring jobs on SGE, Torque, or Condor clusters

Method 1: Server-based installation

When using this approach, Pirana is only installed on the cluster-server, not on the local machine. Pirana is executed from the local machine using X-over-SSH window tunneling. This has the advantage of requiring only one central installation of Pirana for the entire modeling group, and Pirana and other modeling software is installed in a controllable environment. A disadvantage is that the interface is usually a bit slower. Especially when using this method over larger distances (i.e., across internet), the performance of Pirana may be impaired due to the server-client transmission of the full GUI, but this of course depends on the bandwith of your connection and can be tested easily. Also, all auxiliary software (Office suite, HTML-browser, R and an R-GUI, etc.) resides on the cluster.

X-over-SSH tunneling

On the local machine it is necessary to have an X window system installed. For Linux users this is likely already installed. Mac OSX users need to install the XQuartz system. For Windows, a good X window manager is Xming, which can be obtained for free from http://sourceforge.net/projects/xming. After installation of Xming, start the Xming X window server. An alternative to Xming is Cygwin/X.

Using the cluster

If everything is set up correctly, and the X window server is started, Pirana on the cluster can be accessed through SSH, by using the SSH client. If you get an error saying that the display cannot be started on localhost, you may have to enable X window forwarding in OpenSSH or in PuTTY. When using PuTTY, it is essential to use the PuTTY terminal directly, and not plink.exe. The latter program can cause Pirana to crash often, probably due to terminal incompatibility. OpenSSH can also be used.

Method 2: Local installation

The other method is to install Pirana on the local machine, and connect to the cluster using Pirana and third-party SSH software. This installation approach offers a more stable interface (independent of network speed), and does not require installation of auxiliary software on the cluster. It will, however, require a few additional local installations.

First, you need to mount the cluster drive with your data on your local PC (using sshfs on Linux/Mac or ExpanDrive on Windows). For example, ExpanDrive could be used to connect to the cluster through SFTP. While ExpanDrive technically supports use on Mac, experience indicates that sshfs shows much better performance than ExpanDrive. Therefore, sshfs is recommended when using Mac. Refer to https://github.com/osxfuse/osxfuse/wiki/SSHFS. Alternatively, if a Samba server is installed on the remote cluster, a connection can be established by giving the following command:

NET USE Z: \ \server_name\<name> /user:<name> /persistent:yes

Both on Windows and Linux, the mounted remote disk space and the local location need to be specified through the NONMEM Configuration Settings page (SSH to Cluster sub-tab), as these settings are used by Pirana to translate local paths to paths on the remote cluster.

Secondly, an SSH client needs to be installed, which is typically already available on Linux or Mac. On Windows, PuTTY (http://www.chiark.greenend.org.uk/∼sgt) and OpenSSH (download from http://sshwindows.sourceforge.net/) are good choices.

Installing public and private authentication keys

Either on Windows or Linux, type in a shell/console window: (If you use PuTTY instead of OpenSSH, use the Keypair generator program instead.)

ssh-keygen -t rsa

When asked for a passphrase, press <Enter>. Now a public and a private key have been created in c:\Documents and Settings\<Name>\.ssh (Windows) or /home/username/.ssh (Linux). In your home directory on the cluster, if it does not exist already, create the folder .ssh. In this folder, create the file authorized_keys (no extension) and add the contents of id_rsa.pub to that file and save it. Now you should be able to login without being asked for a password. If SSH asks if you want to accept the cluster as a valid host, accept. Keep your private key secret. In the Pirana NONMEM Configuration Settings page (SSH to Cluster sub-tab), specify the username to connect to the cluster (ssh_login).

Tip: if you experience delays (about 5 secs) when logging in to the server by SSH, this may be caused by a reverse DNS lookup. You can circumvent this by adding useDNS no to the file /etc/ssh/sshd_config on the server. Restart the ssh server for the changes to take effect:
sudo /etc/init.d/ssh restart.