ssh username@polaris.cllrnet.ca

Users not familiar with UNIX will find a brief introduction to the UNIX shell here.

Uploading your data

For security reasons standard FTP services are not available on Polaris. Instead, you can use sftp and scp protocols, which are secure and function similarly to the more familiar UNIX ftp and rcp commands. For example, if you wish to copy files from directory "work" to your home directory on Polaris account, you would type:

scp -r work/* username@polaris.cllrnet.ca:~/

Disk usage and backups

The good news: Polaris currently boasts a 175 GB RAID-5 disk server, which is capable of storing data redundantly across multiple hard disks. It also uses uninterruptable power supplies to maintain power during brief outages. Finally, we strive to maintain maximum network security by using only secure services, firewalling, enforcing good password habits.

The bad news: No system is perfectly safe. while the RAID system does afford users some protection against data loss, user data is not backed up. Therefore, users must work under the assumption that data are always susceptible catastrophic loss due to circumstances beyond our control (e.g., fire, flood, virii and other malicious activity). Individual users are urged to backup their data to their home system on a regular basis. Likewise, be aware that files and folders that are accidentally deleted from the disk are not recoverable unless they are backed up.

In terms of disk usage, please be aware that we reserve the right to limit disk space on a per-user basis. We also appreciate your cooperation in removing old files as you offload them to your local system.

The bottom line: Access is provided to users in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.

Scratch space

Each node has a 20MB disk drive that can be used for temporary scratch space. This space is located in the /tmp/ of each node, and is different across each drive. Please note however that each node is a dual processor machine, and that both processors will have access to the same /tmp/ space.

Email

Please don't user your user account on Polaris for receiving email. Also be sure you are forwarding email to your regular account by including a .forward file in your home directory that lists your regular email address.

Compiling and running

Compiling binaries

Currently, the primary package for parallel code is MPI. MPI compilers are: mpicc, mpiCC (C and C++, respectively) mpi90 and mpif77 (FORTRAN 90 and 77). These work similarly to their non-MPI equivalents.

Other packages such as PVM can be installed as required, resource-permitting.

Running jobs

All processes must be submitted to the batch scheduler, which is responsible for assigning individual nodes for each process. Running processes directly from the command line or through mpirun will execute processes to the head node (polaris) only, which is not permitted.

Users should use the 'cllrnet' queue, which is used for both serial and batch jobs. Queueing priority is currently on a first-come first-served basis.

Polaris uses the Sun Grid Engine (SGE) scheduler. A complete users guide is available here. For the impatient, the relevant commands include: qsub qalter qhold qrls qmon qrsh qstat.

Serial jobs

Interactive single-process jobs can be submitted using the qrsh command, which allocates a single process and creates a shell. However, if no processes are currently available, the user must wait until a process is available to be allocated before a shell is opened.

The qsub command can be used to submit a single process to be run. This is best done by creating a script that executes the desired command, and using qsub to execute the script. An example script is found here.

Parallel jobs

Parallel jobs are submitted similarly, using the qsub command and a script containing an mpirun command. An example script is found here.

Getting started with MPI

Introduction to MPI that includes programs to get you started here.