Standard Linux Compute

Getting started

OIT currently has three general purpose Linux (CentOS) computational servers. These systems are typically used to run standard research applications that require more system resources than available on a typical desktop or workstation class system.

More equipment specifications can be found on the OIT website - computational servers and systems

Linux Servers

- circe.rc.pdx.edu (relatively smaller jobs)
- hecate.rc.pdx.edu (high memory compute jobs)
- agamede.rc.pdx.edu (multi-threaded jobs)

These servers can handle most standard Linux single and multiple-threaded processing tasks. They also have access to central NFS volumes.

- /vol/shares research network shares
- 63TB scratch on /workspace
- circe and hecate have 10TB of local scratch space, though this will be deprecated as moved to /workspace

Request an account

1. Do you qualify for account access? You must have an Odin ID (generally PSU faculty, students or staff) or have a sponsorship/affiliate account.
2. Second, do you know your computational system requirements? Refer to the Before Getting Started page for more information.
3. Follow these instructions for how to request account access.

How to connect?

Command Line Interface

If you are not accustomed to using a Linux command line interface (CLI), we recommend familiarizing yourself with introductory material such as http://www.pcworld.com/article/214370/12_commands_every_linux_newbie_should_learn.html. The ability to navigate and manage files at the Linux command line is important in order to work effectively.

Secure Shell (SSH) client

To connect to these servers you will need to use Secure Shell (ssh) run through a terminal emulation client application. If you use Linux or MacOS X terminal applications are included with the operating system. Windows users will need to download a client such as MobaXterm. Refer to the guide at Stonybrook for using SSH on Windows. These clients give you access to the Linux Command Line Interface (CLI).

*** BEST PRACTICE: For security reasons, you are encouraged to using password-less SSH with public authentication keys. Refer to Stonybrook for a complete guide on SSH keys for both Linux and Windows (MobaXterm). ***

File Transfer with sFTP or SCP

To move files to OIT-RC Linux systems you will have to use a secure File Transfer protocol such as sFTP, scp, or rsync. There are many free graphical client programs such as WinSCP (compatible with PuTTY), Fugu for OSX, and CyberDuck and FileZilla for OSX and Windows. scp and rsync can be used from the Linux and OSX CLI as well.

X Server

If you require a graphical interface (for example, to run MatLab with the graphic interface) you will need an X server. There are excellent free X servers, such as XQuartz for OSX and Xming and MobaXterm for Windows. Linux distributions will have native support via ssh -X <odin ID>@<server>, but you may need to install the proper packages and enable and configure the X Window System.

Remote access to login nodes

Direct ssh access to the login nodes is limited to on PSU campus IP range (i.e. doesn’t include the guest wireless.) There are two options to access login nodes from off campus.

- Use campus VPN. This is the considered the most secure method of off-campus access. OIT provides FAQs for installing and configuring the campus VPN. This requires using 2-factor authentication.

Software

Each of these systems mount the /vol/apps/modulefiles volume where a broad range of installed software. Some example of the software installed on this volume:

- - GCC 6.3.0 with earlier versions available
  - Python 3.6 and 2.7 versions with typical libraries such as numpy, scipy.
  - Blast
  - Matlab, R, SAS
  - Latest versions of HDF5, NetCDF4, zlib, cmake

For more on these, refer to Software.