Introduction to our computing facilities

Rafael A. Irizarry

Key email addresses

Email bitsupport @ jhsph . edu to report problems or to ask for service.

Email bithelp @ jhsph . edu for any question related to using software

Our systems

Our machines

The department has various types of computer systems:

• A file server
• A login server (enigma)
• A commercial application server (post)
• A computing server and/or cluster (usher)
• Desktops (macs and PCs)
• Web server (www.biostat.jhsph.edu)

These are all conceter via the school's network.

• The file server is mounted on enigma, usher, and post. You can also request that it be mounted on your MAC or linux machine.
• enigma - this is the login server. you can log in from anywhere in the world using ssh. It is also a very powerful computing server. It has 16 gigs of RAM. Lots of freeware is installed and actively maintained: R, latex, emacs, C compilers etc... It has four very fast processor.
• www - is our web server. You can login from anywhere in the world using ssh. Your home page will be located in ~/public_html/index.html.
• usher - Computing cluster. 64 processors. very fast.
• blinux workstations - faculty workstations. very fast and some with as much as 4 Gigs of RAM

Access policy

The current policy for the file server is that there is no space limit. The file system is backed up every night. Notice that none of the student computers are backed up so we highly recommend using the file system to store files.

Enigma has only 4 processors so we ask that users only run short (less than 15 minutes) interactive jobs. These should be run at low priority (We will explain this later). Longer jobs and higher priority jobs are permitted by asking bitsupport for permission. Non intensive jobs, such as editing, are permitted without restriction.

The current policy for usher is that you can run as many jobs as you want. This might change. Be sure never to run a jobs directly on usher. Please read this before using it.

The webserver should not be used to run CPU intensive jobs.

To obtain access to the faculty workstations contact them directly.

Getting Started

You should already have an account on enigma. If you don't contact bitsupport. The most convenient way to use enigma is by using ssh to login and running an X server.

X windows, desktop environment, and window managers

By default unix/linux doesn't have a windows system. These are the graphics, buttons, icons, etc... you typically see on a computer. However, in practice all unix systems run X windows and some window manager. Macs are now unix system and you can easily install an X server. PCs require special emulator software. The department has a licence for Humingbird which we recommend you install (contact bitsupport for this)

Linux desktops are useful but most of the powerful tools are run from the command line and don't rely on X.

So the first thing you want to do when you start using a system with desktop environment is open a terminal emulator. This will give you a command line.

When you use ssh you will automatically be on a terminal emulator.

About this document ...

Introduction to unix/linux

This document was generated using the LaTeX2HTML translator Version 2002 (1.62)

Copyright © 1993, 1994, 1995, 1996, Nikos Drakos, Computer Based Learning Unit, University of Leeds.
Copyright © 1997, 1998, 1999, Ross Moore, Mathematics Department, Macquarie University, Sydney.

The command line arguments were:
latex2html -split 0 unix.tex

The translation was initiated by Rafael A. Irizarry on 2004-09-02