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Linux Computational Computing

Bowdoin College offers a number of resources for Linux Computational Computing on the campus, including desktop machines within the lab environment, office desktop machines, large multiprocessor computational servers, and specialized systems such as the Chemistry NMR (Nuclear Magnetic Resonance) spectrometer.

A variety of disciplines at Bowdoin are using the Linux Computational environment, including Biology, Chemistry, Computer Science, Environmental Studies, Geology, History, Math, Physics, and Athletics (Swimming Team). Several computational packages are available in the Linux environment, including ADF, Gaussian, Grass, Mathematica, Matlab, and Sybyl among others, and also a large and diverse offering of Open Source software.

There are two different methods for using the Linux Computational resources; interactively, and via a batch scheduler that manages the supercomputing grid.

Interactive Computing

Interactive Computing is the way that most people use a computer. This is essentially sitting at a single computer, running programs, and interacting with those programs either through a GUI (Graphical User Interface) or command line interface. Checking e-mail, browsing the web, and composing a document are examples of interactive computing. You would use interactive computing if you were running any software that displayed graphics, or required manual interaction with the program while it is running, such as inputting more data, typing additional information, or clicking on an icon. Interactive computing is best used when you are able to accomplish your goals during the time that you will be sitting at the computer, and can quit the program when you leave (ie, you are not leaving the computer running your job when you walk away from it).

Bowdoin Computing Grid

The Bowdoin Computing Grid is a group of Linux servers which appear as one big, multiprocessor, compute server that can run many computationally intensive jobs concurrently. The Grid supports a wide range of jobs from simple shell scripts to heavy computational jobs and parallel processes, including the computational software packages listed above. Jobs taking several days on a typical desktop machine might finish within hours using the Grid environment, thus freeing up the desktop computer for other tasks while the Grid resources process the job on dedicated Compute Nodes. People interact with the Bowdoin Computing Grid via the Grid Headnode, a dedicated computer that runs the Sun Grid Engine (SGE) which is a software environment that coordinates the resources of multiple computers. SGE accepts jobs, puts them in a holding area (queue) until they can be run, sends them to a computational node, manages them during the run, and notifies the person when they are finished.

Typically if a job takes more than a few hours to run on a desktop machine, or the desktop machine needs to be available for other tasks, you should consider running the job on the Grid.

Learn More

If you are on campus or connecting to campus via the VPN and wish to learn more about our Linux environment, please visit our Linux Help Site at http://linuxhelp.bowdoin.edu/.

If you have any questions about the Linux Computational environment at Bowdoin College, contact:
Dj Merrill, Technology Consultant for the Sciences & Research