Minnesota/18 June 2009

From 2009.igem.org

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Today I made a python script to automate some of the more menial tasks required in creating models and running them on the supercomputer.

Our supercomputer programs use .nc-files to obtain the initial conditions and other data about the model. A .pbs file tells the supercomputer how long to run, on how many processors to run it, provides the desired algorithm (available to the supercomputer in a language it understands) with the desired .nc file, and finally produces an .out file and final .nc file as the simulation is run.

These .pbs files can be annoying to make in the Linux interface of the supercomputer, so my python script (ConvertNC.py) is given a directory, finds all the .nc files within the folder, and constructs valid .pbs files for each .nc file (with a given amount of runtime, and number of processors).