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OpenMP
gaussian
massive
octave
README.md
bundler.py
gordon.qsub
tasks
trestles.qsub

README.md

This directory contains all of the files necessary to submit "bundled" jobs to SDSC Gordon or Trestles. The files are

  • bundler.py - this is the job controller script that interfaces MPI with your octave script. You should not have to modify this unless you know exactly what you are doing
  • tasks - this is a text file that contains one line for each invocation of the sub-tasks you want to run. If you want to run sixteen sub-tasks, there should be sixteen lines in this "tasks" file. The lines can be arbitrarily complex if you want; for example, you can put multiple commands on a single line if you separate them with ;, per bash convention.
  • gordon.qsub - this is the script that illustrates how to submit a bundled job to Gordon
  • trestles.qsub - this is the script that illustrates how to submit a bundled job to Trestles

To change the number of bundled sub-tasks, you must

  1. Modify your "tasks" file to contain the correct number of lines, each one representing a sub-task
  2. Modify your submit script (gordon.qsub or trestles.qsub) and change your -l nodes=X:ppn=Y to request the correct number of nodes and processors per node. It is OK to request more cores than you have tasks (e.g., request -l nodes=2:ppn=16 if you only have 24 tasks)

There are also a few subdirectories containing examples for different use cases:

  • massive - how to use the bundler to run a massive amount (thousands to tens of thousands) of short-running, serial tasks
  • OpenMP - how to use the bundler to run several multithreaded jobs that use OpenMP
  • gaussian - how to use the bundler to run several Gaussian jobs that use multiple cores (conceptually the same as OpenMP)
  • octave - how to use the bundler with an application that requires a module such as octave