Description of available scripts

  • The script creates a new run directory and the needed directories and files inside it. Options include the ability to copy the code into the new run directory to keep it contained.
  • The script runs background and first order perturbation simulations and saves the results, by default in results/fo.hf5.
  • The script runs a full source term calculation using the first order results. This may take a long time especially if it is not executed in parallel. The options for this script include the location of the first order results file and simple assignment of task number in a parallel (or multiple serial) environment.
  • The script will merge any separate source files, for example from a parallel run, into one main source file. Rudimentary checking of the existence of each time step is completed. One of the options to this script is to further merge the first order and source term results together. The new merged file is used as the input for the second order calculation.
  • The script uses the source term and first order results from the merged file to calculate the second order perturbation solution.
  • The script combines all the results from the first, source and second order runs into one final results file. In this file the timesteps from the second order run are used so only half the results of the first and source term calculations are stored. For this reason this file is more for ease of analysis then long term data storage.
  • The script is used when the qsub queueing command is available. See the section “Using Qsub” below for more information.

Using Qsub

If you are running Pyflation in a cluster environment or somewhere with the qsub queueing system available, there is an extra script which will be useful. When you create a new run the file qsub-sh.template is created which holds a very general outline of a qsub run script. Change any of the options in the preliminary section to meet your needs. The length of runs and the number of task units can be set in When you run:


a new batch of qsub jobs will be created and submitted, running a full second order calculation. Please note that the full calculation make take some considerable time depending on the available computing power. The scripts which are submitted using qsub are available in the directory qsub-scripts. An additional src_individual.qsub script is useful if one of the tasks in the long source term calculation fails for some reason. To restart just one task with the same options as before use:

$ qsub src_individual.qsub N

where N is the number of the task to restart.

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