Slurm GM Simulation Workflow

Contains the following:

• Scripts for installing and usage of HPC environments, which allow running of the workflow in a sandbox
• Scripts/Code for installing and running the automated workflow. This includes:
  • Scripts for installing the a automated workflow run
  • Execution of the installed simulations
  • Management DB code, along with scripts to keep the management DB up to date during an automated workflow run
  • Slurm templates
  • Code for metadata collection
• Unittests
• Code/Scripts for estimation of core hour usage
• Code/Scripts for collection of HPC usage information and displaying it on a dashboard.
• End-to-End tests of the automated workflow
• Scripts for manual generation and aggregation of empirical intensity measures after the automated workflow has run

Running the automated workflow

Also see cybershake manual.

Setup

To run an automated workflow the following folder strucutre/files are required:

• rootDir/Data/
  • Sources
    • Faults (folder for each)
      • Srf
        • .srf files (one for each realisation)
        • .info files (one for each realisation)
      • Stoch
        • .stoch file (one for each realisation)
  • VMs
    • Faults (folder for each)
      • Lots of files (?)

where rootDir is the directory to which the automated workflow will be installed.

To generate these files see pre-processing and cybershake manual.

Installing

Run the install_cybershake.sh bash script, e.g.

$gmsim/workflow/workflow/automation/install_scripts/install_cybershake path/to/rootDir 
cybershake_version /path/to/list.txt --seed [seed]

where the cybershake version is a string with a relevant subdirectory in the templates folder. Current valid options are 16.1 and 18.5.3.4

and list.txt is a list of the faults to run, along with the number of realisations, e.g.

Hossack 4r
RepongaereF4 10r

seed is an optional integer argument to specify the seed to be used for HF calculations. If it is not given, a value in SEED file will be used if the file exists. Otherwise, a random seed will be chosen and kept in SEED file for next use.

Running

To run the installed simulations, copy the task_config.yaml configuration file to the run directory and modify it to your needs. Run the cybershake with the following script:

python $gmsim/workflow/workflow/automation/execution_scripts/run_cybershake.py /path/to/rootDir /path/to/rootDir/task_config.yaml

this will start submitting the different tasks on the HPC and will keep the database up to date.