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  • 🦠gempyor: modeling infectious disease dynamics
    • Modeling infectious disease dynamics
    • Model Implementation
      • flepiMoP's configuration file
      • Specifying population structure
      • Specifying compartmental model
      • Specifying initial conditions
      • Specifying seeding
      • Specifying observational model
      • Distributions
      • Specifying time-varying parameter modifications
      • Other configuration options
      • Code structure
    • Model Output
  • 📈Model Inference
    • Inference Description
    • Inference Implementation
      • Specifying data source and fitted variables
      • (OLD) Configuration options
      • (OLD) Configuration setup
      • Code structure
    • Inference Model Output
    • Inference with EMCEE
  • 🖥️More
    • Setting up the model and post-processing
      • Config writer
      • Diagnostic plotting scripts
      • Create a post-processing script
      • Reporting
    • Advanced
      • File descriptions
      • Numerical methods
      • Additional parameter options
      • Swapping model modules
      • Using plug-ins 🧩[experimental]
  • 🛠️How To Run
    • Before any run
    • Quick Start Guide
    • Multiple Configuration Files
    • Synchronizing Files
    • Advanced run guides
      • Running with Docker locally 🛳
      • Running locally in a conda environment 🐍
      • Running on AWS 🌳
      • Running On A HPC With Slurm
    • Common errors
    • Useful commands
    • Tips, tricks, FAQ
  • 🗜️Development
    • Git and GitHub Usage
    • Guidelines for contributors
  • Deprecated pages
    • Module specification
  • JHU Internal
    • US specific How to Run
      • Running with Docker locally (outdated/US specific) 🛳
      • Running on Rockfish/MARCC - JHU 🪨🐠
      • Running with docker on AWS - OLD probably outdated
        • Provisioning AWS EC2 instance
        • AWS Submission Instructions: Influenza
        • AWS Submission Instructions: COVID-19
      • Running with RStudio Server on AWS EC2
    • Inference scratch
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  • Deleting model_output/ (or any big folder) is too long on the cluster
  • Use seff to analyze a job
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  1. How To Run

Tips, tricks, FAQ

All the little things to save you time on the clusters

Deleting model_output/ (or any big folder) is too long on the cluster

Yes, it takes ages because IO can be so slow, and there are many small files. If you are in a hurry, you can do

mv model_output/ model_output_old
rm -r model_output_old &

The first command rename/move model_output, it is instantaneous. You can now re-run something. To delete the renamed folder, run the second command. the & at the end makes it execute in the background.

Use seff to analyze a job

After a job has run (either to completion or got terminated/fail), you may run:

seff JOB_ID

to know how much ressources your job used in your node, what was the cause for termination and so on. If you don't remember the JOB_ID, look for the number in the filename of the slurm log (slurm_{JOB_ID}.out).

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Last updated 7 months ago

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