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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      • Running with Docker locally (outdated/US specific) 🛳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      • Running with docker on AWS - OLD probably outdated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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  1. How To Run

Common errors

Common error messages and how to debug them

Docker Issues

Docker Issues - storage full
  • Storage full on submission box

    • there can be so many error patterns in shortage of storage

Add error
// Some code

In this case, a common problem is that multiple unused docker containers remain on the submission box. A simple solution is to prune unused containers:

docker system prune

or belows:

// Remove all stopped containers
% docker rm $(docker ps -a -q)
// or Remove all containers
% docker rm -f $(docker ps -a -q)
docker volume could not be changed even if the container was updated and relaunched
  • Docker volume will not be changed and remained once it was created (except mount with -v). That is to say "exists independently".

  • This is observed as well in using docker-compose. If you define and use volumes: in docker-compose.yml file, be cautious that the created volume will not be removed after invoking docker compose down .

  • a workaround is to delete the docker volume beforehand

# Remove volumes
% docker volume rm <specified volume name>
# or 
% docker volume prune
PreviousRunning On A HPC With SlurmNextUseful commands

Last updated 1 year ago

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