/economic_model-zenodo

Repository for thesis

Primary LanguageNetLogo

Spinning Jenny

This pipeline requires Nextflow and one between Docker or Singularity. For installing Nextflow type:

curl -s https://get.nextflow.io | bash

Docker images

Tools needed for running the pipelines are wrapped into docker images and stored in DockerHub. They are automatically retrieved by Nextflow.

Installing the pipeline

You can clone the repository by doing

git clone git@github.com:lucacozzuto/economic_model.git

Installing the pipeline

Then you can launch it specifying either docker or singularity engines:

With Docker:

cd economic_model;

nextflow run  main.nf -with-docker -bg  > log

or with Singularity:

nextflow run  main.nf -with-singularity -bg  > log

Input and Output

The inputs are specified within the file params.config tha contains:

  • the number of batches: number of times you want to run each execution to obtain 8 repetitions per batch.
  • the template xml file name
  • the values file name
  • the output folder name

You can change those default values by editing the file or using two dashes (--) when running the pipeline:

nextflow run  main.nf -with-singularity -bg --batches 125 > log

The file template contains the xml needed by NetLogo for running the model. The default one is named template.xml and given in this repository. The file values contains the name of the parameters and their starting, final and step values for making several simulations. The output of those simulation will be named:

PLOTS -> {PARAMETER_NAME}_{VALUE}_{PLOT_ID}.pdf 
TXT   -> {PARAMETER_NAME}_{VALUE}_{PLOT_ID}._cat.txt

The default file for value is values.txt and will give those files as output:

initial-labor-price_10_1.pdf    initial-labor-price_15_3.pdf
initial-labor-price_10_2.pdf    initial-labor-price_15_cat.txt
initial-labor-price_10_3.pdf    initial-labor-price_5_1.pdf
initial-labor-price_10_cat.txt  initial-labor-price_5_2.pdf
initial-labor-price_15_1.pdf    initial-labor-price_5_3.pdf
initial-labor-price_15_2.pdf    initial-labor-price_5_cat.txt

Running the pipeline in a cluster

We provide multiple configuration for running the pipeline in different environments. Just using different profiles will allow to use different specifications. For example running the pipeline in a SGE based cluster will be:

nextflow run main.nf -with-singularity -profile sge -bg > log.txt

We provide the following possibilities:

  • awsbatch
  • sge
  • slurm
  • local