megadapt

CoMSES MEGADAPT repository for containerized megadapt models

Setup

Development

To create an interactive environment to work on developing megadapt run

docker-compose up -d

on the command line

Then go to localhost:8787 in your web browser. Enter the default username and password (rstudio and test respectively).

You should now see an rstudio environment.

Now source the megadapt project in RStudio (File > Open Project) and go to code > src > r > megadaptr in the explorer and click megadaptr.Rproj.

Your R environment is now setup for you.

Press Ctnl+Shift+b to build and reload from megadaptr package from rstudio.

High Performance Computing

Build the singularity images

cd deploy
singularity build --fakeroot megadapt-base.sif megadapt-base.def
singularity build --fakeroot megadapt.sif megadapt.def

Then copy the final image to your hpc environment and run

scp megadapt.sif <server>:~/.

Detailed instructions are in the packages vignette.

Code Organization

• Scenarios folder (src/r/scenarios)

  Contains scenario specific setup information

• megadaptr folder (src/r/megadaptr)

  Contains generic code which should apply to many scenarios.

• deploy contains configuration to build the development environment and deploy to hpc with singularity

Resources

• see https://github.com/comses/megadapt/wiki/Developer-Resources for tips on developing R packages and manipulating data