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Run PTArcade

pip and conda

If you have installed PTArcade with pip or conda, open a terminal and run PTArcade with 

ptarcade -m ./model.py
The argument passed to the -m input flag is the path to a model file. In addition to a model file, the following optional arguments can be passed to ptarcade:

  • A configuration file can be passed via the input flag -c. The configuration file allows to control several parameters of the run, including the dataset to be analyzed, the number of MC trials, etc. More details on the model and configuration files can be found in the inputs section.

  • A string to append to the output folder. By default, the chains will be saved in ./chains/np_model/chain_0. Each of the three elements of this path can be controlled by the user. ./chains can be changed by using the out_dir parameter in the configuration file, np_model can be changed via the name parameter in the model file, and chain_0 can be changed via the -n input flag passed to ptarcade. The passed argument will be appended to chain_, so, if you want to save the chains in a folder named chain_42, just pass the argument -n 42. This can be useful if you are running multiple chains for the same model and you want to save them in the same root folder.

Using a docker Container

The commands of the previous section must be slightly modified to run within a Docker container. Docker does not mount any directories into the container by default. You must pass directories to mount inside the container using the syntax -v <source>:<destination>. In the example below, we assume that the only directories you will pass to the command line options of PTArcade are accessible from your current working directory. 

docker run -v $(pwd):$(pwd) -w $(pwd) -i -t ptarcade -m ./model.py

  • -v tells Docker what to mount from the host computer and where to mount it in the container. Here, we mount the current working directory of the host into the container using its full path.
  • -w sets the working directory of the container. In this case, it sets it to the current working directory that was just mounted.
  • -i -t keeps STDIN open and allocates a pseudo-TTY

The PYArcade in the docker run command refers to the name of the Docker image. If you would like to run something else inside the container, then replace the PTArcade options with the program to run. For example, to run an interactive Bash shell

docker run -v $(pwd):$(pwd) -w $(pwd) -i -t ptarcade bash

Using a singularity Container

As with Docker, the commands to run PTArcade must be slightly modified to run using Singularity. However, the commands are much simpler because Singularity will automatically mount your home directory inside the container. Using the ptarcade.sif file you created during the singularity installation, type into a terminal 

singularity run ptarcade.sif -m ./model.py
You can also pass another command to run. For example, to start a Jupyter notebook type

singularity run ptarcade.sif jupyter notebook

If you want an interactive shell, run the following command

singularity shell ptarcade.sif