markuskowa/fspx

Functional Scientific Project Execution

FSPX - Functional Scientific Project Execution

Scientific calculations are very often carried out in an iterative fashion. However, in a more complex project it can become difficult to recreate all steps that lead up to a result or to recalculate parts of the project with changed parameters. FSPX is an experimental attempt to formalize the compute environment and keep track of data input and output. This is done by means of cryptographic hashes, which allow us to determine which jobs in a project need to be recalculated.

Basic Concept

A project consists of one or more jobs. These jobs can depend on each other. A job is a function that takes zero or more inputs (simple files) and produces one or more outputs (files). Job scripts (i.e. the functions) are represented by Nix store paths. The input and output files are kept in a content addressed storage and are hashed with a SHA256 checksum. If the function, an input, or an output changes, all jobs and dependent jobs need to be recalculated.

Usage

In the first step we need to create a config file for the project. The config makes use of the nix module system:

{ pkgs, ... } :
{
  workdir = "/tmp/fspx";
  dstore = "./dstore";
  jobsets = {
    pre-run = {
      outputs = [ "data" ];
      jobScript = pkgs.writeShellScript "run"
      ''
	echo "1 2 3" > data
      '';
    };

    sum = {
      inputs = {
        ":data" = null;
      };
      outputs = [ "sum" ];
      env = pkgs.coreutils;
      jobScript = pkgs.writeShellScript "run"
        ''
          s=0;
          for i in $(cat inputs/data); do
            s=$(($s+$i))
          done;
          echo $s > sum
        '';
    };
  };
}

In this simple example we have a job named pre-run, which creates the data file named "data" and second job named sum, which sums up the numbers in data. Note that the input name in the job sum is prefix with ":". This means: take "data" from another job output. The job sum thus depends on the job pre-run. If something in pre-run changes, sum and pre-run will be automatically recalculated.

We can now build the project configuation with:

fspx build ./config.nix

This will create a directory .fspx/cfg, which points to the nix store and contains the project configuration in project.json.

Next, we need to run all jobs:

fspx run

This now creates the outputs of each job, outputs/data and outputs/sum as well as .fspx/pre-run.manifest and .fspx/sum.manifest, which record the state of inputs outputs and all job scripts.

With

fspx check

one can verify, that all jobs in the project are valid.