Examples

This is a collection of example workflows using Experi demonstrating some different ways of using it for real experiments.

Command Line Options

This is an example of using Experi in my own research which was the reason I developed it. I have a tool sdrun which translates command line options into a molecular dynamics simulation. This experiment is investigating how temperature affects the motion of particles in the simulation. The experiment consists of three separate parts;

1. The creation of a high temperature configuration which is well mixed (create)
2. Cooling the high temperature configuration to each of the desired temperatures for data collection (equil)
3. Collect data on the motion of particles within the simulation (prod)

The terms create, equil, and prod are the arguments to sdrun which reflect these stages. For this simulation I would like each of the steps to be a separate job on the scheduler, hence I use the jobs key. Part of the reason for this is that I am only creating a single configuration for the step which is then used for each temperature in the equil step. By running as separate jobs I will have a job with a single task for the first step which once finished will allow the equilibration array job with 10 elements start.

# experiment.yml
jobs:
  - command: >
     mpirun -np 12
     sdrun
     --pressure {pressure}
     --init-temp {init_temp}
     --temperature {create_temp}
     --lattice-lengths {cell_dims}
     --output {output}
     --steps {create_steps}
     create
     Trimer-P{pressure:.2f}-T{create_temp:.2f}.gsd

  - command: >
     mpirun -np 12
     sdrun
     --pressure {pressure}
     --init-temp {create_temp}
     --temperature {temperature}
     --output {output}
     --steps {equil_steps}
     equil
     Trimer-P{pressure:.2f}-T{create_temp:.2f}.gsd
     Trimer-P{pressure:.2f}-T{temperature:.2f}.gsd

  - command: >
     mpirun -np 12
     sdrun
     --pressure {pressure}
     --temperature {temperature}
     --output {output}
     --steps {steps}
     prod
     Trimer-P{pressure:.2f}-T{temperature:.2f}.gsd

variables:
create_temp: 0.80
create_steps: 10_000_000
equil_steps: 100_000_000
output: output
steps: 200_000_000
pressure: 1.00
temperature:
  - 0.30
  - 0.32
  - 0.34
  - 0.36
  - 0.38
  - 0.40
  - 0.42
  - 0.44
  - 0.46
  - 0.50

pbs:
  setup:
    - export PATH="$HOME/.pyenv/versions/crystal/bin:$PATH"
  cpus: 12
  memory: 16gb
  walltime: 100:00:00
  project: PRJ-CrysGrowth
  o: logs
  j: oe