Running calphy on computing clusters

The easiest way to run calphy on computing clusters is by using queue block in the input file. The queue block looks like this:

queue:
  scheduler: slurm
  cores: 20
  jobname: fec
  walltime: "23:50:00"
  queuename: shorttime
  memory: 3GB
  commands:
    - source ~/.bashrc
    - conda activate calphy

The default scheduler is local, which means that the calculations are run on the local machine. Instead slurm or sge can be specified to run on computing clusters. The number of cores, walltime, queue name etc can be set during the respective keywords. Note that if you are using a conda environment, it needs to be activated. This can be done using the commands argument. Anything listed within the commands argument is copied directly to the submission script.

Adding a new scheduler

In the current version only slurm and sge schedulers are supported. There are two ways in which a new scheduler can be added, they are described below:

Editing scheduler.py

The scheduler are implemented in calphy within calphy/scheduler.py file. An existing class can be copied and modified to support the new submission script.

Adding calphy to a submission script

An easier method would be to add calphy manually within a submission script. calphy offers a calphy_kernel command line interface which can be used for direct submission. The above queue block can be translated to an equivalent submission script as follows:

#!/bin/bash
#SBATCH --job-name=fec
#SBATCH --time=23:50:00
#SBATCH --partition=shorttime
#SBATCH --ntasks=20
#SBATCH --mem-per-cpu=3GB

source ~/.bashrc
conda activate calphy

calphy_kernel -i input.yaml -k 0

Note that calphy_kernel is called instead of calphy. Additionally an extra argument -k or --kernel is required, which takes an integer argument. This argument refers to the which calculation needs to be run from the input file. For example if the calculationsblock of the input file is as follows:

calculations:
- mode: ts 
  temperature: [1200, 1400]
  pressure: [0]
  lattice: [FCC, LQD]
  repeat: [5, 5, 5]
  reference_phase: [solid, liquid]
  n_iterations: 1

Specify -k 0 will run a calculation block equivalent to:

- mode: ts 
  temperature: [1200, 1400]
  pressure: [0]
  lattice: [FCC]
  repeat: [5, 5, 5]
  reference_phase: [solid]
  n_iterations: 1

and -k 1 will run:

- mode: ts 
  temperature: [1200, 1400]
  pressure: [0]
  lattice: [LQD]
  repeat: [5, 5, 5]
  reference_phase: [liquid]
  n_iterations: 1