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Custodian

Custodian is a simple, robust and flexible just-in-time (JIT) job management framework written in Python. Using custodian, you can create wrappers that perform error checking, job management and error recovery. It has a simple plugin framework that allows you to develop specific job management workflows for different applications.

Error recovery is an important aspect of many high-throughput projects that generate data on a large scale. When you are running on the order of hundreds of thousands of jobs, even an error rate of 1% would mean thousands of errored jobs that would be impossible to deal with on a case-by-case basis.

The specific use case for custodian is for long running jobs, with potentially random errors. For example, there may be a script that takes several days to run on a server, with a 1% chance of some IO error causing the job to fail. Using custodian, one can develop a mechanism to gracefully recover from the error, and restart the job with modified parameters if necessary.

The current version of Custodian also comes with several sub-packages for error handling for Vienna Ab Initio Simulation Package (VASP), NwChem, QChem, FEFF, Lobster and CP2K calculations. See change log for latest updates.

Getting custodian

Stable version

The version at the Python Package Index (PyPI) is always the latest stable release that will be hopefully, be relatively bug-free. The easiest way to install custodian on any system is to use pip, as follows::

pip install custodian

Some plugins (e.g., vasp management) require additional setup (please see pymatgen docs.

Developmental version

The bleeding edge developmental version is at the custodian’s Github repo. The developmental version is likely to be more buggy, but may contain new features. The Github version include test files as well for complete unit testing. After cloning the source, you can type::

pip install -e .

to install the package in editable mode.

Requirements

Custodian requires Python 3.8+. There are no other required dependencies.

Optional dependencies

Optional libraries that are required if you need certain features:

  1. Python Materials Genomics (pymatgen) 2022.1+: To use the plugin for VASP, NwChem and Qchem. Please install using::

    pip install pymatgen

    For more information, please consult pymatgen docs.

  2. pytest - For complete unittesting.
  3. pycodestyle - For checking pep8 compliance.

Usage

The main class in the workflow is known as Custodian, which manages a series of jobs with a list of error handlers. The general workflow for Custodian is presented in the figure below.

Overview of the Custodian workflow.

The Custodian class takes in two general inputs - a list of Jobs and a list of ErrorHandlers. Jobs should be subclasses of the :class:custodian.custodian.Job abstract base class and ErrorHandlers should be subclasses of the :class:custodian.custodian.ErrorHandler abstract base class. To use custodian, you need to implement concrete implementations of these abstract base classes.

Simple example

A very simple example implementation is given in the custodian_examples.py script in the scripts directory. We will now go through the example in detail here.

The ExampleJob has the following code.

class ExampleJob(Job):

    def __init__(self, jobid, params=None):
        if params is None:
            params = {"initial": 0, "total": 0}
        self.jobid = jobid
        self.params = params

    def setup(self):
        self.params["initial"] = 0
        self.params["total"] = 0

    def run(self):
        sequence = [random.uniform(0, 1) for i in range(100)]
        self.params["total"] = self.params["initial"] + sum(sequence)

    def postprocess(self):
        pass

    @property
    def name(self):
        return f"ExampleJob{self.jobid}"

The ExampleJob simply sums a random sequence of 100 numbers between 0 and 1, adds it to an initial value and puts the value in ‘total’ variable. The ExampleJob subclasses the Job abstract base class, and implements the necessary API comprising of just three key methods: setup(), run(), and postprocess().

Let us now define an ErrorHandler that will check if the total value is >= 50, and if it is not, it will increment the initial value by 1 and rerun the ExampleJob again.

class ExampleHandler(ErrorHandler):

    def __init__(self, params):
        self.params = params

    def check(self):
        return self.params["total"] < 50

    def correct(self):
        self.params["initial"] += 1
        return {"errors": "total < 50", "actions": "increment by 1"}

As you can see above, the ExampleHandler subclasses the ErrorHandler abstract base class, and implements the necessary API comprising just two key methods: check() and correct().

The transfer of information between the Job and ErrorHandler is done using the params argument in this example, which is not ideal but is sufficiently for demonstrating the Custodian API. In real world usage, a more common transfer of information may involve the Job writing the output to a file, and the ErrorHandler checking the contents of those files to detect error situations.

To run the job, one simply needs to supply a list of ExampleJobs and ErrorHandlers to a Custodian.

n_jobs = 100
params = {"initial": 0, "total": 0}
c = Custodian([ExampleHandler(params)],
              [ExampleJob(i, params) for i in xrange(n_jobs)],
              max_errors=n_jobs)
c.run()

If you run custodian_example.py in the scripts directory, you will noticed that a custodian.json file was generated, which summarizes the jobs that have been run and any corrections performed.

Practical example: Electronic structure calculations

A practical example where the Custodian framework is particularly useful is in the area of electronic structure calculations. Electronic structure calculations tend to be long running and often terminates due to errors, random or otherwise. Such errors become a major issue in projects that performs such calculations in high throughput, such as the Materials Project.

The Custodian package comes with a fairly comprehensive plugin to deal with jobs (custodian.vasp.jobs) and errors (custodian.vasp.handlers) in electronic structure calculations based on the Vienna Ab Initio Simulation Package (VASP). To do this, Custodian uses the Python Materials Genomics ([pymatgen]) package to perform analysis and io from VASP input and output files.

A simple example of a script using Custodian to run a two-relaxation VASP job is as follows:

from custodian.custodian import Custodian
from custodian.vasp.handlers import VaspErrorHandler, \
    UnconvergedErrorHandler, PoscarErrorHandler, DentetErrorHandler
from custodian.vasp.jobs import VaspJob

handlers = [VaspErrorHandler(), UnconvergedErrorHandler(),
            PoscarErrorHandler(), DentetErrorHandler()]
jobs = VaspJob.double_relaxation_run(args.command.split())
c = Custodian(handlers, jobs, max_errors=10)
c.run()

The above will gracefully deal with many VASP errors encountered during relaxation. For example, it will correct ISMEAR to 0 if there are insufficient KPOINTS to use ISMEAR = -5.

Using custodian, you can even setup potentially indefinite jobs, e.g. kpoints convergence jobs with a target energy convergence. Please see the converge_kpoints script in the scripts for an example.

cstdn - A yaml-spec controlled job

Custodian now comes with a cstdn script, which allows you to do fine-grained control of a job using a yaml spec file. Below is an annotated example of how you can specify a double VASP relaxation followed by a static calculation. Minor modifications would allow very customizable calculations, though this is obviously not meant for highly complex workflows. For those, usage of FireWorks is highly recommended.

Sample yaml spec::

# Specifies a list of jobs to run.
# Each job is specified by a `jb: <full class path>` with parameters specified
# via the params dict.

jobs:
- jb: custodian.vasp.jobs.VaspJob
  params:
    final: False
    suffix: .relax1
- jb: custodian.vasp.jobs.VaspJob
  params:
    final: False
    suffix: .relax2
    settings_override:
    - {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
- jb: custodian.vasp.jobs.VaspJob
  params:
    final: True
    suffix: .static3
    settings_override:
    - {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
    - {"dict": "INCAR", "action": {"_set": {"NSW": 0}}}


# This key specifies parameters common to all jobs.
# Keys starting with $ are expanded to the environmental values.
# The example below means the parameter vasp_cmd is set to the value with
# $PBS_NODEFILE expanded.

jobs_common_params:
  $vasp_cmd: ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "24", "vasp"]


# Specifies a list of error handlers in the same format as jobs. Similarly,
# parameters passed to the handler __init__ can be configured the same
# way as for jobs.
handlers:
- hdlr: custodian.vasp.handlers.VaspErrorHandler
- hdlr: custodian.vasp.handlers.AliasingErrorHandler
- hdlr: custodian.vasp.handlers.MeshSymmetryErrorHandler

# Specifies a list of error handlers in the same format as jobs.
validators:
- vldr: custodian.vasp.validators.VasprunXMLValidator

#This sets all custodian running parameters.
custodian_params:
  max_errors: 10
  scratch_dir: /tmp
  gzipped_output: True
  checkpoint: True

You can then run the job using the following command::

cstdn run <path to yaml file>

API/Reference Docs

The API docs are generated using Sphinx auto-doc and outlines the purpose of all modules and classes, and the expected argument and returned objects for most methods. They are available at the link below.

How to cite custodian

If you use custodian in your research, especially the VASP component, please consider citing the following work::

Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier,
Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A.
Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
Open-Source Python Library for Materials Analysis.* Computational
Materials Science, 2013, 68, 314–319. `doi:10.1016/j.commatsci.2012.10.028
<http://dx.doi.org/10.1016/j.commatsci.2012.10.028>`_

License

Custodian is released under the MIT License. The terms of the license are as follows::

The MIT License (MIT)
Copyright (c) 2011-2012 MIT & LBNL

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software")
, to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
© Copyright 2011, Materials Project