A simple JIT job management framework in Python.
Project description
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.
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 potentially restart the job if necessary.
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 easy_install or pip, as follows:
easy_install custodian
or:
pip install custodian
Some plugins (e.g., vasp management) require additional setup (please see pymatgen’s documentation).
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:
python setup.py install
or to install the package in developmental mode:
python setup.py develop
Requirements
Custodian requires Python 2.7+. There are no other required dependencies.
Optional dependencies
Optional libraries that are required if you need certain features:
pymatgen 2.6.2+: To use the plugin for VASP. Please install using:
pip install pymatgen
For more information, please consult pymatgen’s documentation.
nose - For complete unittesting.
Basic usage
The main class in the workflow is known as Custodian, which manages a series of jobs with a list of error handlers. To use custodian, you need to implement concrete implementation of the abstract base classes custodian.custodian.Job and custodian.custodian.ErrorHandler. An very simple example implementation is given in the custodian_examples.py script in the scripts directory.
Other specific examples for electronic structure calculations based on the Vienna Ab Initio Simulation Package (VASP) are implemented in the custodian.vasp package. 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
from custodian.vasp.jobs import VaspJob
handlers = [VaspErrorHandler(), UnconvergedErrorHandler(),
PoscarErrorHandler()]
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.
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