Biomolecular simulation remote job submission tool.
Project description
Longbow
Longbow is an automated simulation submission and monitoring tool. Longbow is designed to reproduce the look and feel of using software on the users local computer with the difference that the heavy lifting is done by a supercomputer.
Longbow will automatically generate the necessary submit files and handle all initial file transfer, monitor jobs, transfer files at configurable intervals and perform final file transfer and cleanup.
Longbow can be used to launch one-off jobs, generate ensembles of similar jobs or even run many different jobs over many different supercomputers.
Out of the box, Longbow is currently supporting the PBS/Torque, LSF, SGE, Slurm, SoGE schedulers and ships with application plugins for commonly used bio-molecular simulation softwares AMBER, CHARMM, GROMACS, LAMMPS, NAMD. Longbow is however highly configurable and will function normally with generic software without plugins, however plugins can easily be made to extend Longbow to fully support applications and schedulers that do not ship out of the box.
Using Longbow can be as simple as the following example:
local: executable -a arg1 -b arg2 -c arg3
remote: longbow executable -a arg1 -b arg2 -c arg3
Longbow is also available to developers of applications which require support for automating job submission. Longbow is available as a convenient and light-weight python API that can be integrated in a number of different way.
Licensing
Longbow is released under the BSD 3-clause license. A copy of this license is provided when Longbow is downloaded and installed.
Citing
If you make use of Longbow in your own code or in production simulations that result in publishable output, then please reference our paper:
Gebbie-Rayet, J, Shannon, G, Loeffler, H H and Laughton, C A 2016 Longbow: A Lightweight Remote Job Submission Tool. Journal of Open Research Software, 4: e1, DOI: http://dx.doi.org/10.5334/jors.95
Installation
Releases can be installed either via pip or can be installed manually, to install via pip:
pip install longbow
or to install manually (see docs) Longbow can be downloaded here:
http://www.hecbiosim.ac.uk/longbow
and then extract and run the setup.py script to install.
Documentation
Documentation for Longbow users can be found here:
Examples
Example files can be installed either through the Longbow command-line or by downloading from the HECBioSim website manually:
longbow –examples
Support
Support for any issues arising from using Longbow, whether these are questions, to report a bug or to suggest new ideas. You should use the Longbow forums here:
Developers
Developers that wish to contribute to Longbow are welcome. We do ask that if you wish to contribute to the Longbow base code that you contact us first.
The following resources are available to developers:
Code repository: https://github.com/hecbiosim/longbow
Unit testing: https://travis-ci.org/HECBioSim/Longbow
Code coverage: https://coveralls.io/github/HECBioSim/Longbow
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