Longbow 1.3.1

Biomolecular simulation remote job submission tool.

Longbow is a piece of software that acts as a job proxying tool for biomolecular simulations, Longbow reproduces the native look and feel of using popular molecular dynamics packages (AMBER, CHARMM, GROMACS, LAMMPS and NAMD), with the difference that when those packages are used through Longbow simulations can be run on High Performance Computing (HPC) resources such as ARCHER. Longbow handles jobs setup in terms of creating job submission scripts, automatically stages input files, launches and monitors jobs and stages back simulation results. The option is also there to persistently monitor and stage (realtime local syncing with remote simulation files) simulation files at a specified time interval.

This is designed to have the jobs running on the HPC remote resource appear to the user as if the simulation has run on their local computer/cluster. Users do not have to concern themselves with writing submission files, nor do they have to worry about staging. Longbow provides a convenient interface for generating large ensembles of simulation jobs which in effect extends the packages it supports.

Licensing

Longbow is released under the GNU GPLv2 license. A copy of this license will be provided with the Longbow application when it 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

Please note: In cases where you run the setup script, Longbow will create the host configuration file in a hidden directory in your user directory. In some cases doing a manual install (not using the setup.py) then you will have to make this yourself.

Documentation

Documentation for Longbow can be found here:

http://www.hecbiosim.ac.uk/longbow-docs

Examples

Example files can be installed either through the Longbow command-line or by downloading from the HECBioSim website manually here:

http://www.hecbiosim.ac.uk/longbow-examples

Support

Support for any issues arising from using Longbow, whether these are questions, to report bug or to suggest new ideas. You should use the Longbow forums here:

http://www.hecbiosim.ac.uk/longbow-support

Developers

Developers of software that wish to contribute to Longbow/integrate Longbow into other software tools 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:

source code: https://github.com/jimboid/longbow

documentation: http://www.hecbiosim.ac.uk/longbow-devdocs