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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

Documentation

Documentation for Longbow users can be found here:

https://longbow.readthedocs.io/

Examples

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

longbow --examples

or

https://file-store.hecbiosim.org/longbow-examples.zip

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:

https://github.com/HECBioSim/Longbow/issues

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://github.com/HECBioSim/Longbow/actions

Code coverage: https://coveralls.io/github/HECBioSim/Longbow

About

Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.

www.hecbiosim.ac.uk

Topics

amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque

Resources

Readme
License
Activity
Custom properties

Stars

18 stars

Watchers

5 watching

Forks

6 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
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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
Documentation
Documentation for Longbow users can be found here:
https://longbow.readthedocs.io/
Examples
Example files can be installed either through the Longbow command-line or by
downloading from the HECBioSim website manually:
longbow --examples
or
https://file-store.hecbiosim.org/longbow-examples.zip
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:
https://github.com/HECBioSim/Longbow/issues
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://github.com/HECBioSim/Longbow/actions
Code coverage: https://coveralls.io/github/HECBioSim/Longbow
About
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines. 
www.hecbiosim.ac.uk
Topics
amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque
Resources
Readme
License
Activity
Custom properties
Stars
18 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
ciPyPI - VersionPyPI - StatusPyPI - DownloadsPepy Total DownloadsCoverage StatusDocs - Status
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
Documentation
Documentation for Longbow users can be found here:
https://longbow.readthedocs.io/
Examples
Example files can be installed either through the Longbow command-line or by
downloading from the HECBioSim website manually:
longbow --examples
or
https://file-store.hecbiosim.org/longbow-examples.zip
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:
https://github.com/HECBioSim/Longbow/issues
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://github.com/HECBioSim/Longbow/actions
Code coverage: https://coveralls.io/github/HECBioSim/Longbow
About
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines. 
www.hecbiosim.ac.uk
Topics
amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque
Resources
Readme
License
Activity
Custom properties
Stars
18 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
ciPyPI - VersionPyPI - StatusPyPI - DownloadsPepy Total DownloadsCoverage StatusDocs - Status
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
Documentation
Documentation for Longbow users can be found here:
https://longbow.readthedocs.io/
Examples
Example files can be installed either through the Longbow command-line or by
downloading from the HECBioSim website manually:
longbow --examples
or
https://file-store.hecbiosim.org/longbow-examples.zip
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:
https://github.com/HECBioSim/Longbow/issues
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://github.com/HECBioSim/Longbow/actions
Code coverage: https://coveralls.io/github/HECBioSim/Longbow
About
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines. 
www.hecbiosim.ac.uk
Topics
amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque
Resources
Readme
License
Activity
Custom properties
Stars
18 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
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ciPyPI - VersionPyPI - StatusPyPI - DownloadsPepy Total DownloadsCoverage StatusDocs - Status
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
Documentation
Documentation for Longbow users can be found here:
https://longbow.readthedocs.io/
Examples
Example files can be installed either through the Longbow command-line or by
downloading from the HECBioSim website manually:
longbow --examples
or
https://file-store.hecbiosim.org/longbow-examples.zip
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:
https://github.com/HECBioSim/Longbow/issues
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://github.com/HECBioSim/Longbow/actions
Code coverage: https://coveralls.io/github/HECBioSim/Longbow
About
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines. 
www.hecbiosim.ac.uk
Topics
amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque
Resources
Readme
License
Activity
Custom properties
Stars
18 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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ciPyPI - VersionPyPI - StatusPyPI - DownloadsPepy Total DownloadsCoverage StatusDocs - Status
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
Documentation
Documentation for Longbow users can be found here:
https://longbow.readthedocs.io/
Examples
Example files can be installed either through the Longbow command-line or by
downloading from the HECBioSim website manually:
longbow --examples
or
https://file-store.hecbiosim.org/longbow-examples.zip
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:
https://github.com/HECBioSim/Longbow/issues
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://github.com/HECBioSim/Longbow/actions
Code coverage: https://coveralls.io/github/HECBioSim/Longbow
About
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines. 
www.hecbiosim.ac.uk
Topics
amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque
Resources
Readme
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18 stars
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5 watching
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6 forks
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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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
Documentation
Documentation for Longbow users can be found here:
https://longbow.readthedocs.io/
Examples
Example files can be installed either through the Longbow command-line or by
downloading from the HECBioSim website manually:
longbow --examples
or
https://file-store.hecbiosim.org/longbow-examples.zip
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:
https://github.com/HECBioSim/Longbow/issues
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://github.com/HECBioSim/Longbow/actions
Code coverage: https://coveralls.io/github/HECBioSim/Longbow
About
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines. 
www.hecbiosim.ac.uk
Topics
amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque
Resources
Readme
License
Activity
Custom properties
Stars
18 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
ciPyPI - VersionPyPI - StatusPyPI - DownloadsPepy Total DownloadsCoverage StatusDocs - Status
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
Documentation
Documentation for Longbow users can be found here:
https://longbow.readthedocs.io/
Examples
Example files can be installed either through the Longbow command-line or by
downloading from the HECBioSim website manually:
longbow --examples
or
https://file-store.hecbiosim.org/longbow-examples.zip
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:
https://github.com/HECBioSim/Longbow/issues
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://github.com/HECBioSim/Longbow/actions
Code coverage: https://coveralls.io/github/HECBioSim/Longbow
About
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines. 
www.hecbiosim.ac.uk
Topics
amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque
Resources
Readme
License
Activity
Custom properties
Stars
18 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages