{ "info": { "author": "Juan Eiros", "author_email": "jeirosz@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5" ], "description": "===============================\nMDRun\n===============================\n\n\n.. image:: https://img.shields.io/pypi/v/JobSubmitter.svg\n :target: https://pypi.python.org/pypi/mdrun\n\n.. image:: https://travis-ci.org/jeiros/MDRun.svg?branch=master\n :target: https://travis-ci.org/jeiros/MDRun\n\n.. image:: https://readthedocs.org/projects/JobSubmitter/badge/?version=latest\n :target: https://JobSubmitter.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://coveralls.io/repos/github/jeiros/JobSubmitter/badge.svg?branch=master\n :target: https://coveralls.io/github/jeiros/JobSubmitter?branch=master\n\n\nI've started developing this Python program to generate the appropriate files for long classic\nMolecular Dynamics (MD) runs in the Imperial College HPC facility, using the AMBER MD engine (GPU version).\n\n\nThe objective is to automate the process, so you can chain several jobs and get the results of each one directly\nto your machine. No more manual edit of your submission scripts, copying restart files back and forth, etc. All is\nneeded is to specify the settings of your simulation in a configuration JSON file and then chain the PBS jobs using\ndependency on each other.\n\nMaybe this can be useful for other people as well, I think this should be fairly general for other HPC facilities.\n\nBefore you start\n----------------\n\nYou need to set up your `passwordless ssh `_ from your local machine to the HPC.\nTo test if it works properly, you should be able to ``scp`` a file from the HPC to your local machine\nand not be prompted for your password. Like so::\n\n $ scp username@HPC-hostname:/home/username/test_file.txt .\n test_file.txt 100% 0 0.0KB/s 00:00\n\nYou should also check that `rsync `_ is available in your HPC cluster,\nsince it is used to transfer the files (should be available in any Linux distribution, I think).\n\nCreate an example input file using the `jobsubmitter example` command.\n\n* Free software: MIT license\n* Documentation: https://JobSubmitter.readthedocs.io.\n\n\nFeatures\n--------\n\n* TODO\n\nCredits\n---------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n\n=======\nHistory\n=======\n\n0.1.0 (2016-10-18)\n------------------\n\n* First release on PyPI.\n", "description_content_type": null, "docs_url": null, "download_url": "https://github.com/jeiros/mdrun/archive/0.1.5.tar.gz", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/jeiros/mdrun", "keywords": "MD", "license": "MIT license", "maintainer": "", "maintainer_email": "", "name": "MDRun", "package_url": "https://pypi.org/project/MDRun/", "platform": "", "project_url": "https://pypi.org/project/MDRun/", "project_urls": { "Download": "https://github.com/jeiros/mdrun/archive/0.1.5.tar.gz", "Homepage": "https://github.com/jeiros/mdrun" }, "release_url": "https://pypi.org/project/MDRun/0.1.5/", "requires_dist": null, "requires_python": "", "summary": "Submission of MD runs to HPC with PBS", "version": "0.1.5" }, "last_serial": 3309952, "releases": { "0.1.5": [ { "comment_text": "", "digests": { "md5": "b29f01bed856ea797cd8ded4885d48c0", "sha256": "bce65abfc081ed621d008c11b7ae94f3048571178fe765566a316a7953b00ba4" }, "downloads": -1, "filename": "mdrun-0.1.5-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "b29f01bed856ea797cd8ded4885d48c0", "packagetype": "bdist_wheel", "python_version": "3.5", "requires_python": null, "size": 13161, "upload_time": "2017-02-27T20:08:35", "url": "https://files.pythonhosted.org/packages/82/9a/b1119d1b04efc0f96d11b08cb4738db5c2c0ad1fd590f9f6776e0806ded6/mdrun-0.1.5-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "cf57af4b128234e63ee9c33fa55c0c9d", "sha256": "0b127414fe9a63ffc0603ac8c73ad0242acb697fcb2731d9ee8a956eed26890c" }, "downloads": -1, "filename": "mdrun-0.1.5.tar.gz", "has_sig": false, "md5_digest": "cf57af4b128234e63ee9c33fa55c0c9d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8146, "upload_time": "2017-02-27T20:08:33", "url": "https://files.pythonhosted.org/packages/0e/e2/434524108a0ed23675332b31d868f3bc77237128bc37f0a080074c8caa44/mdrun-0.1.5.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "b29f01bed856ea797cd8ded4885d48c0", "sha256": "bce65abfc081ed621d008c11b7ae94f3048571178fe765566a316a7953b00ba4" }, "downloads": -1, "filename": "mdrun-0.1.5-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "b29f01bed856ea797cd8ded4885d48c0", "packagetype": "bdist_wheel", "python_version": "3.5", "requires_python": null, "size": 13161, "upload_time": "2017-02-27T20:08:35", "url": "https://files.pythonhosted.org/packages/82/9a/b1119d1b04efc0f96d11b08cb4738db5c2c0ad1fd590f9f6776e0806ded6/mdrun-0.1.5-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "cf57af4b128234e63ee9c33fa55c0c9d", "sha256": "0b127414fe9a63ffc0603ac8c73ad0242acb697fcb2731d9ee8a956eed26890c" }, "downloads": -1, "filename": "mdrun-0.1.5.tar.gz", "has_sig": false, "md5_digest": "cf57af4b128234e63ee9c33fa55c0c9d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8146, "upload_time": "2017-02-27T20:08:33", "url": "https://files.pythonhosted.org/packages/0e/e2/434524108a0ed23675332b31d868f3bc77237128bc37f0a080074c8caa44/mdrun-0.1.5.tar.gz" } ] }