Skip to main content

Submission of MD runs to HPC with PBS

Project description

MDRun Documentation Status

I’ve started developing this Python program to generate the appropriate files for long classic Molecular Dynamics (MD) runs in the Imperial College HPC facility, using the AMBER MD engine (GPU version).

The objective is to automate the process, so you can chain several jobs and get the results of each one directly to your machine. No more manual edit of your submission scripts, copying restart files back and forth, etc. All is needed is to specify the settings of your simulation in a configuration JSON file and then chain the PBS jobs using dependency on each other.

Maybe this can be useful for other people as well, I think this should be fairly general for other HPC facilities.

Before you start

You need to set up your passwordless ssh from your local machine to the HPC. To test if it works properly, you should be able to scp a file from the HPC to your local machine and not be prompted for your password. Like so:

$ scp username@HPC-hostname:/home/username/test_file.txt .
test_file.txt              100%    0     0.0KB/s   00:00

You should also check that rsync is available in your HPC cluster, since it is used to transfer the files (should be available in any Linux distribution, I think).

Create an example input file using the jobsubmitter example command.


  • TODO


This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.


0.1.0 (2016-10-18)

  • First release on PyPI.

Project details

Release history Release notifications

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
mdrun-0.1.5-py2.py3-none-any.whl (13.2 kB) Copy SHA256 hash SHA256 Wheel 3.5 Feb 27, 2017
mdrun-0.1.5.tar.gz (8.1 kB) Copy SHA256 hash SHA256 Source None Feb 27, 2017

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page