OpenMM
======

From the OpenMM website http://openmm.org/

    OpenMM is a high performance toolkit for molecular simulation. Use it as a library, or as an application. We include extensive language bindings for Python, C, C++, and even Fortran. The code is open source and actively maintained on Github, licensed under MIT and LGPL. Part of the Omnia suite of tools for predictive biomolecular simulation.

Installing OpenMM on CSD3
-------------------------
Below are instructions of how to install openmm in a miniconda virtual environment. Part of the installation instructions are located at http://docs.openmm.org/latest/userguide/application.html#installing-openmm . 

Connect to a login node with:
::

    ssh your-username@login.hpc.cam.ac.uk

.. literalinclude:: scripts/openmm/openmm_gpu_setup.sh
    :language: bash
	       

Running OpenMM on CSD3
-------------------------

To submit an OpenMM job please use the following submission script:

.. literalinclude:: scripts/openmm/openmm_gpu_sbatch
    :language: bash


Here, we are using OpenMM's own testing suite to ensure the application is running properly.
The output should be similar to the following (times might be slightly different):

::

    There are 4 Platforms available:

    1 Reference - Successfully computed forces
    2 CPU - Successfully computed forces
    3 CUDA - Successfully computed forces
    4 OpenCL - Successfully computed forces

    Median difference in forces between platforms:

    Reference vs. CPU: 6.29882e-06
    Reference vs. CUDA: 6.73039e-06
    CPU vs. CUDA: 7.76279e-07
    Reference vs. OpenCL: 6.75426e-06
    CPU vs. OpenCL: 8.19109e-07
    CUDA vs. OpenCL: 2.19595e-07


The slurm submit script can be submitted to the queue with ``sbatch``. This will run on one node using one core up to a limit of 10 minutes. To run on more cores the ``-n`` option should be adjusted and the timelimit can be changed with ``-t``.