#########################
--GPU Comp Chem--
#########################

Required Hardware:
    NVIDIA card with compute Compute Capability 2.0
    Tested on: NVIDIA Tesla M2070

Required Software:
    Linux Operating System
        Tested on: SUSE Linux Enterprise Server 11 SP1
    NVIDIA Developer Toolkit
        Download from http://developer.nvidia.com/cuda-downloads based on your
        OS and follow the instructions given to install.
        Tested with: CUDA 4.0

    If you are using the Alabama Supercomputer Center(ASC) configure based on the
    instructions received when you set up your account.

    When you have both of the above installed you should be ready to build.


Build Instructions:
    >> git clone git://github.com/rlyspn/SeniorDesign_COMP4710.git
    >> cd SeniorDesign_COMP4710/
    >> make

    If on the ASC:
    >> git clone git://github.com/rlyspn/SeniorDesign_COMP4710.git
    --scp Senior Design Directory to the ASC into the directory of your choice.
    >> cd /path/to/SeniorDesign_COMP4710/
    >> make

To Run a Simulation on a local machine:
    >> cd /path/to/SeniorDesign_COMP4710/
    >> cd bin/
    >> ./ParallelExample

To Run a Simulation on the Alabama Supercomputer Center:

    >> cd /path/to/SeniorDesign_COMP4710/
    >> run_gpu bin/ParallelExample
    Choose a batch job queue:
     
    Queue                 CPU    Mem # CPUs
    -------------- ---------- ------ ------
    daytime           4:00:00   16gb    1-4 
    express          01:00:00  500mb      1 
    large-parallel  240:00:00  120gb   2-64 
    large-serial    240:00:00   35gb      1 
    medium-parallel 100:00:00   32gb   2-16 
    medium-serial    90:00:00    4gb      1 
    small-parallel   48:00:00    8gb    2-8 
    small-serial     40:00:00    1gb      1 
    
     
    Enter Queue Name (default <cr>: small-serial) <must be a serial queue>
    Enter number of processor cores (default <cr>: 1 ) <enter>
    Enter Time Limit (default <cr>: 40:00:00 HH:MM:SS) <enter time limit>
    Enter memory limit (default <cr>: 500mb ) <enter required memory>
    Enter GPU architecture [t10/fermi/any] (default <cr>: any) <fermi>
    Enter a name for your job (default: bin/parallelTe)
    <name of your job>
    
    You standard out for your job will be written to 
    <jobname>.o<job number>

    For more information see the Alabama Supercomputer Center manual.

Configuration File:
    Configuration files are used to configure a simulation. 
    Line numbers are important
    Example configuration file:
[1]     #line 1 is a comment and will be ignored
[2]     <x dimension>
[3]     <y dimension>
[4]     <z dimension>
[5]     #line 5 is a comment and will be ignored
[6]     <temperature in kelvin>
[7]     #line seven is a comment and will be ignored
[8]     <max translation for an atom in angstroms>
[9]     #line 9 is a comment and is ignored
[10]    <number of steps for which to run the simulation> 
[11]    #line 11 is a commend and is ignored
[12]    <number of molecules in the simulation>
[13]    #line 13 is a comment and is ignored
[14]    <path to the opls file>
[15]    #line 15 is a comment and is ignored
[16]    <path to the z-matrix file to use>
[17]    #line 17 is a comment and is ignored.
[18]    <path to the state input file>
[19]    #line 19 is a comment and is ignored.
[20]    <path to the stateoutput file>
[21]    #line 21 is a comment and is ignored.
[22]    <path to the pdb output file>

There are some known issues and TODOs listed here:
https://github.com/rlyspn/SeniorDesign_COMP4710/wiki/Known-Issues-and-TODOs