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README
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#########################
--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