##Requirements ###Required Hardware:
- Nvidia graphics card with compute Compute Capability 2.0 (or greater)
- Tested on Nvidia Tesla M2070
###Required Software:
- Linux Operating System
- Tested on Ubuntu 14.04 LTS, SUSE Linux Enterprise Server 11 SP2
- Nvidia Developer Toolkit
- Tested with CUDA 4.2, 6.5
Note: If you are using the Alabama Supercomputer Center (ASC), configure based on the instructions received when you set up your account.
##Build
git clone git:https://github.com/orlandoacevedo/MCGPU.git
cd MCGPU/
make
Note: To build in debug mode, use BUILD=debug:
make BUILD=debug
##Run ###To Run a Simulation on a local machine:
cd /path/to/MCGPU/
cd bin/
./metrosim ./[configuration file] [options]
Where [configuration file] is a .config file containing configuration information, and [options] are command-line options. An example demo.config can be found in the resources folder. See below for specific .config file documentation and all command-line options available.
###To Run a Simulation on the Alabama Supercomputer Center:
cd /path/to/MCGPU/
run_gpu demo_script.txt
Choose a batch job queue:
Queue CPU Mem # CPUs
-------------- ---------- ------ ------
small-serial 40:00:00 4gb 1
medium-serial 90:00:00 16gb 1
large-serial 240:00:00 120gb 1
class 2:00:00 64gb 1-64
daytime 4:00:00 16gb 1-4
express 01:00:00 500mb 1
Enter Queue Name (default <cr>: small-serial) <must be a serial queue>
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>
You standard out for your job will be written to
<jobname>.o<job number>
###To Run a Simulation on the Alabama Supercomputer Center in debug mode:
gpu_interactive
What architecture GPU do you want [any,t10,fermi,kepler]: <kepler>
Do you want to use X-windows [y/n]: <n>
cd /path/to/MCGPU/
cd bin/
./metrosim ./[configuration file]
For more information, see the Alabama Supercomputer Center manual.
##Available Command-line Options
--serial: Runs simulation serially (on CPU; default)--parallel: Runs simulation in parallel (on GPU; requries CUDA)--list-devices: Lists available CUDA-capable devices (requires CUDA)--device <index>: Specifies what device to use when running a simulation. Index refers to one given in --list-devices. (requires CUDA)--threads <count>: Specifies number of threads to use when running on CPU (serial only)--name <title>: Specifies the name of the simulation that will be run.--steps <count>: Specifies how many simulation steps to execute in the Monte Carlo Metropolis algorithm. Ignores steps to run in config file, if present (line 10).--silent: Disables real time energy printouts
To view documentation for all command-line flags available, use the --help flag:
./metrosim --help
##Configuration File Configuration files are used to configure a simulation. Line numbers are important
[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 a molecule 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-aa.par 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; overrides z-matrix setting is present>
[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>
[23] #line 23 is a comment and is ignored.
[24] <nonbonded cutoff distance in angstroms>
[25] #line 25 is a comment and is ignored.
[26] <max rotation for a molecule in degrees>
[27] #line 27 is a comment and is ignored.
[28] <random number seed input as integer value>
[29] #line 29 is a comment and is ignored.
[30] <primary atom index to be used during cutoff as integer index of z-matrix atom in molecule>
Contributing Authors: Scott Aldige, Matt Campbell, William Champion, Matthew Hardwick, Andrew Lewis, Alexander Luchs, Robert Sanek, Riley Spahn, Kalan Stowe, Ashley Tolbert, Seth Wooten, Xiao (David) Zhang, and Orlando Acevedo