Getting Started¶
Prerequisites¶
Before you try to build SSAGES, make sure that you have the following packages installed:
| Package | Required version | Package name in Ubuntu repository |
|---|---|---|
| openmpi | 1.8 or higher | openmpi-common, libopenmpi-dev |
| gcc | 4.9 or higher | gcc-4.9 |
| cmake | 2.8 or higher | cmake |
| python | 2.7 | python2.7 |
Get the source code¶
There are two ways of getting the source code for SSAGES: Download a ZIP file from github or clone the git repository. We strongly recommend the second method as it allows you to easily stay up-to-date with the latest version.
To clone the git repository, call
git clone https://github.com/MICCoM/SSAGES-public.git
Build SSAGES¶
SSAGES supports a number of simulation engines including LAMMPS and Gromacs.
It is possible to have SSAGES auto-download the source codes for LAMMPS and Gromacs.
This is done by providing the option -DLAMMPS=YES for LAMMPS and -DGROMACS=YES for
Gromacs to Cmake. However, in many cases it will be necessary to build SSAGES using
your local copy of the MD engine source code. For example, if you have modified it
to fit a special need LAMMPS or Gromacs does not support natively.
mkdir build/
cd build/
cmake .. -DLAMMPS=YES
make
or
mkdir build/
cd build/
cmake .. -DGROMACS=YES
make
This set of commands will automatically download LAMMPS/Gromacs and build it together with SSAGES. Alternatively, you can build SSAGES using a local copy of the MD engine source code.
LAMMPS can be built with optional packages. To enable or disable these packages, you can call
make yes-package
or
make no-package
respectively. For more information on optional packages for LAMMPS, refer to the LAMMPS user manual.
Run SSAGES¶
In order to run ssages you need to use run the executable followed by the input file. For example:
mpiexec -np 6 ./ssages input.json
Where the -np flag dictates the total number of processors you need and input.json is the input file. For a description of the input file click here.
More information on how to run SSAGES with a specific simulation engine can be found here:
Advanced options¶
In case these simple steps do not meet your need, you can find advanced information on building and running SSAGES here.