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. If you have already downloaded an engine’s source files, the general steps for building SSAGES with this engine are as follows. (The example here assumes the engine is called “Engine” and uses the respective CMake flag -DENGINE_SRC.)

mkdir build/
cd build/
cmake .. -DENGINE_SRC=/path/to/engine
make

The different supported engines have respective _SRC flags to specify their source code path. For engine-specific steps and options, consult the Engines page, which provides more in-depth directions. SSAGES supports most CMake flags, including -DCMAKE_BUILD_TYPE or specifying the compilers with -DCMAKE_C_COMPILER= and -DCMAKE_CXX_COMPILER=.

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.

For these and other supported engines, you can build with a local copy of the MD engine source code, as described in the Engines section. This can be useful if you are building on a system that has limited or no connectivity or if you want to add user modifications to the engine’s source code before compiling.

Run SSAGES

In order to run SSAGES, you call the executable followed by the input file. For example, with an input file called input.json, simple single-core jobs can call

./ssages input.json

while jobs running on multiple threads can call

mpiexec -np 6 ./ssages input.json

Here, the -np flag dictates the total number of processors on which the simulation will run and input.json is the input file. For more information, consult the Input Files section.

Advanced Options

In case these simple steps do not meet your need, you can find engine-specific options and advanced information on building and running SSAGES in the Engines section.