Getting Started with AToM
Supported public AToM installations
Users are highly encouraged to make use of the AToM public installations, which we maintain and support.
We currently support an AToM public installation on the Edison supercomputer at NERSC. The project install directory is under:
Users must be part of the
atom unix user group to access the NERSC public installation. If you do not have
an account at NERSC already, fill out this form to request
atom for the repository name.
An AToM installation is also maintained at GA. If you do not have GA computer access, follow the steps for GA cyber access.
Build AToM from source
candy(at)fusion.gat.com to obtain access to the AToM GitHub repository. You will need a GitHub account for this. If you are running MacOS, detailed instructions on building AToM from source can be found here.
To clone the repository:
git clone firstname.lastname@example.org:scidac/atom.git
This will make a atom directory with a Makefile in it:
cd atom ls
The Makefile is capable of downloading the sources of the individual AToM components and building them. The AToM Makefile leverages the GACODE build system, and as such it supports compilation of its components on several platforms:
ALCF_BGP ALCF_CETUS BABBAGE BANACH CAOS CARVER CMODWS DELPHI DROP EDISON_CRAY EDISON_INTEL FT GFORTRAN_CORE2 GFORTRAN_OSX GFORTRAN_OSX_64 GFORTRAN_OSX_BELLI GFORTRAN_OSX_MACPORTS GFORTRAN_OSX_TECHX GFORTRAN_PENRYN GFORTRAN_TECHX HOPPER_CRAY HOPPER_INTEL HPC_ITER IFORT_CORE2 IFORT_PENRYN JAC LINDGREN LOHAN LOKI LOKI_SCRATCH METIUS NEWT OSX_MOUNTAINLION PACER PGFORTRAN_OSX PG_OPT64 PG_OPT64_FFTW PG_OPT64_MUMPS PPPL PPPL_PATHSCALE RANGER SATURN TITAN_CRAY VENUS
AToM components include:
To make individual components (for example GACODE on the VENUS platform):
make GACODE ATOM_PLATFORM=VENUS
To make all of the AToM components:
make all ATOM_PLATFORM=VENUS
The Makefile takes care of satisfying any interdependency between the AToM components.
Maintaining an up-to-date AToM installation
The AToM Makefile is also capable of keeping the components up-to-date and in sync with each others’ versions. To update the AToM installation simply:
cd atom git pull make all ATOM_PLATFORM=VENUS
Edit and build the AToM Website
The AToM documentation website is self-contained in the AToM repository. To edit the AToM documentation one simply needs to follow the aforementioned steps and edit the .rst files in the docs/ directory:
cd atom/docs $EDITOR index.rst
The python packages required for buidling the AToM documentation can be installed with:
sudo yum install sphinx sudo yum install python-sphinx sudo pip install sphinx_rtd_theme sudo pip install sphinxcontrib.bibtex
To build a local copy of the website:
cd atom make ATOM-website
which will generate the HTML pages in the directory:
To see the website locally point your browser to open the index.html contained in that directory. For example
To publish the documentation online (must have write permissions to the AToM GitHub repository):
cd atom make ATOM-online