Getting Started with AToM

Supported public AToM installations

Note

Users are highly encouraged to make use of the AToM public installations, which we maintain and support.

NERSC

We currently support an AToM public installation on the Edison supercomputer at NERSC. The project install directory is under:

/project/projectdirs/atom/atom-install-edison

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 one. Use atom for the repository name.

General Atomics

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

Contact 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 git@github.com: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:

  • OMFIT
  • IPS_ATOM
  • GACODE
  • HARVEST_CLIENT
  • GACODE_ADD
  • EPED

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:

../atom-website/html

To see the website locally point your browser to open the index.html contained in that directory. For example

firefox file:///...../atom-website/html/index.html

To publish the documentation online (must have write permissions to the AToM GitHub repository):

cd atom
make ATOM-online