Atlas

Project home: https://confluence.ecmwf.int/display/ATLAS
Contact: Willem Deconinck (willem.deconinck@ecmwf.int)
Publication:

Deconinck et al, 2017 --- Atlas: A library for numerical weather prediction and climate modelling

Atlas is a ECMWF library for parallel data-structures supporting unstructured grids and function spaces, with the aim to investigate alternative more scalable dynamical core options for Earth System models, and to support modern interpolation and product generation software

Atlas is predominantly C++ code, with main features available to Fortran codes through a F2003 interface. It requires some flavour of Unix (such as Linux). It is known to run on a number of systems, some of which are directly supported by ECMWF.

Requirements

Tested compilers include:

• GCC 4.9.1, 5.3.0, 6.3.0, 7.2.0
• Intel 15.0.2, 16.0.3, 17, 18
• CCE 8.4.5, 8.5.8, 8.6.2
• PGI-Fortran 17.7 combined with GNU-C/C++ 6.3
• PGI 17.7

Known compilers to fail include:

• PGI-Fortran 17.10, 18.1

Required dependencies:

• CMake --- For use and installation see http://www.cmake.org/
• ecbuild --- ECMWF library of CMake macros
• eckit (with MPI support) --- C++ support library

Recommended dependencies:

• fckit --- For enabling Fortran interfaces
• python (only when Fortran bindings are required)

Optional dependencies:

• gridtools-storage --- For GPU interoperability
• transi --- For enabling IFS spherical harmonics transforms ( not open-source )
• CGAL --- For enabling Delaunay triangulation of unstructured grids
• Eigen3 -- For certain linear algebra operations
• FFTW -- For enabling inverse spherical harmonics transforms (TransLocal)

Installation

Atlas employs an out-of-source build/install based on CMake.

Make sure ecbuild, eckit and fckit are installed and the ecbuild executable script is found ( which ecbuild ). Following environment variables help the build system to detect the right dependencies:

```bash

For finding eckit

ECKIT_PATH # Path to eckit prefix

For finding fckit

FCKIT_PATH # Path to fckit prefix ```

Other environment variables that could be required for optional features:

```bash

For finding gridtools-storage

GRIDTOOLSSTORAGEPATH # Path to gridtools-storage prefix

For finding transi

TRANSI_PATH # Path to transi prefix

For finding CGAL

BOOSTROOT # Path to Boost prefix CGALDIR # Path to directory containing CGALConfig.cmake Eigen3DIR # Path to directory containing Eigen3Config.cmake FFTWPATH # Path to FFTW prefix ```

Now proceed with installation as follows

```bash

Environment --- Edit as needed

ATLASSRC=$(pwd) ATLASBUILD=build ATLAS_INSTALL=$HOME/local

1. Create the build directory:

mkdir $ATLASBUILD cd $ATLASBUILD

2. Run CMake

ecbuild --prefix=$ATLASINSTALL -- $ATLASSRC

3. Compile / Install

make -j10 make install

4. Check installation

$ATLAS_INSTALL/bin/atlas --info ```

Extra flags maybe added to step 2 to fine-tune configuration.

• --build=DEBUG|RELEASE|BIT --- Optimisation level
  • DEBUG: No optimisation (-O0 -g)
  • BIT: Maximum optimisation while remaning bit-reproducible (-O2 -g)
  • RELEASE: Maximum optimisation (-O3)
• -DENABLE_OMP=OFF --- Disable OpenMP
• -DENABLE_FORTRAN=OFF --- Disable Compilation of Fortran bindings

Note: By default compilation is done using shared libraries. Some systems have linking problems with static libraries that have not been compiled with -fPIC. In this case, also compile atlas using static linking, by adding to step 2: --static

Runtime Configuration

Atlas behaviour can be configured through some environment variables with defaults marked in square brackets

• ATLAS_INFO=<0|[1]> --- Control printing of Atlas standard information
• ATLAS_DEBUG=<[0]|1> --- Control printing of Atlas debug information
• ATLAS_TRACE=<[0]|1> --- Control printing of Atlas traces (includes timings)

Contributing

Contributions to Atlas are welcome. In order to do so, please open an issue where a feature request or bug can be discussed. Then issue a pull request with your contribution. Pull requests must be issued against the develop branch.

Citing Atlas

If you publish work which mentions Atlas, or Atlas has been useful in your research, please cite the following paper:

bibtex @article{DECONINCK2017188, title = "Atlas : A library for numerical weather prediction and climate modelling", journal = "Computer Physics Communications", volume = "220", pages = "188 - 204", year = "2017", issn = "0010-4655", doi = "https://doi.org/10.1016/j.cpc.2017.07.006", url = "http://www.sciencedirect.com/science/article/pii/S0010465517302138", author = "Willem Deconinck and Peter Bauer and Michail Diamantakis and Mats Hamrud and Christian Kühnlein and Pedro Maciel and Gianmarco Mengaldo and Tiago Quintino and Baudouin Raoult and Piotr K. Smolarkiewicz and Nils P. Wedi", keywords = "Numerical weather prediction, Climate, Earth system, High performance computing, Meteorology, Flexible mesh data structure" }