AQ

Air Quality 4DEnVar suite for the SEEDS project based on the JEDI Data Assimilation environment

Obtaining AQ

git clone git@github.com:andreapiacentini/aq.git

Installation

In order to compile AQ and its prerequisites from JSCDA

Set the following environment variables

AQ_JEDI_SRC - source directory of aq (the one where the git clone has been extracted) AQ_JEDI_BLD - ecbuild directory of the aq bundle AQ_JEDI_DIR - installation directory of the aq and prerequisite include, libs, exe AQ_JEDI_UTI - installation directory of compilation utils AQ_JEDI_TEST TIER - (optional) level of testing, default to 1. 2 for 3d tests AQ_JEDI_LOCAL_PATH_TESTFILES - (optional) path of test data on the local machine

Load the appropriate modules

On kraken:

Currently Loaded Modulefiles:
  1) compiler/gcc/8.3.0
  2) compiler/intel/19.0.5.281
  3) mpi/intelmpi/2019.4.243
  4) lib/phdf5/1.10.4_impi
  5) lib/netcdf-fortran/4.4.4_phdf5_1.10.4
  6) tools/cmake/3.17.0(default)
  7) lib/boost/1.66.0_intel
  8) python/3.7.7

On nemo with intel compilers:

Currently Loaded Modulefiles:
  1) compiler/intel/18.0.1.163
  2) mpi/intelmpi/2018.1.163-ddt
  3) lib/phdf5/1.10.4_impi
  4) lib/netcdf-fortran/4.4.4_phdf5_1.10.4
  5) compiler/gcc/5.4.0
  6) tools/cmake/3.23.3
  7) lib/boost/1.66.0_gcc540
  8) python/2.7-shared
  9) python/3.7.7

On nemo with gnu compilers:

Currently Loaded Modulefiles:
  1) compiler/gcc/9.4.0
  2) mpi/intelmpi/2021.5.1
  3) lib/phdf5/1.10.8_gcc940_impi
  4) lib/netcdf-fortran/4.4.4_phdf5_1.10.8_gcc940
  5) tools/cmake/3.23.2
  6) lib/boost/1.66.0_gcc940
  7) python/3.7.7

On davinci:

Currently Loaded Modulefiles:
  1) compiler/intel/19.0.5.281
  2) mpi/intelmpi/2018.1.163
  3) lib/phdf5/1.10.4_impi
  4) lib/netcdf-fortran/4.4.4_phdf5_1.10.4
  5) lib/boost/1.66.0_intel
  6) python/3.9.0

Recover ecbuild

mkdir -p $AQ_JEDI_UTI
cd $AQ_JEDI_UTI
git clone https://github.com/ecmwf/ecbuild.git

Set PATH for using ecbuild

export PATH=${AQ_JEDI_UTI}/ecbuild/bin:$PATH

You can already set the path for the utilities that will be compiled together with the bundle

export PATH=${AQ_JEDI_DIR}/bin:$PATH

Define extra paths in the .bashrc

NetCDF_INCLUDE_DIRS is undefined and required by ecbuild:ecbuild_find_package

export NetCDF_INCLUDE_DIRS=$NETCDF_DIR/include

or

export NetCDF_INCLUDE_DIRS=$NETCDF4_INCDIR

Make BOOST point to the appropriate recent version (module load lib/boost/1.66.0_intel)

export BOOST_ROOT=/softs/local_intel/boost/1.66.0

or on nemo

export BOOST_ROOT=/data/softs/local/boost/1.66.0_gcc540

On nemo make Eigen3 point to the appropriate recent version

export Eigen3_ROOT=/data/softs/local/eigen/3.3.5_gcc540

Point to the appropriate toolchain for compilation options

For the intel based compilations

export ECBUILD_TOOLCHAIN_DIR=$AQ_JEDI_SRC/cmake
export ECBUILD_TOOLCHAIN=${ECBUILD_TOOLCHAIN_DIR}/cerfacs_intel.cmake

For the gnu based compilations

export ECBUILD_TOOLCHAIN_DIR=$AQ_JEDI_SRC/cmake
export ECBUILD_TOOLCHAIN=${ECBUILD_TOOLCHAIN_DIR}/cerfacs_gnu.cmake

Install the bundle by executing the install script

From $AQ_JEDI_SRC

./install_aq.ksh

Run the tests

From $AQ_JEDI_BLD

cd aq
ctest