Installation on Linux

Follow steps here

Install packages (optional if on HPC)

• Install cmake
• make sure open-mpi, lapack has been installed

  # openmpi
  sudo apt-get install libopenmpi-dev openmpi-bin 
  # lappack
  sudo apt-get install libblas3gf libblas-doc libblas-dev liblapack3gf liblapack-doc liblapack-dev
  

• Get OPENMPI_DIR. The root directory can be found by the following command. Do not include bin/mpicc

  # get the root directory of mpi
  which mpicc 
  # or
  which mpicxx
  which mpiftn
  

Configure environment

• Create set_env.sh file with the following content. ```bash #!/usr/bin/env bash

EDIT THESE!

export ATS_BASE=/software/ATS-master # root dir for the installation export ATS_BUILD_TYPE=Release # other options: Debug, RelWithDebInfo (release with debug info) export ATS_VERSION=master # the branch for both amanzi and ats export OPENMPI_DIR=/usr # this is important to include only the directory instead of /usr/bin if mpirun exists inside /usr/bin

END EDIT THESE!

export AMANZI_TPLS_BUILD_DIR=${ATS_BASE}/amanzi_tpls-build-${ATS_VERSION}-${ATS_BUILD_TYPE} export AMANZI_TPLS_DIR=${ATS_BASE}/amanzi_tpls-install-${ATS_VERSION}-${ATS_BUILD_TYPE}

export AMANZI_SRC_DIR=${ATS_BASE}/repos/amanzi export AMANZI_BUILD_DIR=${ATS_BASE}/amanzi-build-${ATS_VERSION}-${ATS_BUILD_TYPE} export AMANZI_DIR=${ATS_BASE}/amanzi-install-${ATS_VERSION}-${ATS_BUILD_TYPE}

export ATS_SRC_DIR=${AMANZI_SRC_DIR}/src/physics/ats export ATS_DIR=${AMANZI_DIR}

export path. This may not be necessary if using modulefile.

export PATH=${ATS_DIR}/bin:${PATH} export PATH=${AMANZI_TPLS_DIR}/bin:${PATH} export PYTHONPATH=${ATS_SRC_DIR}/tools/utils:${PYTHONPATH} export PYTHONPATH=${AMANZI_TPLS_DIR}/SEACAS/lib:${PYTHONPATH}

- Source the environment
```bash
source set_env.sh

• (optional) to access ats and other binary file, put the following lines in .bash_profile

  export PATH=${ATS_DIR}/bin:${PATH}
  export PATH=${AMANZI_TPLS_DIR}/bin:${PATH}
  

  Download amanzi-ats

# clone amanzi, ats and other repos
git clone -b master --recursive http://github.com/amanzi/amanzi $AMANZI_SRC_DIR

# (optional) when the previous clone does not download ats automatically
git clone -b master http://github.com/amanzi/ats $ATS_SRC_DIR

Edit bootstrap

vi ${AMANZI_SRC_DIR}/build_ATS_generic.sh

# change the following bootstrap flags and options
${AMANZI_SRC_DIR}/bootstrap.sh \
   ${dbg_option} \
   --with-mpi=${OPENMPI_DIR} \
   --enable-shared \
   --disable-clm \
   --disable-structured  --enable-unstructured \
   --disable-stk_mesh --enable-mstk_mesh \
   --enable-hypre \
   --disable-silo \
   --disable-petsc \
   --disable-amanzi_physics \
   --enable-ats_physics \
   --disable-ats_dev \
   --enable-geochemistry \
   --amanzi-install-prefix=${AMANZI_DIR} \
   --amanzi-build-dir=${AMANZI_BUILD_DIR} \
   --tpl-install-prefix=${AMANZI_TPLS_DIR} \
   --tpl-build-dir=${AMANZI_TPLS_BUILD_DIR} \
   --tpl-download-dir=${ATS_BASE}/amanzi-tpls/Downloads \
   --tools-download-dir=${ATS_BASE}/amanzi-tpls/Downloads \
   --tools-build-dir=${ATS_BASE}/build \
   --tools-install-prefix=${ATS_BASE}/install \
   --with-cmake=`which cmake` \
   --with-ctest=`which ctest` \
   --branch_ats=${ATS_VERSION} \
   --parallel=8
   
# If TPLs have already been built, and you don't want to go
# through that long process again, replace
#   --tpl-install-prefix=${AMANZI_TPLS_DIR} \
#   --tpl-build-dir=${AMANZI_TPLS_BUILD_DIR} \
#   --tpl-download-dir=${ATS_BASE}/amanzi-tpls/Downloads \
# with
#   --tpl-config-file=${AMANZI_TPLS_DIR}/share/cmake/amanzi-tpl-config.cmake \   

configure and install Amanzi-tpls, Amanzi, and ATS

• run the bootstrap

  sh ${AMANZI_SRC_DIR}/build_ATS_generic.sh
  

After ~ 1hr, the installation would finish, with ats executable in ats/amanzi-install-master-Release/bin/ats*

• check ats version

  $ which ats
  $ ats --version # this will print out the version with the last 8 digits as hash tag from git commits
  

testing

• download testing problem

cd $ATS_BASE
mkdir testing
cd testing
git clone -b master http://github.com/amanzi/ats-demos

• run test

export PATH="path/to/ats:$PATH"

cd ats-demos
cd 01_richards_steadystate
# serial
ats --xml_file=richards_steadystate.xml &> out.log

# parallel
mpirun -n 4 ats --xml_file=richards_steadystate.xml &> out.log