# 1. Start Docker
# macOS:
open -a Docker
# Linux:
sudo systemctl start docker
# Windows (PowerShell):
Start-Service Docker

# 2. Navigate to the containers/ folder
cd containers

# (optional) Clear all docker images and containers
docker system prune -a

# 3. Create the "docker_openwq" container
docker compose up -d

# (optional) Stop the container
docker compose down
# (optional) See the containers running
docker ps

# 4. Run a shell inside the container
docker exec -it docker_openwq /bin/bash
                        

# (Optional but recommended) Clean previous CMake
# cache to avoid stale configuration issues
rm -f CMakeCache.txt
rm -rf CMakeFiles

# CMake command syntax:
cmake -DHOST_MODEL_TARGET=<target> \
      -DCMAKE_BUILD_TYPE=<type> .

# Examples:
cmake -DHOST_MODEL_TARGET=summa_openwq \
      -DCMAKE_BUILD_TYPE=Release .

cmake -DHOST_MODEL_TARGET=mizuroute_openwq \
      -DCMAKE_BUILD_TYPE=Debug .

cmake -DHOST_MODEL_TARGET=mizuroute_lakes_cslm_openwq \
      -DCMAKE_BUILD_TYPE=Release .

# Then compile:
# With 8 GB container RAM: use make -j1 (sequential, slower but safe)
# With 16 GB container RAM: use make -j2 (parallel, faster)
make -j1
# Note: if you increased container RAM for compilation, consider
# reducing it afterwards to avoid competing with the host machine.
# Executable created in .../openwq/openwq/bin/
                        

# 1. Navigate to the containers/ folder
cd containers

# 2. Build Apptainer/Singularity image
apptainer build openwq.sif openwq_apptainer.def
# or
singularity build openwq.sif openwq_apptainer.def
# Or with --fakeroot (if required by your system):
apptainer build --fakeroot openwq.sif openwq_apptainer.def
# or
singularity build --fakeroot openwq.sif openwq_apptainer.def

# IMPORTANT: Build on same architecture as target HPC
# (x86_64 vs ARM). Contact HPC team for site policies.

# 3. Transfer SIF to HPC (if built locally)
scp openwq.sif user@hpc:/path/to/containers/

# 4. Enter the container (run a shell)
apptainer shell --bind $(pwd):/code openwq.sif
# or
singularity shell --bind $(pwd):/code openwq.sif
                        

# (Optional but recommended) Clean previous CMake
# cache to avoid stale configuration issues
rm -f CMakeCache.txt
rm -rf CMakeFiles

# CMake command syntax:
cmake -DHOST_MODEL_TARGET=<target> \
      -DCMAKE_BUILD_TYPE=<type> \
      -DCMAKE_PREFIX_PATH="<paths>" .

# Examples:
cmake -DHOST_MODEL_TARGET=summa_openwq \
      -DCMAKE_BUILD_TYPE=Release \
      -DCMAKE_PREFIX_PATH="/usr/local/phreeqcrm;/usr/local/sundials" .

cmake -DHOST_MODEL_TARGET=mizuroute_openwq \
      -DCMAKE_BUILD_TYPE=Release \
      -DCMAKE_PREFIX_PATH="/usr/local/phreeqcrm;/usr/local/sundials" .

# Then compile:
# With 8 GB container RAM: use make -j1 (sequential, slower but safe)
# With 16 GB container RAM: use make -j2 (parallel, faster)
make -j1
# Note: if you increased container RAM for compilation, consider
# reducing it afterwards to avoid competing with the host machine.
# Executable created in .../openwq/openwq/bin/
                        

# 1. Install system dependencies (Ubuntu/Debian)
sudo apt-get install g++ gfortran cmake \
  libnetcdf-dev libnetcdff-dev \
  libhdf5-dev libopenblas-dev liblapack-dev

# 2. Install Armadillo
cd openwq/utils
./install_armadillo.sh
# Installs to openwq/utils/armadillo-VERSION

# 3. (Optional) Install SUNDIALS for ODE solver
wget https://github.com/LLNL/sundials/archive/v7.1.1.tar.gz
tar -xzf v7.1.1.tar.gz && cd sundials-7.1.1
mkdir build && cd build
cmake .. -DBUILD_FORTRAN_MODULE_INTERFACE=ON \
         -DCMAKE_INSTALL_PREFIX=/usr/local/sundials
make -j4 && sudo make install

# 4. Compile OpenWQ
cd openwq
cmake -DHOST_MODEL_TARGET=summa_openwq \
      -DCMAKE_BUILD_TYPE=Release .
# With 8 GB container RAM: use make -j1 (sequential, slower but safe)
# With 16 GB container RAM: use make -j2 (parallel, faster)
make -j1
# Note: if you increased container RAM for compilation, consider
# reducing it afterwards to avoid competing with the host machine.
# Executable in bin/ folder