Installing aLENS from scratch

General tasks to do beforehand if developing aLENS

Get github account and collaborator status on aLENS and SimToolbox
Install git and setup up token access in global git config
(Optional) Get Intel license to install MKL on system

Ubuntu (version 22)

WARNING: Make sure you have more than 2Gb of RAM and 30Gb of hard drive storage. There are work arounds for reduced memory and storage but these are not covered in this tutorial.

(Optional) If on virtual machine set up port forwarding to ssh into desktop SSH into virtual machine in virtual box
Upgrade to make sure you have latest apt version
```
sudo apt update
sudo apt upgrade
```

Install MKL on system (from this blog)

wget -P /tmp [https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB](https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB)
sudo apt-key add /tmp/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
sudo sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list'
sudo apt update
sudo apt install intel-mkl-64bit-2020.0-088

apt-key command may throw a warning. This is fine, but for further reading, please see: What commands (exactly) should replace the deprecated apt-key?

Tell computer where to find mkl by setting
```
export MKLROOT=/opt/intel/mkl
```
Linux usually installs the mkl package in /opt directory but check to make sure intel/mkl is there. Otherwise, go searching for it. Be sure to add MKLROOT variable to .bashrc file so that you don’t always have to type above command when you open a new terminal. Quick way to add this command to your path is with the command
```
echo 'export MKLROOT=/opt/intel/mkl' >> ~/.bashrc
```

Install other necessary dependencies

sudo apt install gcc g++ cmake openmpi-bin openmpi-doc libopenmpi-dev lbzip2

Make sure your make version <4.3 otherwise Trilinos12 will not compile. This can be installed by first removing make and then downloading and installing the debian package

sudo apt-get remove make
wget http://ftp.de.debian.org/debian/pool/main/m/make-dfsg/make_4.2.1-1.2_amd64.deb
sudo dpkg -i make_4.2.1-1.2_amd64.deb

Make directories to store program files
```
mkdir -p ~/projects ~/local/aLENS
```

Create project structure and clone

cd ~/projects
git clone --recursive git@github.com:flatironinstitute/aLENS.git
cd aLENS/Dep

Download depency softwares using the provided script
```
python3 download_all.py
```
This can take longer than you think. Just be patient.

Make necessary changes to compile_all.py file which includes changing installation directory to

# your installation destination, use ABSOLUTE PATH
##From
#os.environ["SFTPATH"] = os.environ['HOME'] + \
#    '/envs/alens_env'
##To
os.environ["SFTPATH"] = os.environ['HOME'] + \
    '/local/'

Compile all the dependencies
```
python3 compile_all.py
```
This will take a LONG while. Go take a break and come back.
(Now following the installation guide on github landing page.) Go back to aLENS root directory and create a build directory
```
cd ..
mkdir build
```
Modify cmake-example.sh by replacing the variables SFTPATH and CMAKE_INSTALL_PREFIX definitions with
```
-D CMAKE_INSTALL_PREFIX="${HOME}/local/aLENS" \
-D SFTPATH="${HOME}/local" \
```
Go to build directory, run cmake script, and make executable
```
cd build
sh ../cmake-example.sh
make -j <number_of_compiling_cores>
```
WARNING: Leaving <number_of_compiling_cores> blank creates threads equal to the number of cores on your local machine. If you do this with a virtual machine, it will most likely crash during compilation.

Compiling creates the executable file aLENS.X which you can run in any of the example simulations included in the Examples directory of aLENS.

Flatiron cluster (2022-05-18)

This is much easier but only because all dependencies are already installed on our module system.

Make useful directories to store program files
```
mkdir -p ~/projects ~/local/aLENS
```

Create project structure and clone

cd ~/projects
git clone --recursive git@github.com:flatironinstitute/aLENS.git
cd aLENS

Load essential modules

module purge
module load modules gcc cmake gsl boost lib/fftw3 intel-mkl openmpi4 trilinos/12.18.1-mpi eigen vtk

Export environment variables

export MKL_INTERFACE_LAYER=GNU,LP64
export MKL_THREADING_LAYER=GNU
export BOOST_ROOT=$BOOST_BASE
export FFTWDIR=$FFTW3_BASE
unset OMPI_CC
unset OMPI_CXX
export OMP_DISPLAY_ENV=true
export OMP_MAX_ACTIVE_LEVELS=1

Modify cmake-example.sh by replacing SFTPATH and CMAKE_INSTALL_PREFIX definitions with

-D CMAKE_INSTALL_PREFIX="${HOME}/local/aLENS" \
-D SFTPATH="/cm/shared/sw/nix/store" \

Make and go to build directory, run cmake script, and make the executable
```
mkdir build
cd build
sh ../cmake-example.sh
make -j
```

This will produce an executable file aLENS.X that you can run in any of the simulation directory included in the Examples directory of aLENS.