The supported platforms are Linux and MacOS. If you use Windows, follow these instructions to set up a running Linux platform:
-
Go to Start. Search for "Turn Windows features on or off."
-
Check the option Windows Subsystem for Linux.
-
Open Command Prompt as an administrator.
-
Run the command below to install the Distro (e.g. Ubuntu, Debian, ...) of your choice:
wsl --install -d <Distro> -
Launch the Distro by searching from the start menu and insert a username and password. Remember that when you launch the virtual machine you are opening a terminal in the
$HOMEof your Linux platform.
You can access the files of your virtual machine by opening the Windows File Explorer and looking for the Linux folder. Inside the folder with the name of your Distro you can find your home directory.
First, install on your laptop using a package manager the following fundamental software (dependencies) necessary to compile and run Smilei. With the same steps, you are also installing Python which will allow you to run Python scripts (.py) and jupyter notebooks.
For Debian-based (Ubuntu) OS:
sudo apt-get update
sudo apt-get install git python3-h5py python3-ipython python3-pint python3-sphinx python3-matplotlib python3-dev python3-numpy python3-scipy python3-pip build-essential gcc libhdf5-openmpi-dev
Open your .bashrc or .bash_profile file in your $HOME. For example, if you want to use the nano editor, type in the terminal:
nano $HOME/.bashrc
Add the following lines:
export PYTHONEXE=python3
export HDF5_ROOT_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
and source it:
source $HOME/.bashrc
For Fedora OS:
sudo dnf install gcc-c++ git hdf5-openmpi hdf5-openmpi-devel openmpi-devel python python-devel python3-h5py ipython python3-pint python3-sphinx python3-matplotlib
Open your .bashrc or .bash_profile file in your $HOME. For example, if you want to use the nano editor, type in the terminal:
nano $HOME/.bashrc
Add the following lines:
module load mpi
export HDF5_ROOT_DIR=/usr/lib64/openmpi/
and source it:
source $HOME/.bashrc
For ArchLinux OS:
sudo pacman -S git hdf5-openmpi python-numpy python-sphinx python-h5py-openmpi python-matplotlib python-pint make gcc
If you encounter problems, you may need to install openmpi and/or hdf5 directly from source. To do that, try to follow the instructions here.
Download the source code to the path of your choice:
cd /path/of/your/choice/
git clone https://github.com/SmileiPIC/Smilei.git smilei
Move to the downloaded directory:
cd smilei
then compile:
make -j 2
build the Python module to manage the output:
make happi
Now you can use the command import happi in Python scripts to get access to the functions that allow you to read the output of a Smilei simulation.
First, you will need to install Xcode and the Command Line Tools to be able to compile Smilei:
xcode-select --install
and follow the instructions.
Here we show how to install all dependencies needed by Smilei using Brew.
Install HomeBrew:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Install Smilei:
brew install --HEAD iltommi/brews/smilei
Smilei executables (smilei and smilei_test) and the Python module are now accessible from everywhere.
Install Python packages needed for the happi python module:
pip3 install ipython h5py pint sphinx matplotlib scipy
To run efficiently in parallel on your machine you need to know your architecture.
For example, you can find out the number of threads per core and cores per socket on your machine with the command: lscpu (Linux) or sysctl -a | grep machdep.cpu (MacOS).
Copy from the smilei/bin directory the executable (smilei) and an input file (input.py) in a directory of your choice and move there.
Set the number of threads per core depending on the machine
for example, if Thread(s) per core = 2 (in the output of the lscpu command), then
export OMP_NUM_THREADS=2
export OMP_SCHEDULE=dynamic
and if you have Core(s) per socket = 4, you can run on the 4 cores like this
mpirun -np 4 ./smilei input.py