From e4d433e59ed2908b99709a86a7eb017b9dde576a Mon Sep 17 00:00:00 2001
From: Arianna Formenti <ariannaformenti@lbl.gov>
Date: Fri, 13 Sep 2024 16:18:49 -0700
Subject: [PATCH] update setup

---
 setup.md | 85 ++++++++++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 79 insertions(+), 6 deletions(-)

diff --git a/setup.md b/setup.md
index 015fc19..b8811e7 100644
--- a/setup.md
+++ b/setup.md
@@ -1,25 +1,98 @@
 ---
 title: Setup
 ---
-  
-  
+
 Welcome to the WarpX tutorials!  
 Here you can find a guide on how to set up your system to be able to run and analyze WarpX simulations.  
 Let's roll 💃🕺. 
 
 
-## Install the dependencies 
+## Install the dependencies
 
 We use Conda, that work on most opertive system (Windows, macOS, Linux).  
 As a first step get [Conda](https://docs.conda.io/en/latest/) and configure it with `libmamba`.  
 
-
-```bash markdown-code-runner
+```bash
 conda update -y -n base conda
 conda install -y -n base conda-libmamba-solver
 conda config --set solver libmamba
 conda config --set auto_activate_base false
-```  
+```
+
+Create a virtual environment for WarpX and install the dependencies. 
+
+```bash
+conda create -n warpx -c conda-forge blaspp boost ccache cmake compilers git "heffte=*=mpi_mpich*" lapackpp "openpmd-api=*=mpi_mpich*" openpmd-viewer python make numpy pandas scipy yt "fftw=*=mpi_mpich*" pkg-config matplotlib mamba mpich mpi4py ninja pip virtualenv
+```
+
+Activate your WarpX environment to make all the dependencies accessible. 
+
+```bash
+conda activate warpx
+```
+
+
+## Set up your working directory 
+
+Open a terminal in your machine.  
+For Windows users, we recommend installing [Windows Subsystem for Linux (WSL)](https://ubuntu.com/desktop/wsl), to have access to a full Ubuntu terminal environment.  
+
+Create and/or move to a working directory of your choice.  
+Throughout the tutorials we will assume that the working directory is `$HOME/warpx-tutorials`. 
+
+```bash
+mkdir $HOME/warpx-tutorials
+cd $HOME/warpx-tutorials
+```
+
+Download in this folder the material (input files and analysis scripts) 
+that will be used in the tutorials. 
+
+```bash 
+DOWNLOAD SOMEHOW THE RUNS DIRECTORY
+```
+
+
+## Build WarpX
+
+Get WarpX's source code and move into the cloned folder:  
+
+```bash
+git clone https://github.com/ECP-WarpX/WarpX.git warpx
+cd warpx
+```
+Configure the build in a directory called `build`.
+When configuring, you can pass different flags that enble or disable various options.  
+For example: `cmake -S . -B build -DWarpX_DIMS=1 -DCMAKE_BUILD_TYPE=Debug`
+will compile the code in 1D geometry and in debug mode.  
+You can find the list of the build options and their default values 
+[here](https://warpx.readthedocs.io/en/latest/install/cmake.html#build-options).  
+For these tutorials, we compile in 1D, 2D, 3D and enable FFT calculations.
+
+```bash
+cmake -S . -B build -DWarpX_DIMS="1;2;3" -DWarpX_FFT=ON
+```
+
+Finally, compile!
+
+```bash
+cmake --build build -j 4 
+```
+
+The `-j 4` options executes the compilation on 4 processes in parallel.
+
+The executables will appear in `build/bin/` as `warpx.<DIMS>d.MPI.OMP.DP.PDP.OPMD.FFT.EB.QED`. 
+You will also find `warpx.<DIMS>d` files, which are symbolic links to the executables with a shorter name. 
+
+
+## Run WarpX 
+
+To test that everything works fine, we run a first toy case.  
+
+
+```bash  
+mpirun -np 1 warpx/build/bin/warpx.3d inputs.txt
+```