adapt readme

README.md

@@ -8,6 +8,7 @@ The most recent release can be cited with the following reference
 [![DOI](https://zenodo.org/badge/498376436.svg)](https://zenodo.org/doi/10.5281/zenodo.13928119)
 
 The project is described in two conference papers, which were presented at ISPDC 24 in Chur, Switzerland, July 2024:
+
 - [High-Performance Simulations for Urban Planning: Implementing Parallel Distributed Multi-Agent Systems in MATSim](https://doi.org/10.1109/ISPDC62236.2024.10705395)
 - [Real-Time Routing in Traffic Simulations: A Distributed Event Processing Approach](https://doi.org/10.1109/ISPDC62236.2024.10705399)
 
@@ -16,8 +17,8 @@ The project is described in two conference papers, which were presented at ISPDC
 Install Rust for your operating system as described [here](https://www.rust-lang.org/tools/install). For WSL this would
 be
 
-```
-$ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+```shell
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
 ```
 
 ## Set Up Prerequisites
@@ -28,8 +29,8 @@ compiled with the project, but need to be present on the operating system.
 ### METIS
 
 The project uses the [metis](https://crates.io/crates/metis) crate as a dependency which
-is a wrapper for the [METIS C Library](https://github.com/KarypisLab/METIS). The C-Library is 
-expected to be present on the machine. Also, the `metis` crate requires `libclang` on the machine 
+is a wrapper for the [METIS C Library](https://github.com/KarypisLab/METIS). The C-Library is
+expected to be present on the machine. Also, the `metis` crate requires `libclang` on the machine
 this project is built on.
 
 ### MPI
@@ -51,61 +52,105 @@ The dependencies named above need to be installed before the project can be buit
 
 Install dev versions of required packages because dev stuff is required during compilation
 
-```
-$ sudo apt -y install libclang-dev llvm-dev libmetis-dev libopenmpi-dev
+```shell
+sudo apt -y install libclang-dev llvm-dev libmetis-dev libopenmpi-dev
 ```
 
 #### MacOs
 
 The dependencies are available via [homebrew](https://brew.sh/) on macOS.
 
-```
-$ brew install metis open-mpi
+```shell
+brew install metis open-mpi
 ```
 
 The project contains a `config.toml` which tries to set the `CPATH` and the `RUSTFLAGS` environment variable. In case
 this doesn't work, they need to be set like the following:
-```
-$ export CPATH=$HOMEBREW_PREFIX/include
-$ export RUSTFLAGS="-L$HOMEBREW_PREFIX/lib"
+
+```shell
+export CPATH=$HOMEBREW_PREFIX/include
+export RUSTFLAGS="-L$HOMEBREW_PREFIX/lib"
 ```
 
 Both variables are necessary to compile the METIS and MPI wrapper libraries.
 
 #### Math Cluster
 
 The math cluster has all dependencies installed. They need to be enabled via the module system:
+
+```shell
+module load metis-5.1 ompi/gcc/4.1.2
 ```
-$ module load metis-5.1 ompi/gcc/4.1.2
-```
+
 #### HLRN
 
-The HLRN cluster has all dependencies installed. They need to be enabled via the module system:
+##### Setup conda
+
+Unfortunately, there is no `libclang` dependency installed. You need to install it yourself via `conda`. If you use it
+for the first time, load the conda module and initialize it, such that it is available in your shell whenever you login:
+
+```shell
+module load anaconda3/2023.09
+conda init bash
+```
+
+Then create your own environment and install `libclang`:
+
+```shell
+conda create -n your_env_name
+conda activate your_env_name
+conda install libclang 
+```
+
+##### Load dependencies
+
+The HLRN cluster has **some** dependencies installed. They need to be enabled via the module system:
+
+```shell
+module load intel/2024.2 openmpi/gcc/5.0.3
 ```
-$ module load gcc/9.3.0 llvm/9.0.0 openmpi/gcc.9/4.1.4 metis/5.1.0
+
+So, before you run the project, you need to activate the environment:
+
+```shell
+conda activate your_env_name
 ```
 
+The activation automatically updates the environment variables such that `libclang` files can be found by the compiler.
+
+Source: https://nhr-zib.atlassian.net/wiki/spaces/PUB/pages/430343/Anaconda+conda+and+Mamba
+
 ## Run the project
 
 The project is built using cargo.
 
-```
-$ cargo build --release
+```shell
+cargo build --release
 ```
 
 Then a simulation can be started like the following:
-```
-$ mpirun -np 2 ./target/release/mpi_qsim --config-path /path/to/config.yml
+
+```shell
+mpirun -np 2 ./target/release/mpi_qsim --config-path /path/to/config.yml
 ```
 
 It is also possible to execute a build before running by executing the following. This is way, one doesn't
 forget to re-compile before running.
-```
-$  cargo mpirun --np 2 --release --bin mpi_qsim -- --config-path /path/to/config.yaml
+
+```shell
+cargo mpirun --np 2 --release --bin mpi_qsim -- --config-path /path/to/config.yaml
 ```
 
 We also have a
 
 ### Test
 
 Run `$ cargo test` to execute all tests. To have immediate output use `$ cargo test -- --nocapture`
+
+## Create input files
+
+You need to create protobuf files from the xml files. This can be done with the following command:
+
+```shell
+cargo run --bin convert_to_binary --release -- --network network.xml --population population.xml --vehicles vehicles.xml --output-dir output --run-id run
+```