setup

advection/README.md

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+## Location of data
+The data path is hardcoded such that the following tree structure is assumed:
+```
+data/
+  grid.h5
+  hydrodynamic_U.h5
+  hydrodynamic_V.h5
+interactive-track-and-trace/
+  opening-hdf5/
+     ...
+```
+
+## Compiling
+Let the current directory be the `src` directory. Run:
+```shell
+mkdir build
+cd build
+cmake ..
+make
+```
+
+### Building with Linux
+Makes use of `mdspan` which is not supported by glibc++ at time of writing. See [compiler support](https://en.cppreference.com/w/cpp/compiler_support/23) for `mdspan`. The solution to this is to use Clang and libc++; this is configured in our CMake setup, however the default installation of the `netcdf-cxx` package on at least Arch linux (and suspectedly Debian derivatives as well) specifically builds for the glibc implementation. To get the netcdf C++ bindings functional with the libc++ implementation, one needs to build from source. On Linux, this requires a few changes to the CMake file included with the netcdf-cxx source code, which are detailed below.
+
+Step-by-step to build the program using clang++ and libc++ on linux:
+ 1. Download the source code of netcdf-cxx, found at 'https://github.com/Unidata/netcdf-cxx4/releases/tag/v4.3.1' (make sure to download the release source code, as the master branch contains non-compilable code).
+ 2. Edit the CMakeLists.txt file, by appending '-stdlib=libc++' to the `CMAKE_CXX_FLAGS` variable in line 430. This means line 430 should read: 
+    ```cmake 
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wno-unused-variable -Wno-unused-parameter -stdlib=libc++")
+    ```
+ 2. Build the source code with the following: 
+  ```sh 
+    mkdir build && cd build
+    cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/clang++
+    make
+    ctest
+    sudo make install
+  ```
+ 3. Now the code should compile through the standard steps described in the Compiling section.