pointsource_pde: comparison README.md

-:c4f923017349
+:a0d61ac3719e
+# Numerical implementation of “Leak localisation with a measure source convection–diffusion model”
-# Nuerical implementation of “Leak localisation with a measure source convection–diffusion model”
 These are the codes for the numerical demonstrations of the manuscript
 _“Leak localisation with a measure source convection--diffusion model”_
 ([arXiv:2605.12095](https://arxiv.org/abs/2605.12095)) by Thi Tam Dang and Tuomo Valkonen.
 It should be relatively easy to to use this package and the algorithms it provides
 Sorry, although the core of program is written in Rust with a modern dependency management and build process, we also have legacy C++ and Python dependencies, i.e., the Fenicsx PDE library. Therefore, the build process is difficult.
 (We admit it, we made a mistake by going with the crowd and using Fenicsx. In the end it would have been less effort to write low-level PDE code in Rust.)
-###  Phase 1: Python and Fenics
+### Phase 1: Python and Fenics
 #### Option 1.A that avoids Conda hell, but is more work (macOS and Linux)
 ##### Phase 1.A.1: C++ dependencies of Fenics
 (Fenics recommends ParMETIS instead of Kahip, but only the latter is available from Homebrew at the time of writing this.)
 There's no guarantee that this will install compatible versions of these packages. Homebrew, while better than most Linux distributions, is also obsolete in its philosophy: it does not allow easily installing specific versions of packages. Versions known to work are:
-package | version
+| package  | version |
----------|--------
+| -------- | ------- |
-boost    | 1.90.0
+| boost    | 1.90.0  |
-cmake    | 4.2.1
+| cmake    | 4.2.1   |
-fmt      | 12.1.0
+| fmt      | 12.1.0  |
-hdf5-mpi | 1.14.6
+| hdf5-mpi | 1.14.6  |
-kahip    | 3.22
+| kahip    | 3.22    |
-petsc    | 3.24.3
+| petsc    | 3.24.3  |
-pugixml  | 1.15
+| pugixml  | 1.15    |
-slepc    | 3.24.2
+| slepc    | 3.24.2  |
-spdlog   | 1.17.0
+| spdlog   | 1.17.0  |
-gsl      | 2.8
+| gsl      | 2.8     |
 You can get the list of installed versions with:
 brew list --versions openmpi boost pugixml fmt spdlog hdf5-mpi cmake kahip slepc petsc gsl
 (The last two lines are required later.)
 This template is also available in `misc/_envrc`.
 For changes `.envrc` to take effect, you should use
 direnv allow
 ##### Phase 1.A.3: Fenicx-basix
 Install basix from <https://github.com/FEniCS/basix/releases/tag/v0.10.0.post0> according to
 instructions. First do the C++ bit:
 If you didn't already do these steps with `direnv` above, you should:
 export PYTHONPATH=$(echo .venv/lib/python*/site-packages)
 export PYO3_PYTHON="$(which python)"
 #### Option 1.B: Conda
-You can *try to* install Fenicsx in Conda according to instructions on the Fenics website. Additionally you need to install `scipy`:
+You can _try to_ install Fenicsx in Conda according to instructions on the Fenics website. Additionally you need to install `scipy`:
 conda create -n fenicsx-env
 conda activate fenicsx-env
 conda install -c conda-forge fenics-dolfinx=0.10.0 scipy=1.17.1 mpich
-This is, however, unlikely to not work, as Conda, despite its sandboxing separation attempts, conflicts with system packages, or Conda packages have weird ideas. You're likely to run into runtime problems with the FFCX form compiler (*bad* *bad* *bad* idea, running a C compiler runtime) failing due to something, somewhere, in the extremely fragile Conda setup, trying to load system libraries wrongly, etc.
+This is, however, unlikely to not work, as Conda, despite its sandboxing separation attempts, conflicts with system packages, or Conda packages have weird ideas. You're likely to run into runtime problems with the FFCX form compiler (_bad_ _bad_ _bad_ idea, running a C compiler runtime) failing due to something, somewhere, in the extremely fragile Conda setup, trying to load system libraries wrongly, etc.
 #### Option 1.C: Debian/Ubuntu
 You may be able to use the system package manager, but beware of obsolete and modified versions. As of 2026-03-23, the packages available in Debian/Ubuntu cause massive memory leaks and eventual system crash.
 [alg_tools] also needs to be downloaded separately.
 1.  Install the [Rust] infrastructure (including Cargo) with [rustup].
 2.  Install a “nightly” release of the Rust compiler. With rustup, installed in
 the previous step, this can be done with
 rustup toolchain install nightly
-3. Download [alg_tools], [pointsource_algs], and [measures] and unpack them under
+3.  Download [alg_tools], [pointsource_algs], and [measures] and unpack them under
 the same directory as this package.
 [rustup]: https://rustup.rs
 [alg_tools]: https://tuomov.iki.fi/software/alg_tools/
 [pointsource_algs]: https://tuomov.iki.fi/software/pointsource_algs/
 [measures]: https://tuomov.iki.fi/repos/measures/
 [Rust]: https://www.rust-lang.org/
 [GNU Scientific Library]: https://www.gnu.org/software/gsl/
 [rust-GSL]: https://docs.rs/GSL/6.0.0/rgsl/
 [Homebrew]: https://brew.sh
 [arXiv:2212.02991]: https://arxiv.org/abs/2212.02991
 [arXiv:2502.12417]: https://arxiv.org/abs/2502.12417
 [doi:10.46298/jnsao-2023-10433]: http://doi.org/10.46298/jnsao-2023-10433
 ### Linux / further patching
 Due to both Fenics and typical Linux system being completely broken, you may need to do further patching to get things to compile:
 1. I had to set (in my [direnv](https://direnv.net) `.envrc`)
 export PKG_CONFIG_PATH=/home/linuxbrew/.linuxbrew/lib/pkgconfig:/usr/local/lib/pkgconfig/:/usr/lib/aarch64-linux-gnu/pkgconfig/
 export LD_LIBRARY_PATH=/home/linuxbrew/.linuxbrew/lib
 2. Some libraries, in particular `libfmt` and `libspdlog` installed in Homebrew, may conflict with system versions, that must be removed.
 Lack of proper sandboxing in legacy Linux distributions, effectively prohibits multiple versions of the same library.
-2. I had to add `Libs` in `/usr/local/lib/pkgconfig/dolfinx.pc` the bit `-L/home/linuxbrew/.linuxbrew/lib/ -lopenblas`. Nothing in the fenics stack seems to explicitly require it. Basix, that depends on openblas, is entirely missing a `pkg-config` file.
+3. I had to add `Libs` in `/usr/local/lib/pkgconfig/dolfinx.pc` the bit `-L/home/linuxbrew/.linuxbrew/lib/ -lopenblas`. Nothing in the fenics stack seems to explicitly require it. Basix, that depends on openblas, is entirely missing a `pkg-config` file.
-3. Also `export export OMP_NUM_THREADS=1` (in `.envrc`). We don't do MPI. We cannot do MPI in Fenics' lame “it's all just parallel solution of PDEs, with no other computation, ever” aka “single-program multiple-data, with no controller at all” way. If you don't do this, you may have multiple threads wasting CPU just being there. We try to control the thread count in our code, but OpenMPI on Linux doesn't seem to respect it.
+4. Also `export export OMP_NUM_THREADS=1` (in `.envrc`). We don't do MPI. We cannot do MPI in Fenics' lame “it's all just parallel solution of PDEs, with no other computation, ever” aka “single-program multiple-data, with no controller at all” way. If you don't do this, you may have multiple threads wasting CPU just being there. We try to control the thread count in our code, but OpenMPI on Linux doesn't seem to respect it.
 ## Building and running the experiments
 To compile the program, run
 of iterations.
 The double-dash separates the options for the Cargo build system and `pointsource_pde`.
 ### Visualising the results
 The results may be plotted with
 python3 ./plot.py results/laser_and_mirrors_aux/radon_sliding_fb
 Vary the path to `laser_and_mirrors_aux2` and `radon_fb` for the alternative experiment and basic algorithm.

Mercurial > repos > pointsource_pde / file comparison

comparison: README.md

README.md