Tips

This page provides a few helpful tips for installing auxiliary files and scripts that can streamline your simulation workflow. You may also find it useful to visit the Errors page for common mistakes and troubleshooting guidance.

yt

yt is an open-source python package for analyzing and visualizing volumetric data. It is highly recommended if Python is used for postprocessing and analysis of simulations data. To install

$ python -m pip install --user yt

or using conda environments

$ conda install --channel conda-forge yt

Beware of the combination Python 3.9 and yt. It is recommended to use newer Python, >3.11 recommended. Check yt Website for details and tutorials. Most of the examples in the manual use it for quick analysis and plotting in a (usually named) plot.py script.

In recent systems (for example Ubuntu 24), the use of virtual environments is enforced and the above lines will not work unless a virtual environment is created. For example, if the virtual environment exist, to activate it type:

$ source ~/virtual/bin/activate

You will need to do this to install python packages, such as yt and markdown, required for postprocessing or managing the documentation.

Cerisse script

The cerisse script can help to clean directories, create backups, create visit files for movies quickly, check basic simulation paramenters. It is useful for day to day running and avoid file creep-up. The script is installed in bin and can be used by

$ ../bin/cerisse [options]

or by setting the path in .bashrc or .profile by adding the line at the end

PATH="/home/snm/work/cerisse/bin:$PATH"

where /home/snm/work/cerisse corresponds to the installation directory. Type cerisse help or cerisse to view available options. The script is often used to clean files between runs and maximise MPI run cerisse clean and cerisse run.

Documentation Editing

Although the main documentation is onine in Gitbooks, it is possible to generate the documentation by locally typing in the parent directory: $ mkdocs serve and the point the browser to 127.0.0.1.8000 in your browser. The formatting of this documentation may be off (inline equations in particular) and images will not appear.

You may need to install the python-markdown-math extension for rendering equations. For help visit mkdocs.org. Extensions are listed in the file mkdocs.yaml

Python environments (for poetry)

1- Make sure libffi-dev dependency is installed (other prerequisites may be needed)

$ sudo apt install libffi-dev

2-Install pyenv

$ curl https://pyenv.run | bash

3-Add to your shell ~/.bashrc

export PATH="HOME/.pyenx/bin:$PATH"
eval "$(pyenv init --path)"
eval "$(pyenv init -)"

4-Install a specific python version (<3.11 is required for ceptr, see chemistry)

$ pyenv install 3.10

4-Create a virtual environment (named myenv-310 for example)

$ pyenv shell 3.10
$ python -m venv ~/myenv-310

To use

$ source ~/myenv-310/bin/activate

Install packages as usual (for example cantera)

$ pip install  cantera 

Running on Imperial HPC

To run on Imperial's CX2/3, you need to load the following modules

$ module load tools/prod iimpi/2020a

A typical job script looks like this:

#PBS -l select=2:ncpus=128:mem=256gb
#PBS -l walltime=24:00:00
#PBS -N name_of_the_job

module load tools/prod iimpi/2022a

export FI_MLX_IFACE=eth0
export I_MPI_HYDRA_BOOTSTRAP="rsh"
export I_MPI_HYDRA_BOOTSTRAP_EXEC="/opt/pbs/bin/pbs_tmrsh"
export I_MPI_HYDRA_BRANCH_COUNT=0

cd $PBS_O_WORKDIR

mpirun ./Cerisse3d.gnu.MPI.ex inputs

NOTE: There is an issue with MPI version >2020b on CX3 that causes deadlocks when writing chk or plt files.

Legacy (intel-2019.8.254)

Below is for running with Intel MPI 2019, which is unrecommended by RCS but still works.

$ module load gcc/11.2.0 mpi/intel-2019.8.254

If you see an error relating to icpc: command not found, that is because the mpicxx wrapper uses Intel's compiler by default. To change this to g++, you need to add the following command before running make, as

$ I_MPI_CXX=g++ make