Installation guide updates

[ChocolateCharlie]

Ubuntu 22.04.5

The installation guide combined with the use of the environment.yaml file remains mostly valid.

Anaconda

• We could add that if conda init fails, then user could try source ~/anaconda3/etc/profile.d/conda.sh.

• In addition, manual installation of packages should now be replaced by the environment.yml file, which correctly ensures compatibility of the environment with SPARCED.

• We could also add that one may use conda instead of source keyword

AMICI

• We should add @JonahRileyHuggins's helpfull commands:

conda activate sparced
conda install gcc_linux-64
conda install gxx_linux-64
conda install -c conda-forge openmpi
export BLAS_LIBS=-lopenblas
pip install swig==4.0.0
pip install amici==0.11.12
pip install antimony==2.12.0.2

The installation of SPARCED on that version of Ubuntu remains relatively smooth.

Ubuntu 24.04.1

It turns out that some dependencies are actually "transitionnal dummy packages" that got deprecated.

• libgl1-mesa-glx should be replaced by libgl1 and libglx-mesa0

• libegl1-mesa should be replaced by libegl1

• libasound should now be installed through liboss4-salsa-asound2

Note that apparently, Anaconda's official documentation is not up to date regarding those deprecations.

Moreover, all the suggested additions for the 22.04 installation guide are crucial to succeed installing SPARCED on the 24.04 version.

[ChocolateCharlie]

I again face installation issues for the correct version of AMICI on Ubuntu 24.04.1 although I was following the exact same steps as this morning. How difficult would it be to upgrade ?

[ChocolateCharlie]

On Ubuntu 22.04.5 I was facing issues again and it turns out repeating:

conda install -c conda-forge openmpi
export BLAS_LIBS=-lopenblas

a random number of times (between first shot to 3 re-installs) at some point will allow AMICI to successfully install. I'm too tired of this to try again on Ubuntu 24.04.1.