How to properly run cmdstan in apptainer container, as it needs write access

[e-kotov]

In an Apptainer container in HPC cluster, when trying to build a model with cmdstanr/cmdstan there is an error due to read-only file system inside the container. This is only an issue for Apptainer containers. If running under Docker, all is fine (different file system permissions?).

file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
mod <- cmdstan_model(file)
>> Compiling Stan program...
>> <built-in>: fatal error: opening dependency file src/cmdstan/main.d: Read-only file system
>> compilation terminated.

Note to self: similar issue discussed here stan-dev/cmdstan#1175, with some suggested solutions too.

Also a discussion here: https://discourse.mc-stan.org/t/problem-running-cmdstan-on-computing-cluster/34747/4