How to use cmdstan in a singularity (apptainer) container?

Question

The default install location for cmdstan is $HOME/.cmdstan .

In a singularity container, I can install cmdstan somewhere else (eg, /opt/cmdstan ).

The problem is cmdstan sometime requires writing permission during compiling models but I don't have the permission for /opt/cmdstan in the singularity container.

Where should I install cmdstan in a container, and how should I solve this permission problem especially when I use HPC?

Answer 1

Keeping it /opt/cmdstan seems a good place. As far as the writing issue goes, you have two main choices:

1. Write to the host OS

This is simplest option if you can control or know where the writing happens. Since $PWD is one of the system-defined auto mount directories , you can just write there.

If you know instead that they are written to /opt/cmdstan/cache , you can explicitly mount a directory from the host OS with eg, -B /scratch:/opt/cmdstan .

This option is particularly useful if you want to have access to the generated files outside of the running container.

2. Use a tmpfs overlay

If you don't know where the files are being generated and/or don't care what they are, you can you use the --writable-tmpfs flag with your singularity command.

A limitation here is that the size of the overlay is the size of /dev/shm on the host OS. This can sometimes be smaller than expected (I've noticed as low as 32-64MB in some cloud VMs), which will cause the writes to fail complaining about no disk space when there is still space on the host partition.