Javier Ortiz-Tudela

Javier Ortiz-Tudela

he/him

Tips for Singularity

less than 1 minute read

Published:

Tips gathered after too-many trial-and-error attempts. Note: Singularity was renamed to Apptainer in 2021, so if you’re setting this up today look for the equivalent config under that name too.

Failed to set effective UID to 0

From this GitHub issue I got that the easiest way is to look for a singularity.conf file and change allow setuid=yes to allow setuid=no. That file should be located in your Singularity installation directory. If you used spack for the installation, the path would look something like this:

/path/to/spack/opt/spack/linux-scientific7-haswell/gcc-4.8.5/singularity-3.5.2-k2cgya4v4mjzvfay2n4jfmy7wbda5ucq/etc/singularity/singularity.conf

See also: how to run fmriprep on an HPC cluster with Singularity.

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