diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md index 824b46f..194dc7b 100644 --- a/docs/troubleshooting.md +++ b/docs/troubleshooting.md @@ -12,6 +12,23 @@ Singularity also uses some temporary directories to build the squashfs filesyste In many HPC platform, limited space is assigned to `$HOME`. So to make the pipeline more robust, it is recommended to set `SINGULARITY_CACHEDIR` to make sure enough space can be used. +## BoltDB Corruption Errorsīƒ + +The library that SingularityCE uses to retrieve and cache Docker/OCI layers keeps track of them using a single-file database. If your home directory is on a network filesystem which experiences interruptions, or you run out of storage, it is possible for this database to become inconsistent. + +If you observe error messages that mention github.com/etcd-io/bbolt when trying to run SingularityCE, then you should remove the database file: + +``` +rm ~/.local/share/containers/cache/blob-info-cache-v1.boltdb +``` + +Here are the discussions useful for this issue: + +https://github.com/apptainer/singularity/issues/5329#issuecomment-637595826 +https://docs.sylabs.io/guides/main/user-guide/build_env.html#boltdb-corruption-errors +https://github.com/apptainer/singularity/issues/5329#issuecomment-1062000005 + + ## Issue with NIH VPN When the program inside a container needs to connect to a database via API or download some data, the error message below might be threwn out: