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Add issue related to BoltDB Corruption Errors
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xies4 committed May 3, 2024
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Expand Up @@ -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 Errors

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:
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