Build Environment

Overview

You may wish to customize your build environment by doing things such as specifying a custom cache directory for images or sending your Docker Credentials to the registry endpoint. Here we will discuss these and other topics related to the build environment.

Cache Folders

Singularity will cache SIF container images generated from remote sources, and any OCI/docker layers used to create them. The cache is created at $HOME/.singularity/cache by default. The location of the cache can be changed by setting the SINGULARITY_CACHEDIR environment variable.

When you run builds as root, using sudo, images will be cached in root’s home at /root and not your user’s home. Use the -E option to sudo to pass through the SINGULARITY_CACHEDIR environment variable, if you set it.

$ export SINGULARITY_CACHEDIR=/tmp/user/temporary-cache

# Running a build under your user account
$ singularity build --fakeroot myimage.sif mydef.def

# Running a build with sudo, must use -E to pass env var
$ sudo -E singularity build myimage.sif mydef.def

If you change the value of SINGULARITY_CACHEDIR be sure to choose a location that is:

  • Unique to you. Permissions are set on the cache so that private images cached for one user are not exposed to another. This means that SINGULARITY_CACHEDIR cannot be shared.

  • Located on a filesystem with sufficient space for the number and size of container images anticipated.

  • Located on a filesystem that supports atomic rename, if possible.

Warning

If you are not certain that your $HOME or SINGULARITY_CACHEDIR filesystems support atomic rename, do not run Singularity in parallel using remote container URLs. Instead use singularity pull to create a local SIF image, and then run this SIF image in a parallel step. An alternative is to use the --disable-cache option, but this will result in each Singularity instance independently fetching the container from the remote source, into a temporary location.

Inside the cache location you will find separate directories for the different kinds of data that are cached:

$HOME/.singularity/cache/blob
$HOME/.singularity/cache/library
$HOME/.singularity/cache/net
$HOME/.singularity/cache/oci-tmp
$HOME/.singularity/cache/shub

You can safely delete these directories, or content within them. Singularity will re-create any directories and data that are needed in future runs.

You should not add any additional files, or modify files in the cache, as this may cause checksum / integrity errors when you run or build containers. If you experience problems use singularity cache clean to reset the cache to a clean, empty state.

BoltDB Corruption Errors

The library that Singularity 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 when trying to run Singularity that mention github.com/etcd-io/bbolt then you should remove the database file:

rm ~/.local/share/containers/cache/blob-info-cache-v1.boltdb

Cache commands

The cache command for Singularity allows you to view and clean up your cache, without manually inspecting the cache directories.

Note

If you have built images as root, directly or via sudo, the cache location for those builds is /root/.singularity. You will need to use sudo when running cache clean or cache list to manage these cache entries.

Listing Cache

To view a summary of cache usage, use singularity cache list:

$ singularity cache list
There are 4 container file(s) using 59.45 MB and 23 oci blob file(s) using 379.10 MB of space
Total space used: 438.55 MB

To view detailed information, use singularity cache list -v:

$ singularity cache list -v
NAME                     DATE CREATED           SIZE             TYPE
0ed5a98249068fe0592edb   2020-05-27 12:57:22    192.21 MB        blob
1d9cd1b99a7eca56d8f2be   2020-05-28 15:19:07    0.35 kB          blob
219c332183ec3800bdfda4   2020-05-28 12:22:13    0.35 kB          blob
2adae3950d4d0f11875568   2020-05-27 12:57:16    51.83 MB         blob
376057ac6fa17f65688c56   2020-05-27 12:57:12    50.39 MB         blob
496548a8c952b37bdf149a   2020-05-27 12:57:14    10.00 MB         blob
5a63a0a859d859478f3046   2020-05-27 12:57:13    7.81 MB          blob
5efaeecfa72afde779c946   2020-05-27 12:57:25    0.23 kB          blob
6154df8ff9882934dc5bf2   2020-05-27 08:37:22    0.85 kB          blob
70d0b3967cd8abe96c9719   2020-05-27 12:57:24    26.61 MB         blob
8f5af4048c33630473b396   2020-05-28 15:19:07    0.57 kB          blob
95c3f3755f37380edb2f8f   2020-05-28 14:07:20    2.48 kB          blob
96878229af8adf91bcbf11   2020-05-28 14:07:20    0.81 kB          blob
af88fdb253aac46693de78   2020-05-28 12:22:13    0.58 kB          blob
bb94ffe723890b4d62d742   2020-05-27 12:57:23    6.15 MB          blob
c080bf936f6a1fdd2045e3   2020-05-27 12:57:25    1.61 kB          blob
cbdbe7a5bc2a134ca8ec91   2020-05-28 12:22:13    2.81 MB          blob
d51af753c3d3a984351448   2020-05-27 08:37:21    28.56 MB         blob
d9cbbca60e5f0fc028b13c   2020-05-28 15:19:06    760.85 kB        blob
db8816f445487e48e1d614   2020-05-27 12:57:25    1.93 MB          blob
fc878cd0a91c7bece56f66   2020-05-27 08:37:22    32.30 kB         blob
fee5db0ff82f7aa5ace634   2020-05-27 08:37:22    0.16 kB          blob
ff110406d51ca9ea722112   2020-05-27 12:57:25    7.78 kB          blob
sha256.02ee8bf9dc335c2   2020-05-29 13:45:14    28.11 MB         library
sha256.5111f59250ac94f   2020-05-28 13:14:39    782.34 kB        library
747d2dbbaaee995098c979   2020-05-28 14:07:22    27.77 MB         oci-tmp
9a839e63dad54c3a6d1834   2020-05-28 12:22:13    2.78 MB          oci-tmp

There are 4 container file(s) using 59.45 MB and 23 oci blob file(s) using 379.10 MB of space
Total space used: 438.55 MB

All cache entries are named using a content hash, so that identical layers or images that are pulled from different URIs do not consume more space than needed.

Entries marked blob are OCI/docker layers and manifests, that are used to create SIF format images in the oci-tmp cache. Other caches are named for the source of the image e.g. library and oras.

You can limit the cache list to a specific cache type with the -type / -t option.

Cleaning the Cache

To reclaim space used by the Singularity cache, use singularity cache clean.

By default singularity cache clean will remove all cache entries, after asking you to confirm:

$ singularity cache clean
This will delete everything in your cache (containers from all sources and OCI blobs).
Hint: You can see exactly what would be deleted by canceling and using the --dry-run option.
Do you want to continue? [N/y] n

Use the --dry-run / -n option to see the files that would be deleted, or the --force / -f option to clean without asking for confirmation.

If you want to leave your most recent cached images in place, but remove images that were cached longer ago, you can use the --days / -d option. E.g. to clean cache entries older than 30 days:

$ singularity cache clean --days 30

To remove only a specific kind of cache entry, e.g. only library images, use the type / -T option:

$ singularity cache clean --type library

Temporary Folders

When building a container, or pulling/running a Singularity container from a Docker/OCI source, a temporary working space is required. The container is constructed in this temporary space before being packaged into a Singularity SIF image. Temporary space is also used when running containers in unprivileged mode, and performing some operations on filesystems that do not fully support --fakeroot.

The location for temporary directories defaults to /tmp. Singularity will also respect the environment variable TMPDIR, and both of these locations can be overridden by setting the environment variable SINGULARITY_TMPDIR.

The temporary directory used during a build must be on a filesystem that has enough space to hold the entire container image, uncompressed, including any temporary files that are created and later removed during the build. You may need to set SINGULARITY_TMPDIR when building a large container on a system which has a small /tmp filesystem.

Remember to use -E option to pass the value of SINGULARITY_TMPDIR to root’s environment when executing the build command with sudo.

Warning

Many modern Linux distributions use an in-memory tmpfs filesystem for /tmp when installed on a computer with a sufficient amount of RAM. This may limit the size of container you can build, as temporary directories under /tmp share RAM with runniing programs etc. A tmpfs also uses default mount options that can interfere with some container builds.

Set SINGULARITY_TMPDIR to a disk location, or disable the tmpfs /tmp mount on your system if you experience problems.

Encrypted Containers

Beginning in Singularity 3.4.0 it is possible to build and run encrypted containers. The containers are decrypted at runtime entirely in kernel space, meaning that no intermediate decrypted data is ever present on disk or in memory. See encrypted containers for more details.

Environment Variables

  1. If a flag is represented by both a CLI option and an environment variable, and both are set, the CLI option will always take precedence. This is true for all environment variables except for SINGULARITY_BIND and SINGULARITY_BINDPATH which is combined with the --bind option, argument pair if both are present.

  2. Environment variables overwrite default values in the CLI code

  3. Any defaults in the CLI code are applied.

Defaults

The following variables have defaults that can be customized by you via environment variables at runtime.

Docker

SINGULARITY_DOCKER_LOGIN Used for the interactive login for Docker Hub.

SINGULARITY_DOCKER_USERNAME Your Docker username.

SINGULARITY_DOCKER_PASSWORD Your Docker password.

RUNSCRIPT_COMMAND Is not obtained from the environment, but is a hard coded default (“/bin/bash”). This is the fallback command used in the case that the docker image does not have a CMD or ENTRYPOINT. TAG Is the default tag, latest.

SINGULARITY_NOHTTPS This is relevant if you want to use a registry that doesn’t have https, and it speaks for itself. If you export the variable SINGULARITY_NOHTTPS you can force the software to not use https when interacting with a Docker registry. This use case is typically for use of a local registry.

Library

SINGULARITY_BUILDER Used to specify the remote builder service URL. The default value is our remote builder.

SINGULARITY_LIBRARY Used to specify the library to pull from. Default is set to our Cloud Library.

SINGULARITY_REMOTE Used to build an image remotely (This does not require root). The default is set to false.

Encryption

SINGULARITY_ENCRYPTION_PASSPHRASE Used to pass a plaintext passphrase to encrypt a container file system (with the --encrypt flag). The default is empty.

SINGULARITY_ENCRYPTION_PEM_PATH Used to specify the location of a public key to use for container encryption (with the --encrypt flag). The default is empty.