Bind Paths and Mounts

Unless disabled by the system administrator, Apptainer allows you to map directories on your host system to directories within your container using bind mounts. This allows you to read and write data on the host system with ease.

Overview

When Apptainer ‘swaps’ the host operating system for the one inside your container, the host file systems becomes inaccessible. However, you may want to read and write files on the host system from within the container. To enable this functionality, Apptainer will bind directories back into the container via two primary methods: system-defined bind paths and user-defined bind paths.

System-defined bind paths

The system administrator has the ability to define which bind paths will be included automatically inside each container. Some bind paths are derived (e.g. a user’s home directory), and some are statically defined with a bind path entry in the Apptainer configuration.

In the default configuration, the default bind mounts are:

  • The user’s home directory ($HOME)

  • The current working directory (CWD), unless its path contains symlinks resolving to different locations on the host vs inside the container.

  • /dev

  • /etc/hosts

  • /etc/localtime

  • /proc

  • /sys

  • /tmp

  • /var/tmp

Additionally, customized system configuration files /etc/resolv.conf, /etc/group, and /etc/passwd are mounted into the container. These are adapted at container startup to match the requested configuration of the container.

Disabling System Binds

The --no-mount flag allows specific system mounts to be disabled, even if they are set in the apptainer.conf configuration file by the administrator.

For example, if Apptainer has been configured with mount hostfs = yes then every filesystem on the host will be bind mounted to the container by default. If, e.g. a /project filesystem on your host conflicts with a /project directory in the container you are running, you can disable the hostfs binds:

$ apptainer run --no-mount hostfs mycontainer.sif

Multiple system mounts can be disabled by specifying them separated by commas:

$ apptainer run --no-mount tmp,sys,dev mycontainer.sif

When the administrator has configured custom bind path entries in apptainer.conf, to mount specific paths into the container by default, you can disable them individually. To do this, specify the path(s) to disable with the --no-mount flag. For example, if the adminstrator has configured apptainer.conf to always mount /data2. you can disable this with --no-mount /data2:

$ apptainer run --no-mount /data2 mycontainer.sif

To disable all bind path entries set in apptainer.conf, use --no-mount bind-paths:

$ apptainer run --no-mount bind-paths mycontainer.sif

User-defined bind paths

Unless the system administrator has disabled user control of binds, you will be able to request your own bind paths within your container.

The Apptainer action commands (run, exec, shell, and instance start) will accept the --bind/-B command-line option to specify bind paths, and will also honor the $APPTAINER_BIND and $APPTAINER_BINDPATH environment variables (in that order). The argument for this option is a comma-delimited string of bind path specifications in the format src[:dest[:opts]], where src and dest are paths outside and inside of the container respectively. If dest is not given, it is set equal to src. Mount options (opts) may be specified as ro (read-only) or rw (read/write, which is the default). The --bind/-B option can be specified multiple times, or a comma-delimited string of bind path specifications can be used.

Apptainer also has a --mount flag, which provides a longer-form method of specifying binds in --mount type=bind,src=<source>,dst=<destination>[,<option>]... format. This is compatible with the --mount syntax for binds in Docker and other OCI runtimes.

--bind Examples

Here’s an example of using the --bind option and binding /data on the host to /mnt in the container (/mnt does not need to already exist in the container):

$ ls /data
bar  foo

$ apptainer exec --bind /data:/mnt my_container.sif ls /mnt
bar  foo

You can bind multiple directories in a single command with this syntax:

$ apptainer shell --bind /opt,/data:/mnt my_container.sif

This will bind /opt on the host to /opt in the container and /data on the host to /mnt in the container.

Using the environment variable instead of the command line argument, this would be:

$ export APPTAINER_BINDPATH="/opt,/data:/mnt"

$ apptainer shell my_container.sif

Using the environment variable $APPTAINER_BINDPATH, you can bind paths even when you are running your container as an executable file with a runscript. If you bind many directories into your Apptainer containers and they don’t change, you could even benefit by setting this variable in your .bashrc file.

Note

Inside an Apptainer container all the paths that were bound in are set in the $APPTAINER_BIND variable. That means they will be automatically bound in again by default if another apptainer command is run nested inside the first container. You can change that variable if you choose before that point, but if you want to avoid interfering with nested containers it’s better to use $APPTAINER_BINDPATH.

--mount Examples

The --mount flag takes a mount specification in the format type=bind,src=<source>,dst=<dest>. Additional options can be specified, comma delimited.

Apptainer only supports the bind type for --mount, and will infer type=bind if it is not provided.

src or source can be used interchangeably. dst, destination, or target are also equivalent.

To mount data on the host to /mnt inside the container:

$ apptainer exec \
    --mount type=bind,src=/data,dst=/mnt \
    my_container.sif ls /mnt
bar  foo

To mount the same directory read-only in the container, add the ro option:

$ apptainer exec \
    --mount type=bind,source=/data,dest=/mnt,ro \
    my_container.sif touch /mnt/test
touch: cannot touch '/mnt/test': Permission denied

You can bind multiple directories in a single command with multiple --mount flags:

$ apptainer shell --mount type=bind,src=/opt,dst=/opt \
                    --mount type=bind,src=/data,dst=/data \
                    my_container.sif

This will bind /opt on the host to /opt in the container and /data on the host to /mnt in the container.

The mount string can be quoted and escaped according to CSV rules, wrapping each field in double quotes if necessary characters. --mount allows bind mounting paths that are not possible with the --bind flag. For example:

# Mount a path containing ':' (not possible with --bind)
$ apptainer run \
    --mount type=bind,src=/my:path,dst=/mnt \
    mycontainer.sif

# Mount a path containing a ','
$ apptainer run \
    --mount type=bind,"src=/comma,dir",dst=/mnt \
    mycontainer.sif

Mount specifications are also read from then environment variable $APPTAINER_MOUNT. Multiple bind mounts set via this environment variable should be separated by newlines (\n).

Using --bind or --mount with the --writable flag

To mount a bind path inside the container, a bind point must be defined within the container. The bind point is a directory or file within the container that Apptainer can use as a destination to bind a directory or file from the host system. Under most circumstances, Apptainer will automatically create any missing bind points within the container using an overlay.

However, binding paths to non-existent points within the container can result in unexpected behavior when used in conjunction with the --writable flag, and is therefore disallowed. If you need to specify bind paths in combination with the --writable flag, please ensure that the appropriate bind points exist within the container. If they do not already exist, it will be necessary to modify the container and create them.

Using --no-home and --containall flags

--no-home

When starting a container, Apptainer allows you to mount your current working directory (CWD) without mounting your host $HOME directory by using the --no-home flag. This is equivalent to --no-mount home:

$ apptainer shell --no-home my_container.sif

-or-

$ apptainer shell --no-mount home my_container.sif

Disabling the mount of $HOME may be useful if your container image has files at $HOME, which would otherwise be hidden by the bind mount from the host.

Note

If your current working directory is under $HOME, and you do not want to mount it, you will need to disable both cwd and home mounts:

$ apptainer shell --no-mount home,cwd my_container.sif

--contain / --containall

When using the --contain / --containall (or -c / -C for short) flags, $HOME from the host is not mounted, and an in-memory temporary directory is created at the $HOME point inside the container instead. An in-memory temporary directory is also used for /tmp and /var/tmp inside the container.

If the container image includes files within $HOME, the mounted temporary directory will hide them unless you also specify --no-home or --no-mount home:

$ apptainer shell --containall my_container.sif
Apptainer> ls -lah $HOME
total 4K
drwxr-xr-x    2 user group      60 Sep  1 11:45 .
drwxr-xr-x    1 user group      60 Sep  1 11:44 ..

$ apptainer shell --containall --no-home my_container.sif
Apptainer> ls -lah $HOME
total 52K
drwxr-xr-x    2 user group        60 Sep  1 11:45 .
drwxr-xr-x    1 user group        60 Sep  1 11:44 ..
drwxr-xr-x    1 user group     38672 Sep  1 11:44 mydata.csv
drwxr-xr-x    1 user group     14235 Sep  1 11:44 myimage.jpg

FUSE mounts

Filesystem in Userspace (FUSE) is an interface to allow filesystems to be mounted using code that runs in userspace, rather than in the Linux Kernel. Unprivileged (non-root) users can mount filesystems that have FUSE drivers. For example, the fuse-sshfs package allows you to mount a remote computer’s filesystem to your local host, over ssh:

$ mount.fuse sshfs#ythel:/home/dave other_host/

# Now mounted to my local machine:
$ ythel:/home/dave on /home/dave/other_host type fuse.sshfs (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)

Apptainer has a --fusemount option, which allows you to directly expose FUSE filesystems inside a container. The FUSE command / driver that mounts a particular type of filesystem can be located on the host, or in the container.

Requirements

The FUSE command invoked with the --fusemount option must be based on libfuse3 3.3.0 or greater to work correctly with Apptainer. Older versions do not support the way in which the Apptainer runtime passes a pre-mounted file descriptor into the container.

If you are using an older distribution that provides FUSE commands such as sshfs based on FUSE 2 then you can install FUSE 3 versions of the commands you need inside your container.

FUSE mount definitions

A fusemount definition for Apptainer consists of 3 parts:

--fusemount <type>:<fuse command> <container mountpoint>

  • type specifies how and where the FUSE mount will be run. The options are:

    • host - use a FUSE command on the host, to mount a filesystem into the container, with the fuse process attached.

    • container - use a FUSE command inside the container, to mount a filesystem into the container, with the fuse process attached.

    • host-daemon - use a FUSE command on the host, to mount a filesystem into the container, with the fuse process detached.

    • container-daemon - use a FUSE command inside the container, to mount a filesystem into the container, with the fuse process detached.

  • fuse command specifies the name of the executable that implements the FUSE mount, and any arguments. E.g. sshfs server:over-there/ for mounting a remote filesystem over SSH, where the remote source is over-there/ in my home directory on the machine called server.

  • container mountpoint is an absolute path at which the FUSE filesystem will be mounted in the container.

FUSE mount with a host executable

To use a FUSE sshfs mount in a container, where the fuse-sshfs package has been installed on my host, I run with the host mount type:

$ apptainer run --fusemount "host:sshfs server:/ /server" docker://ubuntu
Apptainer> cat /etc/hostname
localhost.localdomain
Apptainer> cat /server/etc/hostname
server

FUSE mount with a container executable

If the FUSE driver / command that you want to use for the mount has been added to your container, you can use the container mount type:

$ apptainer run --fusemount "container:sshfs server:/ /server" sshfs.sif
Apptainer> cat /etc/hostname
localhost.localdomain
Apptainer> cat /server/etc/hostname
server

Image Mounts

In Apptainer you can mount a directory contained in an image file into a container. This may be useful if you want to distribute directories containing a large number of data files as a single image file.

You can mount from image files in ext3 format, squashfs format, or SIF format.

The ext3 image file format allows you to mount it into the container read/write and make changes, while the other formats are read-only. Note that you can only use a read/write image in a single container. You cannot mount it to multiple container runs at the same time.

To mount a directory from an image file, use the -B/--bind option and specify the bind in the format:

-B <image-file>:<dest>:image-src=<source>

Alternatively use the --mount option, and specify the bind in the format:

--mount type=bind,src=<image-file>,dst=<dest>,image-src=<source>

This will bind the <source> path inside <image-file> to <dest> in the container.

If you do not add :image-src=<source> to your bind specification, then the <image-file> itself will be bound to <dest> instead.

Ext3 Image Files

If you have a directory called inputs/ that holds data files you wish to distribute in an image file that allows read/write:

# Create an image file 'inputs.img' of size 100MB and put the
# files inputs/ into it's root directory
$ mkfs.ext3 -d inputs/ inputs.img 100M
mke2fs 1.45.6 (20-Mar-2020)
Creating regular file inputs.img
Creating filesystem with 102400 1k blocks and 25688 inodes
Filesystem UUID: e23c29c9-7a49-4b82-89bf-2faf36b5a781
Superblock backups stored on blocks:
    8193, 24577, 40961, 57345, 73729

Allocating group tables: done
Writing inode tables: done
Creating journal (4096 blocks): done
Copying files into the device: done
Writing superblocks and filesystem accounting information: done

# Run Apptainer, mounting my input data to '/input-data' in
# the container.
$ apptainer run -B inputs.img:/input-data:image-src=/ mycontainer.sif
Apptainer> ls /input-data
1           3           5           7           9
2           4           6           8           lost+found

# Or with --mount instead of -B
$ apptainer run \
    --mount type=bind,src=inputs.img,dst=/input-data,image-src=/ \
    mycontainer.sif

SquashFS Image Files

If you have a directory called inputs/ that holds data files you wish to distribute in an image file that is read-only, and compressed, then the squashfs format is appropriate:

# Create an image file 'inputs.squashfs' and put the files from
# inputs/ into it's root directory
$ mksquashfs inputs/ inputs.squashfs
Parallel mksquashfs: Using 16 processors
Creating 4.0 filesystem on inputs.squashfs, block size 131072.
...

# Run Apptainer, mounting my input data to '/input-data' in
# the container.
$ apptainer run -B inputs.squashfs:/input-data:image-src=/ mycontainer.sif
Apptainer> ls /input-data/
1  2  3  4  5  6  7  8  9

# Or with --mount instead of -B
$ apptainer run \
    --mount type=bind,src=src-inputs.squashfs,dst=/input-data,image-src=/ \
    mycontainer.sif

SIF Image Files

Advanced users may wish to create a standalone SIF image, which contains an ext3 or squashfs data partition holding files, by using the apptainer sif commands similarly to the persistent overlays instructions:

# Create a new empty SIF file
$ apptainer sif new inputs.sif

# Add the squashfs data image from above to the SIF
$ apptainer sif add --datatype 4 --partarch 2 --partfs 1 --parttype 3 inputs.sif inputs.squashfs

# Run Apptainer, binding data from the SIF file
$ apptainer run -B inputs.sif:/input-data:image-src=/ mycontainer.sif
Apptainer> ls /input-data
1  2  3  4  5  6  7  8  9

# Or with --mount instead of -B
$ apptainer run \
    --mount type=bind,src=inputs.sif,dst=/input-data,image-src=/ \
    mycontainer.sif

If your bind source is a SIF then Apptainer will bind from the first data partition in the SIF, or you may specify an alternative descriptor by ID with the additional option id=n, where n is the descriptor ID.