Singularity Configuration Files¶

As a Singularity Administrator, you will have access to various configuration files, that will let you manage container resources, set security restrictions and configure network options etc, when installing Singularity across the system. All these files can be found in /usr/local/etc/singularity by default (though its location will obviously differ based on options passed during the installation). This page will describe the following configuration files and the various parameters contained by them. They are usually self documenting but here are several things to pay special attention to:

singularity.conf¶

Most of the configuration options are set using the file singularity.conf that defines the global configuration for Singularity across the entire system. Using this file, system administrators can have direct say as to what functions the users can utilize. As a security measure, for setuid installations of Singularity it must be owned by root and must not be writable by users or Singularity will refuse to run. This is not the case for non-setuid installations that will only ever execute with user priviledge and thus do not require such limitations. The options for this configuration are listed below. Options are grouped together based on relevance, the order of options within singularity.conf differs.

Setuid and Capabilities¶

ALLOW SETUID: To use all features of Singularity containers, Singularity will need to have access to some privileged system calls. One way singularity achieves this is by using binaries with the setuid bit enabled. This variable lets you enable/disable users ability to utilize these binaries within Singularity. By default, it is set to “yes”, but when disabled, various Singularity features will not function. Please see Unprivileged Installations for more information about running Singularity without setuid enabled.

ROOT DEFAULT CAPABILITIES: Singularity allows the specification of capabilities kept by the root user when running a container by default. Options include:

full: all capabilities are maintained, this gives the same behavior as the --keep-privs option.
file: only capabilities granted in /usr/local/etc/singularity/capabilities/user.root are maintained.
no: no capabilities are maintained, this gives the same behavior as the --no-privs option.

Note

The root user can manage the capabilities granted to individual containers when they are launched through the --add-caps and drop-caps flags. Please see Linux Capabilities in the user guide for more information.

Loop Devices¶

Singularity uses loop devices to facilitate the mounting of container filesystems from SIF images.

MAX LOOP DEVICES: This option allows an admin to limit the total number of loop devices Singularity will consume at a given time.

SHARED LOOP DEVICES: This allows containers running the same image to share a single loop device. This minimizes loop device usage and helps optimize kernel cache usage. Enabling this feature can be particularly useful for MPI jobs.

Namespace Options¶

ALLOW PID NS: This option determines if users can leverage the PID namespace when running their containers through the --pid flag.

Note

For some HPC systems, using the PID namespace has the potential of confusing some resource managers as well as some MPI implementations.

Configuration Files¶

Singularity allows for the automatic configuration of several system configuration files within containers to ease usage across systems.

Note

These options will do nothing unless the file or directory path exists within the container or Singularity has either overlay or underlay support enabled.

CONFIG PASSWD: This option determines if Singularity should automatically append an entry to /etc/passwd for the user running the container.

CONFIG GROUP: This option determines if Singularity should automatically append the calling user’s group entries to the containers /etc/group.

CONFIG RESOLV_CONF: This option determines if Singularity should automatically bind the host’s /etc/resolv/conf within the container.

Session Directory and System Mounts¶

SESSIONDIR MAX SIZE: In order for the Singularity runtime to create a container it needs to create a sessiondir to manage various components of the container, including mounting filesystems over the base image filesystem. This option specifies how large the default sessiondir should be (in MB) and will only affect users who use the --contain options without also specifying a location to perform default read/writes to via the --workdir or --home options.

MOUNT PROC: This option determines if Singularity should automatically bind mount /proc within the container.

MOUNT SYS: This option determines if Singularity should automatically bind mount /sys within the container.

MOUNT DEV: Should be set to “YES”, if you want Singularity to automatically bind mount /dev within the container. If set to ‘minimal’, then only ‘null’, ‘zero’, ‘random’, ‘urandom’, and ‘shm’ will be included.

MOUNT DEVPTS: This option determines if Singularity will mount a new instance of devpts when there is a minimal /dev directory as explained above, or when the --contain option is passed.

Note

This requires either a kernel configured with CONFIG_DEVPTS_MULTIPLE_INSTANCES=y, or a kernel version at or newer than 4.7.

MOUNT HOME: When this option is enabled, Singularity will automatically determine the calling user’s home directory and attempt to mount it into the container.

MOUNT TMP: When this option is enabled, Singularity will automatically bind mount /tmp and /var/tmp into the container from the host. If the --contain option is passed, Singularity will create both locations within the sessiondir or within the directory specified by the --workdir option if that is passed as well.

MOUNT HOSTFS: This option will cause Singularity to probe the host for all mounted filesystems and bind those into containers at runtime.

MOUNT SLAVE: Singularity automatically mounts a handful host system directories to the container by default. This option determines if filesystem changes on the host should automatically be propogated to those directories in the container.

Note

This should be set to yes when autofs mounts in the system should show up in the container.

MEMORY FS TYPE: This option allows admins to choose the temporary filesystem used by Singularity. Temporary filesystems are primarily used for system directories like /dev when the host system directory is not mounted within the container.

Note

For Cray CLE 5 and 6, up to CLE 6.0.UP05, there is an issue (kernel panic) when Singularity uses tmpfs, so on affected systems it’s recommended to set this value to ramfs to avoid a kernel panic

Bind Mount Management¶

BIND PATH: This option is used for defining a list of files or directories to automatically be made available when Singularity runs a container. In order to successfully mount listed paths the file or directory path must exist within the container, or Singularity has either overlay or underlay support enabled.

Note

This option is ignored when containers are invoked with the --contain option.

You can define the a bind point where the source and destination are identical:

bind path = /etc/localtime

Or you can specify different source and destination locations using:

bind path = /etc/singularity/default-nsswitch.conf:/etc/nsswitch.conf

USER BIND CONTROL: This allows admins to decide if users can define bind points at runtime. By Default, this option is set to YES, which means users can specify bind points, scratch and tmp locations.

Limiting Container Execution¶

There are several ways to limit container execution as an admin listed below. If stricter controls are required, check out the Execution Control List.

LIMIT CONTAINER OWNERS: This restricts container execution to only allow conatiners that are owned by the specified user.

Note

This feature will only apply when Singularity is running in SUID mode and the user is non-root. By default this is set to NULL.

LIMIT CONTAINER GROUPS: This restricts container execution to only allow conatiners that are owned by the specified group.

Note

This feature will only apply when Singularity is running in SUID mode and the user is non-root. By default this is set to NULL.

LIMIT CONTAINER PATHS: This restricts container execution to only allow containers that are located within the specified path prefix.

Note

This feature will only apply when Singularity is running in SUID mode and the user is non-root. By default this is set to NULL.

ALLOW CONTAINER ${TYPE}: This option allows admins to limit the types of image formats that can be leveraged by users with Singularity. Formats include squashfs which is used by SIF and v2.x Singularity images, extfs which is used for writable overlays and some legacy Singularity images, dir which is used by sandbox images and encrypted which is only used by SIF images to encrypt filesystem contents.

Note

These limitations do not apply to the root user.

GPU Options¶

Singularity provides integration with GPUs in order to facilitate GPU based workloads seamlessly. Both options listed below are particularly useful in GPU only environments. For more information on using GPUs with Singularity checkout GPU Library Configuration.

ALWAYS USE NV ${TYPE}: Enabling this option will cause every action command (exec/shell/run/instance) to be executed with the --nv option implicitly added.

ALWAYS USE ROCM ${TYPE}: Enabling this option will cause every action command (exec/shell/run/instance) to be executed with the --rocm option implicitly added.

Supplemental Filesystems¶

ENABLE FUSEMOUNT: This will allow users to mount fuse filesystems inside containers using the --fusemount flag.

ENABLE OVERLAY: This option will allow Singularity to create bind mounts at paths that do not exist within the container image. This option can be set to try, which will try to use an overlayfs. If it fails to create an overlayfs in this case the bind path will be silently ignored.

ENABLE UNDERLAY: This option will allow Singularity to create bind mounts at paths that do not exist within the container image, just like ENABLE OVERLAY, but instead using an underlay. This is suitable for systems where overlay is not possible or not working. If the overlay option is available and working, it will be used instead.

External Tooling Paths¶

Internally, Singularity leverages several pieces of tooling in order to provide a wide breadth of features for users. Locations for these tools can be customized by system admins and referenced with the options below:

CNI CONFIGURATION PATH: This option allows admins to specify a custom path for the CNI configuration that Singularity will use for Network Virtualization.

CNI PLUGIN PATH: This option allows admins to specify a custom path for Singularity to access CNI plugin executables. Check out the Network Virtualization section of the user guide for more information.

MKSQUASHFS PATH: This allows an admin to specify the location of mksquashfs if it is not installed in a standard location. If set, mksquashfs at this path will be used instead of a mksquashfs found in PATH.

CRYPTSETUP PATH: The location for cryptsetup is recorded by Singularity at build time and will use that value if this is undefined. This option allows an admin to set the path of cryptsetup if it is located in a custom location and will override the value recorded at build time.

Updating Configuration Options¶

In order to manage this configuration file, Singularity has a config global command group that allows you to get, set, reset, and unset values through the CLI. It’s important to note that these commands must be run with elevated priveledges because the singularity.conf can only be modified by an administrator.

Example¶

In this example we will changing the BIND PATH option described above. First we can see the current list of bind paths set within our system configuration:

$ sudo singularity config global --get "bind path"
/etc/localtime,/etc/hosts

Now we can add a new path and verify it was successfully added:

$ sudo singularity config global --set "bind path" /etc/resolv.conf
$ sudo singularity config global --get "bind path"
/etc/resolv.conf,/etc/localtime,/etc/hosts

From here we can remove a path with:

$ sudo singularity config global --unset "bind path" /etc/localtime
$ sudo singularity config global --get "bind path"
/etc/resolv.conf,/etc/hosts

If we want to reset the option to the default at installation, then we can reset it with:

$ sudo singularity config global --reset "bind path"
$ sudo singularity config global --get "bind path"
/etc/localtime,/etc/hosts

And now we are back to our original option settings. You can also test what a change would look like by using the --dry-run option in conjunction with the above commands. Instead of writing to the configuration file, it will output what would have been written to the configuration file if the command had been run without the --dry-run option:

$ sudo singularity config global --dry-run --set "bind path" /etc/resolv.conf
# SINGULARITY.CONF
# This is the global configuration file for Singularity. This file controls
[...]
# BIND PATH: [STRING]
# DEFAULT: Undefined
# Define a list of files/directories that should be made available from within
# the container. The file or directory must exist within the container on
# which to attach to. you can specify a different source and destination
# path (respectively) with a colon; otherwise source and dest are the same.
# NOTE: these are ignored if singularity is invoked with --contain.
bind path = /etc/resolv.conf
bind path = /etc/localtime
bind path = /etc/hosts
[...]
$ sudo singularity config global --get "bind path"
/etc/localtime,/etc/hosts

Above we can see that /etc/resolv.conf is listed as a bind path in the output of the --dry-run command, but did not affect the actual bind paths of the system.

cgroups.toml¶

Cgroups or Control groups let you implement metering and limiting on the resources used by processes. You can limit memory, CPU. You can block IO, network IO, set SEL permissions for device nodes etc.

Note

The --apply-cgroups option can only be used with root privileges.

Examples¶

When you are limiting resources, apply the settings in the TOML file by using the path as an argument to the --apply-cgroups option like so:

$ sudo singularity shell --apply-cgroups /path/to/cgroups.toml my_container.sif

Limiting memory¶

To limit the amount of memory that your container uses to 500MB (524288000 bytes):

[memory]
    limit = 524288000

Start your container like so:

$ sudo singularity instance start --apply-cgroups path/to/cgroups.toml my_container.sif instance1

After that, you can verify that the container is only using 500MB of memory. (This example assumes that instance1 is the only running instance.)

$ cat /sys/fs/cgroup/memory/singularity/*/memory.limit_in_bytes
  524288000

Do not forget to stop your instances after configuring the options.

Similarly, the remaining examples can be tested by starting instances and examining the contents of the appropriate subdirectories of /sys/fs/cgroup/.

Limiting CPU¶

Limit CPU resources using one of the following strategies. The cpu section of the configuration file can limit memory with the following:

shares

This corresponds to a ratio versus other cgroups with cpu shares. Usually the default value is 1024. That means if you want to allow to use 50% of a single CPU, you will set 512 as value.

[cpu]
    shares = 512

A cgroup can get more than its share of CPU if there are enough idle CPU cycles available in the system, due to the work conserving nature of the scheduler, so a contained process can consume all CPU cycles even with a ratio of 50%. The ratio is only applied when two or more processes conflicts with their needs of CPU cycles.

quota/period

You can enforce hard limits on the CPU cycles a cgroup can consume, so contained processes can’t use more than the amount of CPU time set for the cgroup. quota allows you to configure the amount of CPU time that a cgroup can use per period. The default is 100ms (100000us). So if you want to limit amount of CPU time to 20ms during period of 100ms:

[cpu]
    period = 100000
    quota = 20000

cpus/mems

You can also restrict access to specific CPUs and associated memory nodes by using cpus/mems fields:

[cpu]
    cpus = "0-1"
    mems = "0-1"

Where container has limited access to CPU 0 and CPU 1.

Note

It’s important to set identical values for both cpus and mems.

Limiting IO¶

You can limit and monitor access to I/O for block devices. Use the [blockIO] section of the configuration file to do this like so:

[blockIO]
    weight = 1000
    leafWeight = 1000

weight and leafWeight accept values between 10 and 1000.

weight is the default weight of the group on all the devices until and unless overridden by a per device rule.

leafWeight relates to weight for the purpose of deciding how heavily to weigh tasks in the given cgroup while competing with the cgroup’s child cgroups.

To override weight/leafWeight for /dev/loop0 and /dev/loop1 block devices you would do something like this:

[blockIO]
    [[blockIO.weightDevice]]
        major = 7
        minor = 0
        weight = 100
        leafWeight = 50
    [[blockIO.weightDevice]]
        major = 7
        minor = 1
        weight = 100
        leafWeight = 50

You could limit the IO read/write rate to 16MB per second for the /dev/loop0 block device with the following configuration. The rate is specified in bytes per second.

[blockIO]
    [[blockIO.throttleReadBpsDevice]]
        major = 7
        minor = 0
        rate = 16777216
    [[blockIO.throttleWriteBpsDevice]]
        major = 7
        minor = 0
        rate = 16777216

ecl.toml¶

The execution control list is defined here. You can authorize the containers by validating both the location of the SIF file in the filesystem and by checking against a list of signing entities.

[[execgroup]]
  tagname = "group2"
  mode = "whitelist"
  dirpath = "/tmp/containers"
  keyfp = ["7064B1D6EFF01B1262FED3F03581D99FE87EAFD1"]

Only the containers running from and signed with above-mentioned path and keys will be authorized to run.

Three possible list modes you can choose from:

Whitestrict: The SIF must be signed by ALL of the keys mentioned.

Whitelist: As long as the SIF is signed by one or more of the keys, the container is allowed to run.

Blacklist: Only the containers whose keys are not mentioned in the group are allowed to run.

Note

The ECL checks will use the new signature format introduced in Singularity 3.6.0. Containers signed with older versions of Singularity Singularity will not pass ECL checks.

To temporarily permit the use of legacy insecure signatures, set legacyinsecure = true in ecl.toml.

GPU Library Configuration¶

When a container includes a GPU enabled application, Singularity (with the --nv or --rocm options) can properly inject the required Nvidia or AMD GPU driver libraries into the container, to match the host’s kernel. The GPU /dev entries are provided in containers run with --nv or --rocm even if the --contain option is used to restrict the in-container device tree.

Compatibility between containerized CUDA/ROCm/OpenCL applications and host drivers/libraries is dependent on the versions of the GPU compute frameworks that were used to build the applications. Compatibility and usage information is discussed in the GPU Support section of the user guide

NVIDIA GPUs / CUDA¶

If the nvidia-container-cli tool is installed on the host system, it will be used to locate any Nvidia libraries and binaries on the host system.

If nvidia-container-cli is not present, the nvliblist.conf file is used to specify libraries and executables that need to be injected into the container when running Singularity with the --nv Nvidia GPU support option. The default nvliblist.conf is suitable for CUDA 10.1, but may need to be modified if you need to include additional libraries, or further libraries are added to newer versions of the Nvidia driver/CUDA distribution.

AMD Radeon GPUs / ROCm¶

The rocmliblist.conf file is used to specify libraries and executables that need to be injected into the container when running Singularity with the --rocm Radeon GPU support option. The default rocmliblist.conf is suitable for ROCm 2.10, but may need to modified if you need to include additional libraries, or further libraries are added to newer versions of the ROCm distribution.

GPU liblist format¶

The nvliblist.conf and rocmliblist files list the basename of executables and libraries to be bound into the container, without path information.

Binaries are found by searching $PATH:

# put binaries here
# In shared environments you should ensure that permissions on these files
# exclude writing by non-privileged users.
rocm-smi
rocminfo

Libraries should be specified without version information, i.e. libname.so, and are resolved using ldconfig.

# put libs here (must end in .so)
libamd_comgr.so
libcomgr.so
libCXLActivityLogger.so

If you receive warnings that binaries or libraries are not found, ensure that they are in a system path (binaries), or available in paths configured in /etc/ld.so.conf (libraries).

capability.json¶

Note

It is extremely important to recognize that granting users Linux capabilities with the capability command group is usually identical to granting those users root level access on the host system. Most if not all capabilities will allow users to “break out” of the container and become root on the host. This feature is targeted toward special use cases (like cloud-native architectures) where an admin/developer might want to limit the attack surface within a container that normally runs as root. This is not a good option in multi-tenant HPC environments where an admin wants to grant a user special privileges within a container. For that and similar use cases, the fakeroot feature is a better option.

Singularity provides full support for admins to grant and revoke Linux capabilities on a user or group basis. The capability.json file is maintained by Singularity in order to manage these capabilities. The capability command group allows you to add, drop, and list capabilities for users and groups.

For example, let us suppose that we have decided to grant a user (named pinger) capabilities to open raw sockets so that they can use ping in a container where the binary is controlled via capabilities.

To do so, we would issue a command such as this:

$ sudo singularity capability add --user pinger CAP_NET_RAW

This means the user pinger has just been granted permissions (through Linux capabilities) to open raw sockets within Singularity containers.

We can check that this change is in effect with the capability list command.

$ sudo singularity capability list --user pinger
CAP_NET_RAW

To take advantage of this new capability, the user pinger must also request the capability when executing a container with the --add-caps flag. pinger would need to run a command like this:

$ singularity exec --add-caps CAP_NET_RAW library://sylabs/tests/ubuntu_ping:v1.0 ping -c 1 8.8.8.8
PING 8.8.8.8 (8.8.8.8) 56(84) bytes of data.
64 bytes from 8.8.8.8: icmp_seq=1 ttl=52 time=73.1 ms

--- 8.8.8.8 ping statistics ---
1 packets transmitted, 1 received, 0% packet loss, time 0ms
rtt min/avg/max/mdev = 73.178/73.178/73.178/0.000 ms

If we decide that it is no longer necessary to allow the user pinger to open raw sockets within Singularity containers, we can revoke the appropriate Linux capability like so:

$ sudo singularity capability drop --user pinger CAP_NET_RAW

Now if pinger tries to use CAP_NET_RAW, Singularity will not give the capability to the container and ping will fail to create a socket:

$ singularity exec --add-caps CAP_NET_RAW library://sylabs/tests/ubuntu_ping:v1.0 ping -c 1 8.8.8.8
WARNING: not authorized to add capability: CAP_NET_RAW
ping: socket: Operation not permitted

The capability add and drop subcommands will also accept the case insensitive keyword all to grant or revoke all Linux capabilities to a user or group.

For more information about individual Linux capabilities check out the man pages or use the capability avail command to output available capabilities with a description of their behaviors.

seccomp-profiles¶

Secure Computing (seccomp) Mode is a feature of the Linux kernel that allows an administrator to filter system calls being made from a container. Profiles made up of allowed and restricted calls can be passed to different containers. Seccomp provides more control than capabilities alone, giving a smaller attack surface for an attacker to work from within a container.

You can set the default action with defaultAction for a non-listed system call. Example: SCMP_ACT_ALLOW filter will allow all the system calls if it matches the filter rule and you can set it to SCMP_ACT_ERRNO which will have the thread receive a return value of errno if it calls a system call that matches the filter rule. The file is formatted in a way that it can take a list of additional system calls for different architecture and Singularity will automatically take syscalls related to the current architecture where it’s been executed. The include/exclude-> caps section will include/exclude the listed system calls if the user has the associated capability.

Use the --security option to invoke the container like:

$ sudo singularity shell --security seccomp:/home/david/my.json my_container.sif

For more insight into security options, network options, cgroups, capabilities, etc, please check the Userdocs and it’s Appendix.

remote.yaml¶

Sylabs introduced the online Sylabs Cloud to enable users to Create, Secure, and Share their container images with others.

Singularity allows users to login to an account on the Sylabs Cloud, or configure Singularity to use an API compatable container service such as a local installation of Singularity Enterprise, which provides an on-premise private Container Library, Remote Builder and Key Store.

System-wide remote endpoints are defined in a configuration file typically located at /usr/local/etc/singularity/remote.yaml (this location may vary depending on installation parameters) and can be managed by administrators with the remote command group with the --global flag so that they are easily available for users.

Note

A fresh installation of Singularity is automatically configured to connect to the public Sylabs Cloud services.

Examples¶

Use the remote command group with the --global flag to create a system-wide remote endpoint:

$ sudo singularity remote add --global company-remote https://enterprise.example.com
[sudo] password for dave:
INFO:    Remote "company-remote" added.
INFO:    Global option detected. Will not automatically log into remote.

Conversely, to remove a system-wide endpoint:

$ sudo singularity remote remove --global company-remote
[sudo] password for dave:
INFO:    Remote "company-remote" removed.

Note

Once users login to a system wide endpoint, a copy of the endpoint will be listed in a their ~/.singularity/remote.yaml file. This means modifications or removal of the system-wide endpoint will not be reflected in the users configuration unless they remove the endpoint themselves.

For more insight into the remote command group, using remote endpoints, etc, please check the Remote Userdocs.