Containers Guide

Overview
Known limitations
Prerequisites
Required software
Example configurations for various OCI Runtimes
Testing OCI runtime outside of Slurm
Requesting container jobs or steps
Integration with Rootless Docker
Integration with Podman
OCI Container bundle
Example OpenMPI v5 + PMIx v4 container
Container support via Plugin

Overview

Containers are being adopted in HPC workloads. Containers rely on existing kernel features to allow greater user control over what applications see and can interact with at any given time. For HPC Workloads, these are usually restricted to the mount namespace. Slurm natively supports the requesting of unprivileged OCI Containers for jobs and steps.

Setting up containers requires several steps:

Set up the kernel and a container runtime.
Deploy a suitable oci.conf file accessible to the compute nodes (examples below).
Restart or reconfigure slurmd on the compute nodes.
Generate OCI bundles for containers that are needed and place them on the compute nodes.
Verify that you can run containers directly through the chosen OCI runtime.
Verify that you can request a container through Slurm.

Known limitations

The following is a list of known limitations of the Slurm OCI container implementation.

All containers must run under unprivileged (i.e. rootless) invocation. All commands are called by Slurm as the user with no special permissions.
Custom container networks are not supported. All containers should work with the "host" network.
Slurm will not transfer the OCI container bundle to the execution nodes. The bundle must already exist on the requested path on the execution node.
Containers are limited by the OCI runtime used. If the runtime does not support a certain feature, then that feature will not work for any job using a container.
oci.conf must be configured on the execution node for the job, otherwise the requested container will be ignored by Slurm (but can be used by the job or any given plugin).

Prerequisites

The host kernel must be configured to allow user land containers:

sudo sysctl -w kernel.unprivileged_userns_clone=1
sudo sysctl -w kernel.apparmor_restrict_unprivileged_unconfined=0
sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0

Docker also provides a tool to verify the kernel configuration:

$ dockerd-rootless-setuptool.sh check --force
[INFO] Requirements are satisfied

Required software:

Fully functional OCI runtime. It needs to be able to run outside of Slurm first.
Fully functional OCI bundle generation tools. Slurm requires OCI Container compliant bundles for jobs.

Example configurations for various OCI Runtimes

The OCI Runtime Specification provides requirements for all compliant runtimes but does not expressly provide requirements on how runtimes will use arguments. In order to support as many runtimes as possible, Slurm provides pattern replacement for commands issued for each OCI runtime operation. This will allow a site to edit how the OCI runtimes are called as needed to ensure compatibility.

For runc and crun, there are two sets of examples provided. The OCI runtime specification only provides the start and create operations sequence, but these runtimes provides a much more efficient run operation. Sites are strongly encouraged to use the run operation (if provided) as the start and create operations require that Slurm poll the OCI runtime to know when the containers have completed execution. While Slurm attempts to be as efficient as possible with polling, it will result in a thread using CPU time inside of the job and slower response of Slurm to catch when container execution is complete.

The examples provided have been tested to work but are only suggestions. Sites are expected to ensure that the resultant root directory used will be secure from cross user viewing and modifications. The examples provided point to "/run/user/%U" where %U will be replaced with the numeric user id. Systemd manages "/run/user/" (independently of Slurm) and will likely need additional configuration to ensure the directories exist on compute nodes when the users will not log in to the nodes directly. This configuration is generally achieved by calling loginctl to enable lingering sessions. Be aware that the directory in this example will be cleaned up by systemd once the user session ends on the node.

oci.conf example for runc using create/start:

EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeQuery="runc --rootless=true --root=/run/user/%U/ state %n.%u.%j.%s.%t"
RunTimeCreate="runc --rootless=true --root=/run/user/%U/ create %n.%u.%j.%s.%t -b %b"
RunTimeStart="runc --rootless=true --root=/run/user/%U/ start %n.%u.%j.%s.%t"
RunTimeKill="runc --rootless=true --root=/run/user/%U/ kill -a %n.%u.%j.%s.%t"
RunTimeDelete="runc --rootless=true --root=/run/user/%U/ delete --force %n.%u.%j.%s.%t"

oci.conf example for runc using run (recommended over using create/start):

EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeQuery="runc --rootless=true --root=/run/user/%U/ state %n.%u.%j.%s.%t"
RunTimeKill="runc --rootless=true --root=/run/user/%U/ kill -a %n.%u.%j.%s.%t"
RunTimeDelete="runc --rootless=true --root=/run/user/%U/ delete --force %n.%u.%j.%s.%t"
RunTimeRun="runc --rootless=true --root=/run/user/%U/ run %n.%u.%j.%s.%t -b %b"

oci.conf example for crun using create/start:

EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeQuery="crun --rootless=true --root=/run/user/%U/ state %n.%u.%j.%s.%t"
RunTimeKill="crun --rootless=true --root=/run/user/%U/ kill -a %n.%u.%j.%s.%t"
RunTimeDelete="crun --rootless=true --root=/run/user/%U/ delete --force %n.%u.%j.%s.%t"
RunTimeCreate="crun --rootless=true --root=/run/user/%U/ create --bundle %b %n.%u.%j.%s.%t"
RunTimeStart="crun --rootless=true --root=/run/user/%U/ start %n.%u.%j.%s.%t"

oci.conf example for crun using run (recommended over using create/start):

EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeQuery="crun --rootless=true --root=/run/user/%U/ state %n.%u.%j.%s.%t"
RunTimeKill="crun --rootless=true --root=/run/user/%U/ kill -a %n.%u.%j.%s.%t"
RunTimeDelete="crun --rootless=true --root=/run/user/%U/ delete --force %n.%u.%j.%s.%t"
RunTimeRun="crun --rootless=true --root=/run/user/%U/ run --bundle %b %n.%u.%j.%s.%t"

oci.conf example for nvidia-container-runtime using create/start:

EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeQuery="nvidia-container-runtime --rootless=true --root=/run/user/%U/ state %n.%u.%j.%s.%t"
RunTimeCreate="nvidia-container-runtime --rootless=true --root=/run/user/%U/ create %n.%u.%j.%s.%t -b %b"
RunTimeStart="nvidia-container-runtime --rootless=true --root=/run/user/%U/ start %n.%u.%j.%s.%t"
RunTimeKill="nvidia-container-runtime --rootless=true --root=/run/user/%U/ kill -a %n.%u.%j.%s.%t"
RunTimeDelete="nvidia-container-runtime --rootless=true --root=/run/user/%U/ delete --force %n.%u.%j.%s.%t"

oci.conf example for nvidia-container-runtime using run (recommended over using create/start):

EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeQuery="nvidia-container-runtime --rootless=true --root=/run/user/%U/ state %n.%u.%j.%s.%t"
RunTimeKill="nvidia-container-runtime --rootless=true --root=/run/user/%U/ kill -a %n.%u.%j.%s.%t"
RunTimeDelete="nvidia-container-runtime --rootless=true --root=/run/user/%U/ delete --force %n.%u.%j.%s.%t"
RunTimeRun="nvidia-container-runtime --rootless=true --root=/run/user/%U/ run %n.%u.%j.%s.%t -b %b"

oci.conf example for Singularity v4.1.3 using native runtime:

IgnoreFileConfigJson=true
EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeRun="singularity exec --userns %r %@"
RunTimeKill="kill -s SIGTERM %p"
RunTimeDelete="kill -s SIGKILL %p"

oci.conf example for Singularity v4.0.2 in OCI mode:

Singularity v4.x requires setuid mode for OCI support.

EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeQuery="sudo singularity oci state %n.%u.%j.%s.%t"
RunTimeRun="sudo singularity oci run --bundle %b %n.%u.%j.%s.%t"
RunTimeKill="sudo singularity oci kill %n.%u.%j.%s.%t"
RunTimeDelete="sudo singularity oci delete %n.%u.%j.%s.%t"

WARNING: Singularity (v4.0.2) requires sudo or setuid binaries for OCI support, which is a security risk since the user is able to modify these calls. This example is only provided for testing purposes.

WARNING: Upstream singularity development of the OCI interface appears to have ceased and sites should use the user namespace support instead.

oci.conf example for hpcng Singularity v3.8.0:

EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
OCIRunTimeQuery="sudo singularity oci state %n.%u.%j.%s.%t"
OCIRunTimeCreate="sudo singularity oci create --bundle %b %n.%u.%j.%s.%t"
OCIRunTimeStart="sudo singularity oci start %n.%u.%j.%s.%t"
OCIRunTimeKill="sudo singularity oci kill %n.%u.%j.%s.%t"
OCIRunTimeDelete="sudo singularity oci delete %n.%u.%j.%s.%t

WARNING: Singularity (v3.8.0) requires sudo or setuid binaries for OCI support, which is a security risk since the user is able to modify these calls. This example is only provided for testing purposes.

WARNING: Upstream singularity development of the OCI interface appears to have ceased and sites should use the user namespace support instead.

oci.conf example for Charliecloud (v0.30)

IgnoreFileConfigJson=true
CreateEnvFile=newline
EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeRun="env -i PATH=/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin/:/sbin/ USER=$(whoami) HOME=/home/$(whoami)/ ch-run -w --bind /etc/group:/etc/group --bind /etc/passwd:/etc/passwd --bind /etc/slurm:/etc/slurm --bind %m:/var/run/slurm/ --bind /var/run/munge/:/var/run/munge/ --set-env=%e --no-passwd %r -- %@"
RunTimeKill="kill -s SIGTERM %p"
RunTimeDelete="kill -s SIGKILL %p"

oci.conf example for Enroot (3.3.0)

IgnoreFileConfigJson=true
CreateEnvFile=newline
EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
RunTimeRun="/usr/local/bin/enroot-start-wrapper %b %m %e -- %@"
RunTimeKill="kill -s SIGINT %p"
RunTimeDelete="kill -s SIGTERM %p"

/usr/local/bin/enroot-start-wrapper:

#!/bin/bash
BUNDLE="$1"
SPOOLDIR="$2"
ENVFILE="$3"
shift 4
IMAGE=

export USER=$(whoami)
export HOME="$BUNDLE/"
export TERM
export ENROOT_SQUASH_OPTIONS='-comp gzip -noD'
export ENROOT_ALLOW_SUPERUSER=n
export ENROOT_MOUNT_HOME=y
export ENROOT_REMAP_ROOT=y
export ENROOT_ROOTFS_WRITABLE=y
export ENROOT_LOGIN_SHELL=n
export ENROOT_TRANSFER_RETRIES=2
export ENROOT_CACHE_PATH="$SPOOLDIR/"
export ENROOT_DATA_PATH="$SPOOLDIR/"
export ENROOT_TEMP_PATH="$SPOOLDIR/"
export ENROOT_ENVIRON="$ENVFILE"

if [ ! -f "$BUNDLE" ]
then
        IMAGE="$SPOOLDIR/container.sqsh"
        enroot import -o "$IMAGE" -- "$BUNDLE" && \
        enroot create "$IMAGE"
        CONTAINER="container"
else
        CONTAINER="$BUNDLE"
fi

enroot start -- "$CONTAINER" "$@"
rc=$?

[ $IMAGE ] && unlink $IMAGE

exit $rc

Handling multiple runtimes

If you wish to accommodate multiple runtimes in your environment, it is possible to do so with a bit of extra setup. This section outlines one possible way to do so:

Create a generic oci.conf that calls a wrapper script

IgnoreFileConfigJson=true
RunTimeRun="/opt/slurm-oci/run %b %m %u %U %n %j %s %t %@"
RunTimeKill="kill -s SIGTERM %p"
RunTimeDelete="kill -s SIGKILL %p"

Create the wrapper script to check for user-specific run configuration (e.g., /opt/slurm-oci/run)

#!/bin/bash
if [[ -e ~/.slurm-oci-run ]]; then
	~/.slurm-oci-run "$@"
else
	/opt/slurm-oci/slurm-oci-run-default "$@"
fi

Create a generic run configuration to use as the default (e.g., /opt/slurm-oci/slurm-oci-run-default)

#!/bin/bash --login
# Parse
CONTAINER="$1"
SPOOL_DIR="$2"
USER_NAME="$3"
USER_ID="$4"
NODE_NAME="$5"
JOB_ID="$6"
STEP_ID="$7"
TASK_ID="$8"
shift 8 # subsequent arguments are the command to run in the container
# Run
apptainer run --bind /var/spool --containall "$CONTAINER" "$@"

Add executable permissions to both scripts

chmod +x /opt/slurm-oci/run /opt/slurm-oci/slurm-oci-run-default

Once this is done, users may create a script at '~/.slurm-oci-run' if they wish to customize the container run process, such as using a different container runtime. Users should model this file after the default '/opt/slurm-oci/slurm-oci-run-default'

Testing OCI runtime outside of Slurm

Slurm calls the OCI runtime directly in the job step. If it fails, then the job will also fail.

Go to the directory containing the OCI Container bundle:
```
cd $ABS_PATH_TO_BUNDLE
```
Execute OCI Container runtime (You can find a few examples on how to build a bundle below):
```
$OCIRunTime $ARGS create test --bundle $PATH_TO_BUNDLE
```
```
$OCIRunTime $ARGS start test
```
```
$OCIRunTime $ARGS kill test
```
```
$OCIRunTime $ARGS delete test
```
If these commands succeed, then the OCI runtime is correctly configured and can be tested in Slurm.

Requesting container jobs or steps

salloc, srun and sbatch (in Slurm 21.08+) have the '--container' argument, which can be used to request container runtime execution. The requested job container will not be inherited by the steps called, excluding the batch and interactive steps.

Batch step inside of container:

sbatch --container $ABS_PATH_TO_BUNDLE --wrap 'bash -c "cat /etc/*rel*"'

Batch job with step 0 inside of container:

sbatch --wrap 'srun bash -c "--container $ABS_PATH_TO_BUNDLE cat /etc/*rel*"'

Interactive step inside of container:

salloc --container $ABS_PATH_TO_BUNDLE bash -c "cat /etc/*rel*"

Interactive job step 0 inside of container:

salloc srun --container $ABS_PATH_TO_BUNDLE bash -c "cat /etc/*rel*"

Job with step 0 inside of container:

srun --container $ABS_PATH_TO_BUNDLE bash -c "cat /etc/*rel*"

Job with step 1 inside of container:

srun srun --container $ABS_PATH_TO_BUNDLE bash -c "cat /etc/*rel*"

Integration with Rootless Docker (Docker Engine v20.10+ & Slurm-23.02+)

Slurm's scrun can be directly integrated with Rootless Docker to run containers as jobs. No special user permissions are required and should not be granted to use this functionality.

Prerequisites

slurm.conf must be configured to use Munge authentication.
```
AuthType=auth/munge
```
scrun.lua must be configured for site storage configuration.
Configure kernel to allow pings
Configure rootless dockerd to allow listening on privileged ports
scrun.lua must be present on any node where scrun may be run. The example should be sufficent for most environments but paths should be modified to match available local storage.
oci.conf must be present on any node where any container job may be run. Example configurations for known OCI runtimes are provided above. Examples may require paths to be correct to installation locations.

Limitations

JWT authentication is not supported.
Docker container building is not currently functional pending merge of Docker pull request.
Docker does not expose configuration options to disable security options needed to run jobs. This requires that all calls to docker provide the following command line arguments. This can be done via shell variable, an alias, wrapper function, or wrapper script:
```
--security-opt label:disable --security-opt seccomp=unconfined --security-opt apparmor=unconfined --net=none
```
Docker's builtin security functionality is not required (or wanted) for containers being run by Slurm. Docker is only acting as a container image lifecycle manager. The containers will be executed remotely via Slurm following the existing security configuration in Slurm outside of unprivileged user control.
All containers must use the "none" networking driver . Attempting to use bridge, overlay, host, ipvlan, or macvlan can result in scrun being isolated from the network and not being able to communicate with the Slurm controller. The container is run by Slurm on the compute nodes which makes having Docker setup a network isolation layer ineffective for the container.
docker exec command is not supported.
docker swarm command is not supported.
docker compose/docker-compose command is not supported.
docker pause command is not supported.
docker unpause command is not supported.
docker swarm command is not supported.
All docker commands are not supported inside of containers.
Docker API is not supported inside of containers.

Setup procedure

Install and configure Rootless Docker
Rootless Docker must be fully operational and able to run containers before continuing.
Setup environment for all docker calls:
```
export DOCKER_HOST=unix://$XDG_RUNTIME_DIR/docker.sock
```
All commands following this will expect this environment variable to be set.
Stop rootless docker:
```
systemctl --user stop docker
```
Configure Docker to call scrun instead of the default OCI runtime.
- To configure for all users:
```
/etc/docker/daemon.json
```
- To configure per user:
```
~/.config/docker/daemon.json
```
Set the following fields to configure Docker:
```
{
    "experimental": true,
    "iptables": false,
    "bridge": "none",
    "no-new-privileges": true,
    "rootless": true,
    "selinux-enabled": false,
    "default-runtime": "slurm",
    "runtimes": {
        "slurm": {
            "path": "/usr/local/bin/scrun"
        }
    },
    "data-root": "/run/user/${USER_ID}/docker/",
    "exec-root": "/run/user/${USER_ID}/docker-exec/"
}
```
Correct path to scrun as if installation prefix was configured. Replace ${USER_ID} with numeric user id or target a different directory with global write permissions and sticky bit. Rootless docker requires a different root directory than the system's default to avoid permission errors.
It is strongly suggested that sites consider using inter-node shared filesystems to store Docker's containers. While it is possible to have a scrun.lua script to push and pull images for each deployment, there can be a massive performance penalty. Using a shared filesystem will avoid moving these files around.
Possible configuration additions to daemon.json to use a shared filesystem with vfs storage driver:
```
{
  "storage-driver": "vfs",
  "data-root": "/path/to/shared/filesystem/user_name/data/",
  "exec-root": "/path/to/shared/filesystem/user_name/exec/",
}
```
Any node expected to be able to run containers from Docker must have ability to atleast read the filesystem used. Full write privileges are suggested and will be required if changes to the container filesystem are desired.

Configure dockerd to not setup network namespace, which will break scrun's ability to talk to the Slurm controller.

To configure for all users:

/etc/systemd/user/docker.service.d/override.conf

To configure per user:

~/.config/systemd/user/docker.service.d/override.conf

[Service]
Environment="DOCKERD_ROOTLESS_ROOTLESSKIT_PORT_DRIVER=none"
Environment="DOCKERD_ROOTLESS_ROOTLESSKIT_NET=host"

Reload docker's service unit in systemd:
```
systemctl --user daemon-reload
```
Start rootless docker:
```
systemctl --user start docker
```

Verify Docker is using scrun:

export DOCKER_SECURITY="--security-opt label=disable --security-opt seccomp=unconfined  --security-opt apparmor=unconfined --net=none"
docker run $DOCKER_SECURITY hello-world
docker run $DOCKER_SECURITY alpine /bin/printenv SLURM_JOB_ID
docker run $DOCKER_SECURITY alpine /bin/hostname
docker run $DOCKER_SECURITY -e SCRUN_JOB_NUM_NODES=10 alpine /bin/hostname

Integration with Podman (Slurm-23.02+)

Slurm's scrun can be directly integrated with Podman to run containers as jobs. No special user permissions are required and should not be granted to use this functionality.

Prerequisites

Slurm must be fully configured and running on host running podman.
slurm.conf must be configured to use Munge authentication.
```
AuthType=auth/munge
```
scrun.lua must be configured for site storage configuration.
scrun.lua must be present on any node where scrun may be run. The example should be sufficent for most environments but paths should be modified to match available local storage.
oci.conf must be present on any node where any container job may be run. Example configurations for known OCI runtimes are provided above. Examples may require paths to be correct to installation locations.

Limitations

JWT authentication is not supported.
All containers must use host networking
podman exec command is not supported.
podman-compose command is not supported, due to only being partially implemented. Some compositions may work but each container may be run on different nodes. The network for all containers must be the network_mode: host device.
podman kube command is not supported.
podman pod command is not supported.
podman farm command is not supported.
All podman commands are not supported inside of containers.
Podman REST API is not supported inside of containers.

Setup procedure

Install Podman

Configure rootless Podman

Verify rootless podman is configured

$ podman info --format '{{.Host.Security.Rootless}}'
true

Verify rootless Podman is fully functional before adding Slurm support:
- The value printed by the following commands should be the same:
```
$ id
$ podman run --userns keep-id alpine id
```
```
$ sudo id
$ podman run --userns nomap alpine id
```
Configure Podman to call scrun instead of the default OCI runtime. See upstream documentation for details on configuration locations and loading order for containers.conf.
- To configure for all users: /etc/containers/containers.conf
- To configure per user: $XDG_CONFIG_HOME/containers/containers.conf or ~/.config/containers/containers.conf (if $XDG_CONFIG_HOME is not defined).
Set the following configuration parameters to configure Podman's containers.conf:
```
[containers]
apparmor_profile = "unconfined"
cgroupns = "host"
cgroups = "enabled"
default_sysctls = []
label = false
netns = "host"
no_hosts = true
pidns = "host"
utsns = "host"
userns = "host"
log_driver = "journald"

[engine]
cgroup_manager = "systemd"
runtime = "slurm"
remote = false

[engine.runtimes]
slurm = [
	"/usr/local/bin/scrun",
	"/usr/bin/scrun"
]
```
Correct path to scrun as if installation prefix was configured.
The "cgroup_manager" field will need to be swapped to "cgroupfs" on systems not running systemd.
It is strongly suggested that sites consider using inter-node shared filesystems to store Podman's containers. While it is possible to have a scrun.lua script to push and pull images for each deployment, there can be a massive performance penalty. Using a shared filesystem will avoid moving these files around.
- To configure for all users:
```
/etc/containers/storage.conf
```
- To configure per user:
```
$XDG_CONFIG_HOME/containers/storage.conf
```
Possible configuration additions to storage.conf to use a shared filesystem with vfs storage driver:
```
[storage]
driver = "vfs"
runroot = "$HOME/containers"
graphroot = "$HOME/containers"

[storage.options]
pull_options = {use_hard_links = "true", enable_partial_images = "true"}


[storage.options.vfs]
ignore_chown_errors = "true"
```
Any node expected to be able to run containers from Podman must have ability to atleast read the filesystem used. Full write privileges are suggested and will be required if changes to the container filesystem are desired.

Verify Podman is using scrun:

podman run hello-world
podman run alpine printenv SLURM_JOB_ID
podman run alpine hostname
podman run alpine -e SCRUN_JOB_NUM_NODES=10 hostname
salloc podman run --env-host=true alpine hostname
salloc sh -c 'podman run -e SLURM_JOB_ID=$SLURM_JOB_ID alpine hostname'

Optional: Create alias for Docker:

alias docker=podman

alias docker='podman --config=/some/path "$@"'

Troubleshooting

Podman runs out of locks:

$ podman run alpine uptime
Error: allocating lock for new container: allocation failed; exceeded num_locks (2048)

Try renumbering:
```
podman system renumber
```
Try reseting all storage:
```
podman system reset
```

OCI Container bundle

There are multiple ways to generate an OCI Container bundle. The instructions below are the method we found the easiest. The OCI standard provides the requirements for any given bundle: Filesystem Bundle

Here are instructions on how to generate a container using a few alternative container solutions:

Create an image and prepare it for use with runc:

Use an existing tool to create a filesystem image in /image/rootfs:

debootstrap:

sudo debootstrap stable /image/rootfs http://deb.debian.org/debian/

yum:

sudo yum --config /etc/yum.conf --installroot=/image/rootfs/ --nogpgcheck --releasever=${CENTOS_RELEASE} -y

docker:

mkdir -p ~/oci_images/alpine/rootfs
cd ~/oci_images/
docker pull alpine
docker create --name alpine alpine
docker export alpine | tar -C ~/oci_images/alpine/rootfs -xf -
docker rm alpine

Configure a bundle for runtime to execute:

Use runc to generate a config.json:

cd ~/oci_images/alpine
runc --rootless=true spec --rootless

Test running image:

srun --container ~/oci_images/alpine/ uptime

Use umoci and skopeo to generate a full image:

mkdir -p ~/oci_images/
cd ~/oci_images/
skopeo copy docker://alpine:latest oci:alpine:latest
umoci unpack --rootless --image alpine ~/oci_images/alpine
srun --container ~/oci_images/alpine uptime

Use singularity to generate a full image:

mkdir -p ~/oci_images/alpine/
cd ~/oci_images/alpine/
singularity pull alpine
sudo singularity oci mount ~/oci_images/alpine/alpine_latest.sif ~/oci_images/alpine
mv config.json singularity_config.json
runc spec --rootless
srun --container ~/oci_images/alpine/ uptime

Example OpenMPI v5 + PMIx v4 container

Minimalist Dockerfile to generate a image with OpenMPI and PMIx to test basic MPI jobs.

Dockerfile

FROM almalinux:latest
RUN dnf -y update && dnf -y upgrade && dnf install -y epel-release && dnf -y update
RUN dnf -y install make automake gcc gcc-c++ kernel-devel bzip2 python3 wget libevent-devel hwloc-devel

WORKDIR /usr/local/src/
RUN wget --quiet 'https://github.com/openpmix/openpmix/releases/download/v5.0.7/pmix-5.0.7.tar.bz2' -O - | tar --no-same-owner -xvjf -
WORKDIR /usr/local/src/pmix-5.0.7/
RUN ./configure && make -j && make install

WORKDIR /usr/local/src/
RUN wget --quiet --inet4-only 'https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.7.tar.bz2' -O - | tar --no-same-owner -xvjf -
WORKDIR /usr/local/src/openmpi-5.0.7/
RUN ./configure --disable-pty-support --enable-ipv6 --without-slurm --with-pmix --enable-debug && make -j && make install

WORKDIR /usr/local/src/openmpi-5.0.7/examples
RUN make && cp -v hello_c ring_c connectivity_c spc_example /usr/local/bin

Container support via Plugin

Slurm allows container developers to create SPANK Plugins that can be called at various points of job execution to support containers. Any site using one of these plugins to start containers should not have an "oci.conf" configuration file. The "oci.conf" file activates the builtin container functionality which may conflict with the SPANK based plugin functionality.

The following projects are third party container solutions that have been designed to work with Slurm, but they have not been tested or validated by SchedMD.

Shifter

Shifter is a container project out of NERSC to provide HPC containers with full scheduler integration.

Shifter provides full instructions to integrate with Slurm.
Presentations about Shifter and Slurm:
- Never Port Your Code Again - Docker functionality with Shifter using SLURM
- Shifter: Containers in HPC Environments

ENROOT and Pyxis

Enroot is a user namespace container system sponsored by NVIDIA that supports:

Slurm integration via pyxis
Native support for Nvidia GPUs
Faster Docker image imports

Sarus

Sarus is a privileged container system sponsored by ETH Zurich CSCS that supports:

Slurm image synchronization via OCI hook
Native OCI Image support
NVIDIA GPU Support
Similar design to Shifter

Overview slides of Sarus are here.

Last modified 27 November 2024

Slurm Workload Manager

Containers Guide

Contents

Overview

Known limitations

Prerequisites

Required software:

Example configurations for various OCI Runtimes

oci.conf example for runc using create/start:

oci.conf example for runc using run (recommended over using create/start):

oci.conf example for crun using create/start:

oci.conf example for crun using run (recommended over using create/start):

oci.conf example for nvidia-container-runtime using create/start:

oci.conf example for nvidia-container-runtime using run (recommended over using create/start):

oci.conf example for Singularity v4.1.3 using native runtime:

oci.conf example for Singularity v4.0.2 in OCI mode:

oci.conf example for hpcng Singularity v3.8.0:

oci.conf example for Charliecloud (v0.30)

oci.conf example for Enroot (3.3.0)

Handling multiple runtimes

Testing OCI runtime outside of Slurm

Requesting container jobs or steps

Integration with Rootless Docker (Docker Engine v20.10+ & Slurm-23.02+)

Prerequisites

Limitations

Setup procedure

Integration with Podman (Slurm-23.02+)

Prerequisites

Limitations

Setup procedure

Troubleshooting

OCI Container bundle

Example OpenMPI v5 + PMIx v4 container

Dockerfile

Container support via Plugin

Shifter

ENROOT and Pyxis

Sarus