Skip to content

fix(apptainer): ensure apptainer jobs run as privileged #62

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

fix(apptainer): ensure apptainer jobs run as privileged #62

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 4 additions & 24 deletions snakemake_executor_plugin_kubernetes/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -260,29 +260,6 @@ def run_job(self, job: JobExecutorInterface):
"Must be 'nvidia' or 'amd'."
)

# capabilities
if (
job.is_containerized
and DeploymentMethod.APPTAINER
in self.workflow.deployment_settings.deployment_method
):
# TODO this should work, but it doesn't currently because of
# missing loop devices
# singularity inside docker requires SYS_ADMIN capabilities
# see
# https://groups.google.com/a/lbl.gov/forum/#!topic/singularity/e9mlDuzKowc
# container.capabilities = kubernetes.client.V1Capabilities()
# container.capabilities.add = ["SYS_ADMIN",
# "DAC_OVERRIDE",
# "SETUID",
# "SETGID",
# "SYS_CHROOT"]

# Running in priviledged mode always works
container.security_context = kubernetes.client.V1SecurityContext(
privileged=True
)

# Add service account name if provided
if self.k8s_service_account_name:
pod_spec.service_account_name = self.k8s_service_account_name
Expand Down Expand Up @@ -370,7 +347,10 @@ def run_job(self, job: JobExecutorInterface):
if not scale_value:
container.resources.limits["nvidia.com/gpu"] = gpu_count
# Privileged mode
if self.privileged:
if self.privileged or (
DeploymentMethod.APPTAINER
in self.workflow.deployment_settings.deployment_method
):
container.security_context = kubernetes.client.V1SecurityContext(
privileged=True
)
Expand Down