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When Singularity is called with --containall, since it has to separate the PID namespaces, it tries to create its own proc filesystem as it can't take the existing proc from the external container. When running in a Kubernetes pod the kernel doesn't seem to allow this though, and returns an operation not permitted error:
FATAL: container creation failed: mount proc->/proc error: while mounting proc: can't mount proc filesystem to /proc: operation not permitted
I'm able to replicate this by launching a Kubernetes instance on AWS, launching a pod, and running singularity --verbose exec --pwd /mnt/miniwdl_task_container/work --containall --no-mount hostfs docker://ubuntu:latest ls inside the pod. The yaml I'm using for kubernetes is:
The default MiniWDL configuration has --containall as part of the singularity command, which causes issues in Toil when running it on Kubernetes. Maybe the default config options for singularity shouldn't have --containall or MiniWDL should detect if --containall works.
When Singularity is called with
--containall
, since it has to separate the PID namespaces, it tries to create its own proc filesystem as it can't take the existing proc from the external container. When running in a Kubernetes pod the kernel doesn't seem to allow this though, and returns an operation not permitted error:I'm able to replicate this by launching a Kubernetes instance on AWS, launching a pod, and running
singularity --verbose exec --pwd /mnt/miniwdl_task_container/work --containall --no-mount hostfs docker://ubuntu:latest ls
inside the pod. The yaml I'm using for kubernetes is:The default MiniWDL configuration has
--containall
as part of the singularity command, which causes issues in Toil when running it on Kubernetes. Maybe the default config options for singularity shouldn't have--containall
or MiniWDL should detect if--containall
works.It looks like this issue is also related to this: apptainer/singularity#5857
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