Bug #17244: Make sure cgroupsV2 works with Arvados - Arvados

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Bug #17244

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Make sure cgroupsV2 works with Arvados

Added by Nico César over 3 years ago. Updated over 1 year ago.

Status:

New

Priority:

Normal

Assigned To:

Category:

Crunch

Target version:

Start date:

Due date:

% Done:

Estimated time:

Story points:

Release:

Postponed

Release relationship:

Auto

Description

Reading

https://docs.docker.com/config/containers/runmetrics/

Running Docker on cgroup v2

Docker supports cgroup v2 experimentally since Docker 20.10. Running Docker on cgroup v2 also requires the following conditions to be satisfied:

containerd: v1.4 or later
runc: v1.0.0-rc91 or later
Kernel: v4.15 or later (v5.2 or later is recommended)

Note that the cgroup v2 mode behaves slightly different from the cgroup v1 mode:

The default cgroup driver (dockerd --exec-opt native.cgroupdriver) is “systemd” on v2, “cgroupfs” on v1.
The default cgroup namespace mode (docker run --cgroupns) is “private” on v2, “host” on v1.
The docker run flags --oom-kill-disable and --kernel-memory are discarded on v2.

With all this changes, we have to make sure that:

We can run a distro that has cgroup v2 by default (As in Fedora 2020) or kernel parameters that boot up with cgroups v2 enabled in systemd (kernel param systemd.unified_cgroup_hierarchy=1) and docker version >= 2020.04
We can guide the admin to upgrade to cgroup v2 and have a test case easy to check that arvados will run

The last point is important because the current error is kindof cryptic:

applying cgroup configuration for process caused: cannot enter cgroupv2 "/sys/fs/cgroup/docker" with domain controllers

There also cryptic messages with a cgroupsv2 enabled host and Docker 19.03.13

Status: Downloaded newer image for hello-world:latest
docker: Error response from daemon: cgroups: cgroup mountpoint does not exist: unknown.
ERRO[0005] error waiting for container: context canceled

https://www.kernel.org/doc/html/latest/admin-guide/cgroup-v2.html

Related issues

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Updated by Nico César over 3 years ago

Category set to Crunch
Target version set to 2021-01-20 Sprint

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Updated by Javier Bértoli over 3 years ago

I tried Arvados with the following setup:

1. Built binaries/images from current master (commit e98f4df4a@arvados)
2. Created a cluster
3. Run the test script from the salt-install test dir
4. With kernel Linux 5.9.0-5-amd64 & cgroups2 (as documented here, I have /sys/fs/cgroup/cgroup.controllers)
5. Using docker 20.10
6. Using containerd 1.4.3
7. When I run the script, I get:

+ cwl-runner hasher-workflow.cwl hasher-workflow-job.yml
INFO /usr/bin/cwl-runner 2.1.1, arvados-python-client 2.1.1, cwltool 3.0.20200807132242
INFO Resolved 'hasher-workflow.cwl' to 'file:///usr/src/arvados/tests/hasher-workflow.cwl'
INFO hasher-workflow.cwl:36:7: Unknown hint WorkReuse
INFO hasher-workflow.cwl:50:7: Unknown hint WorkReuse
INFO hasher-workflow.cwl:64:7: Unknown hint WorkReuse
INFO Using cluster arvie (https://arvie.arv.local:8000/)
INFO Upload local files: "test.txt" 
INFO Using collection f55e750025853f5b8ccae3ca79240f65+54 (arvie-4zz18-zbm7cmmt5h9d5rg)
INFO Using collection cache size 256 MiB
INFO [container hasher-workflow.cwl] submitted container_request arvie-xvhdp-7jpooik0zd8aj1t
INFO [container hasher-workflow.cwl] arvie-xvhdp-7jpooik0zd8aj1t is Final
ERROR [container hasher-workflow.cwl] (arvie-dz642-4v8xcwcvjvp5j2f) error log:

  2021-01-11T20:56:51.604627332Z crunch-run crunch-run dev (go1.15) started
  2021-01-11T20:56:51.604709650Z crunch-run Executing container 'arvie-dz642-4v8xcwcvjvp5j2f'
  2021-01-11T20:56:51.604763728Z crunch-run Executing on host '27d4cb3c42e2'
  2021-01-11T20:56:51.871544244Z crunch-run Fetching Docker image from collection '0428f2e88f4b398b8489f6c454e7e9ae+261'
  2021-01-11T20:56:51.940054697Z crunch-run Using Docker image id 'sha256:0dd5078a5bec49810c1fcb86b60e1bda6b9c1e12dc2c3de75453b2fd37a55885'
  2021-01-11T20:56:51.943832124Z crunch-run Docker image is available
  2021-01-11T20:56:51.952139500Z crunch-run Running [arv-mount --foreground --allow-other --read-write --crunchstat-interval=10 --file-cache 268435456 --mount-tmp tmp0 --mount-by-pdh by_id /tmp/crunch-run.arvie-dz642-4v8xcwcvjvp5j2f.288172359/keep406717434]
  2021-01-11T20:56:52.454639768Z crunch-run Creating Docker container
  2021-01-11T20:56:52.509556810Z crunch-run Attaching container streams
  2021-01-11T20:56:53.205291750Z crunch-run Starting Docker container id '7d91dac5eb133131cc9b131d1f0280810acf9c4eda6209b674546bb885c90606'
  2021-01-11T20:56:53.397951196Z crunch-run error in Run: could not start container: Error response from daemon: OCI runtime create failed: container_linux.go:370: starting container process caused: process_linux.go:326: applying cgroup configuration for process caused: cannot enter cgroupv2 "/sys/fs/cgroup/docker" with domain controllers -- it is in an invalid state: unknown
  2021-01-11T20:56:53.752428822Z crunch-run Cancelled
ERROR Overall process status is permanentFail
INFO Final output collection None
{}
WARNING Final process status is permanentFail

Using same images and setup with