We want to make you aware of an upstream Linux kernel issue that can prevent EPI2ME workflows from starting on some Ubuntu 24.04 (“Noble”) systems. This is of particular note, as this is the operating system on which Oxford Nanopore Technologies’ sequencing systems are based.

First and foremost:

Your data is not at risk.
The issue only affects workflow launch, not stored results.
A fixed kernel is now available, and we outline how to move to it below.

The underlying problem originates from changes in the Linux kernel and Java, which are outside our direct control.

This is an extended form article of that originally published in the Nanopore Community

Summary

Under certain Ubuntu 24.04 configurations, EPI2ME workflows fail to start with an error similar to:

ERROR ~ Cannot invoke "jdk.internal.platform.CgroupInfo.getMountPoint()" because "anyController" is null

This happens when:

The system is running Ubuntu 24.04.3 LTS (or a 24.04 installation updated to a newer hardware enablement kernel), and
The Linux kernel is 6.12 or later but earlier than 6.14.0-36 (for example, 6.14.0-27-generic), and
EPI2ME is using a Java Runtime that is affected by a known OpenJDK bug.

We have verified that the issue is resolved by upgrading to the fixed 6.14.0-36-generic kernel from the package

linux-generic-hwe-24.04 version 6.14.0-36.36~24.04.1

EPI2ME workflows run as normal on systems using this kernel.

Who is affected?

You are likely affected if all of the following are true:

You are running Ubuntu 24.04.3 LTS (Noble)
Your kernel version is between 6.12 and 6.14.0-36 (for example: 6.14.0-27-generic).
When launching an EPI2ME workflow, you see a Java/Nextflow error mentioning CgroupInfo and anyController being null.

You are unlikely to be affected if:

You are on Ubuntu 24.04.2 LTS with kernel 6.8.x (our typical shipping configuration), or
You are already on kernel 6.14.0-36-generic or later.

How to check if you are affected?

You can check your Ubuntu version by running the following command in a console:

lsb_release -d

and looking for something like:

Description: Ubuntu 24.04.3 LTS

This will confirm the version of the Ubuntu operating system. The OS kernel version can be checked using:

uname -r

If you see:

6.8.* you are not in the known problematic range.
6.14.0-27-generic or another 6.12–6.14.x kernel earlier than 6.14.0-36, you have a troublesome kernel.
6.14.0-36-generic (or later) you should already be on a fixed kernel.

The characteristic error of the incompatible OS kernels is seeing the following error in workflow logs:

N E X T F L O W ~ version 23.04.2 ... ERROR ~ Cannot invoke "jdk.internal.platform.CgroupInfo.getMountPoint()" because "anyController" is null

Corrective actions (if you are already affected)

We strongly recommend moving to the fixed HWE kernel if your environment allows it. On Ubuntu 24.04, as a user with administrative rights:

sudo apt update sudo apt install --install-recommends linux-generic-hwe-24.04
sudo reboot

After rebooting verify that:

uname -r

shows the updated kernel:

6.14.0-36-generic

In our internal testing, 6.14.0-36-generic (from linux-generic-hwe-24.04 6.14.0-36.36~24.04.1) fully resolves the issue.

Preventative actions (for systems that are still working)

If EPI2ME is currently running without issues on your Ubuntu 24.04 system:

Check your kernel version by running:
```
uname -r
```
If you are on 6.8.x or another kernel version known to work, make a note of it. Avoid jumping to intermediate 6.12–6.14 kernels that do not include the 6.14.0-36 fix.
Plan upgrades carefully:
- Before applying OS or kernel upgrades, verify that the target kernel 6.14.0-36-generic or later.
- If your system is managed by an IT team, share this notice and ask them to pin or select a known-good kernel.
Avoid unsupported combinations:
- Do not assume that any future kernel in the 6.12+ family will “just work” with existing Java and Nextflow versions.
- Where possible, follow our published platform requirements and compatibility notes.

Background

This issue is fundamentally an interoperability bug between newer Linux kernels (≥ 6.12), the cgroups v2 control-group interface, and the Java runtime used by Nextflow (and therefore by EPI2ME workflows).

In version 6.12, the Linux kernel changed how certain cgroup controllers (notably cpuset and memory) are exposed under /proc/cgroups and /sys/fs/cgroup. Many Java runtimes use these files to detect available CPU and memory constraints inside containers.

On affected kernels the cpuset and memory controllers no longer appear where the Java runtime expects them. This causes Java’s internal cgroup-detection code to encounter a missing controller and throw a fatal error. All this happens before Nextflow starts an analysis workflow, so EPI2ME workflows fail immediately at startup.

We have confirmed that:

Ubuntu 24.04.3 systems running kernel 6.14.0-27-generic show this failure.
Upgrading those systems to kernel 6.14.0-36-generic restores correct behaviour and resolves the problem for EPI2ME workflows.

We expect to move EPI2ME to a newer Nextflow version in a future release so that we can take advantage of the OpenJDK 21 fix. The underlying OpenJDK issue has been fixed in the Java 21 development branch and is targeted for a future Java 21.0.10 update. That release is expected as part of the normal quarterly Java update cycle in January 2026.

In the meantime, the most practical and reliable fix is the kernel update to 6.14.0-36-generic.

Contact us

We recognise that kernel and Java issues are not what you want to be dealing with when you are trying to run experiments. We are now validating new kernel and Java combinations against MinKNOW and EPI2ME, and updating our internal QA processes and platform guidance to reduce the chance of similar surprises in the future.

If you believe you are affected and need help applying any of the corrective actions above, please contact our support team with: