google-deepmind / google-deepmind/alphafold

Endless "[Perf]: MatMul reference implementation being executed generated" messages and dramatic inference slowdown upon updating to docker 27.3.1

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Description

Hello,

One of my systems, running Ubuntu 22.04, updated docker to version 27.3.1 (build ce12230)... after which running AlphaFold2 produces a neverending series of messages like the following once it reaches the "Running predict with shape" stage:

```
I0923 14:01:56.716146 129352767932224 run_docker.py:258] 2024-09-23 12:01:56.715574: W external/xla/xla/service/cpu/onednn_matmul.cc:293] [Perf]: MatMul reference implementation being executed
I0923 14:01:56.741649 129352767932224 run_docker.py:258] 2024-09-23 12:01:56.741240: W external/xla/xla/service/cpu/onednn_matmul.cc:293] [Perf]: MatMul reference implementation being executed
(...)
```

This issue dramatically impacts runtime, and could be fixed by reverting docker and preventing it from re-updating:

```
> sudo apt-get install docker-ce=5:26.1.4-1~ubuntu.20.04~focal docker-ce-cli=5:26.1.4-1~ubuntu.20.04~focal containerd.io
> sudo apt-mark hold docker-ce docker-ce-cli
> docker --version
Docker version 26.1.4, build 5650f9b
```

However, I thought I should nonetheless report it as other users may have the same issue, and you can most likely fix it in a straightforward way.

Thanks,

Luca

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