"Aw snap. Out of memory" error with Chrome

[AxelBigOmics]

This has been a common complain among Chrome users. After a while the Platform crashes with the error below.

This is a recent problem that started about 3-4 weeks ago. Previous versions of Chrome did not show this error.

[stefanreifenberg]

So far i could not reproduce this error. I might need a larger dataset compared to the example data. Let me know if you can provide one a dataset for testing via dropbox or so.

[AxelBigOmics]

Hi Stefan,

The error does not appear with a specific task. What normally happens is that after 15-30 minutes the platform crashes with the "out of memory" error. Sometimes I can see the platform struggle to load the dataset into memory as well and there being long delays before I can click on any tab.

The dataset I normali experience this problem with is GSE162475, which you can download from our public dataset collection (https://public.bigomics.ch/app/omicsplayground_contrib).

[stefanreifenberg]

Hey Axel,

from your description it sounds like a memory leak. The app allocates more and more memory without clearing unneeded data from the memory, resulting in Chrome crashing at some point.

[AxelBigOmics]

Sounds about right...how can this problem be fixed? Or is it an issue with Chrome itself?

[stefanreifenberg]

The issue stems from the shiny app. We should implement garbage collection to get rid of obsolete data in the memory.
Here is some information: https://bookdown.org/content/d1e53ac9-28ce-472f-bc2c-f499f18264a3/releasememory.html#use-gc

[AxelBigOmics]

Thanks for the explanation, Stefan. That is an important issue for some of our clients, so hopefully it can be fixed relatively easily (not a programmer myself btw, so no idea how long that can take).

[stefanreifenberg]

Good to know, i'll try to replicate the issue and start working on it

[ivokwee]

Not sure if garbage collection will do. Garbage collection will only clear the memory on the server side, and the error seems on the browser side. We saw this error especially with Chrome and got worse after the Windows 11 update. We don't see this problem on Linux or Mac.

[AxelBigOmics]

Just a quick update...I did not seem to experience the issue today. Will keep an eye on it. Maybe Chrome/Win11 fixed whatever the issue was? Or did any of you guys work your magic?

[stefanreifenberg]

Nice to hear, we did not touch anything today. You could also enable the chrome task manager (top-right the three dots > More Tools > task manager) to see how much memory the tab is using. Would be helpful to know. I tested it on linux and macos, both were between 310mb and 340mb with spikes to 450 here and there.

[JohnCoene]

This happens after the load of the data, when @AxelBigOmics showed me it was very quick to occur: after load Chrome seems to hang then presents the "Aw snap!" popup.

[AxelBigOmics]

Just to update, I experienced the problem again this morning while using v2.8.5 on chrome. I uploaded a fresh dataset, tasked the platform with computing it and when I looked back after about 1h and the "Aw Snap" message had appeared. I did not even access any of the tabs, just had the platform turn the CSV files into a PGX file. It did that, so the crash happened afterwards

[stefanreifenberg]

Good to know. So its not the app crashing after leaving it running for some time. The problem is related to the data preprocessing. Our plan is to move the whole preprocessing step to a separate service which is running on the server. That should eliminate the memory error.