Docker - web service becomes unresponsive after some time

[Marc Hoeppner]

Hi,

after fighting Apollo through manual installation, I eventually decided to move to Docker for running the service. This is on a 4 core server with Ubuntu 20.04 + 32GB Ram. For setup, I followed the docker instructions. 

However, I have a persisting issue with the service becoming "unavailable" after some time. It will run fine for a day, sometimes more, but eventually I can no longer reach it via its remote URL. I can still upload "user tracks" from the local machine (gff3_load_features) and navidate to it using lynx tho, so its still running. 

I am looking for some pointers regarding possible causes here, since I cannot find anything useful in the console output. 

My docker command looks as follows:

sudo docker run --memory=8g -e CATALINA_OPTS="-Xms1G -Xmx4G" -e JAVA_OPTS="-Xmx6g" [...] gmod/apollo:release-2.6.6

Currently, I have no forwarding through apache (etc) set up, so this is just the "naked" container talking to the internet. 

Any advice would be appreciated. 

[Colin]

Possibly you might check the memory usage of the instance. It is weird that it would work in some cases e.g. with uploading tracks but not others.

In my case I saw unresponsiveness of intermine (not apollo) and did a lot of debugging and in the end just increased the memory allotment e.g. increase the Xmx argument to a high value

A pair of posts I made on issue long time back

https://cmdcolin.github.io/posts/2015-10-15

https://cmdcolin.github.io/posts/2015-09-16

-Colin

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[Nathan Dunn]

Disk space within the container might be another culprit as well as what the docker image itself allocates for both disk space and memory. 

Probably easiest to go into the container itself and see.  

Still weird that it is able to run gff3_load_features

I wonder if the rest of the REST functionality works.    Might be worth testing with this: https://pypi.org/project/apollo/

Nathan