I am trying to mount a volume to dsa_girder using the docker run -v command it returns a getsocketopt failed strangley error. This is in order to mount a large number images from the host system to be accessible by DSA. Am I approaching this incorrectly, would girder mount be used in this case?
docker run -v is the usual way to mount volumes for a dockerized install of Girder or DSA (or using the equivalent volume command inside a docker-compose file).
girder mount is used in the same container as girder to provide file-like access to resources regardless of whether they are on local or remote assetstores; it is not used to mount specific volumes.
Thank you, would I use docker run -v on the dsa_girder image or would it be another?
I was able to successfully mount the desired volume using docker compose. But I am having an issue importing the data into DSA. It hangs after a certain number of files, would there be something I am missing?
There shouldn’t be any resource exhaustion based on number of files. There are some cases where, if they are large image files, the default cache options can end up using up available memory – but the default docker-compose for DSA should be set to not have such issues.
Are there any distinct properties of your files that you can share to help diagnose this?
It is a large .ndpi (3.2GB). I tried to view its metadata using openslide but was unsuccessful, I will try to get more information.
What would I need to change in the docker-compose to alleviate the cache issue. I did leave everything default excecpt adding the volume.