DSA + HistomicsTK on Singularity

HistomicsTK
1

Does anyone have a Singularity recipe to run Digital Slide Archive + HistomicsTK + Mongo + memcached?

Is there any way to run the non-minimal version of DSA on Singularity?

Thanks for the help.

Best,
Evan

2

Based on the minimal version here:

you could add in memcached much like mongo is started.
For the non-minimal version, you’ll need to start rabbitmq to communicate with the worker, and start a worker process. The sticking point is to get the worker to start jobs. I don’t think anyone has done this recently, and it might need some change to girder_worker to invoke singularity rather than docker.

– David

3

Hi David,

I appreciate the reply. Memcached is my priority, so to start it, could I run singularity run memcached_latest.sif -m 4096 --max-item-size 8M &? Or do I need to bind anything/specific ports?

Thanks for the help.

Best
Evan

4

Update here for anyone facing the same issue: You need to update girder.cfg within singularity-minimal to use large_image caching.