Time: Day 2, 9:30 – 10:00 am CDT
Host: Matt Kelsey, Washington University School of Medicine
Panelists: Sarah Keefe (Washington University School of Medicine), Kate Alpert (Radiologics), Baxter Rogers (Vanderbilt University), and Ryan Sullivan (University of Sydney)
Other Participants: Pradeep Reddy Raamana (University of Pittsburgh), Isabel Restrepo (Brown University), David Cash (University College London), Simon Doran (Institute for Cancer Research, London), and Alexander Bartnik (SUNY Buffalo)
Questions and Answers
When possible and as time permitted, questions that were brought up in the Q&A module during each talk were addressed in real time by the presenter. Other responses were entered in the Q&A interface itself. Those written responses are included below.
|Are there any training resources ("Hello World" examples, FAQs, etc.) on using XNAT container service?|
|Are containers required for running pipelines? I hope not!||(Answered live in session)|
The files are copied to the build directory - isn't this slow? (I know, probably more secure) Could it not be an option instead? Some of my pipelines manipulated the XML files as well as image files and I've not easily been able to convert these.
Also - any plans for custom execution forms?
|Does Freesurfer 711 container service works with batch launch processing dashboard?||(Answered live in session)|
|Containerization is the way forward for reproducible research. However, Docker's business model and support is changing, and Docker Swarm often isn't allowed to run on HPC. I've been discussing potential work to support Kubernetes with Kate and Tim, but I'm curious on how many other institutions support Kubernetes on their HPC|
|How close would singluarity/slurm implementation be as we are using this at our HPC and looking into how to leverage the current container service with this environment?|
|... Relation to BIDS-Apps?|
|I hope if Slurm is supported, Sub Grid Engine will be too - the submission API is very similar|
|A lot of great work has been done creating dockerized BIDS apps, but this always needs conversion from the XNAT storage to the BIDS format. The xnat2bids command that I found on the NRG github is a few years old and I haven't had any success with it. Are there plans to update or improve how the container service works with BIDS apps? Open to unmuting myself to discuss more!|
|When trying to use the batch plugin, it only shows the old pipeline options. Is there any extra setting needed to activate the connection between batch and container service?|
|Is it possible to adapt the Container Service plugin to issue jobs to an IBM-LSF queue manager?|
|Did you consider some standardization on container interfacing in any way? It could be worthwhile to have a look at biocontainers for instance.|
|For people who do processing using xnat containers, is this made possible because their XNAT is used just by one lab, or do lots of different labs have very similar processing pipelines? I ask because where I am we have maybe 40 different users of our XNAT and no two of them do the same thing to their data, so we haven't seen any advantage to doing processing on the XNAT server vs on the cluster as individual users.|
|I'm new to Containers. If I use a Container on RHEL 8, is everything "bundled" (ie no configuration etc. needed)?|