Joss-reviews: [PRE REVIEW]: Singularity Compose: Orchestration for Singularity Instances

[whedon]

Submitting author: @vsoch (Vanessa Sochat)
Repository: https://github.com/singularityhub/singularity-compose
Version: 0.0.15
Editor: @gkthiruvathukal
Reviewers: @daissi

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Thanks for submitting your paper to JOSS @vsoch. Currently, there isn't an JOSS editor assigned to your paper.

@vsoch if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kyleniemeyer]

Hi @vsoch, thanks for your submission. At first glance, while this looks like valuable software, I don't see anything that indicates that it is research software—nothing in the README or paper seems to connect it to research. Could you clarify how it has an obvious research application?

[vsoch]

Think of any kind of research application that involves a database (mongodb, postgres, etc.) along with an application to interact with it. For example, Singularity Compose is going to fit in nicely with being used on our SLURM cluster to start a database on a node for a researcher's (containerized) scripts to interact with. A second example is with respect to interactive applications. I'm not a huge fan, but jupyter notebooks (and similar) are becoming more popular, and tools like OnDemand (Ohio Supercomputing Center) now allow for running rstudio/jupyter via a Singularity container. An integration with Singularity compose would allow for a user to do similar, but with the interactive applications and services that are relevant for their work (and custom defined by them).

The use cases are strong with this one, and there is no tool that can provide what I outlined above. It is niche as it's for Singularity containers, however they are the unit of reproducible operability on HPC. You are correct that it's a general purpose tool, and not something like a package for a specific scientific domain. But the reasons that I outlined above, and what can be developed for research with such a tool, are exactly what makes it so exciting. I've been waiting years (since 2016) to develop this, and the base unit (Singularity) is finally ready to support it.

[vsoch]

And of course reproducibility of all of the above - given that I run my specific database service + application, by placing the singularity-compose.yml alongside the version controlled code and container recipes, this ensures not just reproducibility of the container build, but also deployment of the services to do some analysis. I believe I stated this in the paper. :)

[vsoch]

@kyleniemeyer please let me know if you have other questions, or if you'd like me to suggest reviewers (those with experience with reproducibility and/or container technologies would be well suited!)

[vsoch]

oh that's so cool! @whedon extracts labels now! You're the best robot, @whedon <3

[kyleniemeyer]

@vsoch great, thank you for the information. I do think that both the README and JOSS paper need to emphasize the research application a bit more, so it's clear, but that can happen through the review process.

[kyleniemeyer]

@gkthiruvathukal can you take on this submission? otherwise, @danielskatz also looks like a good fit.

[gkthiruvathukal]

@kyleniemeyer I think I can. I have a few reviews nearing completion so I should be fine with it.

[kyleniemeyer]

@whedon assign @gkthiruvathukal as editor

[whedon]

OK, the editor is @gkthiruvathukal

[gkthiruvathukal]

@vsoch Can you help suggest a a few reviewers from this list of people? We now require 2 reviewers for all JOSS submissions.

[vsoch]

Sure thing! It looks like @nuest is the only other one that lists containers, so he might be familiar with Docker Compose (Singularity Compose's counterpart). The next tag that might imply container experience would be reproducibility, and from that I can suggest @cole-brokamp and @daissi.

[gkthiruvathukal]

@nuest, @cole-brokamp, @daissi: Would you be willing to contribute a review for this JOSS submission? I need two reviewers to begin review.

[cole-brokamp]

I am out traveling for the next three weeks, but would be glad to take a look when I get back.

On Jun 27, 2019, at 3:18 PM, George K. Thiruvathukal [e-mail] wrote:

@nuest, @cole-brokamp, @daissi: Would you be willing to contribute a review for this JOSS submission? I need two reviewers to begin review.

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[gkthiruvathukal]

@cole-brokamp this works for me. Could you wrap up your review a week or two after travel?

[vsoch]

Works for me too! Safe travels @cole-brokamp :airplane:

[cole-brokamp]

Sure, sounds good!

On Jun 27, 2019, at 3:32 PM, Vanessasaurus [e-mail] wrote:

Works for me too! Safe travels @cole-brokamp ✈️

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[daissi]

Unfortunately, I will not be available to do it before September. It should be better to find someone else, but if nobody appears until September, I will be happy to review this one.

[gkthiruvathukal]

@daissi I'm going to go ahead and add you for now so I can get started. Given that this is summer and many people are busy, I'm noticing that many reviews are taking longer. You'l be the second reviewer with @cole-brokamp, who is also on some travel.

[gkthiruvathukal]

@whedon assign @cole-brokamp as reviewer

[whedon]

OK, the reviewer is @cole-brokamp

[gkthiruvathukal]

@whedon assign @daissi as reviewer

[whedon]

OK, the reviewer is @daissi

[gkthiruvathukal]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1578. Feel free to close this issue now!