Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

D2.13: Micromagnetic VRE completed and online #38

Open
minrk opened this issue Sep 8, 2015 · 11 comments
Open

D2.13: Micromagnetic VRE completed and online #38

minrk opened this issue Sep 8, 2015 · 11 comments

Comments

@minrk
Copy link
Contributor

@minrk minrk commented Sep 8, 2015

The primary focus of the OpenDreamKit project is to improve e-infrastructure for research in mathematics. However, significant parts of these investments go to the general purpose Jupyter ecosystem and are thus of applicability to a wide range of activities outside mathematics research.

With this deliverable we want to demonstrate the power of (improved) Jupyter based Virtual Research Environments with an application to the computational magnetism research domain, as a representative of the growing field of computational science and engineering.

We have exposed the computational capabilities of a well established Micromagnetic simulation package (OOMMF) in Python, defining and implementing a domain specific language for Micromagnetic problems and their numerical solutions. The work is structured so that future computational solvers can be driven from the same problem definition language, and demonstrated the feasibility with another Micromagnetic simulation package (Mumax3). Data retrieval and analysis methods are provided, making use of the Jupiter based virtual research environment which was developed further through OpenDreamKit. Maybe most importantly, we have applied developed tools such as NBVAL and NBDIME, Binder and 3d visualisation to a real world problem, taught this to hundreds of researchers, and used their feedback to improve our designs and processes.

The Ubermag Virtual Research Environment can be explored and tested online here with Binder.

Parts of the work are described in Marijan Beg, Ryan A. Pepper, Hans Fangohr:
User interfaces for computational science: a domain specific language for OOMMF embedded in Python, AIP Advances 7, 056025 (2017)
.

@bpilorget

This comment has been minimized.

Copy link
Contributor

@bpilorget bpilorget commented Jan 11, 2018

#155 was merged into #38 after 3rd amendment to the contract

@nthiery

This comment has been minimized.

Copy link
Contributor

@nthiery nthiery commented Aug 23, 2019

Hey @marijanbeg, @fangohr
I am reviewing your report; thanks so much for completing it so much in advance! It reads very nicely.
Here are some suggestions:

  • Maybe use past tense in the early part of the introduction to highlight that this was how it was before the work carried out here.
  • Please add some context to the introduction to explain how the work fits within ODK: in particular that it was a demonstrator for the claim that ODK work would not only impact mathematics but also other sciences.
  • The introduction speaks about the integration in Jupyter. State that this makes it readily available as an online VRE (via Binder). Provide a direct link.
  • Mention in the introduction all the work done to disseminate the work, and assess how the VRE impacted this.
  • Whenever relevant in the text, mention which other pieces of work in ODK impacted this work
@nthiery

This comment has been minimized.

Copy link
Contributor

@nthiery nthiery commented Aug 23, 2019

Viviane won't be much available to review WP2 reports. So it would be good to get some additional reviewers.

@minrk: would you volunteer?

@mikecroucher, @trallard : would you be so kind to do one last piece of work for us?

@minrk

This comment has been minimized.

Copy link
Contributor Author

@minrk minrk commented Aug 23, 2019

I'll be happy to review this on Monday.

@nthiery

This comment has been minimized.

Copy link
Contributor

@nthiery nthiery commented Aug 25, 2019

For reference, I copy-paste here the offline discussion we had in late June:

Marijan and I are working on the deliverable report
Excellent. Always a soothing news for the coordinator when things are
tackled well in advance :-)
and would like to refer back to other OpenDreamKit results to
connect this as much as possible.
+1

We can think of k3d and nbval, and will add references to the deliverables.

Are there are tasks / deliverables in OpenDreamKit that we can refer to, for example

  • ipywidgets

Jeroen did quite some work on ipywidgets integration in SageMath. I believe this lead to some contribution back to ipywidgets, notably on interact. Please have a look at D4.5. I don't know if this has
impacted the Micromagnetics VRE :-)

  • contributions to conda

That would be T3.3 and D3.10. Let's see: a lot of ODK effort around conda has been on packaging math software, so mostly irrelevant for the micromagnetics VRE; but you did conda packaging on your side for JOOMMF and co; right? Worth a mention. And it's a good occasion to highlight that having conda packages very much helps setting up VRE's, to justify back the efforts on T3.3 and D3.10.

  • nbconvert
  • other improvements of Jupyter / Jupyterlab?

Many contributions here and there. E.g. @minrk says that there have been lots of improvements to JupyterLab from ODK, particularly around extensions: https://github.com/jupyterlab/jupyterlab/pulls?q=is%3Apr+is%3Aclosed+author%3Avidartf

  • Binder

We did some work around Binder (lobbying, promoting, advertising material like the picture and the video, writing a proposal, ...); but I don't really see a specific deliverable/task to refer to. We do say a few words in our internal reports D1.5.

  • bookbook
  • ThebeLab (T4.6, D4.7)

  • Live collaboration? Even if it's not used by your VRE yet, you could mention that as soon as JupyterLab will have support for live collaboration, that feature will come for free to your VRE? Proof of concept support was delivered last year in D4.15. @minrk says: @minrk: Live collaboration has a prototype which can be followed here. I can set up a Binder with the WIP branch for demo purposes by the final report. Hopefully it will be landed in JupyterLab master by then.

@nthiery

This comment has been minimized.

Copy link
Contributor

@nthiery nthiery commented Aug 25, 2019

The upcoming D3.10 #59 reports on our packaging efforts. If relevant, please suggest some language there about the packaging efforts about JOOMMF.

@nthiery nthiery closed this Aug 25, 2019
@nthiery nthiery reopened this Aug 25, 2019
@nthiery

This comment has been minimized.

Copy link
Contributor

@nthiery nthiery commented Aug 25, 2019

Sorry for the accidental closing ...

@nthiery

This comment has been minimized.

Copy link
Contributor

@nthiery nthiery commented Aug 25, 2019

Btw: while having a look at https://joommf.github.io/get_started.html, I noticed the Get Started page dates back from 2016, and does not mention the possibility to try JOOMMF online. Presumably something to be updated?
Also, could you add a JOOMMF item on http://opendreamkit.org/try/ (click on quick-link -> edit this page)?
Thanks in advance!

@minrk

This comment has been minimized.

Copy link
Contributor Author

@minrk minrk commented Aug 26, 2019

I made some small edits. I think this report is in really good shape. In particular, I made sure to note that nbval was itself an ODK deliverable, so we show that our work is coordinated and fixed some typos.

My only other feedback is to perhaps add more language to emphasize the conda work further as part of a coordinated effort for easing installation ODK components (cross-ref D3.10).

Great job!

@fangohr

This comment has been minimized.

Copy link
Contributor

@fangohr fangohr commented Aug 28, 2019

Thanks @minrk and @nthiery . We have addressed the feedback, and suggest the current state as the final draft. If you look at this again, please focus on the (new) introduction and the (new) summary: the introduction is setting the scene and explains the role of this work in ODK. The summary was meant to show a somewhat reflective perspective (to counteract the impression that everything is perfect), but if you find anything rough/edgy in there, please say.

@nthiery nthiery added Submitted and removed needs review labels Aug 29, 2019
@nthiery

This comment has been minimized.

Copy link
Contributor

@nthiery nthiery commented Aug 29, 2019

Congrats on this being the second submitted deliverable for this reporting period.

Thanks @fangohr and @marijanbeg for the hard work and nice report!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.