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[REVIEW]: Julia for HPC: In Situ data Analysis with Julia for Climate Simulations at Large Scale #134
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @simonbyrne, @williamfgc it looks like you're currently assigned to review this paper 🎉. Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post. ⭐ Important ⭐ If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/JuliaCon/proceedings-review) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿 To fix this do the following two things:
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@luraess the links to the conflict of interest policy and code of conduct don't work. |
@simonbyrne thanks for flagging, while we work on a fix, you can access those here https://juliacon.github.io/proceedings-guide/reviewer/#review_guidelines_and_process |
👋 @simonbyrne, please update us on how your review is going (this is an automated reminder). |
👋 @williamfgc, please update us on how your review is going (this is an automated reminder). |
@simonbyrne @williamfgc Human asking about the status of the revision? Ideally, we can try to get this done in the coming weeks (2 ideally). Thanks so much for your contribution! |
I'm on it, will update later this week. |
Same here, I did a quick pass, but I need to go through it more carefully. |
@simonbyrne @williamfgc also let me know if you still have issue checking tick-boxes. |
This was an interesting application of embedding Julia inside another program for in situ analysis. Although I am not able to assess the scientific validity of the analysis (which seems incomplete), from a technical perspective, this is an important problem: as simulations reach higher resolutions, it becomes more expensive and difficult to store all the data for post-processing analysis, thus it is helpful if such analysis can be done while the simulation is running ("in situ"). Overall, I thought the paper was reasonable, but the exposition could be improved in a few places. There is no linked code, (other than the TributaryPCA.jl package, and this doesn't meet most of the above criteria, such as documentation), so I can't really check off those relevant boxes. While the code may not strictly be required, it is a shame as I think this could be of interest to others who are attempting something similar. I would encourage the authors to make those available if possible. Specific comments3.3 C Interface
This is not what the C code in code 2 is doing: as described in https://docs.julialang.org/en/v1/manual/embedding/#Memory-Management, the 3.5 Noninvasive CompilationSome more details could be useful here: how did you load the Julia code? (e.g. did you make use of a precompiled system image?) How did you switch between (or switch off) the in situ analysis codes? Again, having the actual code available could make this easier. 4.1 Sudden Stratospheric Warming (SSW)I'm not sure Algorithm 1 is correct: shouldn't it reset the There isn't much detail on the actual GEV fitting, and I found it difficult to understand. Is it fitting a different GEV distribution at every point? What is the prior distribution used for the GEV parameters? Some more details on this would be helpful (as well as linking to the code). 4.2 TributaryPCAWhile I understand the problem it is trying to solve, I found it difficult to understand algorithm, and the Code 4 block is somewhat unclear:
(I don't have access to the TributaryPCA paper, so couldn't look it up there either). I would suggest either having a mathematical exposition of the algorithm, and/or making the code a bit more readable. Is the data centered (i.e. do you subtract the mean)? The lack of red in Fig 3, PC1 suggests that it isn't, but that isn't clear. If you aren't then the interpretation changes slightly. 5.2 In Situ SSW Detection and Characterization ResultsI don't quite understand this: it doesn't actually analyse the SSW case? It just seems to be an illustration of how one might do an analysis. 5.3 PCA ResultsThe details are a bit lacking. Was the data collected every time step? Or is it based on daily snapshots or averages? How long was the simulation? I disagree with the interpretation of figure 3: you can't really assign "warmer vs colder" to principal components (the sign of eigenvectors doesn't matter). My interpretation of the figures is that:
While it's useful that you can capture this, it's not particularly scientifically interesting. 5.4 PerformanceThe SSW seems to have negligible overhead (which is not surprising since it is evaluated infrequently), so there is not much to say about the analysis. It could be helpful if you could add the number of MPI ranks to Table 1? I'd be interested to know more about the performance bottlenecks of the PCA code? Which parts were the most expensive? Did the Julia garbage collector cause problems with scaling? Minor comments
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Review: Julia for HPC In Situ Data Analysis with Julia for Climate Simulations at Large Scale The work present the implementation of an “in-situ” framework with components written in Julia coupled with the well-known E3SM framework model. Two main post-processing tasks are evaluated: Sudden Stratospheric Warming (SSW) and principal component analysis (PCA). SSW is a smaller component while PCA is more computationally intensive due to the required Cholesky decomposition execution. I must admit I am not a doing expert in E3SM, but I can appreciate the computational effort in plugging Julia into an existing framework for a novel application. Computational experiments show that in-situ provides reasonable overheads for a larger number of processing elements (PEs) usage per node. Overall, it’s a straight-forward application of how Julia can be added to an existing framework and add value for post-processing tasks. Major points:
Minor points:
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Thanks for handing in your revision @simonbyrne @williamfgc . IMPORTANT Please go through the tick-box list and check all points that are addressed leaving the remaining as "to-dos". All tick-boxes will have to be checked upon publication. |
@ltang85 now that the 2 reviewers gave you feedback, please address their comments as soon as possible. Also, please take a look at #134 (comment) as you'd need to fix those references as well. |
@ltang85 just checking in about the status of the revisions, given that you've got feedback since one month ago. Please try to address the issues raised by the reviewers in the coming weeks, and do not hesitate to reach out if there is anything we can help you with. Thanks. |
@luraess I am still working on it and should be able to address all the comments in 2 weeks. Thanks. |
Thanks - take your time. Was just checking in about progress. |
@ltang85 seems there was no activity update for a while here. Can we get the process to a final stage in the coming week? |
@luraess sorry for the delay, I will try to finish it by next week. |
Excellent. We would like to wrap up the previous submissions ideally in the coming 1-2 weeks and then open the system for JuliaCon23. |
@luraess Hi, here is the update: we have addressed most of the reviewers' comments but will need a few more days for the rest of the comments. |
Great, thanks @ltang85 for the update and looking forward to finalising your submission! |
@whedon generate pdf |
My name is now @editorialbot |
@editorialbot generate pdf |
@luraess I have addressed all the comments and uploaded the revised version. However, I failed to generate the pdf here. Will fix it tomorrow or Tuesday. |
Thanks! Seems some figure is missing (https://github.com/JuliaCon/proceedings-papers/actions/runs/8683268959/job/23809007037#step:3:543). |
@editorialbot generate pdf |
@editorialbot generate pdf |
@editorialbot generate pdf |
@luraess I have fixed the pdf issues and it is working now. I have also uploaded a response letter adressing all the reviewers' comments in the paper folder. Thanks. @simonbyrne @williamfgc Thank you very much for reviewing this paper and provding the comments. |
@ltang85 Thanks for submitting the revised version of the manuscript. I am checking it now and will let you know if any further changes are needed before we can accept the manuscript. @simonbyrne @williamfgc If you find some time, I'd like to get your general feedback on whether the author addressed your suggestions in a way you are happy with. Also, please take some time to thick the boxes in here #134 (comment) . Thanks! |
Bump @simonbyrne @williamfgc - Thanks for swiftly verifying ☝️ such that we can finalise the publication! 🙏 |
@luraess I couldn't check the boxes in #134 (comment) |
I recall now this issue we had already at the beginning - let's leave that out. Could you however briefly assess whether the revised version of the manuscript draft adresses your comments and suggestions @williamfgc ? Thanks! |
I just spotted typos: e.g. consqeuent...please proof-read. Other than that, my comments were addressed. Thanks! |
Thanks for the comments. We just proof-read it again and have fixed the typo you mentioned and a few other typos. |
@editorialbot generate pdf |
@ltang85 Thanks for addressing the proof reading. While in the process of accepting your submission, I bumped on the README you link to from your paper regarding the steps to reproduce your research https://github.com/ltang85/In-Situ-data-Analysis-with-Julia-for-Climate-Simulations-at-Large-Scale/tree/main/src . Please format this README using standard markdown syntax, in order to clearly separate code blocks from plain text. Use heading hierarchy to structure the content as well, and please remove the redundant horizontal lines. Once this last bit is fixed, we could proceed with final publication. Thanks! |
Submitting author: @ltang85 (Li Tang)
Repository: https://github.com/ltang85/In-Situ-data-Analysis-with-Julia-for-Climate-Simulations-at-Large-Scale
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Editor: @luraess
Reviewers: @simonbyrne, @williamfgc
Archive: Pending
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