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[REVIEW]: A parallel global multiobjective framework for optimization: pagmo #2338
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dgoldri25, @jangmys 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/openjournals/joss-reviews) 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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Dear @dgoldri25 and @jangmys, thanks for agreeing to review this submission! As you can see, I have started the review process, whereby the original issue has been closed and a new (this) one has been opened, with further directions for you. Please take a moment to go over the instructions and checklists above, and let me know if anything is unclear. Please notice that this is a slightly unusual submission with respect to standard JOSS practice, in that you will not find the source code under the paper repository above, as the submission consists of two separate packages: https://github.com/esa/pagmo2 This should not impact the review process, but let me know if you need further clarifications. I look forward to your comments! |
Concerning the point "State of the field": The paper (which is globally very well written) starts directly with the general formulation of the optimization problem. I am aware that a complete comparison of functionalities/documentation/etc is a huge task which is certainly beyond the scope of this paper - however at least a summary comparison with existing frameworks would clearly enhance the quality of the paper and give interested readers additional motivation to use pagmo. Maybe this comparision could be restricted to frameworks that offer some parallel processing support... In the (now 8 years old) paper by Parejo, José Antonio, et al., "Metaheuristic optimization frameworks: a survey and benchmarking.", Soft Computing 16.3 (2012): 527-561 (https://core.ac.uk/reader/51388224) the authors perform a complete comparative study of metaheuristic optimization frameworks. The results of this study are (at least partially) outdated, but it could still be a good starting point (and/or a reference to give to the reader!). |
The paper says "The parallel evaluation can be performed by multiple threads, processes, nodes in an HPC cluster or even by GPU devices (via, e.g., OpenCL or CUDA)" (p.3) - I could not find a "GPU batch evaluator" in the code (please help me out if I missed it). Of course, conceptually, a batch of solutions could be evaluated on a GPU - technically, however, there are some challenges (for example: (1) no std library in device code -> DS for individuals on the device?; (2) need to explicitly copy problem data to the device and separate implementation of __device__ fitness function (alternatively "Unified Memory" + __host__ __device__ lambdas...which are still experimental: performance?); (3) thread-data mapping on the device (only 1 thread/fitness eval or possibility of parallelizing fitness evaluation itself? If a GPUbatchEval has already been implemented (and I just didn't see it), the paper should provide some explanations and instructions for using GPU acceleration should appear in the documentation... otherwise, if GPU support for batch evaluation is future work, the paper should clarify this. |
Minor remarks (typos): |
I was able to install pygmo/pagmo easily, following the instructions, and the provided tutorials helped me to get started quickly. Therefore, in order to increase the software's visibility and allow researchers to properly cite pagmo/pygmo (the last (only?) pagmo-related paper I found is from 2010, "A global optimization toolbox for massively parallel engineering optimisation"), publishing this paper in JOSS definitely makes sense. |
Thanks for your comments, @jangmys! Could you raise any future issues in the respective repositories? This will ensure your suggestions will enter the package histories and be properly credited. You can create a mention here by using this issue's URL in a repository's issue, if you wish (see https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#guiding-principles). |
@dgoldri25, do you concur with @jangmys' suggestions regarding a comparison with the state of the art? Is this why you have left the corresponding box unticked? |
@eloisabentivegna I second @jangmys' suggestion. While I found the paper to be high quality overall, the review of the state of the art should be expanded. |
@bluescarni, does the request by @jangmys and @dgoldri25 make sense to you? Can you expand the literature review? |
@eloisabentivegna @jangmys @dgoldri25 thanks for the review! We can certainly expand the literature review. Currently all the authors are still on vacation, so apologies for the late reply. We should be able to revise the paper next week. |
@whedon generate pdf |
@eloisabentivegna @jangmys @dgoldri25 @darioizzo we have added a section about related projects/frameworks and fixed the typos. Please let us know if there is anything else. @jangmys regarding your question about the GPU: what pagmo provides is an API to compute the fitness evaluation of a group of independent decision vectors in a (possibly) parallel fashion. Such API can then be used by optimisation algorithms capable of taking advantage of parallel fitness evaluation (in pagmo we have a handful of such algorithms, mostly genetic/evolutionary ones). Thus you are absolutely right that we don't directly address the specifics of GPU programming from within pagmo (such as data transfer, compilation model, etc.). This is left to the author of an optimisation problem, who is free to choose between CUDA/OpenCL/SYCL for the implementation of the batch evaluation API in his/her specific optimisation problem. We expanded a bit on this point in the latest revision of the paper, please let us know if this clarifies the matter. |
@bluescarni @eloisabentivegna @dgoldri25 @darioizzo I think the additional paragraph addresses the existing state-of-the-art appropriately (and I therefore checked the corresponding box). I also agree with the "Concurrent fitness evaluation" section which now clarifies that there is no "out-of-the-box" GPU support, but rather a clean interface that could allow users to build one on their own. From my side there are no further remarks and I recommend to accept the paper. I hope you'll be able to keep up the good work on this framework in the future ;-) |
@bluescarni @eloisabentivegna @jangmys @darioizzo I concur with jangmys' assessment, I've also checked the box for "State of the Field". I recommend to accept the paper as well. |
We need the authors to make a single archive with e.g. Zenodo of all of the software associated with the submission. This will likely require a little extra work on the part of the authors compared with some of the automated methods for doing this with GitHub. |
@arfon would it be enough to make an archive of the latest releases of pagmo and pygmo (i.e., from the released tarballs on github)? |
We would like the archive to include any changes that have been made as a result of this review. Would that be the case if you used the latest releases? |
@arfon No, there were no code changes as a result of the review. |
@arfon where should the archive be uploaded? |
We need an archive DOI from e.g. Zenodo or figshare. |
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@eloisabentivegna @dgoldri25 @jangmys Thanks for the review and all the help! @danielskatz Thanks for the review, I updated the paper with your corrections/suggestions. Regarding the missing links for the Jakob and Johnson references, I have used the bibtex entries suggested in the documentation of those software projects. Perhaps those entries don't play well with JOSS's bib style? |
Unfortunately, bibtex entries are often built for a particular style, and don't work quite right for other styles. I think, rather than putting URLs in a note field, you should put them in a url field (going from https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography) Can you try this? |
@whedon generate pdf |
@whedon check references |
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@danielskatz Cheers for the suggestion, it seems like now the URLs are showing up in the bibliography. |
@whedon accept |
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published. Check final proof 👉 openjournals/joss-papers#1725 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1725, then you can now move forward with accepting the submission by compiling again with the flag
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@whedon accept deposit=true |
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Congratulations to @bluescarni (Francesco Biscani) and co-author!! Thanks to @dgoldri25 & @jangmys for reviewing, and @eloisabentivegna for editing! |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
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@danielskatz @eloisabentivegna @dgoldri25 @jangmys great to hear, and thank you all! |
@danielskatz @eloisabentivegna @dgoldri25 @jangmys thanks indeed! |
🎉 and congratulations to @eloisabentivegna for editing her first JOSS paper through to completion! |
Thanks to you, @arfon and @danielskatz, for your kind guidance and patience. :) |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
This is how it will look in your documentation: We need your help! Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
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Submitting author: @bluescarni (Francesco Biscani)
Repository: https://github.com/esa/pagmo2-paper
Version: v2.15.0
Editor: @eloisabentivegna
Reviewer: @dgoldri25, @jangmys
Archive: 10.5281/zenodo.4013250
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