Closed editorialbot closed 1 year ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.20 s (964.8 files/s, 90787.3 lines/s)
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Java 170 2040 2164 12510
XML 10 0 0 580
Markdown 9 89 0 324
Maven 1 26 1 264
TeX 1 9 0 92
YAML 2 8 12 43
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SUM: 193 2172 2177 13813
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1238
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1155/2017/7494313 is OK
- 10.1155/2017/1967645 is OK
- 10.1016/j.rser.2015.12.169 is OK
- 10.3390/en13153920 is OK
- 10.1016/j.energy.2016.03.038 is OK
- 10.1007/s10462-009-9105-x is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
In general I find it difficult to review the project FAME-code in itself as it should be reviewed and analyzed taking into account the entire FAME-framework.
I have a few comments or questions related to the review items.
- [ ] Contribution and authorship: Has the submitting author (@KriNiTi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
I'm assuming that the submitting author (KriNiTi) is actually Kristina Nienhaus, but this is just a wild guess, since the GitHub account doesn't provide additional identification elements. Most contributions to the codebese are by Christoph Schimeczek, which is also first author of the paper.
- [ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
The paper claims "In single-core mode, FAME-Core executes the AMIRIS model with low overhead – performing a simulation of the German wholesale electricity market for one year in hourly resolution on a desktop computer within about 20 seconds. In multi-core mode, FAME demonstrated high parallelisation efficiency for a setup of 16 computationally heavy agents: Computation wall time was roughly proportional to 1/𝑛 as 𝑛 ∈ 1, 2, 4, 8 cores were utilised." I'm not sure if, by the standard of JOSS, this is considered original result and hence should be cross checked by reviewers.
- [ ] Installation: Does installation proceed as outlined in the documentation?
In general the installation is well documented and the project follows industrial standards. I managed to install FAME-core and, as suggested, FAME-demo.
I just notice that the file PrepareToInstallFameCore.launch
, referenced by installation instructions is not present.
- [ ] Functionality: Have the functional claims of the software been confirmed?
The FAME-demo shows basic functional features of the the software. An extensive analysis should be carried on to assess every aspect of the claimed functionalities. It's important to take into account that FAME-core is part of a broader software suite, part of which is currently under review for JOSS.
- [ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
The claimed performace are basically the same claimed on #5041
Since the project has been submited split in sevaral different papares it's hard to evaluate performances claims of the core package alone.
- [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
I guess that the AMIRIS project under review on #5041 should be considered a real-world analysis problem. But since we are here reviewing FAME-code I guess at least a more explicit reference to AMIRIS should be made. The FAME-demo project is also a good usage example (even though a not real-world one).
- [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
There is a wiki shared by all the projects of the FAME suite (https://gitlab.com/fame-framework/wiki/-/wikis/home). The wiki is certainly clear and complete to a satisfactory level.
- [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
Authors list several other ABM frameworks and claim that they evaluated more than 40 other software but beside that there is no proper comparison. That said, personally, I don't think there is the strict need of an analytical comparison to justify the existence of a new ABM framework and therefore I judge the requirement fulfilled but nonetheless I pointed this out for the sake of the public discussion.
Last note. In the context of the review #4958 FAME-Io, the paper has been modified to include an UML diagram replacing the diagram previously used in common with the one used in FAME-Core. My opinion is that both diagrams convey useful information and both should be used.
@pgranato : Thanks for your effort so far. Regarding your question "The paper claims "In single-core mode, FAME-Core executes the AMIRIS model with low overhead – performing a simulation of the German wholesale electricity market for one year in hourly resolution on a desktop computer within about 20 seconds. In multi-core mode, FAME demonstrated high parallelisation efficiency for a setup of 16 computationally heavy agents: Computation wall time was roughly proportional to 1/𝑛 as 𝑛 ∈ 1, 2, 4, 8 cores were utilised." I'm not sure if, by the standard of JOSS, this is considered original result and hence should be cross checked by reviewers."
I think this could be rather crosschecked by reviewers of https://github.com/openjournals/joss-reviews/issues/5041 .
@KriNiTi : Please let us know what you think about the comments by @pgranato
Dear @pgranato & @fraukewiese
thank you for your comments. Please find our response below:
- [ ] Contribution and authorship: Has the submitting author (@KriNiTi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
I'm assuming that the submitting author (KriNiTi) is actually Kristina Nienhaus, but this is just a wild guess, since the GitHub account doesn't provide additional identification elements. Most contributions to the codebese are by Christoph Schimeczek, which is also first author of the paper.
Kristina Nienhaus was leading the software project in which the original FAME code was created (originally not hosted on Gitlab). Most of the code was indeed written by me (Christoph Schimeczek). Kristina submitted the paper to JOSS on my behalf as I was leaving for a longer period of holidays just days before we got clearance to submit it. I am sorry if this latter issue caused confusion. I will serve as contact person from now on.
- [ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
The paper claims "In single-core mode, FAME-Core executes the AMIRIS model with low overhead – performing a simulation of the German wholesale electricity market for one year in hourly resolution on a desktop computer within about 20 seconds. In multi-core mode, FAME demonstrated high parallelisation efficiency for a setup of 16 computationally heavy agents: Computation wall time was roughly proportional to 1/𝑛 as 𝑛 ∈ 1, 2, 4, 8 cores were utilised." I'm not sure if, by the standard of JOSS, this is considered original result and hence should be cross checked by reviewers.
We agree that it makes sense to consider the general runtime of AMIRIS as original result of the AMIRIS paper. However, we originally intended to make performance claims for FAME-Core regarding “low overhead” & “parallelization efficiency” in this paper using AMIRIS as an example. Since FAME-Core is the execution library of AMIRIS, the former is in fact co-responsible for its runtime. If you think this is not appropriate or confusing to keep it that way, we suggest the following to amend it: we could provide a dedicated performance testing suite for FAME-Core if you would be willing to verify our claims (Please note that this requires open-mpi compiled with Java)? If you think you could check that, we would provide such a suite of tests to measure parallelization efficiency and overhead of FAME - although it might take a few days to write that suite...
- [ ] Installation: Does installation proceed as outlined in the documentation?
In general the installation is well documented and the project follows industrial standards. I managed to install FAME-core and, as suggested, FAME-demo. I just notice that the file
PrepareToInstallFameCore.launch
, referenced by installation instructions is not present.
Thanks for pointing this out. The mentioned file & tedious setup process is no longer required. We updated the README accordingly (as newer information was only available on the Wiki).
- [ ] Functionality: Have the functional claims of the software been confirmed?
The FAME-demo shows basic functional features of the the software. An extensive analysis should be carried on to assess every aspect of the claimed functionalities. It's important to take into account that FAME-core is part of a broader software suite, part of which is currently under review for JOSS.
FAME-demo already uses most functional features of FAME-Core, including scheduling, messaging, input & output management. Do you require further demonstration of functionalities? If so, we would be happy to include additional examples, code or agents within the FAME-Demo project to demonstrate FAME-Core functionality.
- [ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
The claimed performace are basically the same claimed on #5041 Since the project has been submited split in sevaral different papares it's hard to evaluate performances claims of the core package alone.
Our original idea was not to make claims about FAME-Io or AMIRIS, but to hint at the low overhead of FAME-Core and its parallelizability (see also our comment at Reproducibility
). We take this important hint to distinguish more clearly between performance claims for FAME-Core and runtime of FAME-Io or AMIRIS. To validate that FAME-Core is fast, precompiled input files could be used to - thus avoiding the runtime of FAME-Io to interfere. A dedicated suite of tests could allow comparison of runtime with / without FAME-Core. We would prepare such a test suite if you think it makes sense.
- [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
I guess that the AMIRIS project under review on #5041 should be considered a real-world analysis problem. But since we are here reviewing FAME-code I guess at least a more explicit reference to AMIRIS should be made. The FAME-demo project is also a good usage example (even though a not real-world one).
We plan to have a direct reference to JOSS paper of AMIRIS currently under review #5041. The idea is to publish all three papers simultaneously, such that they directly refer to each other. Besides that, would you recommend a longer text describing AMIRIS in the FAME-Core paper as well? Should we add further references to peer-reviewed applications of AMIRIS or do you think the current text suffices?
- [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
There is a wiki shared by all the projects of the FAME suite (https://gitlab.com/fame-framework/wiki/-/wikis/home). The wiki is certainly clear and complete to a satisfactory level.
We also want to point out the API documentation. Since it was easy to miss we added a corresponding badge in the repository.
- [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
Authors list several other ABM frameworks and claim that they evaluated more than 40 other software but beside that there is no proper comparison. That said, personally, I don't think there is the strict need of an analytical comparison to justify the existence of a new ABM framework and therefore I judge the requirement fulfilled but nonetheless I pointed this out for the sake of the public discussion.
We have this comparison available and could add text & tables. However, we originally thought this might blow up the paper and would be out of scope for a JOSS publication. Would you recommend a) including texts, tables and references to other frameworks, b) keep the text as is, or c) drop the reference to other frameworks completely?
Last note. In the context of the review #4958 FAME-Io, the paper has been modified to include an UML diagram replacing the diagram previously used in common with the one used in FAME-Core. My opinion is that both diagrams convey useful information and both should be used.
Do you think we should include both diagrams in this paper of FAME-Core, or would you recommend to keep the current diagram, thus complementing the FAME-Io paper #4958?
Dear @pgranato & @fraukewiese
thank you for your comments. Please find our response below:
- [ ] Contribution and authorship: Has the submitting author (@KriNiTi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
I'm assuming that the submitting author (KriNiTi) is actually Kristina Nienhaus, but this is just a wild guess, since the GitHub account doesn't provide additional identification elements. Most contributions to the codebese are by Christoph Schimeczek, which is also first author of the paper.
Kristina Nienhaus was leading the software project in which the original FAME code was created (originally not hosted on Gitlab). Most of the code was indeed written by me (Christoph Schimeczek). Kristina submitted the paper to JOSS on my behalf as I was leaving for a longer period of holidays just days before we got clearance to submit it. I am sorry if this latter issue caused confusion. I will serve as contact person from now on.
That's fine for me. Checked out this point.
- [ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
The paper claims "In single-core mode, FAME-Core executes the AMIRIS model with low overhead – performing a simulation of the German wholesale electricity market for one year in hourly resolution on a desktop computer within about 20 seconds. In multi-core mode, FAME demonstrated high parallelisation efficiency for a setup of 16 computationally heavy agents: Computation wall time was roughly proportional to 1/𝑛 as 𝑛 ∈ 1, 2, 4, 8 cores were utilised." I'm not sure if, by the standard of JOSS, this is considered original result and hence should be cross checked by reviewers.
We agree that it makes sense to consider the general runtime of AMIRIS as original result of the AMIRIS paper. However, we originally intended to make performance claims for FAME-Core regarding “low overhead” & “parallelization efficiency” in this paper using AMIRIS as an example. Since FAME-Core is the execution library of AMIRIS, the former is in fact co-responsible for its runtime. If you think this is not appropriate or confusing to keep it that way, we suggest the following to amend it: we could provide a dedicated performance testing suite for FAME-Core if you would be willing to verify our claims (Please note that this requires open-mpi compiled with Java)? If you think you could check that, we would provide such a suite of tests to measure parallelization efficiency and overhead of FAME - although it might take a few days to write that suite...
Unfortunately I will not be able to check the suggested performance testing suite. I agree with @fraukewiese that this claim can be cross checked by AMIRIS on #5041
- [ ] Installation: Does installation proceed as outlined in the documentation?
In general the installation is well documented and the project follows industrial standards. I managed to install FAME-core and, as suggested, FAME-demo. I just notice that the file
PrepareToInstallFameCore.launch
, referenced by installation instructions is not present.Thanks for pointing this out. The mentioned file & tedious setup process is no longer required. We updated the README accordingly (as newer information was only available on the Wiki).
Ok, checked.
- [ ] Functionality: Have the functional claims of the software been confirmed?
The FAME-demo shows basic functional features of the the software. An extensive analysis should be carried on to assess every aspect of the claimed functionalities. It's important to take into account that FAME-core is part of a broader software suite, part of which is currently under review for JOSS.
FAME-demo already uses most functional features of FAME-Core, including scheduling, messaging, input & output management. Do you require further demonstration of functionalities? If so, we would be happy to include additional examples, code or agents within the FAME-Demo project to demonstrate FAME-Core functionality.
- [ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
The claimed performace are basically the same claimed on #5041 Since the project has been submited split in sevaral different papares it's hard to evaluate performances claims of the core package alone.
Our original idea was not to make claims about FAME-Io or AMIRIS, but to hint at the low overhead of FAME-Core and its parallelizability (see also our comment at
Reproducibility
). We take this important hint to distinguish more clearly between performance claims for FAME-Core and runtime of FAME-Io or AMIRIS. To validate that FAME-Core is fast, precompiled input files could be used to - thus avoiding the runtime of FAME-Io to interfere. A dedicated suite of tests could allow comparison of runtime with / without FAME-Core. We would prepare such a test suite if you think it makes sense.
- [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
I guess that the AMIRIS project under review on #5041 should be considered a real-world analysis problem. But since we are here reviewing FAME-code I guess at least a more explicit reference to AMIRIS should be made. The FAME-demo project is also a good usage example (even though a not real-world one).
We plan to have a direct reference to JOSS paper of AMIRIS currently under review #5041. The idea is to publish all three papers simultaneously, such that they directly refer to each other. Besides that, would you recommend a longer text describing AMIRIS in the FAME-Core paper as well? Should we add further references to peer-reviewed applications of AMIRIS or do you think the current text suffices?
I think that having the three papers published simultaneously (and referencing each other) solves much of this questions and should be enough for the readers to understand the general concepts of the framework, functionalities and performance claims.
- [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
There is a wiki shared by all the projects of the FAME suite (https://gitlab.com/fame-framework/wiki/-/wikis/home). The wiki is certainly clear and complete to a satisfactory level.
We also want to point out the API documentation. Since it was easy to miss we added a corresponding badge in the repository.
Thanks. Checked.
- [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
Authors list several other ABM frameworks and claim that they evaluated more than 40 other software but beside that there is no proper comparison. That said, personally, I don't think there is the strict need of an analytical comparison to justify the existence of a new ABM framework and therefore I judge the requirement fulfilled but nonetheless I pointed this out for the sake of the public discussion.
We have this comparison available and could add text & tables. However, we originally thought this might blow up the paper and would be out of scope for a JOSS publication. Would you recommend a) including texts, tables and references to other frameworks, b) keep the text as is, or c) drop the reference to other frameworks completely?
I guess that a short paragraph or a small table that briefly describes the comparison with the few you closely analyzed should be added replacing "We closely examined, e.g., Jade, MASS, Repast and Akka."
Last note. In the context of the review #4958 FAME-Io, the paper has been modified to include an UML diagram replacing the diagram previously used in common with the one used in FAME-Core. My opinion is that both diagrams convey useful information and both should be used.
Do you think we should include both diagrams in this paper of FAME-Core, or would you recommend to keep the current diagram, thus complementing the FAME-Io paper #4958?
Since the paper are going to be published together I recommend to keep the current diagram.
@dlr-cjs I fully agree with @pgranato regarding his suggestion: "I guess that a short paragraph or a small table that briefly describes the comparison with the few you closely analyzed should be added replacing "We closely examined, e.g., Jade, MASS, Repast and Akka."" It is a very important point to clarify why the software could not be build upon an existing framework but had to be built from scratch, thus some more explanation in the paper are required.
Dear @fraukewiese & @pgranato,
we rewrote the "Statement of need" to include a more detailed examination of the frameworks we assessed and why we decided to create FAME. We hope that our changes address your comments appropriately.
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Hello @pgranato, here are the things you can ask me to do:
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:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@pgranato : Do you think your comment regarding the statement of need it is addressed adequately?
Hi @fraukewiese, yes I think that this version of the article clarifies sufficiently the state of the field and the need of a new software. Regarding the other two open points, namely Reproducibility and Performance: I think I did what possibile to check the points and I'm personally convinced that the requests are satisfied. Since we discussed that this points could be also cross-checked by reviewers of #5041 and they have been independently verified by reviewers of that submission I marked as checked also here.
@pgranato : Thank you very much for your thorough review!
We will now wait for the further review by @xtruan
Hi @xtruan : Could you update us on how the review is going? Thanks a lot :)
Hey sorry for being the slowpoke here, I will get my review completed by the end of this week!
@xtruan : Great, thanks for the update
@fraukewiese I have completed my review. I was able to successfully run the FAME-Demo with the latest version of FAME-Core with no issues. Your paper was well written and covered all of the information required. I don't believe any additional changes need to be made to satisfy the requirements.
This is a fantastic project! I would like to commend you especially on the depth of the documentation, especially the high quality of code comments within the source. They make understanding the operation of the different FAME components much more approachable.
Dear @xtruan, thank you for your review and your kind words.
@fraukewiese how do we proceed now? shall we manually update the dates in the paper.md, or will this be done automatically? We would plan for a final review of the paper and also like to thank the reviewers for their contributions in the paper, if possible.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@xtruan : Thank you very much for your review!
@KriNiTi All three related submissions #5087 #4958 #5041 have now been reviewed and we can proceed with the final steps. Please make sure the cross-references between the papers are correct and updated - the final DOIs should be 10.21105/joss.05087 10.21105/joss.04958 10.21105/joss.05041
At this point could you:
I can then move forward with accepting the submission.
Dear @fraukewiese
Thank you for your efforts with this publication.
@editorialbot set v1.4.2 as version
@editorialbot set v1.4.2 as version
@editorialbot set 10.5281/zenodo.7755760 as archive
Done! version is now v1.4.2
Done! version is now v1.4.2
Done! Archive is now 10.5281/zenodo.7755760
@editorialbot set 10.5281/zenodo.7755760 as archive
Done! Archive is now 10.5281/zenodo.7755760
@editorialbot recommend-accept
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1155/2017/7494313 is OK
- 10.1155/2017/1967645 is OK
- 10.1016/j.rser.2015.12.169 is OK
- 10.3390/en13153920 is OK
- 10.1016/j.energy.2016.03.038 is OK
- 10.1007/s10462-009-9105-x is OK
MISSING DOIs
- None
INVALID DOIs
- 10.21105/joss.04958 is INVALID
- 10.21105/joss.05041 is INVALID
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1155/2017/7494313 is OK
- 10.1155/2017/1967645 is OK
- 10.1016/j.rser.2015.12.169 is OK
- 10.3390/en13153920 is OK
- 10.1016/j.energy.2016.03.038 is OK
- 10.1007/s10462-009-9105-x is OK
MISSING DOIs
- None
INVALID DOIs
- 10.21105/joss.04958 is INVALID
- 10.21105/joss.05041 is INVALID
:wave: @openjournals/pe-eics, this paper is ready to be accepted and published.
Check final proof :point_right::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4118, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Hello @KriNiT @dlr-cjs, as with the other papers, I made some formatting changes to the paper: https://gitlab.com/fame-framework/fame-core/-/merge_requests/69
Could you merge these?
Thank you @kyleniemeyer for your formatting changes. I merge them as requested.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Submitting author: !--author-handle-->@KriNiTi<!--end-author-handle-- (Kristina Nienhaus) Repository: https://gitlab.com/fame-framework/fame-core Branch with paper.md (empty if default branch): 86-publish-paper Version: v1.4.2 Editor: !--editor-->@fraukewiese<!--end-editor-- Reviewers: @xtruan, @pgranato Archive: 10.5281/zenodo.7755760
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Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
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@xtruan & @pgranato, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
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