[PRE REVIEW]: An Open-Source Tool for Generating Domain-Specific Accelerators for Resource-Constrained Computing

[editorialbot]

Submitting author: !--author-handle-->@dtkerns<!--end-author-handle-- (David Kerns) Repository: https://github.com/dtkerns/d2 Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@gkthiruvathukal<!--end-editor-- Reviewers: @manuel-g-castro, @abhishektiwari Managing EiC: Daniel S. Katz

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (651.9 files/s, 61779.0 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                               2             35             54            652
Bourne Again Shell               11             31             48            632
Python                           10             38             48            532
Markdown                          1             40              0            166
TeX                               1             17              1            147
YAML                              1              1              4             18
--------------------------------------------------------------------------------
SUM:                             26            162            155           2147
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 3890

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/2514740 is OK
- 10.1109/JIOT.2018.2849859 is OK
- 10.1109/32.221135 is OK
- 10.1109/WWC.2001.990739 is OK
- 10.1109/ISCA45697.2020.00041 is OK
- 10.1145/2024716.2024718 is OK

MISSING DOIs

- 10.1093/oso/9780195162929.003.0012 may be a valid DOI for title: Discrete event abstraction: An emerging paradigm for modeling complex adaptive systems
- 10.1145/968280.968304 may be a valid DOI for title: A quantitative analysis of the speedup factors of FPGAs over processors
- 10.1109/32.221135 may be a valid DOI for title: A technique for drawing directed graphs
- 10.1109/hpca.2017.59 may be a valid DOI for title: Needle: Leveraging program analysis to analyze and extract accelerators from whole programs

INVALID DOIs

- 10.1109/ISLPED52811.2021.limaye21_dosage is INVALID

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

DASF: A data analytics software framework for distributed environments Submitting author: @d-eggert Handling editor: @martinfleis (Active) Reviewers: @cjwu, @pritchardn Similarity score: 0.7994

s4rdm3x: A Tool Suite to Explore Code to Architecture Mapping Techniques Submitting author: @tobias-dv-lnu Handling editor: @gkthiruvathukal (Active) Reviewers: @kinow, @xirdneh Similarity score: 0.7940

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences Submitting author: @warrenlr Handling editor: @biorelated (Retired) Reviewers: @andrewjpage Similarity score: 0.7926

SARAS: A general-purpose PDE solver for fluid dynamics Submitting author: @roshansamuel Handling editor: @kyleniemeyer (Active) Reviewers: @dlagrava, @olgadoronina, @nickwimer Similarity score: 0.7914

SimSGamE : Scheduling simulator for modern game engines Submitting author: @baptisteCoye Handling editor: @danielskatz (Active) Reviewers: @azoitl, @hwloidl Similarity score: 0.7911

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

👋 @dtkerns - thanks for your submission. However, I see a number of issues.

First, your paper is about 4 times longer than recommended for a JOSS paper. Please see the example paper. If you want to continue this potential JOSS submission, you will need to reduce the content of your .md file.

In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

But before making changes to the paper or references, we should be sure that this work is in scope for JOSS. Due to the relatively small amount of code, I'm unsure if it meets the substantial scholarly effort criterion for review by JOSS. Can you explain a bit about the C and Python parts of the code?

Additionally, if we do review this, your README will need work. I don't see a lot of the things that are needed, such as a statement of purpose, community contributor guidelines, how the code is supported, etc. See https://joss.readthedocs.io/en/latest/review_criteria.html

[dtkerns]

@editorialbot commands

@editorialbot check references

On Sat, Dec 2, 2023 at 1:46 PM The Open Journals editorial robot < @.***> wrote:

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Hello @dtkerns, here are the things you can ask me to do:

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[dtkerns]

@editorialbot check references

On Sun, Dec 3, 2023 at 11:48 AM The Open Journals editorial robot < @.***> wrote:

Hello @dtkerns https://github.com/dtkerns, here are the things you can ask me to do:

List all available commands

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@editorialbot check references

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[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/968280.968304 is OK
- 10.1145/2514740 is OK
- 10.1109/ISLPED52811.2021.9502501 is OK
- 10.1109/JIOT.2018.2849859 is OK
- 10.1109/32.221135 is OK
- 10.1109/WWC.2001.990739 is OK
- 10.1109/ISCA45697.2020.00041 is OK
- 10.1145/2024716.2024718 is OK
- 10.1109/HPCA.2017.59 is OK

MISSING DOIs

- 10.1093/oso/9780195162929.003.0012 may be a valid DOI for title: Discrete event abstraction: An emerging paradigm for modeling complex adaptive systems
- 10.1109/32.221135 may be a valid DOI for title: A technique for drawing directed graphs

INVALID DOIs

- None

[dtkerns]

Hi Daniel, Thank you for your pre-review comments. I'm employed full-time and have an important milestone at work on Thursday, so time is a bit sparse this week. I am meeting w/ my PhD adviser this afternoon and he will assist me with a proper follow-up. I did address the DOI issues. I have been working on this research and paper for 2.5 years, so a few days tacked on is not detrimental to my schedule. Thank you for your patience.

Dave Kerns

On Sat, Dec 2, 2023 at 1:57 PM Daniel S. Katz @.***> wrote:

👋 @dtkerns https://github.com/dtkerns - thanks for your submission. However, I see a number of issues.

First, your paper is about 4 times longer than recommended for a JOSS paper. Please see the example paper https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography. If you want to continue this potential JOSS submission, you will need to reduce the content of your .md file.

In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

But before making changes to the paper or references, we should be sure that this work is in scope for JOSS. Due to the relatively small amount of code, I'm unsure if it meets the substantial scholarly effort https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort criterion for review by JOSS. Can you explain a bit about the C and Python parts of the code?

Additionally, if we do review this, your README will need work. I don't see a lot of the things that are needed, such as a statement of purpose, community contributor guidelines, how the code is supported, etc. See https://joss.readthedocs.io/en/latest/review_criteria.html

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1837251739, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKGWMQS6ABHORUTCEETYHOI2TAVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZXGI2TCNZTHE . You are receiving this because you were mentioned.Message ID: @.***>

[danielskatz]

@dtkerns - thanks, I'll look forward to hearing more from you soon.

Also, I see two DOIs that still aren't in the bib, so I'm unsure that "I did address the DOI issues" is fully complete.

[dtkerns]

@editorialbot check references

On Sun, Dec 3, 2023 at 12:19 PM The Open Journals editorial robot < @.***> wrote:

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

• 10.1145/968280.968304 is OK
• 10.1145/2514740 is OK
• 10.1109/ISLPED52811.2021.9502501 is OK
• 10.1109/JIOT.2018.2849859 is OK
• 10.1109/32.221135 is OK
• 10.1109/WWC.2001.990739 is OK
• 10.1109/ISCA45697.2020.00041 is OK
• 10.1145/2024716.2024718 is OK
• 10.1109/HPCA.2017.59 is OK

MISSING DOIs

• 10.1093/oso/9780195162929.003.0012 may be a valid DOI for title: Discrete event abstraction: An emerging paradigm for modeling complex adaptive systems
• 10.1109/32.221135 may be a valid DOI for title: A technique for drawing directed graphs

INVALID DOIs

• None

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1837573852, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKFNMPPLUQAL6ZELUETYHTGFJAVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZXGU3TGOBVGI . You are receiving this because you were mentioned.Message ID: @.***>

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/968280.968304 is OK
- 10.1145/2514740 is OK
- 10.1109/ISLPED52811.2021.9502501 is OK
- 10.1109/JIOT.2018.2849859 is OK
- 10.1109/32.221135 is OK
- 10.1109/WWC.2001.990739 is OK
- 10.1109/ISCA45697.2020.00041 is OK
- 10.1145/2024716.2024718 is OK
- 10.1109/HPCA.2017.59 is OK

MISSING DOIs

- 10.1109/32.221135 may be a valid DOI for title: A technique for drawing directed graphs

INVALID DOIs

- None

[dtkerns]

Re: the missing DOIs for 10.1093/oso/9780195162929.003.001 it looks like the text that referenced that work was removed, so I removed it from paper.bib for 10.1109/32.221135, I have an email from the author, who recommended the bib I cited. (see email below, but I'll follow your advice)

After meeting with my advisor (who's delighted you've engaged in dialogue) I came up with this explanation:

The tool, D2, enables computer architects and researchers to easily generate domain-specific accelerators (DSAs) given a set of input workloads based on the super block (SB) granularity. To the best of our knowledge, no such automation tool currently exists. D2 is a shell script “driver” that takes two arguments: the top directory of the user’s source code to be analyzed and a working directory for D2 to store its intermediate data.

The driver calls make on the user’s source (for which the Makefile should have been modified previously, per the documentation, to build the .ll/.llg "targets") The .llvm files and other metadata is copied to the working directory. The driver then walks through the various python and C++ data-processing programs to determine a list of rank ordered SBs. The user is then able to evaluate each SB for appropriateness to implement as a DSA.

The sb.cc program (SB identifier) is the heart of D2 and represents the greatest contribution of this work. It also represents a significant research effort not well represented by the line count. It encompassed a non-trivial search for any already-published Control Flow Graph (CFG) SB identifiers. A second stage of the effort sought to solve the complex problem of determining what metadata to carry along to utilize the results successfully in the context of creating a DSA from the output. Finally, the sb program is actually called twice from within the driver for the following two distinct operations: 1) identifying the constraint list from each basic block (BB) in the CFG and 2) identifying the SBs from the CFG.

---

Finally, I will clean up the README... Apologies that I overlooked that before submission.

Dave

Hello, I'd like to cite your original DOT paper... Google scholar finds it here: https://labs.onb.ac.at/gitlab/wobweger/h_howto/-/raw/8e8aed73e99899f2f2447098343e83cfd6481bba/0_gen/x_gv/dotguide.pdf then gives a BibTeX as:

@misc{gansner2006drawing, title={Drawing graphs with dot}, author={Gansner, Emden and Koutsofios, Eleftherios and North, Stephen}, year={2006}, publisher={Technical report, AT\&T Research. URL http://www. graphviz. org/Documentation~…} }

It would be nice if you hosted it (even hidden) on/in https://graphviz.org/documentation/ ... maybe you already do ;)

thanks,

Dave

Hi,

Actually that paper is on the Graphviz web site here under User's Guides in Documentation. As that was not externally published, we usually recommend the second item under the Graphviz Papers for citations. Or for just the Dot program, there is the article

@article{DBLP:journals/tse/GansnerKNV93, author = {Emden R. Gansner and Eleftherios Koutsofios and Stephen C. North and Kiem{-}Phong Vo}, title = {A Technique for Drawing Directed Graphs}, journal = {{IEEE} Trans. Software Eng.}, volume = {19}, number = {3}, pages = {214--230}, year = {1993}, url = {https://doi.org/10.1109/32.221135}, doi = {10.1109/32.221135}, timestamp = {Wed, 17 May 2017 10:56:38 +0200}, biburl = {https://dblp.org/rec/journals/tse/GansnerKNV93.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }

Emden

On Mon, Dec 4, 2023 at 8:18 AM Daniel S. Katz @.***> wrote:

@dtkerns https://github.com/dtkerns - thanks, I'll look forward to hearing more from you soon.

Also, I see two DOIs that still aren't in the bib, so I'm unsure that "I did address the DOI issues" is fully complete.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1838864661, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKDZ7MP2P3WZMQXZ5FDYHXSVHAVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZYHA3DINRWGE . You are receiving this because you were mentioned.Message ID: @.***>

[danielskatz]

@editorialbot generate pdf

[danielskatz]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (792.0 files/s, 71362.2 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                               2             35             54            652
Bourne Again Shell               11             31             48            632
Python                           10             38             48            532
Markdown                          2             49              0            186
TeX                               1             16              1            168
YAML                              1              1              4             18
make                              1              3              0              7
--------------------------------------------------------------------------------
SUM:                             28            173            155           2195
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 3890

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

DASF: A data analytics software framework for distributed environments Submitting author: @d-eggert Handling editor: @martinfleis (Active) Reviewers: @cjwu, @pritchardn Similarity score: 0.7994

s4rdm3x: A Tool Suite to Explore Code to Architecture Mapping Techniques Submitting author: @tobias-dv-lnu Handling editor: @gkthiruvathukal (Active) Reviewers: @kinow, @xirdneh Similarity score: 0.7940

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences Submitting author: @warrenlr Handling editor: @biorelated (Retired) Reviewers: @andrewjpage Similarity score: 0.7926

SARAS: A general-purpose PDE solver for fluid dynamics Submitting author: @roshansamuel Handling editor: @kyleniemeyer (Active) Reviewers: @dlagrava, @olgadoronina, @nickwimer Similarity score: 0.7914

SimSGamE : Scheduling simulator for modern game engines Submitting author: @baptisteCoye Handling editor: @danielskatz (Active) Reviewers: @azoitl, @hwloidl Similarity score: 0.7911

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/968280.968304 is OK
- 10.1145/2514740 is OK
- 10.1109/ISLPED52811.2021.9502501 is OK
- 10.1109/JIOT.2018.2849859 is OK
- 10.1109/32.221135 is OK
- 10.1109/WWC.2001.990739 is OK
- 10.1109/ISCA45697.2020.00041 is OK
- 10.1145/2024716.2024718 is OK
- 10.1109/HPCA.2017.59 is OK

MISSING DOIs

- 10.1109/32.221135 may be a valid DOI for title: A technique for drawing directed graphs

INVALID DOIs

- None

[danielskatz]

@dtkerns - thanks for your comments and changes so far.

I think, that based on what you've said, this is in scope for JOSS review.

However, there are still two issues to be addressed before that can start, one small and one big.

The small one is the DOI - it looks like your bib file contains items for both gansner17_graphviz and gansner1993technique which are to the same work, but one doesn't have a DOI, which is what editorialbot is catching. I think you should just remove the gansner1993technique entry from your .bib file, and if needed, make sure you reference gansner17_graphviz instead.

The big issue is the paper length. As I wrote previously, this is not a JOSS paper, as it's far too long: about 4000 words vs JOSS asking for 1000 max. The two options you have are:

1. Reduce the size of the paper, more closely following the example paper and the sections in it. Other material that's currently in your paper might be put in the repository and pointed to in the paper.
2. Submit to another journal, such as JORS that has more of a focus on both the paper and the software, unlike JOSS, where the purpose of the paper is mostly to point to and introduce the software and the repository, not to fully explain it.

Please let me know which you want to do.

[dtkerns]

ok. thanks. Let me talk with my advisor and I'll get back to you as soon as possible.

On Thu, Dec 7, 2023 at 2:12 PM Daniel S. Katz @.***> wrote:

@dtkerns https://github.com/dtkerns - thanks for your comments and changes so far.

I think, that based on what you've said, this is in scope for JOSS review.

However, there are still two issues to be addressed before that can start, one small and one big.

The small one is the DOI - it looks like your bib file contains items for both gansner17_graphviz and gansner1993technique which are to the same work, but one doesn't have a DOI, which is what editorialbot is catching. I think you should just remove the gansner1993technique entry from your .bib file, and if needed, make sure you reference gansner17_graphviz instead.

The big issue is the paper length. As I wrote previously, this is not a JOSS paper, as it's far too long: about 4000 words vs JOSS asking for 1000 max. The two options you have are:

1. Reduce the size of the paper, more closely following the example paper https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography and the sections in it. Other material that's currently in your paper might be put in the repository and pointed to in the paper.
2. Submit to another journal, such as JORS https://openresearchsoftware.metajnl.com that has more of a focus on both the paper and the software, unlike JOSS, where the purpose of the paper is mostly to point to and introduce the software and the repository, not to fully explain it.

Please let me know which you want to do.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1846119497, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKBDOKRX5RYRAHDIL6LYIIWK7AVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBWGEYTSNBZG4 . You are receiving this because you were mentioned.Message ID: @.***>

[dtkerns]

I spoke with my advisor and he'd like me to proceed w/ JOSS, so I will start trimming. (I deleted the rogue bib) My advisor would like to review it before you start your review. I plan to work on it tomorrow. I'll give you a heads up when we think we're there. Thanks again!

On Thu, Dec 7, 2023 at 2:17 PM david kerns @.***> wrote:

ok. thanks. Let me talk with my advisor and I'll get back to you as soon as possible.

On Thu, Dec 7, 2023 at 2:12 PM Daniel S. Katz @.***> wrote:

@dtkerns https://github.com/dtkerns - thanks for your comments and changes so far.

I think, that based on what you've said, this is in scope for JOSS review.

However, there are still two issues to be addressed before that can start, one small and one big.

The small one is the DOI - it looks like your bib file contains items for both gansner17_graphviz and gansner1993technique which are to the same work, but one doesn't have a DOI, which is what editorialbot is catching. I think you should just remove the gansner1993technique entry from your .bib file, and if needed, make sure you reference gansner17_graphviz instead.

The big issue is the paper length. As I wrote previously, this is not a JOSS paper, as it's far too long: about 4000 words vs JOSS asking for 1000 max. The two options you have are:

1. Reduce the size of the paper, more closely following the example paper https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography and the sections in it. Other material that's currently in your paper might be put in the repository and pointed to in the paper.
2. Submit to another journal, such as JORS https://openresearchsoftware.metajnl.com that has more of a focus on both the paper and the software, unlike JOSS, where the purpose of the paper is mostly to point to and introduce the software and the repository, not to fully explain it.

Please let me know which you want to do.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1846119497, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKBDOKRX5RYRAHDIL6LYIIWK7AVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBWGEYTSNBZG4 . You are receiving this because you were mentioned.Message ID: @.***>

[dtkerns]

@editorialbot check references

On Thu, Dec 7, 2023 at 6:10 PM david kerns @.***> wrote:

I spoke with my advisor and he'd like me to proceed w/ JOSS, so I will start trimming. (I deleted the rogue bib) My advisor would like to review it before you start your review. I plan to work on it tomorrow. I'll give you a heads up when we think we're there. Thanks again!

On Thu, Dec 7, 2023 at 2:17 PM david kerns @.***> wrote:

ok. thanks. Let me talk with my advisor and I'll get back to you as soon as possible.

On Thu, Dec 7, 2023 at 2:12 PM Daniel S. Katz @.***> wrote:

@dtkerns https://github.com/dtkerns - thanks for your comments and changes so far.

I think, that based on what you've said, this is in scope for JOSS review.

However, there are still two issues to be addressed before that can start, one small and one big.

The small one is the DOI - it looks like your bib file contains items for both gansner17_graphviz and gansner1993technique which are to the same work, but one doesn't have a DOI, which is what editorialbot is catching. I think you should just remove the gansner1993technique entry from your .bib file, and if needed, make sure you reference gansner17_graphviz instead.

The big issue is the paper length. As I wrote previously, this is not a JOSS paper, as it's far too long: about 4000 words vs JOSS asking for 1000 max. The two options you have are:

1. Reduce the size of the paper, more closely following the example paper https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography and the sections in it. Other material that's currently in your paper might be put in the repository and pointed to in the paper.
2. Submit to another journal, such as JORS https://openresearchsoftware.metajnl.com that has more of a focus on both the paper and the software, unlike JOSS, where the purpose of the paper is mostly to point to and introduce the software and the repository, not to fully explain it.

Please let me know which you want to do.

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[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/968280.968304 is OK
- 10.1145/2514740 is OK
- 10.1109/ISLPED52811.2021.9502501 is OK
- 10.1109/JIOT.2018.2849859 is OK
- 10.1109/32.221135 is OK
- 10.1109/WWC.2001.990739 is OK
- 10.1109/ISCA45697.2020.00041 is OK
- 10.1145/2024716.2024718 is OK
- 10.1109/HPCA.2017.59 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[dtkerns]

@editorialbot check references

On Fri, Dec 8, 2023 at 10:53 PM The Open Journals editorial robot < @.***> wrote:

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

• 10.1145/968280.968304 is OK
• 10.1145/2514740 is OK
• 10.1109/ISLPED52811.2021.9502501 is OK
• 10.1109/JIOT.2018.2849859 is OK
• 10.1109/32.221135 is OK
• 10.1109/WWC.2001.990739 is OK
• 10.1109/ISCA45697.2020.00041 is OK
• 10.1145/2024716.2024718 is OK
• 10.1109/HPCA.2017.59 is OK

MISSING DOIs

• None

INVALID DOIs

• None

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1848252138, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKF5ZJXEFGVGHD4IYFTYIP4F3AVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBYGI2TEMJTHA . You are receiving this because you were mentioned.Message ID: @.***>

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/3282307 is OK
- 10.1145/968280.968304 is OK
- 10.1145/2514740 is OK
- 10.1109/ISLPED52811.2021.9502501 is OK
- 10.1109/JIOT.2018.2849859 is OK
- 10.1109/32.221135 is OK
- 10.1109/WWC.2001.990739 is OK
- 10.1109/ISCA45697.2020.00041 is OK
- 10.1145/2024716.2024718 is OK
- 10.1109/HPCA.2017.59 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[dtkerns]

Daniel, Please let me know if I have sufficiently trimmed the paper down. thanks

On Mon, Dec 11, 2023 at 10:42 PM The Open Journals editorial robot < @.***> wrote:

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

• 10.1145/3282307 is OK
• 10.1145/968280.968304 is OK
• 10.1145/2514740 is OK
• 10.1109/ISLPED52811.2021.9502501 is OK
• 10.1109/JIOT.2018.2849859 is OK
• 10.1109/32.221135 is OK
• 10.1109/WWC.2001.990739 is OK
• 10.1109/ISCA45697.2020.00041 is OK
• 10.1145/2024716.2024718 is OK
• 10.1109/HPCA.2017.59 is OK

MISSING DOIs

• None

INVALID DOIs

• None

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1851337634, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKE7M3NOFDBDJZMNRVTYI7VELAVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJRGMZTONRTGQ . You are receiving this because you were mentioned.Message ID: @.***>

[danielskatz]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (773.8 files/s, 69484.8 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                               2             36             63            652
Bourne Again Shell               11             31             48            632
Python                           10             38             48            532
Markdown                          3             65              0            236
TeX                               1             16              1            173
YAML                              1              1              4             18
make                              1              3              0              7
--------------------------------------------------------------------------------
SUM:                             29            190            164           2250
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1224

[danielskatz]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

DASF: A data analytics software framework for distributed environments Submitting author: @d-eggert Handling editor: @martinfleis (Active) Reviewers: @cjwu, @pritchardn Similarity score: 0.8036

dms2dfe: Comprehensive Workflow for Analysis of Deep Mutational Scanning Data Submitting author: @rraadd88 Handling editor: @tracykteal (Retired) Reviewers: @afrubin Similarity score: 0.7981

s4rdm3x: A Tool Suite to Explore Code to Architecture Mapping Techniques Submitting author: @tobias-dv-lnu Handling editor: @gkthiruvathukal (Active) Reviewers: @kinow, @xirdneh Similarity score: 0.7976

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences Submitting author: @warrenlr Handling editor: @biorelated (Retired) Reviewers: @andrewjpage Similarity score: 0.7971

SimSGamE : Scheduling simulator for modern game engines Submitting author: @baptisteCoye Handling editor: @danielskatz (Active) Reviewers: @azoitl, @hwloidl Similarity score: 0.7933

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

@dtkerns - yes, this looks fine for now. I'll next look for an editor

[danielskatz]

👋 @gkthiruvathukal - do you think you could edit this submission?

[danielskatz]

@editorialbot invite @gkthiruvathukal as editor

[editorialbot]

Invitation to edit this submission sent!

[gkthiruvathukal]

@danielskatz Yes, I can take this one. Will self-assign now.

[gkthiruvathukal]

@editorialbot assign me as editor

[editorialbot]

Assigned! @gkthiruvathukal is now the editor

[dtkerns]

I added an example directory. When I ran d2 on the example, I discovered I've been hit by software rot. (the usage of LLVM's opt command changed) I'm working on correcting the issue.

On Tue, Dec 12, 2023 at 7:15 AM The Open Journals editorial robot < @.***> wrote:

Assigned! @gkthiruvathukal https://github.com/gkthiruvathukal is now the editor

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1852121005, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKE6WQAEZK2ZGM5ZEQTYJBRIFAVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJSGEZDCMBQGU . You are receiving this because you were mentioned.Message ID: @.***>

[dtkerns]

It turns out to be a bug in LLVM ... it took a significant amount of patience to discover this. see https://discourse.llvm.org/t/need-usage-help-w-new-pass-manager-for-opt-analysis-natural-loop-information/75874 which ultimately resulted in https://github.com/llvm/llvm-project/issues/76762 I've created an issue against d2 and implemented a work-around in the script.

On Sun, Dec 17, 2023 at 9:57 PM david kerns @.***> wrote:

I added an example directory. When I ran d2 on the example, I discovered I've been hit by software rot. (the usage of LLVM's opt command changed) I'm working on correcting the issue.

On Tue, Dec 12, 2023 at 7:15 AM The Open Journals editorial robot < @.***> wrote:

Assigned! @gkthiruvathukal https://github.com/gkthiruvathukal is now the editor

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6111#issuecomment-1852121005, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVJRKE6WQAEZK2ZGM5ZEQTYJBRIFAVCNFSM6AAAAABAEH5WWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJSGEZDCMBQGU . You are receiving this because you were mentioned.Message ID: @.***>

[gkthiruvathukal]

@cjwu and/or @pritchardn: Are you willing to review this JOSS submission?

[danielskatz]

👋 @gkthiruvathukal - It seems like this has gotten stuck. Can you get it moving again?

[gkthiruvathukal]

@kinow, and @xirdneh, would either or both of you be able to help with this JOSS submission?