[PRE REVIEW]: FlowFPX: Nimble Tools for Debugging Floating-Point Exceptions #135

whedon · 2023-10-27T11:52:39Z

Submitting author: @ashton314 (Ashton Wiersdorf)
Repository: https://github.com/utahplt/juliacon2023-paper
Branch with paper.md (empty if default branch):
Version:
Editor: @lucaferranti
Reviewers: @JeffreySarnoff, @dpsanders
Managing EiC: Mathieu Besançon

Author instructions

Thanks for submitting your paper to JCON @ashton314. Currently, there isn't an JCON editor assigned to your paper.

The author's suggestion for the handling editor is @lucaferranti.

@ashton314 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JCON and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JCON submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

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The text was updated successfully, but these errors were encountered:

whedon · 2023-10-27T11:52:43Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ JOSS reduced service mode ⚠️

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.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon · 2023-10-27T11:52:53Z

Failed to discover a Statement of need section in paper

whedon · 2023-10-27T11:52:54Z

Wordcount for paper.tex is 4721

whedon · 2023-10-27T11:52:56Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.10 s (431.1 files/s, 78048.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              9            461            245           3685
SVG                             29              0              0           3232
Ruby                             1              8              4             45
Racket                           1              5              5             38
YAML                             1              0              0             34
Julia                            1              3              0             14
make                             1              1              0              5
-------------------------------------------------------------------------------
SUM:                            43            478            254           7053
-------------------------------------------------------------------------------


Statistical information for the repository 'cb21e6b90590109945dc6ebd' was
gathered on 2023/10/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ashton Wiersdorf                 1            57              0          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Ashton Wiersdorf             57          100.0          0.0                7.02

whedon · 2023-10-27T11:52:57Z

Failed to discover a valid open source license.

whedon · 2023-10-27T11:52:58Z

PDF failed to compile for issue #135 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
===========Latexmk: Missing input file: 'cleveref.sty' from line
  '! LaTeX Error: File `cleveref.sty' not found.'
Latexmk: Missing input file: 'cleveref.sty' from line
  '! LaTeX Error: File `cleveref.sty' not found.'
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

whedon · 2023-10-27T11:53:14Z

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

OK DOIs

- 10.1145/103162.103163 is OK
- 10.1007/978-3-031-08751-6_9 is OK
- 10.1109/IEEESTD.1985.82928 is OK
- 10.1029/2020MS002246 is OK
- 10.1145/3316279.3316281 is OK
- 10.1109/MCSE.2014.90 is OK
- 10.1145/3579990.3580020 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.1145/3324989.3325721 is OK
- 10.1145/2998441 is OK
- 10.1145/3330345.3330346 is OK
- 10.1002/0471028959 is OK
- 10.1109/Correctness56720.2022.00006 is OK
- 10.1109/Correctness54621.2021.00007 is OK
- 10.1145/3520313.3534655 is OK
- 10.1109/XLOOP56614.2022.00010 is OK
- 10.11578/dc.20230713.4 is OK
- 10.21105/joss.02018 is OK
- 10.1109/ASE.2019.00118 is OK
- 10.1109/IISWC55918.2022.00014 is OK
- 10.5281/ZENODO.5115765 is OK
- 10.1109/MCSE.2014.11 is OK
- 10.1145/2737924.2737959 is OK
- 10.48550/arXiv.2305.10599 is OK
- 10.1109/IPDPS.2007.370254 is OK
- 10.1109/MC.2019.2926614 is OK
- 10.1145/3369583.3392673 is OK
- 10.1007/978-3-319-76526-6 is OK
- 10.48550/arXiv.2209.05433 is OK

MISSING DOIs

- 10.2307/2317055 may be a valid DOI for title: The Art of Computer Programming, Volume 2: Seminumerical Algorithms
- 10.1515/jnum-2012-0013 may be a valid DOI for title: New development in FreeFem++
- 10.1016/j.parco.2021.102870 may be a valid DOI for title: Linear solvers for power grid optimization problems: A review of GPU-accelerated linear solvers

INVALID DOIs

- None

lucaferranti · 2023-10-27T12:09:49Z

@whedon assign @lucaferranti as editor

whedon · 2023-10-27T12:09:54Z

OK, the editor is @lucaferranti

lucaferranti · 2023-10-27T12:52:26Z

HI @ashton314, 👋

thank you for the submission. I will be your editor and will start looking for reviewers.

Meanwhile, it seems the latex compilation is failing for your paper. Would be good if you could look into it and try to fix it.

Note also that there seem to be a few missing DOIs.

If you have any questions, do not hesitate in letting me know.

lucaferranti · 2023-10-27T12:53:15Z

looking at the error

===========Latexmk: Missing input file: 'cleveref.sty' from line
  '! LaTeX Error: File `cleveref.sty' not found.'
Latexmk: Missing input file: 'cleveref.sty' from line
  '! LaTeX Error: File `cleveref.sty' not found.'
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

it seems like a missing library file from the repository

ashton314 · 2023-10-27T16:38:40Z

Hi Luca! Thanks for helping me out with this!

error
I see—thanks for that! I was frustrated with the Whedon bot because I couldn't figure out how to view the compile errors. I see some of them are in this thread though—that's good.

I think cleverref.sty is part of my LaTeX distro; I'll add it manually if I can.

ashton314 · 2023-10-27T17:03:12Z

DOIs:

10.2307/2317055 this is a review of The Art of Computer Programming, not the book itself. I'm having difficulty finding a DOI for the second volume; we have the ISBN in the bibtex file; can we ask the citation generation format to put the ISBN in instead?
10.1515/jnum-2012-0013 added
10.1016/j.parco.2021.102870 added

ashton314 · 2023-10-27T17:03:51Z

@whedon commands

whedon · 2023-10-27T17:03:54Z

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

ashton314 · 2023-10-27T17:04:01Z

@whedon generate pdf

whedon · 2023-10-27T17:04:11Z

PDF failed to compile for issue #135 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
===========Latexmk: Missing input file: 'microtype.sty' from line
  '! LaTeX Error: File `microtype.sty' not found.'
Latexmk: Missing input file: 'microtype.sty' from line
  '! LaTeX Error: File `microtype.sty' not found.'
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

ashton314 · 2023-10-27T17:05:21Z

@whedon generate pdf

whedon · 2023-10-27T17:05:31Z

PDF failed to compile for issue #135 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
===========Latexmk: Missing input file: 'microtype-pdftex.def' from line
  '! LaTeX Error: File `microtype-pdftex.def' not found.'
Latexmk: Missing input file: 'microtype-pdftex.def' from line
  '! LaTeX Error: File `microtype-pdftex.def' not found.'
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

ashton314 · 2023-10-27T17:06:35Z

@whedon generate pdf

whedon · 2023-10-27T17:06:44Z

PDF failed to compile for issue #135 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------

kpathsea: Running mktextfm psyr
/app/.texlive/texmf-dist/web2c/mktexnam: Could not map source abbreviation  for psyr.
/app/.texlive/texmf-dist/web2c/mktexnam: Need to update ?
mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input psyr
This is METAFONT, Version 2.7182818 (TeX Live 2017) (preloaded base=mf)

kpathsea: Running mktexmf psyr

! I can't find file `psyr'.
<*> \mode:=ljfour; mag:=1; nonstopmode; input psyr
                                                  
Please type another input file name
! Emergency stop.
<*> \mode:=ljfour; mag:=1; nonstopmode; input psyr
                                                  
Transcript written on mfput.log.
grep: psyr.log: No such file or directory
mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input psyr' failed to make psyr.tfm.
kpathsea: Appending font creation commands to missfont.log.
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

ashton314 · 2023-10-27T17:10:01Z

Alright, @lucaferranti I'm a little stuck on this: I'm not sure what this error is saying. Have you seen this before?

lucaferranti · 2023-10-27T20:22:21Z

10.2307/2317055 this is a review of The Art of Computer Programming, not the book itself. I'm having difficulty finding a DOI for the second volume; we have the ISBN in the bibtex file; can we ask the citation generation format to put the ISBN in instead?

The references check is not perfect and can have some false-positives sometimes (like in this case). Great that you double-checked! If you find no DOI, it's ok to leave it this way.

LaTeX error

ouch, those can be a bit challenging sometimes.

are you able to compile the paper locally with latexmk ? Does your paper rely on any fancy library / font installed in your system? If yes, those should be included in the source code too, since on CI we only use plain latexmk.

I have not seen that specific error before, but it seems to indicate that some file (maybe some font) is missing.

Googling your error, I found this: https://www.mrunix.de/forums/showthread.php?61988-pdflatex-psyr-und-pcrr7t-not-found (discussion is in German unfortunately, but google translate apparently can translate the page pretty well), which seems to indeed to refer to some missing fonts.

You don't import many packages in the paper

\usepackage{amsmath}
\usepackage{cleveref}
\usepackage{microtype}
\usepackage{pifont}

and amsmath is unlikely to be the issue. So some of those packages is needing something that latexmk does not have by default. Given the error mentions some fonts, my uneducated guess would be to start with pifont, but not sure. Could you try if removing that (and the parts in the paper that rely on it) fixes the error? If it works, then we found the issue, otherwise we can do some more debugging.

Here a quick debugging I could get done on Friday night, hopefully it helps. Let me know how this proceeds. :)

ashton314 · 2023-10-27T20:50:59Z

references check

Well, it was very helpful with the other two missing DOIs that it found!

I can build the paper locally with latexmk, as can the rest of my team. I'll see what exactly the pifont package is doing. Someone else added that.

(I actually speak German, so that page was very helpful! :)

ashton314 · 2023-10-27T20:58:04Z

Looks like the pifont package makes the postscript dingbats accessible. My guess is the font files that it needs are not installed wherever Whedon runs.

Do you know of a way to add fonts? I suppose I could just drop the font file in the repo but that seems a little… overkill. I don't really like the default fonts anyway… I'd love it if I could use JuliaMono for the code samples—it'd be appropriate, no?

arfon · 2024-03-24T07:52:53Z

@editorialbot commands

editorialbot · 2024-03-24T07:52:56Z

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


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set juliacon-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

arfon · 2024-03-24T07:53:45Z

@editorialbot generate pdf

lucaferranti · 2024-03-24T08:02:25Z

I should maybe also point out that this submission has a bit of a peculiar structure, in the sense that the paper is not a paper/ folder in a software repository, but its own repository, so paper.tex etc. are in the base directory, maybe this breaks the workflow? I still don't understand why it doesn't post a comment about the failure, like in other issues. Looking at the actions: https://github.com/JuliaCon/proceedings-papers/actions it seems for this one it does not even start the generation

arfon · 2024-03-24T08:04:00Z

@lucaferranti - it looks like the migration of all of the review issues only happened for the ones under active review (i.e., not pre-reviews) so I think we need @xuanxu to re-run his script for the issues like this one as the metadata structure at the top of the issue is currently incorrect.

lucaferranti · 2024-03-24T08:06:47Z

cool, thank you for the help in debugging!

xuanxu · 2024-04-09T10:36:11Z

@editorialbot generate pdf

editorialbot · 2024-04-09T10:38:16Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

lucaferranti · 2024-04-09T11:08:44Z

@ashton314 new infra ready and paper compilation working 🎉

It seems the paper is missing hte references, could you look into it

lucaferranti · 2024-04-09T14:00:19Z

Hi @JeffreySarnoff 👋 ,

would you be interested in reviewing this submission for the JuliaCon proceedings? You can find reviewer instructions here and you are of course also welcome to ask any questions you may have.

lucaferranti · 2024-04-09T14:02:23Z

Hi @JeffreySarnoff 👋 ,

would you be interested in reviewing this submission for the JuliaCon proceedings? You can find reviewer instructions here and you are of course also welcome to ask any questions you may have.

lucaferranti · 2024-04-09T14:02:48Z

Hi @oscardssmith 👋 ,

would you be interested in reviewing this submission for the JuliaCon proceedings? You can find reviewer instructions here and you are of course also welcome to ask any questions you may have.

bennn · 2024-04-10T03:42:57Z

@editorialbot generate pdf

editorialbot · 2024-04-10T03:53:50Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

bennn · 2024-04-10T17:20:27Z

Thanks everybody + robot, the PDF looks great now!

JeffreySarnoff · 2024-04-10T20:49:36Z

This is nice work, and much appreciated. With regard to "8-bit formats are on the rise", please consider adding this reference:
P3109 Interim Report. That file will continue to be updated periodically, while the link remains the same. Here is additional information on IEEE P3109.

lucaferranti · 2024-04-11T11:42:11Z

@JeffreySarnoff , does this mean you are interested in reviewing this submission?

This issue is at the moment a pre-review, once I find two reviewers, I will start a review issue, where reviewers will have a checklist of things to check and can leave feedback.

Reviewing for JuliaCon proceedings is in general more lightweight (and enjoyable) than normal academic reviews. :)

JeffreySarnoff · 2024-04-11T13:12:10Z

sure

lucaferranti · 2024-04-11T13:47:43Z

@editorialbot add @JeffreySarnoff as reviewer

editorialbot · 2024-04-11T13:47:47Z

@JeffreySarnoff added to the reviewers list!

lucaferranti · 2024-04-11T13:48:18Z

Thanks Jeff, review will start once I find a second reviewer

JeffreySarnoff · 2024-04-11T14:15:44Z

ok .. let me know

…

On Thu, Apr 11, 2024 at 9:48 AM Luca Ferranti ***@***.***> wrote: Thanks Jeff, review will start once I find a second reviewer — Reply to this email directly, view it on GitHub <#135 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAM2VRTI36ILESXN2YFO6RDY42IDPAVCNFSM6AAAAAA6SWKNBCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBZG4ZTMMZSGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

lucaferranti · 2024-04-25T17:07:17Z

Found a second reviewer! 🎉

lucaferranti · 2024-04-25T17:07:24Z

@editorialbot add @dpsanders as reviewer

editorialbot · 2024-04-25T17:07:27Z

@dpsanders added to the reviewers list!

lucaferranti · 2024-04-25T17:07:56Z

@editorialbot start review

editorialbot · 2024-04-25T17:08:00Z

OK, I've started the review over in #148.

whedon added the pre-review label Oct 27, 2023

whedon added the Julia label Oct 27, 2023

whedon added Makefile TeX labels Oct 27, 2023

whedon assigned lucaferranti Oct 27, 2023

editorialbot assigned JeffreySarnoff Apr 11, 2024

editorialbot assigned dpsanders Apr 25, 2024

editorialbot closed this as completed Apr 25, 2024

[PRE REVIEW]: FlowFPX: Nimble Tools for Debugging Floating-Point Exceptions #135

[PRE REVIEW]: FlowFPX: Nimble Tools for Debugging Floating-Point Exceptions #135

Comments

whedon commented Oct 27, 2023 • edited by editorialbot

whedon commented Oct 27, 2023

whedon commented Oct 27, 2023

whedon commented Oct 27, 2023

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ashton314 commented Oct 27, 2023 • edited

ashton314 commented Oct 27, 2023

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ashton314 commented Oct 27, 2023

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ashton314 commented Oct 27, 2023

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arfon commented Mar 24, 2024

editorialbot commented Mar 24, 2024

arfon commented Mar 24, 2024

lucaferranti commented Mar 24, 2024

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xuanxu commented Apr 9, 2024

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bennn commented Apr 10, 2024

editorialbot commented Apr 10, 2024

bennn commented Apr 10, 2024

JeffreySarnoff commented Apr 10, 2024

lucaferranti commented Apr 11, 2024 • edited

JeffreySarnoff commented Apr 11, 2024

lucaferranti commented Apr 11, 2024

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JeffreySarnoff commented Apr 11, 2024 via email

lucaferranti commented Apr 25, 2024

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editorialbot commented Apr 25, 2024

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editorialbot commented Apr 25, 2024

whedon commented Oct 27, 2023 •

edited by editorialbot

ashton314 commented Oct 27, 2023 •

edited

lucaferranti commented Apr 11, 2024 •

edited