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

[whedon]

Submitting author: !--author-handle-->@ashton314<!--end-author-handle-- (Ashton Wiersdorf) Repository: https://github.com/utahplt/juliacon2023-paper Branch with paper.md (empty if default branch): Version: Editor: !--editor-->@lucaferranti<!--end-editor-- 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:

@whedon commands

[whedon]

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

:warning: JOSS reduced service mode :warning:

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]

Failed to discover a Statement of need section in paper

[whedon]

Wordcount for paper.tex is 4721

[whedon]

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]

Failed to discover a valid open source license.

[whedon]

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]

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]

@whedon assign @lucaferranti as editor

[whedon]

OK, the editor is @lucaferranti

[lucaferranti]

HI @ashton314, :wave:

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]

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]

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]

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]

@whedon commands

[whedon]

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]

@whedon generate pdf

[whedon]

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]

@whedon generate pdf

[whedon]

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]

@whedon generate pdf

[whedon]

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]

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

[lucaferranti]

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]

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]

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?

[ashton314]

@whedon generate pdf

[whedon]

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: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
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]

Ok, I've found a workaround for the missing fonts; we just needed an "x" and a checkmark character from the dingbats; I've hacked around that. Now something's wrong with the citations. I can take a look at this more later, but maybe you'd be able to see something right away that's wrong?

[lucaferranti]

Oh gosh, it seems like it does not build the bibilography, since the references don't work.

I am not sure why that happens, fwiw, I could build the paper locally.

I see you have a Makefile with content

paper.pdf: paper.tex ref.bib
    latexmk -bibtex -pdf paper.tex

.PHONY: clean
clean:
    latexmk -c && rm paper.bbl

I am not sure the paper.bbl should be removed though :thinking:

This is just a weak hunch, but maybe Whedon automatically detects the Makefile (which does not come with the template), and runs that, which messes up the bot workflow. Could try

1. Removing the rm paper.bbl OR
2. Removing the Makefile

I know it's a pretty weak guess, but it's the only thing I can think of rn.

(we are in the process of updating the infrastructure, and the process should become much smoother in the foreseable future, but we are not quite there yet, sorry for the inconvenience)

[ashton314]

@whedon generate pdf

[whedon]

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: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
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]

@lucaferranti I've removed the Makefile from the repo (well, moved it to something not called Makefile) and Whedon still isn't happy. The .bbl file isn't checked into our repo anyway.

[ashton314]

Pinging @bennn for visibility

[lucaferranti]

oh my, I'll try to have a closer look. The process should be much smoother (or at least easier to debug) once we complete the infrastructure update, let's see which one I get done first :)

Some random ideas:

• I see from the error message that on CI latexmk v4.55 is used, which is a bit old. Which version are you using locally to build the paper? Maybe the older version does not support some formatting in the .bib file?

[ashton314]

➤ ~ latexmk --version
Latexmk, John Collins, 7 Jan. 2023. Version 4.79

I'm using what looks like a pretty up-to-date version. I think the most recent version is 4.80. Maybe I can try building with the older version of latexmk, but it will take me a minute to figure out how to install that older version.

Thanks so much for your help Luca!

[lucaferranti]

@whedon list reviewers

[whedon]

Here's the current list of reviewers: http://bit.ly/2V9GSFq

[lucaferranti]

A possible strategy to debug could be to comment out most references from the bibtex file and see if it works with a minimal set and gradually reinsert others. My suspect is that the older version does not support some bibtex features and this could help identify the problematic entries.

I am sorry for the incovenience with this, we are upgrading whedon to the new editorial-bot and that should fix all of these issues. Moreover, the new version will use texlive-full which should be fully battery included. The upgrade is going a bit slow, but getting there soon. You can either wait for us to upgrade the infrastructure or try to get latex to work with the old bot. I hope to wrap up the upgrade within a couple of weeks.

[bennn]

Thanks Luca. I'll try debugging the bib.

[bennn]

@whedon generate pdf

[whedon]

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: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
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

[bennn]

@whedon generate pdf

[whedon]

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: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `IEEEStandardBinary1985' on page 1 undefined on input line 140
  Citation `bllmg-xloop-2022' on page 1 undefined on input line 71
  Citation `ddghlllprr-correctness-2022' on page 1 undefined on input line 71
  Citation `fp8' on page 1 undefined on input line 109
  Citation `fpchecker-reports' on page 1 undefined on input line 71
  Citation `github-issues' on page 1 undefined on input line 78
  Citation `gllprt-correctness-2021' on page 1 undefined on input line 71
  Citation `humphreySystematicDebuggingMethods2014' on page 1 undefined on input line 90
  Citation `klowerLowprecisionClimateComputing2021' on page 1 undefined on input line 109
  Citation `knuthArtComputerProgramming1997' on page 1 undefined on input line 134
  Citation `llg-soap-2022' on page 1 undefined on input line 71
  Citation `llsflg-hpdc-2023' on page 1 undefined on input line 93
  Citation `mullerHandbookFloatingPointArithmetic2018' on page 1 undefined on input line 134
  Citation `p-draft-1997' on page 1 undefined on input line 142
  Citation `sdjmrstp-pc-2022' on page 1 undefined on input line 71
  Citation `torontoPracticallyAccurateFloatingPoint2014' on page 1 undefined on input line 134
  Reference `f:real-vs-fp' on page 1 undefined on input line 106
  Reference `s:background' on page 1 undefined on input line 67
  Reference `s:casestudies' on page 1 undefined on input line 83
  Reference `s:flowfpx' on page 1 undefined on input line 81
Latexmk: Summary of warnings:
  Latex failed to resolve 4 reference(s)
  Latex failed to resolve 16 citation(s)
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

[bennn]

@lucaferranti it still fails with an empty bib. I think we're blocked here until editorial-bot arrives.

[lucaferranti]

Hi @bennn and @ashton314 , have you noticed this issue? https://github.com/JuliaCon/JuliaConSubmission.jl/issues/34

it seems having underscore in the DOI may cause issues, maybe that's what broke compilation?

(side note, the infra update should be wrapped up within this month, so this should go forward pretty soon in a way or another)

[bennn]

Hi @lucaferranti , no I hadn't seen that, and we do have an underscore (an escaped one but still).

But, we had the same issue with an empty bib of zero references.

I think the intra update is what we need. Very excited for it!

[lucaferranti]

@editorialbot commands

[editorialbot]

Hello @lucaferranti, 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

# Reject paper
@editorialbot reject

# Withdraw paper
@editorialbot withdraw

# Invite an editor to edit a submission (sending them an email)
@editorialbot invite @(.*) as editor

# 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

# Accept and publish the paper
@editorialbot accept

# Update data on an accepted/published paper
@editorialbot reaccept

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

[lucaferranti]

@editorialbot generate pdf

[lucaferranti]

@editorialbot generate pdf