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[REVIEW]: Basic Threading Examples in JuliaLang v1.3 #54

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9 of 42 tasks
whedon opened this issue Sep 24, 2019 · 50 comments
Closed
9 of 42 tasks

[REVIEW]: Basic Threading Examples in JuliaLang v1.3 #54

whedon opened this issue Sep 24, 2019 · 50 comments

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@whedon
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@whedon whedon commented Sep 24, 2019

Submitting author: @vtjnash (Jameson Nash)
Repository: https://github.com/vtjnash/JuliaCon2019Threading
Editor: @vchuravy
Reviewer: @ArchRobison, @wsmoses
Archive: 10.5281/zenodo.4480494

Status

status

Status badge code:

HTML: <a href="https://submissions.juliacon.org/papers/9ac8bda44df0efa04afdfba84cb90c9e"><img src="https://submissions.juliacon.org/papers/9ac8bda44df0efa04afdfba84cb90c9e/status.svg"></a>
Markdown: [![status](https://submissions.juliacon.org/papers/9ac8bda44df0efa04afdfba84cb90c9e/status.svg)](https://submissions.juliacon.org/papers/9ac8bda44df0efa04afdfba84cb90c9e)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ArchRobison & @wsmoses , please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/JuliaCon/proceedings-reviews/invitations

The reviewer guidelines are available here: https://proceedings.juliacon.org/guide/reviewers. Any questions/concerns please let @vchuravy know.

Please try and complete your review in the next two weeks

Review checklist for @ArchRobison

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Authorship: Has the submitting author (@vtjnash) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Paper format

  • Authors: Does the paper.tex file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
  • Page limit: Is the page limit for full papers respected by the submitted document?

Content

  • Context: is the scientific context motivating the work correctly presented?
  • Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
  • Results: are the results presented and compared to approaches with similar goals?

Review checklist for @wsmoses

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Authorship: Has the submitting author (@vtjnash) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Paper format

  • Authors: Does the paper.tex file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
  • Page limit: Is the page limit for full papers respected by the submitted document?

Content

  • Context: is the scientific context motivating the work correctly presented?
  • Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
  • Results: are the results presented and compared to approaches with similar goals?
@whedon
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@whedon whedon commented Sep 24, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ArchRobison, @wsmoses it looks like you're currently assigned to review this paper 🎉.

Important

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/JuliaCon/proceedings-review) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/JuliaCon/proceedings-review:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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
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@whedon whedon commented Sep 24, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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@whedon whedon commented Sep 24, 2019

PDF failed to compile for issue #54 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/54 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-efe915e61673/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

@vchuravy
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@vchuravy vchuravy commented Sep 24, 2019

@vchuravy
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@vchuravy vchuravy commented Sep 24, 2019

@whedon generate pdf

@whedon
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@whedon whedon commented Sep 24, 2019

Attempting PDF compilation. Reticulating splines etc...

@vchuravy
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@vchuravy vchuravy commented Sep 24, 2019

@whedon commands

@whedon
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@whedon whedon commented Sep 24, 2019

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

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

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

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

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to accept the paper and deposit with Crossref
@whedon accept

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

@whedon
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@whedon whedon commented Sep 24, 2019

@vtjnash
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@vtjnash vtjnash commented Nov 27, 2019

@whedon generate pdf

@whedon
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@whedon whedon commented Nov 27, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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@whedon whedon commented Nov 27, 2019

@vtjnash
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@vtjnash vtjnash commented Dec 5, 2019

@whedon generate pdf

@whedon
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@whedon whedon commented Dec 5, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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@whedon whedon commented Dec 5, 2019

@vtjnash
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@vtjnash vtjnash commented Dec 22, 2019

Is there anything else I need to do? I think I've adopted and incorporated all of Arch's feedback and made it better.

@vtjnash
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@vtjnash vtjnash commented Feb 12, 2020

Am I supposed to bump this? I'm not really sure what its status is or who it's waiting on.

@wsmoses
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@wsmoses wsmoses commented Jun 8, 2020

@vtjnash Do you need to @sync in the merge sort example before merging or am I missing something.

@vtjnash
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@vtjnash vtjnash commented Jun 8, 2020

No, that's implied in the fetch

@wsmoses
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@wsmoses wsmoses commented Jun 8, 2020

Ah that makes sense, in any case here's a more full review/set of comments:

This paper presents a mechanism of embedding dynamic task-based parallelism into the Julia language, allowing Julia programs to benefit from parallelism as distinct from existing Julia mechanisms from concurrency. The core of this contribution is a new scheduler with frontend modifications that allow several front-end improvements to make it easier to use this model. The authors also describe several changes to language constructs needed to integrate their framework with arbitrary code, including a demonstration of using external libraries with their framework.

The authors present several demonstrations of programs (merge sort, number sieve, and a prefix scan), that could benefit from the task-parallelism that they now permit. The additional syntax, while demonstrated in code blocks, isn't explained well for new users hoping to take advantage of it (e.g. no description of @sync/fetch, ambiguity about the guarantees provided by @Spawn).

The authors allude to several limitations in existing Julia threading primitives. There isn't a good description of why the existing threading primitives couldn't be used on the demonstration codes (though I can see why this would be difficult). It would also be useful to do a performance comparison between the new runtime and old systems on some mutually compatible code. This comparison, along with perhaps showing the serial runtime [e.g. without parallel constructs rather than 1-core with parallel constructs] would be helpful to demonstrate that the new runtime doesn't provide significant overhead.

It would also be desirable to provide more quantifiable justification of their performance on FFTW than simply claiming it to be competitive (which is somewhat unclear). The authors should also include additional reference to related work in the field (e.g. existing parallel runtimes, including those outside of Julia) and describe the similarities and differences between prior art and the runtime described in this paper.

As a minor point (and I'm not the most familiar with the types of papers in this venue so take this with a grain of salt): some of the wording e.g. "but on to even more fun stuff..." could be tightened up for a professional audience.

Overall this paper represents a significant contribution to the Julia community in improving the experience of writing high performance parallel code. There are some additional changes to the writeup that would aid in fully demonstrating this contribution.

@vchuravy
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@vchuravy vchuravy commented Jul 27, 2020

@whedon check references

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@whedon whedon commented Jul 27, 2020

Reference check summary:

OK DOIs

- 10.1007/978-3-319-20119-1_10 is OK
- 10.1145/2807591.2807602 is OK
- 10.1145/1248377.1248396 is OK
- 10.1145/359576.359585 is OK
- 10.1145/361020.361216 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@vchuravy
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@vchuravy vchuravy commented Jul 27, 2020

Thank you @wsmoses for your review.

@vtjnash thank you for your patience can you address the reviewer comments and is there an archival DOI that you would like to associate with the publication?

@vtjnash
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@vtjnash vtjnash commented Aug 18, 2020

@whedon generate pdf

@whedon
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@whedon whedon commented Aug 18, 2020

@vtjnash
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@vtjnash vtjnash commented Aug 28, 2020

I don't have an archival DOI, but don't think it'll be useful for this. I think Kiran and I have improved the paper based on the reviewer's comments.

@vtjnash
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@vtjnash vtjnash commented Oct 29, 2020

What's next for us?

@vchuravy
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@vchuravy vchuravy commented Jan 14, 2021

@whedon commands

@whedon
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@whedon whedon commented Jan 14, 2021

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

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

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

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

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# 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

EiC TASKS

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

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

@vchuravy
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@vchuravy vchuravy commented Jan 14, 2021

@whedon accept

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@whedon whedon commented Jan 14, 2021

No archive DOI set. Exiting...

@vchuravy
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@vchuravy vchuravy commented Jan 14, 2021

don't have an archival DOI, but don't think it'll be useful for this.

Can you create one with the example code being used?

@vchuravy
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@vchuravy vchuravy commented Jan 28, 2021

@whedon remind @vtjnash in 1 week

@whedon
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@whedon whedon commented Jan 28, 2021

Reminder set for @vtjnash in 1 week

@vtjnash
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@vtjnash vtjnash commented Jan 30, 2021

@whedon set 10.5281/zenodo.4480494 as archive
@whedon generate pdf

@whedon
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@whedon whedon commented Jan 30, 2021

I'm sorry @vtjnash, I'm afraid I can't do that. That's something only editors are allowed to do.

@vchuravy
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@vchuravy vchuravy commented Jan 30, 2021

@whedon set 10.5281/zenodo.4480494 as archive

@whedon
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@whedon whedon commented Jan 30, 2021

OK. 10.5281/zenodo.4480494 is the archive.

@vchuravy
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@vchuravy vchuravy commented Jan 30, 2021

@whedon generate pdf

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@whedon whedon commented Jan 30, 2021

@vchuravy
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@vchuravy vchuravy commented Jan 30, 2021

@whedon check references

@whedon
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@whedon whedon commented Jan 30, 2021

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

OK DOIs

- 10.1007/978-3-319-20119-1_10 is OK
- 10.1145/2807591.2807602 is OK
- 10.1145/1248377.1248396 is OK
- 10.1145/359576.359585 is OK
- 10.1145/361020.361216 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@vchuravy
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@vchuravy vchuravy commented Jan 30, 2021

@whedon accept

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@whedon whedon commented Jan 30, 2021

Attempting dry run of processing paper acceptance...

@whedon
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@whedon whedon commented Jan 30, 2021

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

OK DOIs

- 10.1007/978-3-319-20119-1_10 is OK
- 10.1145/2807591.2807602 is OK
- 10.1145/1248377.1248396 is OK
- 10.1145/359576.359585 is OK
- 10.1145/361020.361216 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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@whedon whedon commented Jan 30, 2021

👋 @JuliaCon/jcon-eics, this paper is ready to be accepted and published.

Check final proof 👉 JuliaCon/proceedings-papers#37

If the paper PDF and Crossref deposit XML look good in JuliaCon/proceedings-papers#37, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@vchuravy
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@vchuravy vchuravy commented Jan 30, 2021

@whedon accept deposit=true

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@whedon whedon commented Jan 30, 2021

Doing it live! Attempting automated processing of paper acceptance...

@whedon
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@whedon whedon commented Jan 30, 2021

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JCON! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 JuliaCon/proceedings-papers#38
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/jcon.00054
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@vchuravy vchuravy closed this Jan 30, 2021
@whedon
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@whedon whedon commented Jan 30, 2021

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://proceedings.juliacon.org/papers/10.21105/jcon.00054/status.svg)](https://doi.org/10.21105/jcon.00054)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jcon.00054">
  <img src="https://proceedings.juliacon.org/papers/10.21105/jcon.00054/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://proceedings.juliacon.org/papers/10.21105/jcon.00054/status.svg
   :target: https://doi.org/10.21105/jcon.00054

This is how it will look in your documentation:

DOI

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