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[REVIEW]: MyQueue: Task and workflow scheduling system #1844

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whedon opened this issue Oct 29, 2019 · 73 comments
Closed

[REVIEW]: MyQueue: Task and workflow scheduling system #1844

whedon opened this issue Oct 29, 2019 · 73 comments
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@whedon whedon commented Oct 29, 2019

Submitting author: @jjmortensen (Jens Jørgen Mortensen)
Repository: https://gitlab.com/myqueue/myqueue
Version: version-20.1.1
Editor: @danielskatz
Reviewer: @gonsie, @marksantcroos
Archive: 10.5281/zenodo.3607221

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/33edc00feaacaaaca2bb0e22011bb421"><img src="https://joss.theoj.org/papers/33edc00feaacaaaca2bb0e22011bb421/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/33edc00feaacaaaca2bb0e22011bb421/status.svg)](https://joss.theoj.org/papers/33edc00feaacaaaca2bb0e22011bb421)

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

@gonsie & @marksantcroos, 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/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

Please try and complete your review in the next two weeks

Review checklist for @gonsie

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@jjmortensen) 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 functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @marksantcroos

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@jjmortensen) 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 functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
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@whedon whedon commented Oct 29, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @gonsie, @marksantcroos 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/openjournals/joss-reviews) 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/openjournals/joss-reviews:

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
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@whedon whedon commented Oct 29, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 29, 2019

@danielskatz

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@danielskatz danielskatz commented Oct 29, 2019

👋 @gonsie, @marksantcroos - as I think you know, we'll do the review here. Your job is to work through the review checklists, checking off items or creating new issues 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.)

If you have any questions or problems, please let me know

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@gonsie gonsie commented Nov 6, 2019

Thanks for submission @jjmortensen. I've created some issues in the repo:

For the paper, could you include some details on how MyQueue compares with other tools? I think the most relevant tools would come from the workflow tools / managers.

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@danielskatz danielskatz commented Nov 6, 2019

👋 @marksantcroos - how are you doing on your review?

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@jjmortensen jjmortensen commented Nov 8, 2019

Thanks for the links. I'm familiar with Fireworks and Aiida. Will take a look ...

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@marksantcroos marksantcroos commented Nov 8, 2019

I've also started my review by going through installation and testing, but got stuck rather quickly.

Although I might be biased, these errors do trigger my "yet another workflow system that tries (and fails) to integrate with queuing systems".

Putting this out here for now, will continue the review and edit accordingly.

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@jjmortensen jjmortensen commented Nov 13, 2019

Thanks for all your comments so far. There is now a version 19.11.1 available on PyPI with some new features and bug-fixes. There is also an updated version of the paper. See:

https://myqueue.readthedocs.io/en/latest/releasenotes.html
https://gitlab.com/myqueue/myqueue/merge_requests/40

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@danielskatz danielskatz commented Nov 13, 2019

When you update the paper, please rebuild it here (using the following whedon command), as I am now going to do

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@danielskatz danielskatz commented Nov 13, 2019

@whedon generate pdf

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@whedon whedon commented Nov 13, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 13, 2019

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@gonsie gonsie commented Nov 21, 2019

This paper is still missing a ‘state of the field’ summary. Comparing MQ to Slurm/PBS is not the right level of comparison. It needs to be compared to other workflow tools.

In addition, the paper mentions that MQ was used to drive a study of 10,000 jobs. Please provide details on that. How did it handle this large number of jobs? What was the job limit enforced by the underlying scheduler? I believe that this may be the real contribution of MQ (rather than just a front end to a scheduler).

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@danielskatz danielskatz commented Nov 27, 2019

👋 @jjmortensen - note that there are some questions/actions for you here.

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@danielskatz danielskatz commented Nov 27, 2019

👋 @marksantcroos - Can you let us know how your review is proceeding? Are you stuck on anything?

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@jjmortensen jjmortensen commented Nov 28, 2019

We are looking into it ... in the meantime, @gonsie I added a small section on the web-page describing how to work with many jobs:

https://myqueue.readthedocs.io/en/latest/workflows.html#handling-very-many-tasks

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@mortengjerding mortengjerding commented Nov 29, 2019

@whedon generate pdf

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@whedon whedon commented Nov 29, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 29, 2019

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@mortengjerding mortengjerding commented Nov 29, 2019

We have now added a section describing the state of the field, where we compare MyQueue to AiiDA and Fireworks, trying to emphasize what MyQueue can/cannot do. Let us know if you have suggestions for further improvements.

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@marksantcroos marksantcroos commented Nov 29, 2019

I've worked some more with the software and got something out of it. Will go over the new pdf and report my findings.

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@danielskatz danielskatz commented Dec 6, 2019

@marksantcroos - thanks

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@danielskatz danielskatz commented Dec 10, 2019

@marksantcroos - any update?

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@jjmortensen jjmortensen commented Jan 11, 2020

@whedon generate pdf

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@whedon whedon commented Jan 11, 2020

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@jjmortensen jjmortensen commented Jan 11, 2020

Added the missing DOI and upper cased JSSPP

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@danielskatz danielskatz commented Jan 11, 2020

@whedon accept

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@whedon whedon commented Jan 11, 2020

No archive DOI set. Exiting...

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@danielskatz danielskatz commented Jan 11, 2020

At this point could you:

  • Make a tagged release of your software, and list the version tag of the archived version here.
  • Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

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@jjmortensen jjmortensen commented Jan 14, 2020

The MyQueue version is 20.1.1 and the tag name in the Git repository is "version-20.1.1":

https://gitlab.com/myqueue/myqueue/-/tags/version-20.1.1

I've uploaded an archive to Zenodo:

https://zenodo.org/record/3607221

The DOI is "10.5281/zenodo.3607221".

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@danielskatz danielskatz commented Jan 14, 2020

@whedon set version-20.1.1 as version

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@whedon whedon commented Jan 14, 2020

OK. version-20.1.1 is the version.

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@danielskatz danielskatz commented Jan 14, 2020

@whedon set 10.5281/zenodo.3607221 as archive

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@whedon whedon commented Jan 14, 2020

OK. 10.5281/zenodo.3607221 is the archive.

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@danielskatz danielskatz commented Jan 14, 2020

@whedon accept

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@whedon whedon commented Jan 14, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Jan 14, 2020

Reference check summary:

OK DOIs

- 10.1088/2053-1583/aacfc1 is OK
- 10.1007/10968987_3 is OK
- 10.26434/chemrxiv.9971054.v1 is OK
- 10.1002/cpe.3505 is OK
- https://doi.org/10.1016/j.commatsci.2015.09.013 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Jan 14, 2020

Check final proof 👉 openjournals/joss-papers#1214

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1214, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Jan 14, 2020

@whedon generate pdf

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@whedon whedon commented Jan 14, 2020

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@danielskatz danielskatz commented Jan 14, 2020

@whedon accept

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@whedon whedon commented Jan 14, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Jan 14, 2020

Reference check summary:

OK DOIs

- 10.1088/2053-1583/aacfc1 is OK
- 10.1007/10968987_3 is OK
- 10.26434/chemrxiv.9971054.v1 is OK
- 10.1002/cpe.3505 is OK
- https://doi.org/10.1016/j.commatsci.2015.09.013 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Jan 14, 2020

Check final proof 👉 openjournals/joss-papers#1215

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1215, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Jan 14, 2020

@whedon accept deposit=true

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@whedon whedon commented Jan 14, 2020

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Jan 14, 2020
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@whedon whedon commented Jan 14, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Jan 14, 2020

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1216
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01844
  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...

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@danielskatz danielskatz commented Jan 14, 2020

Thanks to @gonsie, @marksantcroos for reviewing!
And congratulations to @jjmortensen and coauthors!

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@whedon whedon commented Jan 14, 2020

🎉🎉🎉 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://joss.theoj.org/papers/10.21105/joss.01844/status.svg)](https://doi.org/10.21105/joss.01844)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01844">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01844/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01844/status.svg
   :target: https://doi.org/10.21105/joss.01844

This is how it will look in your documentation:

DOI

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