[REVIEW]: SCAS dashboard: A tool to intuitively and interactively analyze Slurm cluster usage

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@wathom@danielskatz<!--end-editor-- Reviewers: @aturner-epcc, @phargogh Archive: 10.5281/zenodo.10064783

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Reviewer instructions & questions

@aturner-epcc & @apjez & @verolero86, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

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Checklists

📝 Checklist for @aturner-epcc

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=2.31 s (14.7 files/s, 1937.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                5            437            272           1429
Python                          13            280            349           1037
Markdown                         4             59              0            300
YAML                             3              7              8            126
TeX                              1              4              0             46
Dockerfile                       3             22             19             42
CSS                              1              3              0             14
Bourne Shell                     3              1              2             10
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            34            813            650           3005
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1500

editorialbot commented 1 year ago

Failed to discover a Statement of need section in paper

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/10968987_3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

danielskatz commented 1 year ago

@aturner-epcc, @apjez, and @verolero86 - Thanks for agreeing to review this submission. This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6017 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

danielskatz commented 1 year ago

@wathom - To fix the editorialbot complaint about not finding a Statement of need section, I'm suggesting some changes to how section headings are formatted in https://github.com/Bioinformatics-Munich/scas_dashboard/pull/1 - this is what JOSS papers typically use, and I don't think it makes any difference to the formatted PDF, other than that I've promoted the conclusions header to a 1st level heading. If this seems ok, please merge it.

wathom commented 1 year ago

Dear @danielskatz - many thanks, I merged the pull request.

wathom commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

danielskatz commented 1 year ago

👋 @aturner-epcc, @apjez, and @verolero86, if you could please create your checklist typing: @editorialbot generate my checklist, and check off the two items (code of conduct and COIs), I would appreciate it.

apjez commented 1 year ago

Review checklist for @apjez

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Bioinformatics-Munich/scas_dashboard?
[x] 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 (@wathom) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] 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?

aturner-epcc commented 1 year ago

Review checklist for @aturner-epcc

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Bioinformatics-Munich/scas_dashboard?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wathom) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

danielskatz commented 11 months ago

👋 @verolero86, if you could please create your checklist typing: @editorialbot generate my checklist, and check off the two items (code of conduct and COIs), I would appreciate it.

danielskatz commented 11 months ago

👋 @aturner-epcc and @apjez, how are things coming along in your reviews?

verolero86 commented 11 months ago

Review checklist for @verolero86

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Bioinformatics-Munich/scas_dashboard?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wathom) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] 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?

danielskatz commented 11 months ago

👋 @aturner-epcc, @apjez, and @verolero86, I just wanted to check in with you to see how your reviews are coming, and if there's anything blocking your progress I can help with.

aturner-epcc commented 11 months ago

@wathom I see an failure using the installation instructions provided right at the start.

Build and start containers

Build images an run docker-compose to start the containers (nginx, frontend, backend, postgres):
To build: docker compose build

~/temp/joss/scas_dashboard/docker main                                                                                                                                                                          3.9.16 anaconda3 aturner@MBP-AT
❯ docker compose build
[+] Building 1.3s (3/3) FINISHED                                                                                                                                                                                           docker:desktop-linux
 => [scas-backend internal] load build definition from Dockerfile                                                                                                                                                                          0.0s
 => => transferring dockerfile: 1.32kB                                                                                                                                                                                                     0.0s
 => [scas-backend internal] load .dockerignore                                                                                                                                                                                             0.0s
 => => transferring context: 2B                                                                                                                                                                                                            0.0s
 => ERROR [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5                                                                                                                                                           1.2s
------
 > [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5:
------
failed to solve: rocker/shiny:4.0.5: no match for platform in manifest sha256:4e68438dc5a553b440e148ba04832007a6949361c4c9796c042599a7b2444285: not found

Am I doing something wrong or missing a step?

aturner-epcc commented 11 months ago

@wathom The link to the API documentation seems invalid. It is listed as: https://yourserver.edu/docs/ (this does not exist) Ah! just a minute. Is this only available when you have the framework running? Can the API docs be hosted in such a way that they are accessible without having to run the service?

aturner-epcc commented 11 months ago

@wathom As well as the two issues above, I think the following items are missing from the submission (happy to be pointed at them if I have missed them):

State of the field: Do the authors describe how this software compares to other commonly-used packages?

I see mention of integration with tools like Graphana but expcted to see notes on how this compares to other commonly used tools in this area such as OpenXDMoD and Open OnDemand.

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

This does not seem to really be present other than "Submit an issue". What level of support can be expected (e.g. this is not funded so we will do our best in our spare time)? Are there any contribution guidelines or coding styles that need to be adhered to? What level of information is required for Issues or PRs?

wathom commented 11 months ago

Dear @aturner-epcc, Many thanks for your comments, we will address them. The API documentation is now available also here: https://bioinformatics-munich.github.io/scas_dashboard_api_documentation and the link has been added to the readme.

wathom commented 11 months ago

@wathom I see an failure using the installation instructions provided right at the start.

Build and start containers

Build images an run docker-compose to start the containers (nginx, frontend, backend, postgres): To build: docker compose build

~/temp/joss/scas_dashboard/docker main                                                                                                                                                                          3.9.16 anaconda3 aturner@MBP-AT
❯ docker compose build
[+] Building 1.3s (3/3) FINISHED                                                                                                                                                                                           docker:desktop-linux
 => [scas-backend internal] load build definition from Dockerfile                                                                                                                                                                          0.0s
 => => transferring dockerfile: 1.32kB                                                                                                                                                                                                     0.0s
 => [scas-backend internal] load .dockerignore                                                                                                                                                                                             0.0s
 => => transferring context: 2B                                                                                                                                                                                                            0.0s
 => ERROR [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5                                                                                                                                                           1.2s
------
 > [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5:
------
failed to solve: rocker/shiny:4.0.5: no match for platform in manifest sha256:4e68438dc5a553b440e148ba04832007a6949361c4c9796c042599a7b2444285: not found

Am I doing something wrong or missing a step?

@aturner-epcc Is this error still present, unfortunatley I can't reproduce it on my platforms.

aturner-epcc commented 11 months ago

@wathom I see an failure using the installation instructions provided right at the start.

Build and start containers

Build images an run docker-compose to start the containers (nginx, frontend, backend, postgres): To build: docker compose build

~/temp/joss/scas_dashboard/docker main                                                                                                                                                                          3.9.16 anaconda3 aturner@MBP-AT
❯ docker compose build
[+] Building 1.3s (3/3) FINISHED                                                                                                                                                                                           docker:desktop-linux
 => [scas-backend internal] load build definition from Dockerfile                                                                                                                                                                          0.0s
 => => transferring dockerfile: 1.32kB                                                                                                                                                                                                     0.0s
 => [scas-backend internal] load .dockerignore                                                                                                                                                                                             0.0s
 => => transferring context: 2B                                                                                                                                                                                                            0.0s
 => ERROR [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5                                                                                                                                                           1.2s
------
 > [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5:
------
failed to solve: rocker/shiny:4.0.5: no match for platform in manifest sha256:4e68438dc5a553b440e148ba04832007a6949361c4c9796c042599a7b2444285: not found

Am I doing something wrong or missing a step?

@aturner-epcc Is this error still present, unfortunatley I can't reproduce it on my platforms.

Yes, it is still an issue for me. I think I know what the issue is though. A bit of further digging shows that rocker only provide x86 container images. As I am using an M1 Mac (Arm processor) this is what is causing the error here. I am now testing if I can make this work through Rosetta by setting:

export DOCKER_DEFAULT_PLATFORM=linux/amd64

before the docker compose command

aturner-epcc commented 11 months ago

I have verified that I can perform all the testing using the export DOCKER_DEFAULT_PLATFORM=linux/amd64 option before running the docker compose command. @wathom It may be worth adding a note to the README on this. Do you want to do this or do you want me to submit a PR?

danielskatz commented 10 months ago

👋 @wathom - please do respond to @aturner-epcc's question 👆

danielskatz commented 10 months ago

👋 @apjez and @verolero86 - I'm just checking in post-holidays on how your reviews are going. I look forward to seeing progress, or some discussion about what's blocking you.

verolero86 commented 10 months ago

thanks for the ping @danielskatz - wrapping up EOY activities took many more cycles than expected, but now that those deadlines are behind me, I'll be able to continue the review.

wathom commented 10 months ago

Dear all, Happy new year!

I have verified that I can perform all the testing using the export DOCKER_DEFAULT_PLATFORM=linux/amd64 option before running the docker compose command. @wathom It may be worth adding a note to the README on this. Do you want to do this or do you want me to submit a PR?

Dear @aturner-epcc, Many thanks for testing this and for providing the solution. I am happy if you add the info and if you create a PR. Otherwise I can also add the info, just let me know.

Dear @verolero86, Many thanks, looking forward to your comments.

danielskatz commented 10 months ago

@aturner-epcc - Did you see @wathom's response above?

danielskatz commented 10 months ago

👋 @apjez & @verolero86 - how are your reviews coming?

danielskatz commented 9 months ago

👋 @aturner-epcc, @apjez, @verolero86 - just a ping on keeping your reviews moving along... Thanks!!

danielskatz commented 9 months ago

note via email - @verolero86 feels she will be able to make progress soon

aturner-epcc commented 9 months ago

Sorry for the delay. PR created to address the Apple Silicon issue.

@wathom As far as I can see, the other two points I raised during my review have not been addressed. Repeating them here:

State of the field: Do the authors describe how this software compares to other commonly-used packages?

I see mention of integration with tools like Graphana but expcted to see notes on how this compares to other commonly used tools in this area such as OpenXDMoD and Open OnDemand.

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

This does not seem to really be present other than "Submit an issue". What level of support can be expected (e.g. this is not funded so we will do our best in our spare time)? Are there any contribution guidelines or coding styles that need to be adhered to? What level of information is required for Issues or PRs?

wathom commented 9 months ago

Dear @aturner-epcc,
Many thanks for adding the info and creating the PR, I merged it.
I will address you other points as soon as possible and once the other reviews are in (OpenXDMoD and Open OnDemand references).

danielskatz commented 9 months ago

@wathom - it's generally better practice in JOSS to make changes in response to one reviewer than to wait for other reviewers. This can make the job of other reviewers easier, too.

wathom commented 9 months ago

@wathom - it's generally better practice in JOSS to make changes in response to one reviewer than to wait for other reviewers. This can make the job of other reviewers easier, too.

Dear @danielskatz, Ok.

wathom commented 9 months ago

Dear @aturner-epcc

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 This does not seem to really be present other than "Submit an issue". What level of support can be expected (e.g. this is not funded so we will do our best in our spare time)? Are there any contribution guidelines or coding styles that need to be adhered to? What level of information is required for Issues or PRs?

I have added now community guidelines including Code of Conduct with the workflow how to contribute to the project, and templates for issue/bug reporting and for feature request. Please let me know if you have further suggestions on this topic.

danielskatz commented 9 months ago

👋 @apjez, @verolero86 - again, I'm just checking on your progress on this review. Please let us know how things are coming.

danielskatz commented 9 months ago

@aturner-epcc - Does @wathom's update help you complete your review?

danielskatz commented 9 months ago

👋 @apjez, @verolero86 - again, I'm just checking on your progress on this review. Please let us know how things are coming.

danielskatz commented 9 months ago

👋 @aturner-epcc - Does @wathom's update help you complete your review?

aturner-epcc commented 8 months ago

@wathom Thanks for adding these community guidelines. I have updated my review to note that this is now there.

@danielskatz I do not think there is anything else for me to do now

danielskatz commented 8 months ago

@aturner-epcc - there's one item on your checklist not checked off - can you check it off now?

danielskatz commented 8 months ago

👋 @apjez - How is your review coming? What's blocking you from checking off more items on your checklist?

danielskatz commented 8 months ago

👋 @verolero86 - How is your review coming? What's blocking you from checking off more items on your checklist?

wathom commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

wathom commented 8 months ago

Dear @aturner-epcc , @verolero86 , @apjez and @danielskatz
The manuscript was revised and comparisions and references for OpenXDMoD and Open OnDemand were added as suggested by @aturner-epcc.

danielskatz commented 8 months ago

For the record, I emailed @verolero86 and @apjez two days ago to remind them of this review.

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