Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Closes #195: HPC vs reproducibility post #232

Merged
merged 20 commits into from
Oct 16, 2024
Merged

Closes #195: HPC vs reproducibility post #232

merged 20 commits into from
Oct 16, 2024

Conversation

AleKoure
Copy link
Contributor

@AleKoure AleKoure commented Sep 19, 2024 •
edited
Loading

Thank you for your Pull Request! We have developed this task checklist to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your blog post.

Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the main branch until you have checked off each task.

  • Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update), and make sure the corresponding issue is linked in the Development section on the right hand side
  • Ensure your new post folder is of the form "posts/zzz_DO_NOT_EDIT_<your post title>". This is so that the post date can be auto-updated upon the merge into main.
  • Run the script from CICD.R line by line to first check the spelling in your post and then to make sure your code is compatible with our code-style. Address any incongruences by following the instructions in the file!
  • Choose (possibly several) tag(s) or categories from the current list: c("Metadata", "SDTM", "ADaM", "TLG", "Shiny", "Community", "Conferences", "Submissions", "Technical") for your blog post. If you cannot find anything that fits your blog post, propose a new tag to the maintainers! Note: if you use a tag not from this list, the "Check Post Tags" CICD pipeline will error. We occasionally tidy up all tags for consistency.
  • Add a short description for your blog post in the description field at the top of the markdown document.
  • Blog post is short, personalized, reproducible and readable
  • Add a disclaimer at the top of your post, if appropriate (example: Disclaimer
    This blog contains opinions that are of the authors alone and do not necessarily reflect the strategy of their respective organizations.)
  • Address all merge conflicts and resolve appropriately
  • Assign two of us (@bms63, @manciniedoardo, @StefanThoma, @kaz462) as reviewers in the PR.
  • Pat yourself on the back for a job well done! Much love to your accomplishment!

@manciniedoardo manciniedoardo changed the title Draft: HPC vs reproducibility post (#195) Closes #195: HPC vs reproducibility post Sep 20, 2024
@manciniedoardo manciniedoardo linked an issue Sep 20, 2024 that may be closed by this pull request
Blog Post: The Tension of High-Performance Computing: Reproducibility vs. Parallelization #195
Closed
manciniedoardo
manciniedoardo requested changes Sep 20, 2024
View reviewed changes
Copy link
Collaborator

@manciniedoardo manciniedoardo left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for the post @AleKoure - it's super interesting. I've left some minor suggestions. Wondering if we can also put in a couple more references to pharma/statistical programming in order to fit in even more within the "pharmaverse" sphere?

@bms63 @StefanThoma thoughts?

Also please review the failing CICD checks for spelling and code style.

....../the__tension_of__high-_performance__computing:__reproducibility_vs.__parallelization.qmd Outdated Show resolved Hide resolved
....../the__tension_of__high-_performance__computing:__reproducibility_vs.__parallelization.qmd Outdated Show resolved Hide resolved
....../the__tension_of__high-_performance__computing:__reproducibility_vs.__parallelization.qmd Outdated Show resolved Hide resolved
@AleKoure AleKoure mentioned this pull request Sep 24, 2024
Closed
manciniedoardo
manciniedoardo requested changes Sep 30, 2024
View reviewed changes
Copy link
Collaborator

@manciniedoardo manciniedoardo left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for the updates! I've left one other comment about defining demons.

On a broader note, I didn't notice any mention of the pharmaverse or any pharmaverse packages. As this is the pharmaverseblog I am wondering if you could please adapt your post slightly for a pharmaverse-minded audience? E.g.: How is this discussion relevant to:

  • pharmaverse packages
  • The E2E clinical data flow in R

Thanks in advance.

....../the__tension_of__high-_performance__computing:__reproducibility_vs.__parallelization.qmd Outdated Show resolved Hide resolved
StefanThoma
StefanThoma requested changes Oct 1, 2024
View reviewed changes
Copy link
Collaborator

@StefanThoma StefanThoma left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Great post!
Please try out https://github.com/pharmaverse/logrx and see if you could use that instead 👍

....../the__tension_of__high-_performance__computing:__reproducibility_vs.__parallelization.qmd Outdated Show resolved Hide resolved
....../the__tension_of__high-_performance__computing:__reproducibility_vs.__parallelization.qmd Outdated Show resolved Hide resolved
....../the__tension_of__high-_performance__computing:__reproducibility_vs.__parallelization.qmd Show resolved Hide resolved
@AleKoure
Copy link
Contributor Author

AleKoure commented Oct 8, 2024 •
edited
Loading

Thanks for the updates! I've left one other comment about defining demons.

On a broader note, I didn't notice any mention of the pharmaverse or any pharmaverse packages. As this is the pharmaverseblog I am wondering if you could please adapt your post slightly for a pharmaverse-minded audience? E.g.: How is this discussion relevant to:

  • pharmaverse packages
  • The E2E clinical data flow in R

Thanks in advance.

@manciniedoardo Good points! I added some amendments.

As @StefanThoma also suggested:

  • We use the Pharmavese package logrx to show some complexities in workflow execution.

  • We add some additional clarity to the drug efficacy simulation

@manciniedoardo
Copy link
Collaborator

Thanks @AleKoure for your updates! for me we can go ahead and merge if conflicts are resolved and @StefanThoma is happy.

StefanThoma
StefanThoma approved these changes Oct 11, 2024
View reviewed changes
Copy link
Collaborator

@StefanThoma StefanThoma left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Great post IMO!

@manciniedoardo
Copy link
Collaborator

@AleKoure could you please fix the failing style check?

@AleKoure
Copy link
Contributor Author

AleKoure commented Oct 11, 2024 via email

@AleKoure
Copy link
Contributor Author

@AleKoure could you please fix the failing style check?

I have resolved the checks and after @shikokuchuo's suggestion, I included a minor update for mirai version 1.3.0. Additionally, I added my affiliation.

@manciniedoardo
Copy link
Collaborator

@AleKoure if you fix the final failing link we can go ahead and merge

@manciniedoardo manciniedoardo merged commit 77dc96f into pharmaverse:main Oct 16, 2024
5 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@manciniedoardo manciniedoardo manciniedoardo approved these changes

@StefanThoma StefanThoma StefanThoma approved these changes

@bms63 bms63 Awaiting requested review from bms63

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Blog Post: The Tension of High-Performance Computing: Reproducibility vs. Parallelization
3 participants
@AleKoure @manciniedoardo @StefanThoma