Skip to content

{bio}[foss/2022a] ColabFold v1.5.2, AlphaFold v2.3.4 w/ Python 3.10.4#17751

Merged
verdurin merged 3 commits intoeasybuilders:developfrom
lexming:20230418145246_new_pr_ColabFold152
Apr 25, 2023
Merged

{bio}[foss/2022a] ColabFold v1.5.2, AlphaFold v2.3.4 w/ Python 3.10.4#17751
verdurin merged 3 commits intoeasybuilders:developfrom
lexming:20230418145246_new_pr_ColabFold152

Conversation

@lexming
Copy link
Copy Markdown
Contributor

@lexming lexming commented Apr 18, 2023 •
edited
Loading

(created using eb --new-pr)

ColabFold relies on its own fork of AlphaFold. This PR adds:

  • easyconfigs for this AlphaFold fork with an extra -ColabFold versionsuffix
  • easyconfigs for the actual package of ColabFold

Depends on:

@lexming
adding easyconfigs: ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb, ColabF…
4512e49 
…old-1.5.2-foss-2022a.eb, AlphaFold-2.3.4-foss-2022a-ColabFold.eb, AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb and patches: AlphaFold-ColabFold-2.3.4_data-dep-paths.patch, AlphaFold-ColabFold-2.3.4_fix-scp-path.patch
@lexming lexming mentioned this pull request Apr 18, 2023
Closed
2 tasks
@boegelbot

This comment was marked as outdated.

Sign in to view
@easybuilders easybuilders deleted a comment from boegelbot Apr 19, 2023
@easybuilders easybuilders deleted a comment from boegelbot Apr 19, 2023
@lexming
Copy link
Copy Markdown
Contributor Author

lexming commented Apr 19, 2023

Test report by @lexming
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node401.hydra.os - Linux CentOS Linux 7.9.2009, x86_64, AMD EPYC 7282 16-Core Processor (zen2), 1 x NVIDIA NVIDIA A100-PCIE-40GB, 515.48.07, Python 3.6.8
See https://gist.github.com/lexming/d259af1c2d7ef689d5551e60431b8e61 for a full test report.

Micket
Micket approved these changes Apr 20, 2023
View reviewed changes
Copy link
Copy Markdown
Contributor

@Micket Micket left a comment

Choose a reason for hiding this comment

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

lgtm

@Micket
Copy link
Copy Markdown
Contributor

Micket commented Apr 20, 2023

@boegelbot please test @ generoso
EB_ARGS="AlphaFold-2.3.4-foss-2022a-ColabFold.eb ColabFold-1.5.2-foss-2022a.eb"

@Micket
Copy link
Copy Markdown
Contributor

Micket commented Apr 20, 2023

Test report by @Micket
SUCCESS
Build succeeded for 3 out of 3 (2 easyconfigs in total)
vera-c1 - Linux Rocky Linux 8.6, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/Micket/c7b5617c28917ccd2d053d7e238520c4 for a full test report.

@boegelbot
Copy link
Copy Markdown
Collaborator

boegelbot commented Apr 20, 2023

@Micket: Request for testing this PR well received on login1

PR test command 'EB_PR=17751 EB_ARGS="AlphaFold-2.3.4-foss-2022a-ColabFold.eb ColabFold-1.5.2-foss-2022a.eb" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17751 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 10687

Test results coming soon (I hope)...

Details

- notification for comment with ID 1516252107 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Copy Markdown
Collaborator

boegelbot commented Apr 20, 2023

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/e8b746f3fe16fc236cea98ad7b8caea9 for a full test report.

@lexming
Copy link
Copy Markdown
Contributor Author

lexming commented Apr 24, 2023

@Micket just a ping in case this was missed, it seems ready

@verdurin verdurin added this to the next release (4.7.2) milestone Apr 25, 2023
@verdurin
Copy link
Copy Markdown
Member

verdurin commented Apr 25, 2023

Going in, thanks @lexming!

@verdurin verdurin merged commit ea402a7 into easybuilders:develop Apr 25, 2023
@lexming lexming deleted the 20230418145246_new_pr_ColabFold152 branch April 26, 2023 08:10
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@Micket Micket Micket approved these changes

Assignees

No one assigned

Labels

new update

Projects

None yet

Milestone

4.7.2

Development

Successfully merging this pull request may close these issues.

4 participants

@lexming @boegelbot @Micket @verdurin