Haddock3 container workflow & usage by Comp-era · Pull Request #1318 · haddocking/haddock3

Comp-era · 2025-07-09T03:54:26Z

This PR adds a top-level usage-container/ directory from the Comp-era/HADDOCK3-Container repo,
containing:

README.md (detailed container usage guide)
docs/usage.md (run instructions)
recipe/ (example build definition)
scripts/ (Slurm run scripts)

It also updates the root README.md to link to this guide.

amjjbonvin · 2025-07-25T09:11:43Z

Fine for your own repo - should rather be removed here if distributed with haddock3

The CONTRIBUTING.md has now been removed.

amjjbonvin · 2025-07-25T09:16:10Z

Is this the minimal set of dependencies?

These are the minimal set of dependencies to build and run haddock3

Comp-era · 2025-08-05T11:24:21Z

All requested changes have been made. PR ready for re-review

amjjbonvin

We have now a mix of local haddock3 repo links and links pointing to https://github.com/Comp-era/HADDOCK3-Container
Not sure what is best. If this is mainly documentation, we could rather add the content to the HADDOCK3 user manual instead.
Or we have everything in the haddock3 repo.

amjjbonvin · 2025-08-22T12:32:07Z

+
+A ready-to-use Docker image for HADDOCK3 is published on the GitHub container registry, simply pull:
+```bash
+docker pull ghcr.io/haddocking/haddock3:2025.5.0


We have now released 2025.8.0 - so should this command be made more generic to pull the latest version?

And add a second command to pull a specific version

Pull command has been made generic with :latest and added a second example to pin 2025.8.0 for reproducibility.

amjjbonvin · 2025-08-22T12:33:15Z

+# Or, build with Singularity
+singularity build haddock3_mpi.sif docker://ghcr.io/haddocking/haddock3:2025.5.0
+  ```
+**Note:** Refer to the [**usage.md**](https://github.com/Comp-era/HADDOCK3-Container/blob/main/docs/usage.md) and the example SLURM script available in the `scripts` folder for detailed instructions on how to run HADDOCK3 jobs in an HPC environment.


Is this the same usage.md file as in this pull request? if yes then rather link to the local one

Link has been updated with local HADDOCK3 repo

amjjbonvin · 2025-08-22T12:37:37Z

+
+---
+
+### Build Your Own HADDOCK3 Container


This is still pointing to https://github.com/Comp-era/HADDOCK3-Container - if we make it part of the haddock3 repo, we should rather point to the local haddock3 repo files.

Link updated with local haddock3 repo files.

github-actions · 2025-10-02T02:04:15Z

This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days.

Comp-era · 2025-10-02T19:15:28Z

All comments have been resolved. Happy to make any additional edits if required!

amjjbonvin · 2025-10-03T11:22:53Z

+
+srun --partition=compute \
+     --nodes=1 \
+     --ntasks-per-node=8 \


Would be nice to add somewhere some explanations on how to change the number of cpu used. Now the example gives 8, but is this a dynamic variable that the container will automatically take over? Or do you need to rebuild the container in case a different number of cpus should be used?

Required changes have been incorporated. The documentation now clarifies that the number of CPUs can be adjusted dynamically through the SLURM command and does not require rebuilding the container. Also added relevant information pertaining to usage of the container.

amjjbonvin · 2025-10-03T11:24:09Z

+
+#SBATCH --job-name=HADDOCK3-docking
+#SBATCH --output=HADDOCK3_%j.out
+#SBATCH --nodes=3


Here we are requesting 3 nodes with each 120 tasks. Somewhere it should be made clear that the mpi run mode of HADDOCK3 must then be used in the config file.

The documentation now explicitly mentions that when running on multiple nodes, the HADDOCK3 configuration file must be set to use the MPI run mode. Clarifications on changing the number of CPU cores have also been added, along with the same information reflected in the SLURM batch script.

github-actions · 2025-11-07T02:11:06Z

This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days.

amjjbonvin · 2025-11-07T13:15:50Z

@Comp-era - please check the last comments not yet answered

…r.sh for proper container run behavior

…mages

rvhonorato

After reading trough this, I think it will fit better in https://github.com/haddocking/haddock3-user-manual instead of here.

Comp-era · 2025-11-13T06:26:34Z

Thanks for the suggestion. Is there a designated location within https://github.com/haddocking/haddock3-user-manual where I should submit a pull request for the same?

rvhonorato · 2025-11-13T10:39:24Z

you can just make a PR there and the reviewers can decide where it fits best.

Comp-era · 2025-12-01T08:05:56Z

As suggested, I have created a PR within https://github.com/haddocking/haddock3-user-manual. Once the reviewers decide the location, I’ll update the directory paths accordingly to match the designated structure.

github-actions · 2026-01-01T02:16:22Z

This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days.

rvhonorato · 2026-01-01T13:31:20Z

moved to haddocking/haddock3-user-manual#25

container workflow & usage

fa0d2b3

rvhonorato requested review from a team and amjjbonvin July 9, 2025 13:01

rvhonorato added documentation Improve docs community Feature requests / contribution / issues from users labels Jul 9, 2025

rvhonorato assigned Comp-era Jul 9, 2025

amjjbonvin reviewed Jul 25, 2025

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Comp-era added 3 commits August 5, 2025 16:22

Remove LICENSE

0d4fb11

Removed CONTRIBUTING.md

5efc144

Fix typo and finalize PR feedback changes

e6e5c4f

rvhonorato requested review from a team and amjjbonvin August 14, 2025 15:45

Merge branch 'main' into usage-run-build-container

71cdc53

amjjbonvin reviewed Aug 22, 2025

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docs: update links and docker instructions; fix script filename

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github-actions Bot added the Stale label Oct 2, 2025

rvhonorato requested review from a team and amjjbonvin October 3, 2025 10:35

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github-actions Bot added the Stale label Nov 7, 2025

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Comp-era added 2 commits November 10, 2025 14:22

docs(usage): fix path to recipe directory in README

ee40aa8

update maintainer label in MPI definition

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rvhonorato reviewed Nov 10, 2025

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Comment thread usage-container/recipe/haddock3_mpi.def Outdated

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Comment thread usage-container/README.md

Comp-era added 6 commits November 10, 2025 23:31

docs(usage): update HPC CPU/core explanation and mpi run mode details

0fdbde8

(scripts): remove obsolete slurm_run_singularity.sh script

32a9402

removed singularity command and build argument to contain version

6a55cb6

fix(scripts): remove redundant exec and bind from slurm_run_apptaine…

dcae9eb

…r.sh for proper container run behavior

docs(usage): clarify root access requirement for building Apptainer i…

543d56e

…mages

updated infromation on script usage for number of cpuresource allocation

7fc1c39

rvhonorato reviewed Nov 10, 2025

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Comp-era added 3 commits November 11, 2025 01:55

docs(usage): replace .cfg with .toml in usage.md

30c3f95

removed singularity in intro in README.md

8955a05

minor correction

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rvhonorato requested changes Nov 11, 2025

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Comp-era Aug 25, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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