Haddock3 container workflow & usage #1318
Conversation
rvhonorato
added
documentation
usage-container/CONTRIBUTING.md
Outdated
There was a problem hiding this comment.
Fine for your own repo - should rather be removed here if distributed with haddock3
There was a problem hiding this comment.
The CONTRIBUTING.md has now been removed.
There was a problem hiding this comment.
Is this the minimal set of dependencies?
There was a problem hiding this comment.
These are the minimal set of dependencies to build and run haddock3
|
All requested changes have been made. PR ready for re-review |
There was a problem hiding this comment.
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.
usage-container/README.md
Outdated
|
|
||
| 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 |
There was a problem hiding this comment.
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
There was a problem hiding this comment.
Pull command has been made generic with :latest and added a second example to pin 2025.8.0 for reproducibility.
usage-container/README.md
Outdated
| # 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. |
There was a problem hiding this comment.
Is this the same usage.md file as in this pull request? if yes then rather link to the local one
There was a problem hiding this comment.
Link has been updated with local HADDOCK3 repo
|
|
||
| --- | ||
|
|
||
| ### Build Your Own HADDOCK3 Container |
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
Link updated with local haddock3 repo files.
|
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. |
|
All comments have been resolved. Happy to make any additional edits if required! |
|
|
||
| srun --partition=compute \ | ||
| --nodes=1 \ | ||
| --ntasks-per-node=8 \ |
There was a problem hiding this comment.
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?
|
|
||
| #SBATCH --job-name=HADDOCK3-docking | ||
| #SBATCH --output=HADDOCK3_%j.out | ||
| #SBATCH --nodes=3 |
There was a problem hiding this comment.
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.
3 participants
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.mdto link to this guide.