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SLURM defaults move from results

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Dima
2025-11-26 10:35:04 +01:00
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parent 298e614641
commit 6250f6da80
1 changed files with 20 additions and 15 deletions
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README.md
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@@ -180,6 +180,26 @@ Then open `http://localhost:8501` in your browser.
## Advanced Configuration
### SLURM defaults for structure inference
Override default values to match your cluster:
```yaml
slurm_partition: "gpu" # which partition/queue to submit to
slurm_qos: "normal" # optional QoS if your site uses it
structure_inference_gpus_per_task: 1 # number of GPUs each inference job needs
structure_inference_gpu_model: "3090" # optional GPU model constraint (remove to allow any)
structure_inference_tasks_per_gpu: 0 # <=0 keeps --ntasks-per-gpu unset in the plugin
```
`structure_inference_gpus_per_task` and `structure_inference_gpu_model` are read by the
Snakemake Slurm executor plugin and translated into `--gpus=<model>:<count>` (or `--gpus=<count>` if
no model is specified). We no longer use `slurm_gres`; requesting GPUs exclusively through these
fields keeps the job submission consistent across clusters.
`structure_inference_tasks_per_gpu` toggles whether the plugin also emits `--ntasks-per-gpu`. Leaving
the default `0` prevents that flag, which avoids conflicting with the Tres-per-task request on many
systems. Set it to a positive integer only if your site explicitly requires `--ntasks-per-gpu`.
### Using Precomputed Features
If you have precomputed protein features, specify the directory:
@@ -217,23 +237,8 @@ enable_structure_analysis: true # skip alphaJudge if set to false
generate_recursive_report: true # disable if you do not need all_interfaces.csv
recursive_report_arguments: # optional extra CLI flags for alphajudge
--models_to_analyse: best
# SLURM defaults (override to match your cluster)
slurm_partition: "gpu" # which partition/queue to submit to
slurm_qos: "normal" # optional QoS if your site uses it
structure_inference_gpus_per_task: 1 # number of GPUs each inference job needs
structure_inference_gpu_model: "3090" # optional GPU model constraint (remove to allow any)
structure_inference_tasks_per_gpu: 0 # <=0 keeps --ntasks-per-gpu unset in the plugin
```
`structure_inference_gpus_per_task` and `structure_inference_gpu_model` are read by the
Snakemake Slurm executor plugin and translated into `--gpus=<model>:<count>` (or `--gpus=<count>` if
no model is specified). We no longer use `slurm_gres`; requesting GPUs exclusively through these
fields keeps the job submission consistent across clusters.
`structure_inference_tasks_per_gpu` toggles whether the plugin also emits `--ntasks-per-gpu`. Leaving
the default `0` prevents that flag, which avoids conflicting with the Tres-per-task request on many
systems. Set it to a positive integer only if your site explicitly requires `--ntasks-per-gpu`.
### Changing Folding Backends