Impress fixes

.github/workflows/tests.yml

@@ -14,12 +14,6 @@ jobs:
       fail-fast: false
       matrix:
         include:
-        - os: ubuntu-latest
-          python: '3.9'
-          toxenv: py39
-        - os: ubuntu-latest
-          python: '3.10'
-          toxenv: py310
         - os: ubuntu-latest
           python: '3.11'
           toxenv: py311
@@ -59,12 +53,6 @@ jobs:
       fail-fast: false
       matrix:
         include:
-        - os: ubuntu-latest
-          python: '3.9'
-          toxenv: py39-all
-        - os: ubuntu-latest
-          python: '3.10'
-          toxenv: py310-all
         - os: ubuntu-latest
           python: '3.11'
           toxenv: py311-all

.gitignore

@@ -135,6 +135,11 @@ dmypy.json
 
 # asyncflow related
 asyncflow.session.*
+ddict_*
+
+# ROME runtime outputs
+af_stats_*.csv
+examples/protien_binding_usecase/logs/
 
 # pdzbinder wf outputs
 af_pipeline_outputs_multi/
@@ -146,3 +151,5 @@ ddict*
 b0
 slurm*
 *slurm
+# scratch archives
+arch/

examples/.gitignore

@@ -0,0 +1,14 @@
+# SLURM log output (all workflows)
+*/logs/
+
+# Per-pipeline task directories written to cwd
+*/p*/
+
+# Dragon telemetry session dirs
+*/telemetry/
+
+# Run metadata written to cwd
+*/runinfo
+
+# Legacy output dirs
+*/myoutputs/

examples/protein_binding/SKILL.md

@@ -0,0 +1,131 @@
+# Protein Binding Use Case — SKILL.md
+
+## What it does
+
+5-step adaptive protein design pipeline running on Delta HPC (gpuA40x4):
+
+| Step | Task | Type | Notes |
+|------|------|------|-------|
+| s1 | ProteinMPNN — generate sequences | local (subprocess) | GPU via `CUDA_VISIBLE_DEVICES` |
+| s2 | Sequence ranking | local (pure Python) | sorts by MPNN score |
+| s3 | FASTA generation | local (pure Python) | writes `.fa` for each target |
+| s4 | AlphaFold multimer prediction | local (subprocess) | GPU, runs via Apptainer |
+| s4_post | Copy best models | local (pure Python) | glob → shutil.copy |
+| s5 | pLDDT extraction | local (subprocess) | writes `af_stats_<name>_pass_<n>.csv` |
+
+Passes repeat up to `max_passes` times. The adaptive function reads pLDDT CSVs and can spawn child pipelines for proteins that degrade.
+
+---
+
+## Key files
+
+```
+protien_binding_usecase/
+├── run_protein_binding.py      # entry point — backend, GPU policy, ImpressManager
+├── delta_gpu_run.sh            # SLURM script — Dragon launcher
+├── delta_env_setup.sh          # one-time venv setup (~/ve/impress/)
+├── af2_multimer_reduced.sh     # Apptainer wrapper for AlphaFold multimer
+├── mpnn_wrapper.py             # ProteinMPNN CLI wrapper
+└── plddt_extract_pipeline.py   # reads AF JSON → writes CSV
+```
+
+Pipeline implementation: `/scratch/bblj/mgoliyad1/IMPRESS/src/impress/pipelines/protein_binding.py`
+
+---
+
+## Environment variables
+
+| Variable | Set in | Purpose |
+|----------|--------|---------|
+| `SCRATCH` | user env | base scratch path (`/scratch/bblj`) |
+| `MPNN_PATH` | `delta_gpu_run.sh` | path to ProteinMPNN repo |
+| `AF2_DATABASE` | `delta_gpu_run.sh` | AlphaFold database dir |
+| `AF2_SIF` | `delta_gpu_run.sh` | AlphaFold Apptainer image |
+| `IMPRESS_INPUT_DIR` | `delta_gpu_run.sh` | dir containing `{name}_in/` folders |
+| `IMPRESS_OUTPUT_DIR` | `delta_gpu_run.sh` | output root (af_pipeline_outputs_multi/) |
+| `IMPRESS_SCRIPTS_DIR` | `delta_gpu_run.sh` | dir with mpnn_wrapper.py, af2_multimer_reduced.sh |
+| `SBATCH_ACCOUNT` | user env | SLURM account (e.g. `bblj-delta-gpu`) |
+
+`IMPRESS_PRE_EXEC` was removed — the venv is activated in the SLURM script before `dragon -s`, so all subprocesses inherit the environment.
+
+---
+
+## Dragon integration
+
+**Backend**: `DragonExecutionBackendV2` (flow engine only — no tasks dispatched to Dragon workers).
+
+**Why not V3**: Dragon worker subprocesses silently hang when a subprocess uses GPU ops (`cupy`, `torch`, Apptainer). Same failure mode documented in `DeepDriveSim/workflows/miniapps_workflow/miniapps_workflow.py`.
+
+**Fix**: All pipeline steps are `local_task=True`. GPU steps (s1, s4) run as `asyncio.create_subprocess_shell()` on the Dragon head process, which has direct GPU access from SLURM allocation. Dragon manages the `ImpressManager`/`WorkflowEngine` loop; it never dispatches tasks to workers.
+
+**GPU affinity**: `_find_gpus()` + `_make_policy()` in `run_protein_binding.py` use `dragon.native.machine.System()` to discover GPUs and build a `dragon.infrastructure.policy.Policy` with `gpu_affinity`. The policy's GPU list is passed as `CUDA_VISIBLE_DEVICES` to each subprocess via `_gpu_env()` in the pipeline.
+
+```python
+# To change GPU count per pipeline (default n_gpus=1 for MPNN):
+policy = _make_policy(all_gpus, idx=0, n_gpus=1)
+```
+
+**Launcher** (`delta_gpu_run.sh`):
+```bash
+source ~/ve/impress/bin/activate
+dragon-config add --ofi-runtime-lib="${FAB_LIB}"
+rm -rf asyncflow.session.*
+dragon -s run_protein_binding.py     # -s = single-node
+```
+
+**SLURM resource request**: `--tasks-per-node=4`, `--gpus=4`, `--exclusive` (matches Dragon's single-node layout).
+
+---
+
+## Key design decisions
+
+### Three separate path env vars
+`base_path` was split into `IMPRESS_INPUT_DIR` / `IMPRESS_OUTPUT_DIR` / `IMPRESS_SCRIPTS_DIR` so input data, outputs, and scripts can live in different locations independently.
+
+### Output dirs auto-created in `__init__`
+`os.makedirs(..., exist_ok=True)` is called in `ProteinBindingPipeline.__init__` for all required subdirs. No manual `mkdir` needed in the SLURM script.
+
+### `s4_post` replaces `post_exec`
+`post_exec` in task descriptions is a RADICAL-Pilot artifact — `ConcurrentExecutionBackend` and Dragon never execute it. Replaced with a `local_task=True` coroutine using `glob` + `shutil.copy` to move `ranked_0.pdb` and `ranking_debug.json` to `best_models/` and `best_ptm/`.
+
+### AlphaFold container flags
+- `--no-home`: prevents host's newer Biopython from shadowing the container's version (`SCOPData` import error)
+- `--run_relax` removed: not supported by this container version
+- Database bind: `/scratch/rhaas/SUP-5301/database:/database`
+- Container: `/scratch/rhaas/SUP-5301/alphafold.sif`
+
+---
+
+## One-time setup
+
+```bash
+export SCRATCH=/scratch/bblj
+cd /scratch/bblj/mgoliyad1/IMPRESS/examples/protien_binding_usecase
+bash delta_env_setup.sh          # creates ~/ve/impress/
+
+# Unzip inputs (GNU tar, not zip):
+cd /scratch/bblj/mgoliyad1/IMPRESS_inputs
+tar -xf prod_in.tar              # or whatever archive name
+```
+
+## Submitting a job
+
+```bash
+export SCRATCH=/scratch/bblj
+export SBATCH_ACCOUNT=bblj-delta-gpu
+cd /scratch/bblj/mgoliyad1/IMPRESS/examples/protien_binding_usecase
+sbatch delta_gpu_run.sh
+```
+
+## Checking results
+
+```bash
+# pLDDT scores per pass:
+cat af_stats_p1_pass_1.csv
+
+# AlphaFold best models:
+ls IMPRESS_outputs/af_pipeline_outputs_multi/p1/af/prediction/best_models/
+
+# Full logs:
+tail -f logs/impress_<jobid>.out
+```