ai4science-studio: Skill for Cursor

Material science domain

Scope

The material_science/ domain covers materials, chemistry, and related ML: property prediction, generative models, surrogates for DFT or MD-scale workflows when exposed as Hugging Face models, and similar tasks.

Layout

• Models: material_science/models/<model-slug>/
• Slug rules: material_science/models/README.md (default org__model; public on-disk names such as HydraGNN are allowed when the model README.md states the canonical Hub id)
• Structural template reference: _template/ (repo root)
• Example: material_science/models/HydraGNN/ — atomistic graph foundation models (HydraGNN), Hub id mlupopa/HydraGNN_Predictive_GFM_2024

Agent guidance

• Keep recipes explicit about input representations (graphs, crystals, SMILES, etc.) and any unit conventions (including energy vs force targets and graph vs node outputs where relevant).
• Prefer citing benchmarks and baseline numbers from literature or model cards when adding evaluation snippets.
• Do not commit large proprietary structure databases; link to public sources or describe how users supply their own data.
• Institutional AMD clusters and staging large artifacts (Hugging Face CLI, Globus / Constellation mirrors, OLCF copy-out when applicable) belong in data-access.md-style runbooks for ADIOS or similar scientific I/O when models use them.

HydraGNN multi-node training pattern

HydraGNN uses MPI-based distributed training with ADIOS datasets. Key patterns for AMD clusters:

• Launch: srun --mpi=pmix apptainer exec --rocm --overlay <overlay>:ro $SIF bash <rank_script>. The --mpi=pmix is required because mpi4py calls MPI_Init inside the container.
• Non-DDStore path (phase 1): Use --multi --multi_model_list=<datasets> without --ddstore. Each rank opens ADIOS files directly via AdiosMultiDataset. Simpler and sufficient for moderate scales (1-8 nodes).
• DDStore path (phase 2): Add --ddstore flag plus env vars HYDRAGNN_AGGR_BACKEND=mpi, HYDRAGNN_DDSTORE_METHOD=1, HYDRAGNN_CUSTOM_DATALOADER=1. Required for large-scale (32+ nodes) where per-rank ADIOS I/O becomes a bottleneck.
• Dataset convention: ADIOS datasets are expected at ./dataset/<name>-v2.bp relative to the training script. Symlink from shared storage rather than copying.
• Config file: The upstream gfm_mlip.json is hardware-agnostic and works on any cluster. Use CLI flags (--batch_size, --num_epoch, --precision) to override parameters at runtime without modifying the file.
• Env vars inside container: Set OMP_NUM_THREADS to match --cpus-per-task, MIOPEN_DISABLE_CACHE=1, MIOPEN_USER_DB_PATH=$SCRATCH_LOCAL/<jobid>/miopen (node-local fast storage from .cluster-config.yaml), HYDRAGNN_USE_VARIABLE_GRAPH_SIZE=1.
• Multi-node MPI transport (ob1/tcp): On Pensando/ionic fabrics, data NICs use /31 subnets that don't route between nodes — IB verbs cannot work for MPI. Use OMPI_MCA_pml=ob1, OMPI_MCA_btl=tcp,self, OMPI_MCA_btl_tcp_if_include=$MGMT_NIC, MPI4PY_RC_THREADS=false. RCCL uses ANP plugin (librccl-anp.so) over ionic native transport (RoCEv2/GDRDMA) for GPU allreduce, independent of MPI. The ANP plugin and libionic.so.1 must be bind-mounted from the host into the container.
• Convergence capture: Run with HYDRAGNN_VALTEST=1 to get epoch-level loss reporting. Parse with examples/parse_convergence.py --log <slurm_output>.
• Strong-scaling sweep: Submit matched 1/2/4/8-node runs via examples/run_scaling_study.sh (identical env, HYDRAGNN_VALTEST=0, 6 epochs). Collate steady-state throughput (epochs 2–5) with examples/collate_scaling_study.py. Results table and methodology in recipes/train/README.md §6. sbatch_train_amd.sh defaults TORCH_NCCL_HIGH_PRIORITY=1 and GPU_MAX_HW_QUEUES=2.