Virtual screening is a campaign, not a single benchmark. Preparation, conformer generation, docking, molecular dynamics, feature extraction and AI ranking have different resource shapes. The objective is completed, reviewable compounds per day with enough evidence to reproduce each decision.
Campaign architecture
AxiLattice handles CPU preparation, docking variants, ETL and statistical analysis. AxiForge Max runs four-GPU single-node training or simulation. AxiBastion supports multiple concurrent GPU campaigns and distributed training across twelve 96GB devices. Keep structures and approved results on protected shared storage; stage trajectories to NVMe.
GROMACS execution
Benchmark the exact molecular system because CPU/GPU balance changes with atom count, PME configuration and trajectory output. Allocate CPU cores to keep accelerators fed without stealing capacity from concurrent runs. Write checkpoints to resilient storage at a measured interval and test continuation after interruption.
AI ranking
Use versioned descriptors, sequence/structure inputs and splits that prevent scaffold or temporal leakage. BioNeMo or other domain frameworks can support model development, but validation remains specific to the scientific question. Rank candidates with uncertainty and preserve full-simulation confirmation for high-value decisions.
Scheduler strategy
Use job arrays for independent replicas and compounds; reserve multi-GPU allocations for models that demonstrate scaling. Apply project quotas and fair-share so one campaign cannot crowd out all work. Track licence tokens as schedulable resources where necessary.
Evidence pack
For every selected compound preserve input structures, protonation/parameter choices, seeds, software images, checkpoints, model/version, scores and review outcome. Acceptance tests include energy/trajectory sanity, repeatability within expected stochastic tolerance, throughput and recovery.
Primary technical references
- GROMACS heterogeneous parallelisation
- NVIDIA BioNeMo Framework documentation
- Slurm Quick Start Administrator Guide
- MLflow Tracking documentation
References are provided for software architecture and implementation planning. Validate the versions, licences, support matrix and regulated-use requirements applicable to the final deployment.