arXiv subjects

Ian Johnson

Publications and source records attributed to Ian Johnson.

5 recordsLinked to original sources

arXiv2026

Multi-tenant Kubernetes Use Cases for AI, Secure Computing and Data Services, and More

Kubernetes, as a container orchestration engine, has been widely used in cloud-native ecosystems for several years. In supercomputing ecosystems, especially where bare-metal performance for compute and network devices are considered, the adoption is somewhat limited. However, with the increasing diversity of use cases such as AI, secure and confidential computing for sensitive data, and mixed workload orchestration, a traditional, single-tenant batch computing system does not offer the flexibility and reproducibility to which public cloud users are accustomed. Note that Kubernetes is not considered a replacement for batch scheduling systems, which have powerful features for large-scale MPI jobs with thousands of network end points. Rather, it is a complementary service provided as part of a national AI Research Resource. We evaluate Kubernetes deployment on a Hewlett Packard Enterprise (HPE) Cray EX supercomputerwith HPE Slingshot interconnect, called Isambard-AI, with co-design use cases. One is a Trusted Research Environment used for medical and health sciences. The other combines KubeRay, Ray, and vLLM to provide a distributed, sandboxed, persistent AI model hosting service targeting multi-tenant confidential computing. We discuss challenges and lessons learned, and where further development is needed to offer a production Kubernetes-as-a-Service on HPE Cray EX (and later) platforms.

cs.DC↗

arXiv2025

Mofasa: A Step Change in Metal-Organic Framework Generation

Mofasa is an all-atom latent diffusion model with state-of-the-art performance for generating Metal-Organic Frameworks (MOFs). These are highly porous crystalline materials used to harvest water from desert air, capture carbon dioxide, store toxic gases and catalyse chemical reactions. In recognition of their value, the development of MOFs recently received a Nobel Prize in Chemistry. In many ways, MOFs are well-suited for exploiting generative models in chemistry: they are rationally-designable materials with a large combinatorial design space and strong structure-property couplings. And yet, to date, a high performance generative model has been lacking. To fill this gap, we introduce Mofasa, a general-purpose latent diffusion model that jointly samples positions, atom-types and lattice vectors for systems as large as 500 atoms. Mofasa avoids handcrafted assembly algorithms common in the literature, unlocking the simultaneous discovery of metal nodes, linkers and topologies. To help the scientific community build on our work, we release MofasaDB, an annotated library of hundreds of thousands of sampled MOF structures, along with a user-friendly web interface for search and discovery: https://mofux.ai/ .

cs.LG↗

arXiv2022

Emergence of local geometric laws of step flow in homoepitaxial growth

Below the roughening transition, crystal surfaces exhibit nanoscale line defects, steps, that move by exchanging atoms with their environment. In homoepitaxy, we analytically show how the motion of a step train in vacuum under strong desorption can be approximately described by nonlinear laws that depend on local geometric features such as the curvature of each step, as well as suitably defined effective terrace widths. We assume that each step edge, a free boundary, can be represented by a smooth curve in a fixed reference plane for sufficiently long times. Besides surface diffusion and evaporation, the processes under consideration include kinetic step-step interactions in slowly varying geometries, material deposition on the surface from above, attachment and detachment of atoms at steps, step edge diffusion, and step permeability. Our methodology relies on boundary integral equations for the adatom fluxes responsible for step flow. By applying asymptotics, which effectively treat the diffusive term of the free boundary problem as a singular perturbation, we describe an intimate connection of universal character between step kinetics and local geometry.

cond-mat.mtrl-sci↗

arXiv2021

Real-time interactive 4D-STEM phase-contrast imaging from electron event representation data

The arrival of direct electron detectors (DED) with high frame-rates in the field of scanning transmission electron microscopy has enabled many experimental techniques that require collection of a full diffraction pattern at each scan position, a field which is subsumed under the name four dimensional-scanning transmission electron microscopy (4D-STEM). DED frame rates approaching 100 kHz require data transmission rates and data storage capabilities that exceed commonly available computing infrastructure. Current commercial DEDs allow the user to make compromises in pixel bit depth, detector binning or windowing to reduce the per-frame file size and allow higher frame rates. This change in detector specifications requires decisions to be made before data acquisition that may reduce or lose information that could have been advantageous during data analysis. The 4D Camera, a DED with 87 kHz frame-rate developed at Lawrence Berkeley National Laboratory, reduces the raw data to a linear-index encoded electron event representation (EER). Here we show with experimental data from the 4D Camera that linear-index encoded EER and its direct use in 4D-STEM phase contrast imaging methods enables real-time, interactive phase-contrast from large-area 4D-STEM datasets. We detail the computational complexity advantages of the EER and the necessary computational steps to achieve real-time interactive ptychography and center-of-mass differential phase contrast using commonly available hardware accelerators.

cond-mat.mtrl-sci↗

arXiv2017

Spin nilHecke algebras of classical type

We formulate and study the spin nilHecke algebras ${}^\mathfrak{b}\!{\mathrm{NH}}_n^-$ and ${}^\mathfrak{d}\!{\mathrm{NH}}_n^-$ of type B/D, which differ from the usual nilHecke algebras by some odd signs. The type B spin nilHecke algebra is a nil version of the spin type B Hecke algebra introduced earlier by the second author and Khongsap, but not for the type D one. We construct faithful polynomial representations $\mathrm{Pol}_n^-$ of the nilHecke algebras via odd Demazure operators. We formulate the spin Schubert polynomials, and use them to show that the spin nilHecke algebras are matrix algebras with entries in a subalgebra of $\mathrm{Pol}_n^-$ consisting of spin symmetric polynomials. All these results have their counterparts for the usual nilHecke algebras over the rational field. Our work is a generalization of results of Lauda and Ellis-Khovanov-Lauda in usual/spin type A.

math.RT↗