Evaluation of OpenAI Codex for HPC Parallel Programming Models Kernel Generation

We evaluate AI-assisted generative capabilities on fundamental numerical kernels in high-performance computing (HPC), including AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG. We test the generated kernel codes for a variety of language-supported programming models, including (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numba, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). We use the GitHub Copilot capabilities powered by OpenAI Codex available in Visual Studio Code as of April 2023 to generate a vast amount of implementations given simple + + prompt variants. To quantify and compare the results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. Results suggest that the OpenAI Codex outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general-purpose Python can benefit from adding code keywords, while Julia prompts perform acceptably well for its mature programming models (e.g., Threads and CUDA.jl). We expect for these benchmarks to provide a point of reference for each programming model's community. Overall, understanding the convergence of large language models, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.Comment: Accepted at the Sixteenth International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2), 2023 to be held in conjunction with ICPP 2023: The 52nd International Conference on Parallel Processing. 10 pages, 6 figures, 5 table

Comparing Llama-2 and GPT-3 LLMs for HPC kernels generation

We evaluate the use of the open-source Llama-2 model for generating well-known, high-performance computing kernels (e.g., AXPY, GEMV, GEMM) on different parallel programming models and languages (e.g., C++: OpenMP, OpenMP Offload, OpenACC, CUDA, HIP; Fortran: OpenMP, OpenMP Offload, OpenACC; Python: numpy, Numba, pyCUDA, cuPy; and Julia: Threads, CUDA.jl, AMDGPU.jl). We built upon our previous work that is based on the OpenAI Codex, which is a descendant of GPT-3, to generate similar kernels with simple prompts via GitHub Copilot. Our goal is to compare the accuracy of Llama-2 and our original GPT-3 baseline by using a similar metric. Llama-2 has a simplified model that shows competitive or even superior accuracy. We also report on the differences between these foundational large language models as generative AI continues to redefine human-computer interactions. Overall, Copilot generates codes that are more reliable but less optimized, whereas codes generated by Llama-2 are less reliable but more optimized when correct.Comment: Accepted at LCPC 2023, The 36th International Workshop on Languages and Compilers for Parallel Computing http://www.lcpcworkshop.org/LCPC23/ . 13 pages, 5 figures, 1 tabl

Julia as a unifying end-to-end workflow language on the Frontier exascale system

We evaluate Julia as a single language and ecosystem paradigm powered by LLVM to develop workflow components for high-performance computing. We run a Gray-Scott, 2-variable diffusion-reaction application using a memory-bound, 7-point stencil kernel on Frontier, the US Department of Energy's first exascale supercomputer. We evaluate the performance, scaling, and trade-offs of (i) the computational kernel on AMD's MI250x GPUs, (ii) weak scaling up to 4,096 MPI processes/GPUs or 512 nodes, (iii) parallel I/O writes using the ADIOS2 library bindings, and (iv) Jupyter Notebooks for interactive analysis. Results suggest that although Julia generates a reasonable LLVM-IR, a nearly 50% performance difference exists vs. native AMD HIP stencil codes when running on the GPUs. As expected, we observed near-zero overhead when using MPI and parallel I/O bindings for system-wide installed implementations. Consequently, Julia emerges as a compelling high-performance and high-productivity workflow composition language, as measured on the fastest supercomputer in the world.Comment: 11 pages, 8 figures, accepted at the 18th Workshop on Workflows in Support of Large-Scale Science (WORKS23), IEEE/ACM The International Conference for High Performance Computing, Networking, Storage, and Analysis, SC2

Temporal activity of rural free-ranging dogs: implications for the predator and prey species in the Brazilian Atlantic Forest

Domestic or free-ranging dogs (Canis lupus familiaris) can have deleterious effects on wildlife, acting as predators or competitors to native species. These impacts can be highly important in fragmented pristine habitats or well-preserved areas located in human dominated landscapes and where biodiversity values are usually high, such as those in southeastern Brazil. Here we explored the level of overlap or mismatch in the distributions of activity patterns of rural free-ranging dogs and potential wild prey (Didelphis aurita, Cuniculus paca; Sylvilagus brasiliensis) and a wild predator (Leopardus pardalis) in areas of Atlantic Forest in southeastern Brazil. We further explored the possible influence of the wild predator on the dog presence pattern detected in the territory analyzed. Our camera-trap data (714 camera-trap days) showed that while rural free-ranging dogs display a cathemeral activity pattern, with activity peaks at dusk and dawn, ocelot and prey species are mainly nocturnal. Moreover, we found no evidence of an effect of ocelot presence, the distance to human houses and the presence of native forests on site occupancy by dogs. The ocelot activity patterns in this study were similar to those already reported in previous studies. On the other hand, previous studies have indicated that that free-ranging dogs are often reported to be more diurnal, and it seems that the rural free-ranging dogs in our study area may have adjusted their behaviour to be more active at dawn and dusk periods. This might be to both maintain some overlap with potential prey, e.g. Sylvilagus brasiliensis, and also to avoid ocelots by being less active in periods when this predator is more active (which also coincides with peaks in activity for potential prey species). We hypothesize that the presence of ocelots might be influencing the temporal niche dimension of rural free-ranging dogs. As a sustainable management strategy, we propose conserving territories to promote the presence of medium to large predators in natural areas, in order to control free-ranging dogs and protect their vertebrate prey species

Software engineering to sustain a high-performance computing scientific application: QMCPACK

We provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions runners, and NVIDIA and AMD GPUs in pre-exascale systems, using self-hosted hardware; (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, sustainable maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the sustainability of community HPC codes and scientific discovery at scale.Comment: Accepted at the first US-RSE Conference, USRSE2023, https://us-rse.org/usrse23/, 8 pages, 3 figures, 4 table

Giving RSEs a Larger Stage through the Better Scientific Software Fellowship

The Better Scientific Software Fellowship (BSSwF) was launched in 2018 to foster and promote practices, processes, and tools to improve developer productivity and software sustainability of scientific codes. BSSwF's vision is to grow the community with practitioners, leaders, mentors, and consultants to increase the visibility of scientific software production and sustainability. Over the last five years, many fellowship recipients and honorable mentions have identified as research software engineers (RSEs). This paper provides case studies from several of the program's participants to illustrate some of the diverse ways BSSwF has benefited both the RSE and scientific communities. In an environment where the contributions of RSEs are too often undervalued, we believe that programs such as BSSwF can be a valuable means to recognize and encourage community members to step outside of their regular commitments and expand on their work, collaborations and ideas for a larger audience.Comment: submitted to Computing in Science & Engineering (CiSE), Special Issue on the Future of Research Software Engineers in the U

The Early Stage of Bacterial Genome-Reductive Evolution in the Host

The equine-associated obligate pathogen Burkholderia mallei was developed by reductive evolution involving a substantial portion of the genome from Burkholderia pseudomallei, a free-living opportunistic pathogen. With its short history of divergence (∼3.5 myr), B. mallei provides an excellent resource to study the early steps in bacterial genome reductive evolution in the host. By examining 20 genomes of B. mallei and B. pseudomallei, we found that stepwise massive expansion of IS (insertion sequence) elements ISBma1, ISBma2, and IS407A occurred during the evolution of B. mallei. Each element proliferated through the sites where its target selection preference was met. Then, ISBma1 and ISBma2 contributed to the further spread of IS407A by providing secondary insertion sites. This spread increased genomic deletions and rearrangements, which were predominantly mediated by IS407A. There were also nucleotide-level disruptions in a large number of genes. However, no significant signs of erosion were yet noted in these genes. Intriguingly, all these genomic modifications did not seriously alter the gene expression patterns inherited from B. pseudomallei. This efficient and elaborate genomic transition was enabled largely through the formation of the highly flexible IS-blended genome and the guidance by selective forces in the host. The detailed IS intervention, unveiled for the first time in this study, may represent the key component of a general mechanism for early bacterial evolution in the host

Open innovation in public management: analysis of the Brazilian action plan for Open Government Partnership

Este estudo objetivou analisar o Plano de Ação brasileiro para o Governo Aberto, baseado na teoria da inovação aberta na gestão pública. Utilizou-se de uma pesquisa documental, com vistas a aprofundar o conhecimento do fenômeno em questão. O documento foi escolhido intencionalmente, por ser exemplo basilar das políticas públicas relacionadas à inovação aberta brasileira. Os resultados mostram que os compromissos firmados pelo governo brasileiro estão consoantes com o processo de inovação aberta pública. As ações previstas no Plano estão especificamente relacionadas a transparência, abertura de dados e preparação do corpo estatal para o processo aberto de inovação. _________________________________________________________________________________________ RESUMEN: Este estudio tuvo como objetivo analizar el Plan de Acción de Brasil para el Gobierno Abierto con base en la teoría de la innovación abierta en la gestión pública. Se utilizó una investigación documental, con el fin de profundizar el conocimiento en el fenómeno en cuestión. El documento fue elegido intencionadamente porque es fundamental para las políticas públicas relacionadas con la innovación abierta brasileña. Los resultados muestran que los compromisos asumidos por el gobierno brasileño son compatibles con el proceso de innovación abierta pública. En concreto, las acciones contenidas en el plan están relacionados con la transparencia, los datos abiertos y preparación de la estructura de gobierno para el proceso abierto de innovación. _________________________________________________________________________________________ ABSTRACT: This study aims to analyze the Brazilian action plan for Open Government, based on the theory of open innovation in public management. Documentary research was used, in order to deepen of the knowledge the phenomenon being discussed . The document was intentionally chosen because it is essential for public policies related to Brazilian open innovation The results show that the commitments made by the Brazilian government are compatible with the public open innovation process. The actions in the Plan are related specifically to transparency, open data and preparation of the governance body for the open innovation process