Mark Abraham
Research Software Engineer at Intel Corporation
Stockholm, Sweden
Summary
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Rockstar🎓
Top SchoolMark Abraham is a research software engineer with 16 years of experience specializing in high-performance computing for life sciences, currently contributing to GROMACS development at Intel and previously supporting Sweden's academic and industrial users at ENCCS. He combines deep expertise in parallelization, acceleration, testing and scalability with hands-on build and packaging work—actively improving build systems like Spack and EasyBuild to ensure portable, high-performance deployments. A former global lead for GROMACS development and coordinator of research software engineering at BioExcel, he has driven exascale-readiness for molecular simulation on the largest European supercomputers. His background in computational chemistry (PhD) and prior work on multilingual NLP and voice analytics gives him a rare cross-disciplinary perspective that helps bridge domain science and production-grade HPC software.
16 years of coding experience
10 years of employment as a software developer
Bachelor of Science (B.Sc.), Chemistry, Bachelor of Science (B.Sc.), Chemistry at University of TasmaniaAustralian National UniversityGeelong Grammar School
Stackoverflow
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Github Skills (34)
performance-analytics10
c-language10
performance-monitor10
scite10
python10
decomposition10
memory-management10
mpi10
cmake10
hpc10
performance-measurement10
performance-analysis10
parallel-computing10
scilab10
performance-tuning10
Programming languages (16)
Github contributions (5)
gromacs/gromacs
Nov 2009 - Jan 2023
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
Role in this project:
Backend Developer & Performance Engineer
Backend Developer & Performance EngineerContributions:2161 commits, 8 PRs, 7 branches in 13 years 3 months
Contributions summary:Mark focused on optimizing the GROMACS molecular simulation toolkit by reordering code related to thread-MPI thread spawning and improving data structures. They refactored the code to more cleanly handle the reverse topology, moving responsibilities between different modules. Furthermore, they implemented and optimized various performance related code, including handling the memory for constraints.
gromacspythonissue-trackinggitlabmolecular
spack/spack
Feb 2021 - Aug 2022
A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
Role in this project:Backend & Build Engineer
Backend & Build EngineerContributions:30 reviews, 4 commits, 19 PRs in 1 year 6 months
Contributions summary:Mark primarily contributes to the build system and package management aspects of the spack/spack repository. They modify package configurations for GROMACS, enabling new features and addressing build-related issues. The user also extends support for Intel oneAPI components and enhances the build process for packages like `hwloc` and `rdma-core`, introducing new variants and fixing build errors. These modifications streamline the build process, and ensure compatibility with a variety of systems.
compilerspythonradiussplatformslinux
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