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molecular-dynamics

molecular dynamics

GROMACS

SystemTechniques · 5Primitives · 22 molecular-dynamics Halo exchangedistributed · medium: Each rank stores its block plus a border copy of its neighbours' edge cells, refreshed by small messages every step; communication scales with block surface, not volume.›Checkpoint and restarthardware-os · medium: Periodically save enough state to resume a computation after a crash, preemption or move, with an interval that balances save cost against lost work.›Constraint solvers shake lincsphysics · medium: Hold bond lengths fixed in MD: SHAKE iteration, LINCS matrix expansion, SETTLE for waterParticle mesh ewaldphysics · medium: Split long-range forces: real-space short range plus FFT mesh solve (PME, PPPM, TreePM)Thermostats barostatsphysics · medium: Temperature and pressure control in MD: Langevin, Nose-Hoover, velocity rescale, Parrinello-RahmanVerlet / leapfrognumerics · low: Half-kick, drift, half-kick: a second-order, time-reversible, symplectic integrator with one force evaluation per step whose energy error stays bounded for millions of steps.›Fast Fourier transformnumerics · low: Computes the DFT in O(n log n) by recursively splitting into even and odd halves; the basis of fast convolution and spectral methods.›Neighbor listsphysics · low: Cell lists plus Verlet buffer lists for O(n) short-range pair interactionsPeriodic boundary conditionsphysics · low: Minimum image convention and wrapping for simulations in periodic boxesSIMD programminghardware-os · low: Process 4-16 lanes per instruction with AVX2, AVX-512 or NEON via Rust std::arch, with runtime dispatch and a portable fallback.›CUDA and GPU languageslanguages · low: Programming GPUs: thousands of lockstep threads, bound by memory bandwidth; libraries first, Triton for fused kernels, CUDA C++ for peak speed.›Collective communicationml-training · low: The family of group exchanges (broadcast, reduce, all-gather, reduce-scatter, all-to-all) and the latency-plus-bytes cost model that picks ring, tree or direct algorithms by message size and topology.›Floating-point errornumerics · low: How IEEE 754 rounding error accumulates and how to contain it: compensated (Kahan/Neumaier) and pairwise summation, error-free transformations with FMA, ULP comparisons.›Force field termsphysics · low: Bonded and nonbonded MD potentials: bonds, angles, torsions, Lennard-Jones, Coulomb with cutoffsEager rendezvous protocoldistributed · low: MPI point-to-point: eager sends for small messages, rendezvous handshake for large onesRdmanetworking · low: RDMA verbs over InfiniBand/RoCE: queue pairs, memory registration, one-sided opsZero-copy I/Onetworking · low: Move bytes between files, sockets and NICs by passing page references instead of copying through user space: sendfile, splice, MSG_ZEROCOPY, kTLS.›Copy-on-write forkhardware-os · low: fork() gives the child the parent's whole address space by sharing pages read-only and copying one only when someone writes it; vfork and posix_spawn skip even that.›Dirty page trackinghardware-os · low: Write-protection or PML logs of modified guest/process pagesmmap and the page cachehardware-os · low: How read() and mmap reach file data through the kernel page cache, what readahead and madvise do, and why databases use their own buffer pool instead.›Ptrace process controlhardware-os · low: Ptrace: attach, read and write registers and memory, single-step, intercept signals+ 6 more primitives

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