Hosted GPU tier: endpoint, launcher, reaper, runner image, clients (GJOB-088) by arvandnavabi · Pull Request #1 · forcefieldsilicon/mdengine

arvandnavabi · 2026-09-06T20:32:48Z

Everything behind api.forcefieldsilicon.com and mdengine run --gpu, built 2026-09-03 → 09-06. Merge commit over unrelated histories (local lineage diverged after v0.6.1); merged tree == hosted-2026-09-06, zero conflicts.

hosted/endpoint: stdlib service (hashed API keys, credits ledger, /welcome instant-key page + Stripe webhook, job state machine, RunPod REST v2 launcher with ladder fallback, launch timeout, reaper), admin CLI, Caddy/systemd/bootstrap/deploy, hourly sqlite backup timer — 33 tests
docker/runner-gpu: pull-runner, pod-side TTL, Dockerfile.prebuilt + GHCR workflow → ghcr.io/forcefieldsilicon/mdengine-runner-gpu:ADA89
Clients: HostedClient in LAMMPSCore; CLI run --gpu / login / account / jobs; MCP host=cloud; app "Run accelerated"
hosted/CONTRACT.md: purchase flow + pod-lifecycle invariant

🤖 Generated with Claude Code

macOS MD workbench: Metal trajectory viewer (orbit/pan/zoom, timeline scrubber), mdengine CLI (info/export/decimate/run), and an MCP stdio server with a detached LAMMPS job runner. Fresh public-history repo; internal development history stays in the private working repo. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

…ld Silicon branding - Scrubber shows frame numbers under major ticks; major/minor grid spacing user-selectable (10/20/25/50% and 1/2/5/10%) - Right-side inspector (View menu, ⌥⌘I, or sidebar button): timeline grid, atom size, background, orbit speed, camera reset, element legend — live via the same UserDefaults keys as Settings - Brand: launching under ForceField Silicon (Gitinama Inc. trade name); bundle id com.forcefieldsilicon.mdengine; README/LICENSE/manual updated Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

…t agent-security note - Bundle fe_oxidation.in/.xyz: bcc Fe slab + O2 gas via ffield.reax.Fe_O_C_H (ships with LAMMPS - nothing redistributed); 391 atoms, 13 frames, runs in ~17s on 6 omp threads. First step of the metal-oxidation focus; Al/O ReaxFF pending a force-field licensing check. - CLI + MCP derive LAMMPS_POTENTIALS from the lmp install when unset, so decks can reference bare force-field names out of the box (verified end-to-end). - README: decks-are-programs security note now states plainly that an agent on the MCP server can submit decks that execute with user privileges; sandboxing is scoped to the hosted tier. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- LammpsDumpParser: ITEM: TIMESTEP blocks from dump atom/custom; direct, unwrapped, and scaled (box-mapped) coordinates; element column when present, numeric type token otherwise; rows sorted by id. TrajectoryReader sniffs dump-vs-XYZ, and every reader (app Load File, CLI info/export/decimate, MCP trajectory tools) now goes through it. Verified: scaled and element dump variants parse bit-identical bboxes to the XYZ reference. - Unknown element tokens (numeric types) get stable distinct hash colours. - docker/runner: two-stage LAMMPS stable_29Aug2024 OpenMP build, non-root, potentials baked in; README documents the hardening flags that constitute the sandbox (no network, read-only, resource caps). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

…robustness From peer-session shakedown on real oxidation dumps (RUN-010, id type x y z q): - Reported misparse (element=id, shifted coords, wrong counts) was a STALE RELEASE BINARY on PATH, not parser logic - release now rebuilt with every change; parser verified against 150-frame growing-count dump (8402->8421). - Real fixes/features: -h/--help on subcommands (was 'cannot read --help'); info prints the dump's per-atom field list and charge range; Arv carries q from native dumps; export/decimate --charges writes extended-XYZ (Properties=species:S:1:pos:R:3:charge:R:1); --elements O,Al maps numeric type tokens to symbols; rows with non-finite coords dropped (NaN-poisoned RUN-006 tail frames now parse with finite bbox). MCP: trajectory_info gains fields/charges, export_frame gains charges option. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

…dump) Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- Tests/AppTests: 11 XCTest cases over both parsers, reader sniffing, and the extended-XYZ writer (scaled coords, charges, id sort, growing counts, truncated in-flight tails, NaN drops); test target fixed to match its dir so 'swift test' actually runs it. All green. - MCP: new job_files tool (locate a finished job's outputs); refuse >2GB trajectory loads with actionable guidance (CLI too); serverInfo 0.5.0. - README: full MCP tool table, Claude Desktop registration, platform/limits. - GitHub Actions CI (build + test + release build on macos-14), activates on first push. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

… scaffold - Double-clicking .xyz/.extxyz/.lammpstrj/.traj/.dump now opens in MDEngine (CFBundleDocumentTypes + AppDelegate open-URL buffering for launch races) - scripts/make_dmg.sh packages dist/MDEngine-<version>.dmg with /Applications symlink; make_app.sh signs with DEVELOPER_ID + notarizes/staples when NOTARY_PROFILE is set, ad-hoc otherwise - Apple-day is config-only - Version 0.5.0 across app + MCP Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- Play/pause button beside the timeline with a Loop checkbox beneath it (checked = repeat from frame 1 when playback reaches the end; persisted) - Live following: a loaded file is polled every 2s; frames appended by a running simulation extend the timeline automatically (green 'live' badge). Camera and scrub position are preserved; if the user was at the final frame the view follows the new final frame. Skipped above 512MB. - Gesture terminology unified as Orbit / Pan / Zoom / Reset — window hint, manual, and code comments now all say 'Pan: double-click-drag' Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Root cause (hung on a 343MB growing oxidation dump): load() parsed on the main thread, then live-follow re-parsed the WHOLE file every 2s, also on the main thread. Fixes: - All parsing moved to a background queue; UI shows 'Loading …' and stays responsive; results published on main - Live-follow: in-flight guard (never overlapping parses), poll interval scales with file size (~45s at 350MB), 1GB follow cap, watch invalidated if a different file is loaded meanwhile - App-side 2GB open guard with decimate guidance (CLI/MCP already had one) - Arv drops its unused Identifiable UUID (millions of pointless allocations per parse); renderer builds GPU atom arrays per frame on demand instead of precomputing every frame (~350MB saved on 1276-frame trajectories) Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- Window scene replaces WindowGroup: macOS restoration was resurrecting blank duplicate windows; every window shared one trajectory anyway - View menu + inspector View section: Perspective/Orthographic toggle (⌥⌘P). Ortho frames the height perspective would see at the current distance, so zoom works and switching holds framing; point size pre-divided by distance to match apparent atom size - Window title shows the loaded file name Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Root cause (seen twice in screenshots: restored windows rendering window-bg gray): AppKit recreates the MTKView while the representable's Coordinator - and its uploaded-generation counter - survives. The fresh Renderer never received the trajectory and every draw early-returned without painting. makeNSView now resets the coordinator's generation so the next update re-uploads, and draw() always encodes a clear pass so an atomless view shows the intentional background instead of never painting. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

MTKView's internal display link silently never started for re-hosted windows (process sample showed zero draw calls while UI stayed live). The view now pauses the internal loop and owns a CADisplayLink created in viewDidMoveToWindow — rendering runs exactly while the view is in a window. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Tracked on every successful load (deduped, most recent first, persisted). Menu shows filenames with full-path tooltips; stale entries are pruned with an explanatory alert; Clear Menu resets. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- ZProfileAnalysis in LAMMPSCore: surface plane (top-5% substrate mean z), probe penetration depths, at-surface/in-flight counts, bound-probe mean charge, relative-z histogram; unit-tested; shared by app and MCP. - Inspector: Z-profile section (substrate/probe pickers, live stats, mini histogram) + Scale bar toggle in the View section. - Viewport scale bar: round 1/2/5x10^n A length, driven by camera distance and trajectory normalization via ViewportScale; exact at center depth. - MCP: z_profile tool (frame/substrate/probe args, defaults to the two most abundant elements). - Manual: Inspector analysis section. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Persisted as playbackFPS; retimes a running playback live. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… core - New MDRender target: RenderCore (one shader/camera-math/palette shared by the interactive view and offscreen rendering), OffscreenRenderer, and VideoExporter (AVFoundation H.264 MP4 + ImageIO animated GIF). - Annotations (scale bar + frame counter) baked by default, toggleable. - Cinematic orbit option; sprite sizes scale with output resolution so 4K exports match the window (maxPointSize uniform added to the shader). - App: File > Export Video... (shift-cmd-E) + Inspector Video-export section (resolution/fps/stride-with-auto/annotations/orbit, progress + cancel). - Viewport View menu snaps to canonical Top/Bottom/Front/Rear (z-up rig); Inspector panes 2-4 add extra fixed-view viewports in a CAD-style grid. - MCP: render_video tool (camera in degrees, stride, orbit, annotations, type->element mapping via 'elements'); element mapper moved to LAMMPSCore. - Manual: Views + Video export sections. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…ed state) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… viewport View menu Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… view picker Pane rows show a status summary (view name / Off) collapsed; pane 1 is the main viewport (always on, Free + snap presets synced with the View menu). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…pans Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…deo export second-to-last LazyVGrid collapsed rows after the first because Metal views have no intrinsic size; the viewport grid now uses explicit HStack rows. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… in Restore Defaults Home/reset camera = isometric (corner view, direction cosines 135/45/-45 to the axes). Camera rig gains a roll axis so Left keeps z up. Restore Defaults now resets pane 1-4 (Isometric main; 2/3/4 = Top/Left/Front, off). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>