Load-balance, active-box windowing, block-structured AMR

.lychee.toml

@@ -33,5 +33,6 @@ exclude = [
     "https://code\\.visualstudio\\.com/?$",           # Root page returns 403 to automated requests
     "https://stackoverflow\\.com",                    # Returns 403 to automated requests
     "https://marketplace\\.visualstudio\\.com",        # Returns 503 to automated requests
+    "_8md\\.html$",  # Doxygen auto-links backticked *.md filenames in prose to per-file pages it never generates for markdown inputs; the real md_*.html page links are still checked
     "https://web\\.eng\\.ucsd\\.edu",                    # San Diego mechanism page has an untrusted SSL cert
 ]

.typos.toml

@@ -7,6 +7,9 @@ extend-ignore-identifiers-re = [
 AttributeIDSupressMenu = "AttributeIDSupressMenu"
 
 [default.extend-words]
+# Cray CCE spells it this way in the lib-4425 runtime error; quoted verbatim in the AMR ledger so the
+# message stays greppable against what the machine actually prints.
+Unitialized = "Unitialized"
 INOUT = "INOUT"
 WRONLY = "WRONLY"
 nd = "nd"
@@ -22,6 +25,9 @@ TKE = "TKE"
 HSA = "HSA"
 infp = "infp"
 Sur = "Sur"
+thi = "thi"           # AMR clustering local: tagged-box hi index (tlo/thi)
+alo = "alo"           # AMR clustering local: accepted-box lo array (alo/ahi)
+thr = "thr"           # AMR clustering local: min-separation merge threshold
 equil = "equil"       # abbreviation for "equilibrium" (flamelet chemistry)
 chioces = "chioces"   # typo for "choices" - tests constraint key validation
 reqires = "reqires"   # typo for "requires" - tests dependency key validation

cmake/Fypp.cmake

@@ -119,6 +119,7 @@ macro(HANDLE_SOURCES target useCommon)
                                  -D MFC_COMPILER="${CMAKE_Fortran_COMPILER_ID}"
 				                 -D MFC_CASE_OPTIMIZATION=False
                                  -D chemistry=False
+                                 -D eos_state_dependent=False
                                  --line-numbering
                                  --no-folding
 								 --line-length=999

cmake/GPU.cmake

@@ -90,9 +90,15 @@ elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "Cray")
     add_link_options("SHELL:-hkeepfiles")
 
     if (CMAKE_BUILD_TYPE STREQUAL "Debug")
+        # -h bounds: array-bounds and pointer checking, the Cray equivalent of gfortran's
+        # -fcheck=bounds,pointer / Intel's -check bounds / NVHPC's -Mbounds, all of which the
+        # debug branches above already set. Cray was the ONLY compiler whose debug build had no
+        # bounds checking, so an out-of-bounds write showed up here only as a later, unrelated
+        # allocation failing with an uninitialised descriptor.
         add_compile_options(
                 "SHELL:-h acc_model=auto_async_none"
                 "SHELL: -h acc_model=no_fast_addr"
+                "SHELL: -h bounds"
                 "SHELL: -K trap=fp" "SHELL: -g" "SHELL: -O0"
         )
         add_link_options("SHELL: -K trap=fp" "SHELL: -g" "SHELL: -O0")

docs/documentation/amr_fine_distribution.md

@@ -0,0 +1,172 @@
+@page amr_fine_distribution AMR fine-level distribution
+
+# AMR fine-level distribution (design note)
+
+> **Design record / implementation note.** This documents the internal design and development of AMR
+> fine-block distribution across MPI ranks. For user-facing behavior and parameters, see @ref amr.
+
+## Problem
+
+MFC's AMR uses a **mirror decomposition**: the fine level reuses the coarse rank
+decomposition, so each rank owns exactly the fine cells over its coarse subdomain's
+intersection with the blocks (`s_amr_compute_isect` → `amr_rank_owns_block`). This makes
+coarse↔fine coupling entirely rank-local (zero communication) but leaves fine work
+**unbalanced**: if refinement concentrates in a sub-region, only the ranks owning that
+region do the fine advance while the rest idle. At scale this caps AMR speedup.
+
+## Target
+
+Give the fine level its **own distribution**, decoupled from the coarse decomposition, so
+fine blocks spread across all ranks by measured work — the AMReX per-level
+`DistributionMapping` idea. MFC already enforces an invariant that makes this far simpler
+than the general case: **blocks are kept ≥ `buff_size` apart** (regrid merge), so with
+**whole-block-per-rank** assignment there is *no fine–fine halo at all*
+(`s_mpi_sendrecv_amr_fine_halo` disappears). The only coupling that becomes communication
+is coarse↔fine, block-granular.
+
+## Coupling changes (whole-block-per-rank)
+
+| Step | Today (mirror, local) | Decoupled |
+|---|---|---|
+| Ownership | intersection, multi-owner (`amr_rank_owns_block`) | single owner (`amr_block_owner(k) == proc_rank`) |
+| Ghost fill / prolong (coarse→fine) | read local coarse `q_cons` | **gather** coarse patch (block + `buff_size` halo) from coarse owner(s) to block owner |
+| Reflux + restriction (fine→coarse) | write local coarse cells | **scatter** corrections from block owner back to coarse owner(s) |
+| Fine–fine halo | coarse Cartesian neighbors | none (blocks separated) |
+| Regrid | cluster (global) → mirror | cluster → **assign** (`amr_block_owner`) → **migrate** fine state |
+
+The gather/scatter is the only new communication surface. SFC-ordered assignment keeps a
+block's coarse patch on an SFC-nearby rank, bounding the cost. Conservation exactness is
+preserved because the scatter applies the *same* reflux add / restrict overwrite the
+mirror model applied locally — a pure data-movement change, not a numerics change.
+
+## Reuse
+
+`m_load_weight` (per-cell cost field) and `m_sfc_partition` (Morton order + chains-on-chains
+balanced partition) already exist as an init-time diagnostic. They become the fine-level
+distributor: feed the block list + per-block fine-work weight, return `amr_block_owner(:)`.
+
+## Phasing (each independently mergeable)
+
+1. **Distribution map, computed but not applied** (behavior-preserving). Add
+   `amr_block_owner(:)` + SFC assignment + an imbalance diagnostic; mirror ownership and all
+   coupling unchanged. Goldens bit-identical. *(this note's first increment)*
+2. **Apply the map**: switch `amr_rank_owns_block` to single-owner, add the coarse↔fine
+   gather/scatter, drop the fine–fine halo. Validate conservation + assignment-independence.
+3. **Dynamic rebalance each regrid**; optionally drop the fixed max-size slot pool for
+   right-sized boxes.
+
+Phase 2 carries the correctness risk (gather/scatter exactness) and is the checkpoint gate.
+
+## Phase 2 implementation status (branch `amr-fine-dist-wip`)
+
+Done and np=1 bit-identical (the gather reduces to the local read when the owner is the sole rank):
+
+- **Gather** (`s_amr_gather_coarse_patch`): per-block coarse patch `[region_lo-nmar : region_hi+nmar]`
+  assembled by a sentinel-MAX allreduce into `amr_cg` (a drop-in `scalar_field`). Contribution rule
+  `f_amr_own_coarse` claims interior cells + physical-boundary ghosts only (never inter-rank ghosts), so
+  there is one authoritative contributor per cell and no coarse-ghost halo dependence. `pull_host` flag
+  stages device-resident coarse to host for the runtime callers.
+- **Read side rerouted**: init/regrid host prolongation (`s_interpolate_coarse_to_fine`) and the runtime
+  device ghost-fill (`s_amr_fill_fine_ghosts`, stage + subcycle) now prolong from `amr_cg`.
+- **Restriction scatter** (`s_restrict_fine_to_coarse`): owner restricts on host into the `amr_cg_wp`
+  scratch (sole contributor), sentinel-MAX assembles, each rank overwrites the covered coarse cells it
+  owns. `s_restrict_all_vars` (old local device kernel) deleted.
+- **Fine–fine halo dropped**: `s_mpi_sendrecv_amr_fine_halo` calls removed (whole-block owner has no
+  continuation faces; blocks ≥ buff_size apart). Routine in `m_mpi_proxy` now dead — remove with the
+  reflux rework.
+
+Remaining (the conservation crux — reflux is NOT yet decoupling-correct):
+
+- **Reflux redesign.** `s_amr_reflux_face_flags` derives transverse participation `tv` from `amr_isect`,
+  which is owner-only in the decoupled model, so `own_lo/own_hi` (gating BOTH `creg` capture and the
+  reflux apply) is true only on the block owner — which does not own the outside coarse cells. Fix:
+  (1) recompute `tv` from the replicated block range (`amr_region_lo/hi(t)` overlap with `sidx:sidx+ext`),
+  so any coarse-outside-owner participates; (2) the owner captures `freg` (already correct) and BROADCASTS
+  it (allreduce, replacing the cart-neighbor `s_mpi_sendrecv_amr_reflux_faces`); (3) coarse-outside-owners
+  capture `creg` locally and apply `(freg-creg)` to their owned outside cells — verify the apply's
+  block-relative transverse indexing maps onto each receiver's local coarse slice. Conservation-critical.
+- **QBMM pb/mv** gather/scatter for np≥2 (currently local; non-polytropic QBMM+AMR now **gated fail-closed** at np≥2 in
+  `m_checker` — see "Known open" for the scatter follow-up).
+- np=2 conservation + assignment-independence validation once reflux lands (acceptance goldens:
+  BD21A5C0, 5EFB3277, 79B334C7 — they pass on `up/mega` via the mirror).
+
+## Phase 2 status: DONE and validated (reflux + scalability)
+
+The reflux redesign above landed (block-relative frame, participation from the replicated block range), and the
+whole coupling is now **point-to-point + right-sized** — the fine level distributes with no global collective per
+stage and per-rank memory that scales with the decomposition.
+
+- **Reflux**: `s_amr_reflux_face_flags` derives `tv`/`tlo`/`thi` from the replicated block range; `creg` capture +
+  both applies index block-relative; the owner's `freg` is delivered to the applying coarse-outside-owners.
+- **Point-to-point coupling** (replaced the correctness-first global collectives): a replicated coarse-decomposition
+  table `amr_decomp` (allgathered once at init) lets any rank compute which ranks hold a coarse-cell range.
+  - gather: owner `Irecv`s patch slices from the coarse-owners (`f_amr_rank_coarse_range`).
+  - restriction: owner `Isend`s each coarse-owner its covered slice (`f_amr_rank_interior`).
+  - reflux: owner `Isend`s `freg` only to participants (`f_amr_reflux_participates` = `own_lo/hi` parameterized by
+    rank via `amr_decomp`); `s_amr_p2p_reflux_faces` in `m_amr`.
+  Non-participants exchange nothing.
+- **Right-sized memory**: fine/coord/register arrays sized to `amr_maxc_fit` (min-over-ranks local half-extent = the
+  max block a rank can own, enforced by the scratch-constraint abort), not the global half-domain `amr_maxc` — about
+  `1/num_procs` (and `1/num_procs^(d-1)` for the face registers) the memory at scale.
+- **Coordinate fix**: `s_amr_swap_to_fine` extends fine ghost coords from the global boundaries `amr_g?cb` (the owner
+  need not hold the block's local coarse coord slice).
+
+Validated: np=1 1D/2D/3D goldens bit-identical; np=2 conservation exact in 1D (energy 1.9e-16) and 2D with
+transverse-face appliers (mass 1.4e-14), bounds-clean. `s_mpi_allreduce_array_max` remains only for the
+once-at-init coordinate assembly.
+
+## Phase 3
+
+1. **Block-splitting / tiling** (the coverage gap) — DONE.
+   - **Tiling**: `s_amr_tile_box` splits any box > `amr_maxc_fit` into contiguous ≤`amr_maxc_fit` sub-blocks, wired into
+     the initial-block setup and the regrid pipeline (non-IB); `s_populate_amr_fine` loops over all blocks refreshing
+     per-block mirrors via `s_amr_select_slot`.
+   - **Block-to-block fine-fine halo**: the fine advance is three driver phases — **fill all** (gather + coarse
+     ghost-fill), **`s_amr_fine_fine_halo`** (overwrite each seam ghost with the neighbour's *stage-entry* interior,
+     buff_size-deep, `MPI_Sendrecv` between owners or a local copy when one rank owns both; adjacency from the
+     replicated `amr_region_*_all` via `f_amr_seam`), **advance all** (RHS + RK). `s_advance_amr_fine_stage` split into
+     `s_amr_fine_stage_fill` / `s_amr_fine_stage_advance`.
+   - **Reflux seam-exclusion**: `f_amr_face_is_seam` drops a sub-block face shared with another fine sub-block from
+     `s_amr_reflux_face_flags` `own_lo/own_hi` (fine-fine, not c/f).
+   - **Owner-ordering fix**: `s_amr_assign_block_owners` runs BEFORE the owner-dependent `s_set_amr_fine_geometry` in
+     init, regrid, AND restart — the stale default (rank-0) owner map otherwise sized multi-block owners wrong (only
+     surfaces once tiling makes several blocks). Restart (`s_read_amr_restart`) is a two-pass read (regions → assign →
+     place data) for both the parallel_io and non-parallel_io paths.
+2. **Regrid cross-rank fine-state migration** — DONE (the stretched-np≥2 correctness fix). The regrid overlap-copy
+   preserves a covering old block's fine detail by reading `amr_slots(kk)%%q_cons_stor`, but that was local-only
+   (`if (.not. old_owns(kk)) cycle`). Under fine-level distribution an old block can be owned by a rank *other* than the
+   one now owning a covering new block, so the copy was silently skipped and the new block kept only its
+   coarse-prolonged values — **exact on uniform grids** (prolongation reproduces the fine field) but **~O(1e-4) wrong on
+   stretched grids** (prolongation is not exact). Fix: broadcast every old block's stashed fine state from its owner
+   into the replicated slot's `q_cons_stor` on all ranks (`num_procs>1`; no-op at np=1), copy the overlap from *every*
+   covering old block regardless of ownership, and take `old_ilo`/`old_ext` from the global replicated region (not the
+   owner-only isect). Correctness-first collective; a per-block P2P version mirroring `s_amr_gather_coarse_patch` is
+   future work. Validated (`-b mpirun`): 79B334C7 (1D stretched dynamic-regrid, 2 ranks) passes; F0DDE1B4 (np=1 twin),
+   5EFB3277 + BD21A5C0 (uniform np=2 tiled + restart), and the np=1 AMR batch all pass.
+
+## Golden regeneration note (tiling refines more at np=1)
+
+At np=1, tiling adds a capability the mirror never had: refining a tagged region **larger than `amr_maxc`** (half the
+domain per dim). The old regrid **clamped** any box to `amr_maxc_fit` (`hi = lo + amr_maxc_fit - 1`), so a big tag was
+only partially refined; block-splitting **tiles** it and refines the whole tag. Any np=1 AMR golden whose tag exceeds
+`amr_maxc(dim)` therefore changes (more cells refined) and must be regenerated with the tiled binary — an *intended*
+solution change, not a regression (the tiled advance is bit-identical to the mirror where footprints match, conservation
+is exact, and the seam is exact). Example: **B7704247** (2D stretched-y regrid) — the mirror refined `y4:23` (20 cells,
+clamped); tiling refines the full `y4:35` (`y4:19` + `y20:35`). Golden regenerated. np≥2 goldens are unaffected: the
+mirror splits a block across ranks there, so its footprint already matches tiling.
+
+## Known open
+
+- **QBMM pb/mv** gather/scatter for np≥2 — the pb/mv side-state coarse↔fine coupling (`s_amr_prolong_pbmv` /
+  `s_restrict_pbmv`) and the regrid QBMM overlap-copy are still LOCAL-only (same bug class as the q_cons migration
+  above). Now **gated fail-closed**: `m_checker` PROHIBITs `qbmm .and. .not. polytropic .and. num_procs > 1` for `amr`,
+  so np≥2 non-polytropic QBMM+AMR aborts at case load instead of silently coupling to the wrong coarse side-state.
+  Distributing pb/mv (gather/scatter/migration, mirroring q_cons) is future work for when np≥2 QBMM+AMR is needed and
+  testable. Polytropic QBMM+AMR at np≥2 is unaffected (its moments ride q_cons, which is already distributed).
+- **`amr_g?cb` lacks physical-boundary ghost coords** (sized `-1:m_glb`; the base grid's `x/y/z_cb` carry BC-aware ghosts
+  via `s_populate_grid_variables_buffers`). A near-domain-edge **whole** (untiled) block can drive the fine ghost-coord
+  build out of `amr_gycb` bounds — surfaced only by artificially disabling tiling; tiled blocks stay in bounds. Fix if
+  untiled near-edge whole blocks ever become reachable.
+- Minor: the P2P routines scan all `num_procs` to find participants (integer-only, O(P) per block per stage); the regrid
+  migration broadcasts (correctness-first, → P2P); patch-only device transfers instead of whole-field host round-trips
+  (GPU only); own-only slot allocation.