Fix 8 HPC-sensitive bugs: GPU kernels, MPI broadcast, domain decomposition

[sbryngelson]

User description

Summary

Batches 8 bug fixes that touch GPU parallel regions, MPI broadcasts, or compiler-sensitive code paths. These need HPC CI validation across NVHPC, CCE, and AMD compilers.

Not included: #1225 (3D viscous GPU private clauses) and #1181 (MUSCL-THINC right-state + GPU privates) remain as separate PRs due to higher risk — they add new private clause variables to GPU parallel loops, which is the most compiler-sensitive change possible.

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GPU kernel fixes

Fix z-boundary backward FD stencil (#1173)

• File: src/common/m_finite_differences.fpp
• Bug: At the z-domain boundary, the backward FD stencil reads fields(2) (y-velocity) instead of fields(3) (z-velocity), corrupting divergence/gradient calculations for all 3D viscous, hyperelastic, and hypoelastic simulations.
• Fix: fields(2)%sf(x, y, z-2) → fields(3)%sf(x, y, z-2)
• Impact: Runs inside GPU_PARALLEL_LOOP in m_viscous.fpp, m_hypoelastic.fpp, m_hyperelastic.fpp, and m_derived_variables.fpp. Affects every 3D simulation using these modules.

Fix GRCBC subsonic inflow using wrong L index (#1224)

• File: src/simulation/m_cbc.fpp
• Bug: In the GRCBC characteristic wave amplitude loop do i = 2, momxb, the code writes L(2) = ... instead of L(i) = .... Only the last species' wave amplitude survives; all others are overwritten.
• Fix: L(2) → L(i)
• Impact: Inside a GPU_PARALLEL_LOOP (collapse=2 CBC loop with L as private). Affects multi-species GRCBC subsonic inflow boundary conditions.

Fix G_K exponential degradation in damage model (#1227)

• File: src/common/m_variables_conversion.fpp
• Bug: G_K = G_K * max((1-damage), 0) is inside the do i = strxb, strxe stress component loop, applying the damage factor N times (exponential (1-damage)^N) instead of once.
• Fix: Move the damage line before the loop in both s_convert_conservative_to_primitive and s_convert_primitive_to_conservative.
• Impact: Inside GPU_PARALLEL_LOOP(collapse=3) with G_K as private. Produces exponentially wrong stiffness degradation for multi-component stress tensors.

MPI broadcast fixes

Fix bc_x%ve3 never MPI-broadcast (#1175)

• File: src/simulation/m_mpi_proxy.fpp
• Bug: A fypp loop broadcasts bc_x%ve2 twice and bc_x%ve3 (z-velocity component) never. All non-root ranks receive uninitialized garbage, which is then pushed to GPU via GPU_UPDATE.
• Fix: Change the duplicate 'bc_x%ve2' entry to 'bc_x%ve3' in the fypp broadcast list.
• Impact: Every multi-rank 3D simulation using velocity boundary conditions on x-boundaries reads garbage ve3 on non-root ranks.

Fix fluid_rho broadcast using MPI_LOGICAL instead of mpi_p (#1176)

• File: src/pre_process/m_mpi_proxy.fpp
• Bug: MPI_BCAST(fluid_rho(1), num_fluids_max, MPI_LOGICAL, ...) broadcasts a real(wp) array with the wrong MPI datatype. On 64-bit wp, MPI_LOGICAL (typically 4 bytes) only transfers half the bytes, silently corrupting density values on non-root ranks.
• Fix: MPI_LOGICAL → mpi_p
• Impact: MPI-implementation-dependent. May appear to work with some stacks (if byte layout aligns) and produce garbage with others. Affects pre-process perturbation IC density initialization.

MPI / compiler-sensitive fixes

Fix loc_violations used uninitialized in MPI_Allreduce (#1186)

• File: src/pre_process/m_data_output.fpp
• Bug: loc_violations is passed to s_mpi_allreduce_sum without initialization. Whether this matters depends on the compiler: GCC may zero-initialize stack variables in debug mode, NVHPC and CCE may not.
• Fix: Initialize to 0 and restructure as a local variable (not module-level, avoiding implicit SAVE).
• Impact: Pre-process grid validation. Compiler-dependent behavior makes HPC testing essential.

Fix domain decomposition overwriting muscl_order (#1229)

• File: src/common/m_mpi_common.fpp
• Bug: An else branch in s_mpi_decompose_computational_domain unconditionally sets recon_order = weno_order for all non-IGR cases, even when recon_type == MUSCL_TYPE where muscl_order was already correctly assigned.
• Fix: Remove the else branch (2 lines deleted).
• Impact: Wrong reconstruction order causes incorrect ghost-cell counts in domain decomposition for MUSCL cases. Needs multi-rank MPI validation.

Fix NaN check reading wrong index in MPI unpack (#1231)

• File: src/common/m_mpi_common.fpp
• Bug: ieee_is_nan(q_comm(i)%sf(j, k, l)) should be q_comm(i)%sf(j + unpack_offset, k, l) — the check reads a stale element instead of the just-unpacked one.
• Fix: Add unpack_offset to the appropriate index in all 3 directions (x, y, z).
• Impact: Only compiles under #if defined(__INTEL_COMPILER). Dead code on NVHPC/CCE/GCC, but the diagnostic would miss real NaNs in ghost cells on Intel builds.

Supersedes

Closes #1173, closes #1175, closes #1176, closes #1186, closes #1224, closes #1227, closes #1229, closes #1231

Test plan

• All GitHub CI checks pass
• HPC (NVHPC): 3D viscous case, GRCBC multi-species case, damage model case
• HPC (CCE/AMD): Multi-rank 3D with velocity BCs (validates bc_x%ve3 broadcast)
• HPC (any): MUSCL multi-rank case (validates domain decomposition fix)
• Verify no regressions in existing test suite

🤖 Generated with Claude Code

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CodeAnt-AI Description

Fix multiple HPC-sensitive bugs that caused corrupted 3D results and incorrect MPI communication

What Changed

• Corrected the z-boundary finite-difference term so the z-velocity is used, preventing corrupted divergence/gradient in 3D viscous and elastic simulations
• Restored correct MPI broadcasts and reductions so quantities are consistent across ranks: x-boundary third velocity is broadcast, fluid densities are broadcast with the correct numeric type, and local violation counters are zeroed before global reduction
• Fixed out-of-bounds/incorrect-index NaN checks in MPI receives so received data is validated correctly
• Adjusted damage-modifier order so damage properly reduces shear/elastic moduli when damage is active

Impact

✅ Fewer incorrect 3D divergence/gradient results
✅ Consistent boundary velocity and density values across MPI ranks
✅ Fewer spurious downsample warnings and reduction-related errors

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No issues found across 7 files

Confidence score: 5/5

• Automated review surfaced no issues in the provided summaries.
• No files require special attention.

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🔒 No security issues identified

⚡ Recommended areas for review Potential OOB (L array) The new GRCBC inflow loop assigns to L(i) for i=2..momxb and later accesses L at indices like momxb+1, momxb+2, and advxe. L is declared conditionally as dimension(sys_size) or dimension(20) (for AMD). Verify that in all build/config combinations L has sufficient length (>= max(advxe, momxb+2)) to avoid out-of-bounds writes/reads when the GRCBC branch is enabled. Also ensure GPU/private usage of L matches the declared size (private arrays in GPU regions must be properly sized). MPI count mismatch The broadcast of fluid_rho uses num_fluids_max as the count. If the actual number of fluids is num_fluids (broadcast earlier), broadcasting the full max length may send or expect uninitialised padding. Verify intended behaviour and consider using num_fluids to limit the count to active entries. Boundary stencil safety The z-boundary backward finite-difference stencil was corrected to reference fields(3) (z-velocity). Verify that the index z-2 is always valid for the code path that runs this branch (no out-of-bounds reads). Confirm the boundary indexes and halo/padded ranges used by the GPU kernel guarantee z-2 is in-bounds in all configurations (including small local subdomains). MPI broadcast list consistency The MPI broadcast list was corrected to include distinct bc_x%vb*/bc_x%ve* members (previously there was a duplicate). Confirm that the newly added members exist on the derived types, that their Fortran types match the MPI datatype mpi_p used in the call, and that the ordering/number of MPI_BCAST calls matches the receiving side expectations. A mismatch in types/counts or a missing member can lead to silent data corruption across ranks. MPI datatype correctness The call uses mpi_p as the MPI datatype token for fluid_rho. Confirm mpi_p matches the Fortran kind real(wp) (e.g. MPI_DOUBLE_PRECISION or an appropriate alias). A mismatch between mpi_p and the variable kind can lead to incorrect data transfer across MPI implementations or compilers.

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[Copilot]

Pull request overview

This PR batches several correctness fixes in GPU-executed kernels and MPI communication paths (broadcasts + halo exchange diagnostics), plus a domain-decomposition bug affecting reconstruction order—aimed at eliminating silent corruption and compiler/MPI-stack-dependent behavior in HPC runs.

Changes:

• Fix multiple GPU-path physics/kernel correctness issues (FD stencil component, GRCBC wave amplitudes indexing, damage-model shear modulus degradation).
• Fix MPI communication correctness (missing broadcast field, wrong MPI datatype, Intel-only NaN check indexing) and a domain decomposition reconstruction-order overwrite.
• Fix compiler-sensitive undefined behavior in pre_process by initializing a reduction input.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
src/common/m_finite_differences.fpp	Corrects z-boundary backward FD stencil to use fields(3) (z-velocity) consistently.
src/simulation/m_cbc.fpp	Fixes GRCBC subsonic inflow loop to write L(i) instead of overwriting L(2).
src/common/m_variables_conversion.fpp	Applies continuous damage factor to G_K/G once (outside the stress-component loop) to avoid exponential compounding.
src/simulation/m_mpi_proxy.fpp	Fixes user-input broadcast list to include bc_x%ve3 (was duplicating bc_x%ve2).
src/pre_process/m_mpi_proxy.fpp	Broadcasts fluid_rho with the correct MPI real datatype (mpi_p) instead of MPI_LOGICAL.
src/pre_process/m_data_output.fpp	Initializes loc_violations before MPI reduction to avoid undefined values on some compilers.
src/common/m_mpi_common.fpp	Fixes Intel-only NaN check to read the just-unpacked element and prevents non-IGR runs from clobbering MUSCL recon order.

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Claude Code Review

No issues found. Checked for bugs and CLAUDE.md compliance.