Fix 1D multi-rank MPI_GATHERV bug in post-process silo output

[sbryngelson]

Summary

• Fix undefined behavior in s_mpi_gather_spatial_extents and s_mpi_gather_data_extents in src/post_process/m_mpi_proxy.fpp for 1D multi-rank runs
• The shared recvcounts/displs arrays are sized for grid defragmentation (m+1 per rank) but were being reused for scalar extent gathers where each rank sends exactly 1 element — a sendcount/recvcounts mismatch that is undefined behavior per the MPI standard
• Additionally, the 1D spatial extents path used a displacement multiplier of 4*displs instead of 2*displs, causing buffer overflows on the root process
• Replace MPI_GATHERV with MPI_GATHER + temp buffer for the 1D case, avoiding the mismatched shared arrays entirely

Bug details

The 1D -> 2 MPI Ranks test (UUID 0FCCE9F1) was failing nondeterministically on the Intel no-debug CI job (Github (ubuntu, mpi, no-debug, true)) with:

h5dump error: unable to open file ".../tests/0FCCE9F1/silo_hdf5/p0/50.silo"

This was a latent bug exposed when the Intel oneAPI packages were unpinned (from intel-oneapi-mpi-2021.7.1 to latest). Newer Intel MPI versions are stricter about the MPI_GATHERV sendcount/recvcounts mismatch, causing crashes that prevent silo files from being written. The bug was masked with GCC/OpenMPI (which tolerates the mismatch) and in debug mode (which changes stack/heap layout).

Test plan

• 1D -> 2 MPI Ranks test passes on Intel no-debug CI
• All other tests unaffected (2D/3D paths unchanged, 1D defragmentation functions unchanged)

Summary by CodeRabbit

• Refactor

  • Updated internal MPI communication handling for 1D simulations to optimize data gathering operations.

• Chores

  • Minor documentation updates in module declarations.

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[qodo-code-review]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 1 🔵⚪⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review

[qodo-code-review]

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[coderabbitai]

📝 Walkthrough

Walkthrough

Adds 1D-specific MPI gather handling to spatial/data extent collection in src/post_process/m_mpi_proxy.fpp, and updates a single comment in src/post_process/m_data_output.fpp. Functional behavior for multi-D remains unchanged; 1D gathers now use intermediate buffers and root-only assembly.

Changes

Cohort / File(s)	Summary
Module Comment Update src/post_process/m_data_output.fpp	Minor comment change in a module use statement; no semantic or behavioral impact.
MPI gather logic for extents src/post_process/m_mpi_proxy.fpp	Introduces 1D-specific gather flow: uses temporary ext_temp buffers and MPI_GATHER on non-root ranks, then root assembles per-rank extents; preserves existing MPI_GATHERV behavior for multi-dimensional cases. Changes affect routines handling spatial and data extents and add provisional buffers and conditional control flow for proc_rank == 0 assembly. Review focus: correctness of buffer sizing/initialization, root-only assignments, and unchanged multi-D semantics.

Sequence Diagram(s)

sequenceDiagram
    rect rgba(200,200,255,0.5)
    participant Rank_i as Non-root Rank
    end
    rect rgba(180,255,200,0.5)
    participant Root as Root Rank (proc_rank==0)
    end
    rect rgba(255,220,180,0.5)
    participant MPI as MPI Library
    end

    Note over Rank_i,Root: 1D path (n==0 && grid_geometry!=3) flow
    Rank_i->>MPI: MPI_GATHER(ext_scalar -> ext_temp[rank_index])
    MPI->>Root: deliver ext_temp array
    Root->>Root: assemble spatial_extents/data_extents from ext_temp per rank

    Note over Rank_i,Root: Multi-D path (n>0 or grid_geometry==3) flow
    Rank_i->>MPI: MPI_GATHERV(local_extent, recvcounts, displs)
    MPI->>Root: deliver gathered arrays
    Root->>Root: assign spatial_extents/data_extents from gathered arrays

Loading

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Poem

🐰 I hopped through buffers, soft and neat,
Collected extents on every seat.
For 1D I bundled, then handed to root,
Multi-D stayed steady, unchanged in its route.
A tiny comment flicked, and the meadow's complete.

🚥 Pre-merge checks | ✅ 3 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Merge Conflict Detection	⚠️ Warning	❌ Merge conflicts detected (11 files): ⚔️ .typos.toml (content) ⚔️ CMakeLists.txt (content) ⚔️ docs/Doxyfile.in (content) ⚔️ docs/documentation/case.md (content) ⚔️ docs/documentation/readme.md (content) ⚔️ docs/documentation/references.md (content) ⚔️ docs/documentation/visualization.md (content) ⚔️ src/post_process/m_data_output.fpp (content) ⚔️ src/post_process/m_mpi_proxy.fpp (content) ⚔️ toolchain/mfc/lint_docs.py (content) ⚔️ toolchain/mfc/params/definitions.py (content) These conflicts must be resolved before merging into master.	Resolve conflicts locally and push changes to this branch.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately and specifically describes the main change: fixing a 1D multi-rank MPI_GATHERV bug in the post-process silo output module.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description check	✅ Passed	The PR description is comprehensive and addresses all required template sections with clear technical detail about the bug, fix rationale, and test plan.

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[cubic-dev-ai]

No issues found across 1 file

Confidence score: 5/5

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

[Copilot]

Pull request overview

This PR updates a comment in the post-processing data output module (m_data_output) to slightly simplify the description of the m_global_parameters import.

Changes:

• Updated the inline comment on use m_global_parameters from “Global parameters for the code” to “Global parameters”.

[codeant-ai]

Nitpicks 🔍

🔒 No security issues identified

⚡ Recommended areas for review Namespace pollution The added module import brings in all public entities from m_global_parameters into m_data_output's namespace. This can cause accidental symbol collisions, make the code harder to reason about, and increase build time. Prefer restricting imports to only the symbols required.

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[codecov]

Codecov Report

❌ Patch coverage is 9.52381% with 19 lines in your changes missing coverage. Please review.
✅ Project coverage is 44.02%. Comparing base (0ba6c02) to head (0a79011).
⚠️ Report is 4 commits behind head on master.

Files with missing lines	Patch %	Lines
src/post_process/m_mpi_proxy.fpp	9.52%	18 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1138      +/-   ##
==========================================
- Coverage   44.03%   44.02%   -0.01%     
==========================================
  Files          70       70              
  Lines       20649    20658       +9     
  Branches     2053     2059       +6     
==========================================
+ Hits         9093     9095       +2     
- Misses      10368    10373       +5     
- Partials     1188     1190       +2     

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