Reconcile bpsi/develop base into develop (bpsi↔fork merge baseline, CI-green) - #226
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For web-client EQ→TR file coupling. Adds ~25 lines to eq_api.f90. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Exposes the eq_save C-ABI symbol (added in Task 1.1 / SHA eb55843) as Eq.save(path): sets KNAMEQ then calls eq_save, raising EqlibError on non-zero rc. Adds ctypes prototype in _ffi.py and a TDD integration test that verifies file existence and non-zero size. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add handle_save handler and @mcp.tool() save registration; update --print-tools list and the test_print_tools_output count from 11 → 12. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
… channel Fortran's WRITE(6,...) maps to OS fd 1 (process stdout), which is the same fd the MCP stdio transport uses for JSON-RPC framing. Any Fortran diagnostic line written to fd 1 corrupts the channel and causes 'Connection closed'. Add _redirect_fortran_stdout_to_stderr() context manager to eq_mcp and tr_mcp servers: saves fd 1, dup2s fd 2 (stderr) over fd 1 before Fortran calls, then restores fd 1 afterwards. Applied to eq.run(), eq.save(), and tr.run(). Do NOT use fflush(NULL): on macOS/Python it also flushes the Python-level asyncio write buffer while fd 1 still points to stderr, sending the pending JSON response to stderr and causing Connection closed on the client side. Fortran WRITE(6,...) is line-buffered, so output reaches stderr before fd 1 is restored without an explicit flush. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Previous redirect protected fd 1 during the Fortran call but didn't flush libc's stdout buffer. Pending Fortran output then leaked into the MCP pipe after restoration, corrupting JSON-RPC on subsequent calls (notably get_state after run). Now we fflush() libc's C-level stdout FILE* before restoring fd 1; this does NOT affect Python's asyncio writes because Python writes via syscalls, not via C stdout. Also extend the redirect to cover set_param, set_param_str, set_params, get_state, and finalize in both eq_mcp and tr_mcp, since those handlers also call Fortran routines that may print.
Add setvbuf(stdout, NULL, _IONBF, 0) at server startup in both eq_mcp and tr_mcp so that any Fortran WRITE(6,...) output is emitted immediately rather than staying in libc's buffer after the fd-level redirect has been torn down. Also add _gfortran_flush_i4 (Fortran-level I/O buffer flush for unit 6) inside _redirect_fortran_stdout_to_stderr() so that gfortran's own internal buffer is drained into stderr before fd 1 is restored to the JSON-RPC pipe. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…imi#194) Adds belt-and-suspenders fd-isolation at module load time, beyond the per-call redirect already in 69d3d9d4. Disables _gfortran_flush_i4 in the long-lived server path to avoid SIGABRT during teardown. Uses os._exit(0) in main() to bypass Python finalizers that race with Fortran cleanup. Local-only patch on kyoshimi-develop; will be re-evaluated after upstream macOS build support (f8f5c9e) lands and macos_stubs.f90 is dropped (which may make the SIGABRT-on-teardown class obsolete).
…clickable GitHub links Per user request: 1. Remove the 'Lessons learned' frame. 2. Merge the 'Status' frame into 'Repositories & current result' -> a single closing frame 'Repositories, links & current result' (repo table + result badges + 'P0 delivered/P1 underway' + Thank you), placed after 'Future plan'. 3. Add clickable GitHub links via hyperref \href (colorlinks): the three GitHub repos, the merge PR k-yoshimi#1, and direct links to the engineering report + the slides on the fork. Adds \hypersetup. Now 15 frames; static-checked (env/brace/tikz balance, 5 \href, no bad URL char, underscore escaping) -- no local TeX to compile.
…he deck Per-slide (15) companion to 2026-06-30-merge-trx-beamer.tex: a short bilingual explanation of each slide plus a natural spoken speaker script in English and Chinese (中英对照演讲词). Drafted by a 4-agent workflow constrained to the verified facts brief (topology SHAs, 736-passed CI, tot_ht6m physics, the reactivity comparison, Option A), assembled + spot-verified.
…-4 merge inputs Pre-push review (codex) on the speaker notes caught two real inaccuracies that were also latent in the deck/report/plan: - [HIGH] the '<=1.2% over 1-30 keV' agreement was based on a log-log spline; libnf actually SPL1Ds the RAW <sigma v> vs log10(T) (trx/libnf.f90:327,414). Re-derived: at core/fusion temps (T>=5 keV) it holds ~1-2%, but the raw-value spline overshoots enormously at the low-T edge (>2000% at 1.5 keV) where the reactivity is negligible and no fusion occurs -- immaterial to fusion power. Corrected the claim in the deck (Slide 12), report (5.2), plan (RECORDED DECISIONS), and notes (Slide 12 EN+ZH). Option A is unaffected (indeed the analytic MDLNF is the smoother path). - [MED] the Motivation diagram/Slide-4 notes implied ats-fukuyama is a merge input; the actual merge parents are the Phase-L fork 58f1fe2 + bpsi fa9dd49. Relabelled the diagram node to the Phase-L fork; fixed Slide-4 notes EN+ZH.
…n consistency) Second-reviewer (codex) pass on the correction commit flagged three items: - [HIGH] 'the spline holds ~1-2% of SIGMAM' is ambiguous (reads as spline=1-2% OF SIGMAM). Reworded to 'stays within ~1-2% of SIGMAM' in report/beamer/plan. - [MED] Beamer Goal slide labelled the GitHub line as 'ats-fukuyama'; the active GitHub line is the Phase-L fork kyoshimi-develop (ats-fukuyama is only its stale ancestor, not a merge input). Relabelled in the deck + speaker-notes Slide 3. - [MED] Plan body still had actionable 'replace/retire MDLNF' steps contradicting the Option-A RECORDED DECISION. Added an OVERRIDE note + reworded Step-3 heading, sub-bullets, table row, and the sample commit message to 'additive, MDLNF kept'.
…econcile-2026-07 # Conflicts: # .gitignore
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Careful review completed. I found three correctness issues that should be addressed before merge:
I opened #227 with reproduction details, required fixes, and regression-test expectations, and assigned it to @HengyuLi-Ozaki-lab. Please also run the required GitHub Actions against the updated PR head. At review time, this PR reports no checks for fb80991. Review outcome: changes requested pending #227. |
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Non-MCP follow-up review is complete. It found additional merge-blocking regressions outside the MCP servers, including:
I opened a separate follow-up issue for the full evidence, affected lines, verification results, and acceptance criteria: #228 Recommendation remains do not merge yet. This issue is separate from the MCP findings tracked in #227. |
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A further non-MCP audit found six additional defects, including three new P1 merge blockers:
The additional P2/P3 findings cover FPX debug output inside deep NBI loops, WF2DT use of deallocated RGB arrays, and validation of the wrong WIM record index. Full evidence, reproduction output, affected lines, and acceptance criteria were added to #228: The recommendation remains do not merge yet pending the P1 fixes. |
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Clavius runtime verification found three additional P1 merge blockers and one regression-harness defect at the current PR head
WIM wave-dump generation/conversion and changed W1, WM/WMX, WR/WRX, FP, and OB library builds succeeded on clavius. WF2DT end-to-end plotting remains unverified because all committed GLAST inputs stop at the antenna setup error. Full reproduction details and acceptance criteria: Recommendation remains do not merge yet until the P1 items and regression contract are resolved. |
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An independent re-audit at the current head
Details added to #228 (findings 18-19): #228 (comment) Additionally, five defects in the Positive verification results: |
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A fifth review wave audited defect classes not covered by the earlier findings: statement-level verification of the equ/ fixed→free-form conversion against the original sources, a repository-wide impact sweep of the newly introduced shared symbols and moved APIs (including unmodified components), and CI-workflow logic. It found four additional P1 merge blockers, nine P2 defects, and ~25 smaller issues at the current PR head
Notable P2s: the plasmaf-overflow this PR fixes in Full evidence, line references, and acceptance criteria:
Recommendation remains do not merge yet until the P1 items across #227/#228 are resolved and the workflows run green on the PR head. |
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A fresh re-review of the unchanged head The PR moves Fresh clavius results: Both runs calculate and reach Full evidence and acceptance criteria were added as finding 32: The same re-review also reconfirmed the existing EQ regression failures, TRX input error, TXNEW |
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Thank you both — five review waves plus an independent re-audit, including real runs on clavius, is far more scrutiny than this PR had any right to expect, and it found real problems. I've now worked through every finding in #227/#228/#229 and re-verified each one against Below: what's ours and being fixed, one thing I need from a maintainer, two corrections with reproductions, and a proposal for how to land this. 1. What I need from a maintainer (this is the blocker)The workflows are not failing — they were never allowed to start. Zero jobs were dispatched. This also gates the EQ baseline regeneration you asked for (§4): 2. Confirmed ours — being fixedFour P1s are unambiguously mine, and one methodology failure that I think is worse than any of them. 2.1 2.2 MCP import mutates process-wide stdout (#227 item 1). Confirmed. 2.3 tr_mcp lifecycle is self-contradictory (#227 item 2). Confirmed. 2.4 2.5 The EQ baseline gap — you're right, and my justification was invalid. The decision record for the One correction to the root-cause attribution, though: it isn't Plan: regenerate 2.6 One defect nobody found: 2.7 CI never compiles 3. Two corrections, with reproductions3.1 The The mechanism claim doesn't reproduce. Same result on macOS/BSD There is a small real residue nobody flagged: on a repo literally named 3.2 There's a hard check: Suggest closing that item as not-a-defect. (The Fortran-side 80-char limit is real and undocumented at the C ABI — worth a doc note, but nothing is silently truncated.) 4. Proposed de-scoping (evidence for each)
For the rest: of 162 changed files, 94 are byte-identical to bpsi My proposed split for those: fix here anything that breaks the build or is unguarded UB on a default path — findings 1, 5, 8, 9, 10+15, 12, 14, 20, 21, 23, 24 (~9 small changes; note 10 and 15 must land together, since routing 5. How I'd like to land thisCopilot declined this diff for exceeding 20,000 lines, and that's a fair signal. But I don't think splitting #226 helps: the bulk is Instead I propose buying review confidence with CI rather than with smaller diffs:
If you'd rather I fold everything into #226 instead, I'm happy to — just say which you prefer. Sorry for the volume of work this created. The |
…not deallocate Addresses k-yoshimi#228 finding 32 (P1, integrated-lifecycle regression). The merge landed bpsi's ownership move of DEALLOCATE_TRCOMM from the standalone program into the reusable menu. bpsi can do that safely because bpsi has no integrated TOT regression path (`git ls-tree -r fa9dd49 tot/` = 12 files, no totregress.f90; k-yoshimi's tree has 29 and does). On this tree, tot/totmenu.f90:48 calls tr_menu, so exiting the TR submenu destroyed RN/RT/AJ/QP before TOT could read them. Reproduced locally before the fix, on tot_demo2014_short (the input enters `tr`, runs, then `x` exits the submenu — exactly the 9000 path): TOT_REGRESS_DUMP=1 tot/tot < test_run/inputs/tot_demo2014_short.in -> TR_PRESENT=0 (matches the reviewer's clavius result) After: -> TR_PRESENT=1, NT=100, NRMAX=50, NSMAX=2, WPT=1.6203558665082904E+00 Fix: drop the call from tr/trmenu.f90's 9000 handler and restore it in tr/trmain.f90 before STOP, i.e. back to the arrangement develop already had. Cleanup stays owned at the other two layers too — tr/tr_api.f90 (tr_finalize) for the library/MCP path, and tr/trcomm.f90's ALLOCATE_TRCOMM is self-healing on re-entry — so removing the menu-level call leaks nothing. Verified the standalone path still runs clean (tr2 on tr_m0904: exit 0, full dump, no double-free). The USE list keeps only GTCPU1 + DEALLOCATE_TRCOMM; NFM/NGM/NSM/NTM are not referenced anywhere in trmain.f90 (grep confirms zero hits).
Addresses k-yoshimi#227 item 1 (P1). eq_mcp/server.py and tr_mcp/server.py performed the JSON-RPC fd-isolation dance -- dup(1), dup2(2, 1), rebuild sys.stdout -- at *module scope*. Importing either module therefore mutated the host process: pytest collection, an embedding application, or a bare `python -c "import eq_mcp.server"` had its fd 1 redirected to stderr and its sys.stdout replaced, irreversibly and process-wide. The shim now lives in `_install_fd_isolation()` (idempotent, sets _FD_ISOLATION_INSTALLED) and is called from main() immediately before `build_server()` / `server.run()` -- i.e. only when the module actually runs as the stdio server. The --help / --print-tools / MCP-SDK-missing paths all return before that point, so the previous `_is_oneshot` guard is no longer needed and the dead `_ONESHOT_FLAGS`/`_is_oneshot` pair is removed. One knock-on: `_HAS_GFORTRAN_FLUSH` was forced False at import time whenever the permanent redirect was active (the flush is unnecessary once fd 1 is stderr, and _gfortran_flush_i4 SIGABRTs 10-40% of the time on this libgfortran). That decision can no longer be made at import time, so it moved to the call site in `_redirect_fortran_stdout_to_stderr`: `if _HAS_GFORTRAN_FLUSH and not _FD_ISOLATION_INSTALLED`. Same behaviour for the server, correct behaviour for an importing process. Verification: - New regression test python/mcp-servers/eq_mcp/tests/test_import_isolation.py probes both modules in fresh subprocesses. It PASSES with this change and FAILS on the pre-fix code (checked by stashing), so it genuinely pins the contract rather than just passing. before: fd1_unchanged=False sys.stdout_unchanged=False (both modules) after : fd1_unchanged=True sys.stdout_unchanged=True (both modules) - The real stdio path is unaffected: with eq/libeqapi.so built, test_get_psi_rz_tool.py::test_get_psi_rz_via_mcp -- which spawns the server as a subprocess and speaks JSON-RPC over the pipe -- passes. That test is the one that would break if the isolation were lost. - Full suites: eq_mcp + tr_mcp = 77 passed, 3 skipped, 0 failed (--forked). (Without a built libeqapi.so the psi_rz test fails on both the pre- and post-fix code with a JSONDecodeError -- a missing-.so artifact, not a regression.)
Addresses k-yoshimi#227 item 2 (P1). handle_finalize marked the Trlib handle closed *without* calling tr_finalize, to dodge a SIGABRT in the Fortran cleanup path. Two consequences, both real: - tr_init is idempotent (tr/tr_api.f90:77 "already initialized, just return OK"), so leaving g_initialized set made a subsequent init a no-op that did not restore defaults. Verified: set NSMAX=3, finalize, init -> still 3. - handle_run_and_get_state needs a genuine reset for its documented fresh-init contract, so it kept calling STATE.close() -- the very tr_finalize path handle_finalize was avoiding. The server contradicted itself, and eq_mcp (plain STATE.close()) disagreed with tr_mcp. The SIGABRT it was working around is a double DEALLOCATE, and it is already fixed on this tree: DEALLOCATE_TRCOMM gained an idempotency guard (`IF(.NOT.ALLOCATED(PNSS)) RETURN`, tr/trcomm.f90) that develop does not have -- `git show 4a5d977:tr/trcomm.f90` has the unguarded body. tr/tr_api.f90 itself is unchanged vs develop, so the fix is entirely in the deallocator. Measured on the merged tree (gfortran-15, macOS, fresh subprocess per run): init + close 40/40 exit 0 init + run(1) + close 40/40 exit 0 init + run + close + an explicit second tr_finalize 30/30 exit 0 (2nd returns TR_OK via the not-initialized guard) So both lifecycle paths now use the honest one: handle_finalize is `with _redirect_fortran_stdout_to_stderr(): STATE.close()`, structurally identical to eq_mcp's. Contract restored -- set NSMAX=3, finalize, init -> 2. New tests in python/mcp-servers/tr_mcp/tests/test_lifecycle.py cover finalize->init reset, finalize idempotency, and run_and_get_state isolation. The reset test FAILS on the pre-fix code (checked by stashing) and passes now. Full eq_mcp + tr_mcp suites: 83 passed, 0 failed. Caveat worth stating: the crash-rate measurements are macOS/gfortran-15. The authoritative check is this PR's Linux/gfortran-13.2 CI, which is still awaiting the fork-PR workflow approval.
Addresses k-yoshimi#227 item 3 (P1). eqfile::EQSAVE is a bare external subroutine with no IERR out-argument: on an FWOPEN failure (blank KNAMEQ, missing directory, permission denied) it prints a message and RETURNs, leaving no file. eq_api_save then returned EQ_OK unconditionally. Our own docstrings admitted this on both sides -- eq_api.f90 said "EQ_OK is returned unconditionally ... The caller is expected to verify the file's existence", and eqlib.py said "callers should verify file existence after the call". Shipping a known false-success with a comment instead of a guard was the wrong call. Fortran layer (eq/eq_api.f90) -- verify the artefact rather than trust the call: - blank KNAMEQ -> EQ_ERR_INVALID - no file, or a zero-length file -> EQ_ERR_CALC_FAILED - otherwise -> EQ_OK EQSAVE's own signature is untouched, so eqmenu.f90:98 (`CALL EQSAVE`, the interactive path) is unaffected. Python layer (python/eqlib/eqlib.py) -- the same check after raise_for_rc, as defense in depth so a stale libeqapi.so built before this fix also cannot report a success that did not happen. Both docstrings rewritten to state the contract instead of apologising for its absence. Verified against the rebuilt .so: missing directory -> EqlibCalculationFailedError (rc=3) blank path -> EqlibInvalidParamError (rc=1) valid path -> OK, 45956-byte file written Control (pre-fix eq_api.f90 + eqlib.py restored, .so rebuilt): save() to a missing directory returned SUCCESS -- exactly the reported defect. New regression tests in python/eqlib/tests/test_save.py cover the missing directory and blank-path cases. Suites: eqlib + eq_mcp + tr_mcp = 133 passed, 2 skipped, 0 failed.
… 6 more components Addresses k-yoshimi#228 findings 1, 20, 21 (P1). The merge carries two bpsi changes to shared pl state: - plcomm_parm gained a bare PT(NSM) (pl/plcomm.f90:66). develop has no PT in that declaration block at all -- verified with `git show 4a5d977:pl/plcomm.f90`. - pl_view moved plparm -> the new pl/plview.f90 (develop's plparm has 3 refs; head has 0). Our earlier CI-greening commits (17f21f2, 9242c12) contained this for ti, wm, wmx and four menus, but only for the components CI builds. CI never compiles trm/ wmf/ wmfn/ wmseki/ dpseki/, so the rest went unnoticed. All six victim files are byte-identical to develop -- they are untouched casualties of a change we are the courier for. Reproduced before fixing (`make -C <dir>` from a clean worktree): trm Error: Symbol 'pt' conflicts with symbol from module 'plcomm_parm' wmf Error: Incompatible ranks 0 and 1 in assignment (wmfem_vmec.f:517) wmfn Error: Incompatible ranks 0 and 1 in assignment wmseki Error: Incompatible ranks 0 and 1 in assignment dpseki Error: Symbol 'pl_view' referenced at (1) not found in module 'plparm' Fixes use the pattern the earlier commits established: - `USE plcomm,pt_pl=>PT` / `USE dpcomm,pt_dp=>PT` in trm, wmf, wmfn, wmseki. wmf needed BOTH routes (it imports plcomm and dpcomm; dpcomm_parm re-exports plcomm_parm's PT) -- the same double rename wmx/wmcomm.f90:11,24 already has. This restores the pre-merge meaning exactly: before bpsi added PT to plcomm_parm, bare PT in these legacy fixed-form files was an implicit local scalar, which is what the rename gives back. - `USE plview,ONLY: pl_view` in dpseki/dpmenu.f and dpseki/dpcont.f (the latter split from a combined `USE plparm,ONLY: pl_parm,pl_view`). Separately, wm/wmsetg.f:310-311 is the silent variant of the same defect and is the more dangerous one: `PT=(PTPR(1)+2*PTPP(1))/3.D0` is a legal Fortran broadcast that overwrites the WHOLE shared PT(NSM) array with the electron temperature, and `PT(1)` then reads it back. It compiles cleanly, so CI could never have caught it -- wm builds green today. Changed to the local scalar PTAV, matching the correct sibling at wm/wmsetg.f:185-186 (and wmvmec.f:530, wmbooz.f:570). After: trm, wmf, wmfn, wm, wmx, ti all compile. dpseki compiles (its remaining link failure is a missing ../mtxp/libmtxbndmpi.o, an MPI artifact not built in this worktree, not a code defect). Two things found while doing this that are NOT ours, for the de-scope list: - fpx fails on fpcomm.f90:621 `IF(ALLOCATED(SAVPOS))` where SAVPOS is not declared ALLOCATABLE in that scope. fpx/fpcomm.f90 is byte-identical to develop, so fpx has never compiled -- pre-existing, unrelated to plcomm. - wmseki, after the PT fix, next fails on 'pl_wmxprf'/'wmspl_prof' not found in module plprof. pl/plprof.f90 is byte-identical to develop -- also pre-existing. wmseki additionally has no mod/ directory in the repo while 55 other mod/ files are tracked; that packaging gap is left alone here. Full python suite: 601 passed, 169 skipped, 0 failed.
…den its fallback Addresses k-yoshimi#228 findings 10 and 15 (P1). They must land together -- see below. Finding 10: the new MDLPCK=2 block-tridiagonal solver calls raw DGETRF/DGETRS (7 sites, txnew/txexec.f90:1197-1271). Nothing in the tree defines those symbols, and the repository default is a LAPACK-free build (make.header.org:13-14 `LAPACK = nolapack.f`, `LIBLA =`), so `make -C txnew` cannot link at all. Every other solver in the tree goes through the LAPACK_* shim in lib/ instead -- which had wrappers for DGBTRF/DGBTRS/DGBSV/DSBTRD/DSTEBZ/DGESV but none for DGETRF/DGETRS. Added the two missing wrappers to lib/lapack.f (real calls) and lib/nolapack.f (INFO=-1 stubs, matching the file's existing style), and pointed the 7 call sites at them. Finding 15: fixing 10 alone would have converted a loud link error into a silent wrong answer. TXSOLV_BLOCKTRI maps a LAPACK failure to `IER = 200000/220000 + 1000*k + info` (txexec.f90:1199,1212,1222,1229) -- always POSITIVE -- while the caller's fallback fired only on `ierr_la == -2` (txexec.f90:237, the "BL has non-zero far blocks" case). So with the nolapack stubs returning INFO=-1, IER lands at 200000+1000k-1, the fallback is skipped, and control drops into the error branch with the solution vector never solved. The fallback now fires on any non-zero ierr_la, so a factorization failure -- from the stubs or from a genuine numerical problem -- degrades to the band solver (LAPACK_DGBSV/GBSV) that the rest of the file already relies on. If that also fails, the existing `if(ierr_la /= 0)` error branch still catches it. Provenance: txnew/txexec.f90 is byte-identical to Kyoto bpsi/develop (fa9dd49); develop (4a5d977) has no raw LAPACK calls in txnew at all. This is Kyoto's code that our merge is the courier for, but it breaks the default build, so it is fixed here rather than deferred. Verified: - `make -C txnew libtx3.a` -> exit 0 (was: "Undefined symbols ... _dgetrf_"). - `nm -gU lib/libtask.a` shows _lapack_dgetrf_ / _lapack_dgetrs_ in BOTH the real-LAPACK build and a `LAPACK=nolapack.f` rebuild. - No undefined _dgetrf_/_dgetrs_ remain in the txnew objects.
Addresses k-yoshimi#228 findings 5, 8, 9, 12, 14, 18, 19, 23, 24. All ten sites are byte-identical to Kyoto bpsi/develop (fa9dd49) -- this merge is their courier, not their author -- and each was independently reproduced before patching. equ/ [9, P1] equ_convert.f90:42 `DO n=n,LEN(line)` reads n uninitialised as its own loop bound. Reproduced: gfortran -Wuninitialized flags it; the same extract with `DO n=1,` compiles clean. Garbage > 256 => zero commas => ALLOCATE(...(0)) then a read of element 1; garbage < 1 => out-of-bounds substring. Bound is 1, not 5: the record is `hdr,L1,...,Ln` with the header's comma at column 4 and no trailing comma, so counting from column 1 yields exactly ndata commas for ndata labels. [18] equpl.f90:91 restores `plasmaf%nrmax=0`, dropped by the F77->F90 conversion (`git show 7d18264:equ/eqpl.f`:91) while the sibling eqpl_get kept it at :163. NOTE FOR THE REVIEWER: this is symmetry / F77 fidelity, NOT the claimed P1. Against the bpsd this build pins (../bpsd @ 6a85985), bpsd_get_plasmaf takes its argument intent(out) and assigns nrmax unconditionally, so the store is provably dead -- demonstrated with a standalone intent(out) test. It was load-bearing under an older intent(inout) bpsd, which is why the line existed. wf2dt/ [8, P1] wfgsubn.f90: the PABS plot wrote rnode into BOTH coordinates (every triangle drawn at y=R, collapsing the mesh) and passed a 3-element vertex array to poly2D(...,4). Elements are triangles (ndelm(1:3,...)), and the fill loop above is DO i=1,3, so 3 is the true count and the 4th read was pure garbage. Now ya <- znode and poly2D(...,3). [12+31] wfglib.f90: rgbf_a/rgbf_b DEALLOCATEd rgb_a/rgb_b and then read them in the clamp branches below (f < f_a(1) fires on any negative pabs) -- rgbf_c already had this right and frees only the scratch array. Same patch also unwinds all three SPL1D failure paths, which previously RETURNed with the arrays allocated and INIT still 0, so the next call re-ALLOCATEd allocated arrays and aborted. [19] wfglib.f90:567-568 `1.-12` parses as -11.0, so `ABS(fmax).LE.-11.0` is never true and the near-zero colour-range fallback never fired. Now 1.D-12. (Provenance note: terasakisatoshi filed this as PR-introduced; it is byte-identical to fa9dd49, i.e. carried, not authored here.) trx/ [5, P1] trpnb.f90:477 zero-initialises VCD3/VCT3/VCA3 before the three IF(NS_x.NE.0) guards. develop assigns all three unconditionally; the new guards leave a term undefined when a species is absent, and VC3 = VCD3+VCT3+VCA3 is then used as a divisor. [24] trprep.f90:131 `DO NS=1,MAX(NSMAX,4)` -> `DO NS=1,NSMAX`, restoring develop's bound. Labelling species past NSMAX defeats libnf's presence STOP and enables out-of-bounds writes in tr_pnf. Applied TOGETHER with finding 5 by design: reverting the bound without the zero-init would widen finding 5's exposure. [23] trexec.f90: the new "Kawamura correction" dropped the NSTN.EQ.0 guard every sibling branch has, reading X(0) when the equation is excluded. Restored, with develop's pre-Kawamura formula in the NSTN==0 arm. [14, P1] in/test01.in, in/test02.in: `model_nnf(1)=4` is not in NAMELIST /TR/, so every shipped run printed '## PARM INPUT ERROR' and then continued with an unintended configuration. The variable is a late-allocated ALLOCATABLE outside the namelist scope and no physics reads it, so removing the key is the correct fix rather than extending the namelist. Verified from trx/ (the cwd the binary needs -- running elsewhere makes GSFOPN fail and the menu never reaches the namelist read, which invalidated my first attempt at this check): before: PARM INPUT ERROR = 1 on both inputs after : PARM INPUT ERROR = 0 on both inputs Verification: equ, trx, wf2dt, trm, wm, wmx, wmf, wmfn, tot, lib, pl, eq, tr all compile. Python suite 601 passed / 0 failed. TOT still TR_PRESENT=1. The tr_m0904 TR_REGRESS dump is byte-identical to the pre-refactor baseline (sha256 56d09887...cb9ad869), i.e. none of this perturbs tr numerics. Separate observation for the PR thread, NOT patched here: develop's trx/in/test01.in set `model_pnf=1`; bpsi's copy does not, and the merge took bpsi's file, so the shipped sample no longer exercises the fusion model at all. That is a test-coverage regression worth a maintainer decision rather than a unilateral edit.
… step Two CI changes, both prompted by PR k-yoshimi#226's review. 1. New `uncovered-modules-build` job (compile-only). The pytest job builds tr/fp/ti/wr/wrx/eq/tot, and `make -C tot libs` adds pl/dp/wmx/ob/adf11/adpost. equ/ trx/ txnew/ wf2dt/ wim/ wm/ trm/ wmf/ wmfn/ have had NO CI coverage at all -- and every one of them is substantially touched by the bpsi merge. That gap is the structural reason a batch of hard compile/link breakages reached human review in k-yoshimi#226 instead of the pipeline: a bare PT added to plcomm_parm colliding with local PTs (trm, wmf, wmfn, wmseki), pl_view moving plparm->plview without migrating its callers (dpseki), and raw DGETRF/DGETRS with no LAPACK shim (txnew). Nine directories, library targets only -- the standalone binaries pull in graphics (gsaf) and MPI link paths this headless runner deliberately does not provide, while compiling every source is what catches the defect class above. Deliberately excluded, with the reason recorded in the job comment so the omission is auditable rather than silent: fpx, wmseki and dpseki do not build on `develop` either (their failing files are byte-identical there), so including them would make the job red on day one for defects this PR did not introduce. All nine targets verified green locally before wiring them up. 2. Path-equality guard on the `../task` symlink step (both workflows). The step's own comment claimed it was a "no-op when the repo is already named task". It is not: when the destination is a real directory, `ln -sfn` falls back to link-into-directory mode and creates a self-referential `task -> .` symlink INSIDE the checkout. Reproduced on GNU coreutils 8.32 (the CI toolchain) and on BSD ln -- both exit 0, so it is silent. Harmless for the current job graph, but a symlink loop for any future recursive find/tar/artifact-glob step. Now guarded on path equality, and both stale comments corrected. Note for the record: this is NOT why PR k-yoshimi#226 reports no checks. That run (29195792410) is `conclusion: action_required` with `{"total_count": 0, "jobs": []}` -- the fork-PR approval gate, so no step ran at all. regen-baselines.yml is additionally `workflow_dispatch`-only and can never contribute a PR check.
…atch
Two independent reviews found two blockers and several real gaps. Both blockers
were in work I had already called verified, so the corrections are recorded here
rather than folded silently into the earlier commits.
BLOCKER 1 (channel A) — the new CI job could not have passed.
My "all nine targets verified green locally" was a dirty-worktree false green:
this worktree carries untracked trlib/mod/*.mod and equ objects from earlier
builds. Re-tested properly in a PRISTINE clone of HEAD, 3 of 9 failed:
trx, trm Cannot open module file 'cytran_mod.mod'
equ Cannot open module file 'aaa_mod.mod'
Root causes, both real Makefile facts rather than environment:
- trx/ and trm/ compile against trlib's .mod files via `-I../trlib/$(MOD)`,
and neither libtr2.a target bootstraps trlib. Only trlib/mod/dummy is
tracked, so a fresh clone has none of them.
- equ/'s `libequ.a: $(OBJS)` covers SRCS only, but equcomm.f90 -- which
defines aaa_mod, USEd across SRCS -- lives in the separate SRCC/OBJC
variable, so the library target alone can never build from clean.
Added `make -C trlib libtrm.a` and `make -C equ obj/equcomm.o` to the support
step. Re-verified in a pristine clone: 9/9 green, job exits 0.
BLOCKER 2 (channel B) — k-yoshimi#228 finding 21 was only 2 of 6 sites.
b4c07ef migrated dpseki/dpmenu.f and dpseki/dpcont.f but missed
fpx/fpmenu.f90:23, fp.anzai/fpmenu.f90:19, fp.nuga/fpmenu.f90:19 and
fp.ota/fpmenu.f90:19 -- all four still `USE plparm` and `CALL pl_view`, and
pl/plparm.f90 no longer re-exports pl_view, so they carry the identical hard
compile error the commit claimed to have swept. Now routed via `USE plview`
like fp/fpmenu.f90 already was.
Also fixed:
- [A-MED] txnew/txexec.f90: the widened fallback `ierr_la /= 0` also swallowed
IER=-1 (BL/BX too small, :1092) and would have called LAPACK_DGBSV with the
very dimensions just found unsatisfied. Narrowed to `== -2 .or. > 0`, so the
dimension error keeps its loud path.
- [B-MED] eq_save's artefact check could not tell "written now" from "already
there": channel B reproduced a false success by saving once, setting MODEFW=3
(so FWOPEN refuses to reopen), and saving again -- the first run's file made
both the Fortran INQUIRE and the Python os.path check pass. EQSAVE now takes a
real IERR out-argument and propagates FWOPEN's failure; eq_api_save honours it
before falling back to the artefact check. Both call sites updated
(eq/eqmenu.f90:98, eq/eq_api.f90). New regression test reproduces the exact
repeat-save scenario and asserts the earlier file is left untouched.
- [A-MED] Stale docstrings in eq_mcp/tr_mcp still said the fd shim runs "at
startup (BEFORE any mcp/logging import)" and "at module load time", and that
the context manager is "effectively a no-op" -- false for an importer, which
is now exactly the case it protects. Rewritten.
- [A-MED] tr/trcomm.f90's idempotency-guard comment cited "tr_menu calls this
unconditionally at exit" -- the call 98ba1e2 removes. Now cites trmain and
tr_api_finalize.
- [B-LOW] "wm owns a local PT" in wmf/wmfn/wmseki was wrong: those trees have no
declared local PT, they rely on implicit REAL*8 typing. Comment corrected.
(Accurate as written for trm and wmx, which do declare one.)
- [A-MED] test_finalize_is_idempotent's docstring claimed to exercise the
double-DEALLOCATE guard; _ServerState.close() nulls the handle so the second
call never re-enters Fortran. Docstring now says what the test actually covers.
Disclosed but deliberately NOT changed here (for the PR thread):
- Restoring `DO NS=1,NSMAX` (finding 24) leaves NS_T/NS_He4 at 0 for NSMAX<4,
which several unguarded trx/ sites would index as PZ(0)/PA(0)/PIN(NR,0).
Upstream trm/ has always used this bound with the same half-guards, several of
those routines hardcode species 3/4 regardless, and both committed inputs pin
NSMAX=4 -- so NSMAX<4 was never supported. Reverting the bound would instead
re-break libnf's presence STOP, which is the defect being fixed.
- Channel B also found pre-existing defects this batch does not claim: NS_He5
never reset by tr_prep_ns; libnf CASE(1,12,13) vs the documented model_pnf=14;
eq/eqfile.f90's transposed PSI/DELPSI/HJT write-vs-read; tr/trloop.f90's two
bare `return`s; missing IOSTAT on equ_convert's READs; txmain never inspecting
IERR. All are worth issues; none are regressions from this PR.
Verification: full python suite 602 passed / 169 skipped / 0 failed. TOT still
TR_PRESENT=1. tr_m0904 dump still byte-identical to the pre-refactor baseline
(sha256 56d09887...cb9ad869). CI job re-verified 9/9 on a pristine clone.
Review note: codex was unavailable in this environment (the CLI rejects the
default model as too new, and the account cannot select gpt-5.2/gpt-5.2-codex),
so the second channel was an independent adversarial reviewer with a different
mandate rather than the usual codex pass.
|
Pushed 9 commits (head Each fix was reproduced before being written and re-verified after; where I could not reproduce a reported mechanism I say so below rather than patching on faith. What landed
Two things I got wrong, and correctedWorth stating plainly since both were in work I had already called verified. The new CI job could not have passed. My "all nine targets green locally" was a dirty-worktree false green — this checkout had #228-21 was only 2 of 6 sites. I migrated And one hole in my own The CI gap is the part I'd most like your view on
Proposed de-scoping, with evidenceBoth of these surfaced while fixing the PT/
Together with the items already moved to #229 and #224, and #227 item 4 (refuted earlier — Pre-existing defects worth their own issuesFound while reviewing this work; all verified NOT to be regressions from this PR, so I have not touched them:
Two disclosures on my own changes#228-24. Restoring Test coverage. Still blocked on the same thingThe workflows have still never run. The new head has its own run — Once CI is green I will regenerate |
Contributing the bpsi↔fork merge baseline back to
k-yoshimi/taskCover letter for an upstream contribution — what the baseline is, what changed, and how it was tested.
Prepared 2026-07-10. Full engineering detail:
docs/2026-06-TASK-merge-and-TRX-report.md.0. TL;DR for a reviewer
This proposes bringing the Kyoto
bpsi/developbase and the GitHub Phase-L modernization forkinto one reconciled, CI-green baseline. The merge is already done, resolved, and validated:
0254aa91— 1st parent58f1fe2e(Phase-L fork tip), 2nd parentfa9dd493(
bpsi/develop, +23 commits). i.e.bpsi/developmerged into the fork, keeping everymodernization and grafting bpsi's intent.
d1f7f9e7— 736 passed on Python 3.11 + 3.13; three1e-10equivalencebaselines regenerated on the CI compiler (gfortran-13.2), one of them for an owner-approved physics
refinement.
intent (table in §3).
Upstream already incorporated (§6): this branch merges current
k-yoshimi/developin (73 commits —mono-
libtotapirouting #201/#204/#208, the Linux-canonical equivalence policy #213, the Pythonfixture-parity backfill #215, and more) and adds the 57-commit bpsi baseline on top: 58 ahead / 0
behind. Only
.gitignoreneeded manual conflict resolution (unioned); the merge co-modifies just 5non-Fortran files (all clean unions) and no Fortran file, so nothing upstream is dropped. Offered as
a PR, never a force-push.
1. What the baseline is
Three git lines had drifted apart:
bpsi.nucleng.kyoto-u.ac.jp/pub/git/taskgithub.com/k-yoshimi/taskforklibXapi.so+ Python wrappers + MCP servers,trcommsplit into 6 sub-modulesgithub.com/ats-fukuyama/taskThe merge brings the latest upstream base onto the modernized fork without regression. An audit
established
bpsi/developis the latest base (not a 3-way upstream merge):ats-fukuyama/developis 119commits behind bpsi and its "unique" commits are superseded backups. So the merge is bpsi base → the
Phase-L fork.
2. What the contribution changes, in aggregate
Before this merge, the baseline was 57 commits ahead / 73 behind the current
k-yoshimi/develop(this PR incorporates all 73 — see §6, now 0 behind). The 57ahead touch 162 files (+9,637 / −5,522). The bulk is the bpsi merge itself (the
0254aa91mergealone reconciles 128 files) plus the CI-greening fixes and the design/plan docs. The net intent:
eq/trq-solver refinement (finerflux-surface grid,
EQLOOPunder-relaxation) used by themodelg=3eq_loadpath.libXapi.solayer, Python wrappers, MCP servers,and the 6-way
trcommsplit.3. Conflict resolutions (10 files)
Each conflict = keep fork modernization, graft bpsi intent:
eq/eqinit.f90NTVMAX200→400,NLPMAX20→100eq/eqcalc.f90EQLOOPadaptive under-relaxationeq/eqcalq.f90NPRINTprint +NMAX200→400eq/eqsub.f90pl/Makefilenoeqlibrecipes + take bpsiSRCS_NOEQ+plview.f90tr/trcomm.f90DEALLOCATE_TRCOMMtr/trcomm_param.f90PNM/PTM/PTPR/PTPP/PUM/PUPR/PUPP)tr/trmain.f90txnew/txcalv.f90wrx/wrcalpwr.f90dx4. How it was tested
4.1 The build had never been CI-green on the sandbox
Even the pure base
developfailed — the build never reached pytest. Getting to green surfaced issuesclass by class (auto-merge artifacts, a
PTsymbol clash betweenti/wm, apl_viewmodule move thatbroke
fpat link time, a repo-name assumption, and test-env gaps). Final:d1f7f9e7carries a two-reviewer pre-push sign-off marker.4.2 The
1e-10equivalence gateThe project keeps per-case regression baselines compared at a
1e-10tolerance. Three drifted onthe CI compiler (gfortran-13.2), for two distinct reasons:
wrx_demo/wrx_iter01— pure compiler-version FP reordering (gf8.5 ≠ gf13.2 ≠ Mac gf15, allwithin ~
1e-9). Lesson recorded:1e-10binary equivalence is too tight for FP-heavy modules acrosscompiler versions; baselines must be captured on the exact CI compiler. Regenerated on gf13.2.
tot_ht6m_short— a real ~1e-4physics shift (see §5), owner-approved and re-baselined.Because the CI env couldn't regenerate these directly, an env-gated capture (
REGEN_OUTPUT_DIR)dumps each case's freshly computed metrics as a CI artifact; those gf13.2 values were committed as the
new baselines.
4.3 Reproduce
5. The one deliberate physics change:
tot_ht6mq-solver refinementtot_ht6m_short(integrated eq→tr coupled run) shifted by ~1e-4. Root cause: bpsi's mergedEQ-solver refinements — finer flux-surface grid (
NMAX200→400) +EQLOOPunder-relaxation — on themodelg=3eq_loadpath. Signature (all 50 radial rows):jup in the core, down mid-radius to −7.9e-4 @ ρ=0.74, up at theedge;
qis its integral: down core, up outer);AJTΔ 3.9e-5 ≪ local Δ 7.9e-4);Reviewed and owner-approved as an intended higher-accuracy solve; the baseline was regenerated on
gf13.2 accordingly. (A truncated CI log initially mis-characterized this as core-localized; two
independent reviewers caught it against the full committed baseline — the write-up was corrected to
global redistribution.)
6. What this PR actually contains, and how it was validated
It is a merge, not a rewrite. The branch is
merge/upstream-reconcile-2026-07; its tip is a mergecommit whose parents are the delivered baseline (
c6cee542) and the currentk-yoshimi/develop(
4a5d977d). Result: 58 ahead / 0 behinddevelop.The merge is clean by construction — the two sides co-modify only 5 non-Fortran files, each a
verified clean union:
.gitignore,.github/workflows/python-tests.yml,python/eqlib/_ffi.py,python/totlib/tests/test_equivalence.py,python/wrxlib/tests/test_equivalence.py..gitignoreproduced a conflict marker (resolved as the union of both rule sets); the other fourauto-merged, and each was checked to keep both sides' additions (e.g.
_ffi.pykeeps oureq_save/psi_rzprototypes and upstream'sMONO_LIB_PATHrouting; the CI workflow keeps ournumpy/REGEN steps and upstream's
mono-buildjob).tot/, so the mergedtot(the mono-libtotapiwork, L-7b-ii Phase 2: monolithic mode + BPSD coupling activation (umbrella) #201/L-7b-ii follow-up: add Linux CI build job for libtotapi_mono.so #204/L-7b-ii Phase 2c: wrapper mono routing + activate ('eq','tr') BPSD coupling #208) is byte-identical to upstream's and known-good;and upstream's 73 commits changed no
tr/eq/pl/bpsdFortran, so those come wholly from thebaseline. There is therefore no semantic-merge risk in the Fortran.
Local validation (macOS, gfortran-15):
make -C tr tr2(static) builds from the merged sources;lib/mtxp/pl/eq/bpsdall compile.pytest --collect-only python/trlib python/totlibcollects 229 tests with no import/fixture breakage.Deferred to this PR's Linux CI — by upstream's own policy:
1e-10equivalence tests are now Linux-canonical (fplib + wrxlib equivalence tests fail 1e-10 tolerance on develop (mismatches ~1e-9) #213,@skipUnless(IS_LINUX)), so they donot run on macOS; the authoritative equivalence run is the Linux CI on this PR.
libtotapi_mono.sois a Linux-only build (L-7b-ii follow-up: add Linux CI build job for libtotapi_mono.so #204), so the mono routing/coupling tests likewise runon CI, not locally.
So the full 736-test suite (including the equivalence gate that this whole exercise protects) is
re-verified by the CI attached to this PR, against the merged tree.
7. Key commits