Native Windows (MSYS2/MinGW-w64) build for ABACUS

[ErjieWu]

Summary

This PR adds the ability to build and run ABACUS natively on Windows (without WSL), and fixes several latent bugs uncovered along the way. The native build supports plane-wave (PW) and numerical-atomic-orbital (LCAO) bases, in both serial and MPI (MS-MPI) configurations, using the MSYS2/MinGW-w64 GCC toolchain with OpenBLAS, FFTW, and ScaLAPACK.

The guiding principle throughout: do not change working Linux code. Every Windows-specific change is isolated behind #if defined(_WIN32) (or a macro that expands to the exact upstream token on non-Windows), so Linux/macOS builds are byte-for-byte unchanged. The only exceptions are genuine bug fixes (noted below), which improve correctness on all platforms.

New feature: native Windows build

Rather than introducing bespoke Windows scripts, the build plugs into the existing toolchain/ infrastructure and the existing integration-test harness, mirroring the other backends (gnu, intel, gcc-mkl, …):

• toolchain/toolchain_windows.sh — installs the prerequisites via MSYS2 pacman (gcc/gfortran, cmake, ninja, openblas, fftw, cereal, ms-mpi, scalapack, bc).
• toolchain/build_abacus_windows.sh — configures and builds (default: MPI + LCAO). It bundles the dependent DLLs next to abacus.exe (so the binary is self-contained), drops an mpirun→mpiexec shim for the test harness, and caps default build parallelism by available RAM to avoid cc1plus OOM.

cd toolchain
./toolchain_windows.sh
./build_abacus_windows.sh        # default: MPI + LCAO; -j N to override
source abacus_env.sh
abacus                           # serial run
./build_abacus_windows.sh        # default: MPI + LCAO; -j N to override
source abacus_env.sh
abacus                           # serial run
mpiexec -n 4 abacus              # parallel run (MS-MPI)

Testing uses the standard harness unchanged — no separate Windows test script and no separate case list:

cd tests/01_PW
bash ../integrate/Autotest.sh -a abacus       # MPI (default np=4)
bash ../integrate/Autotest.sh -a abacus -n 0  # serial (no MPI launcher)

Three Windows-specific gaps were closed so the unmodified harness can drive MS-MPI: MS-MPI ships only mpiexec (not mpirun); MSYS2's OpenBLAS is OpenMP-threaded so OMP_NUM_THREADS (not OPENBLAS_NUM_THREADS) must be pinned to avoid its allocator failing under multiple ranks; and mpiexec doesn't propagate PATH to child ranks when stdout is redirected, which the bundled DLLs solve.

Build-system / portability changes (Linux unaffected)

• CMakeLists.txt — WIN32/MSVC-guarded defines (_USE_MATH_DEFINES, NOMINMAX, _CRT_SECURE_NO_WARNINGS); skip -O3 -g/-lm/the post-install symlink on MSVC/Windows; require ScaLAPACK only when ENABLE_MPI (a serial build is distributed-memory-free — no effect on MPI builds).
• cmake/FindBlas.cmake, FindLapack.cmake — save/restore CMAKE_MODULE_PATH around the builtin find_package so the wrapper doesn't recurse into itself on case-insensitive filesystems (Windows/macOS). No-op on Linux.
• source/source_base/fs_compat.h (new) — a portable make_directory() (_mkdir on Windows, mkdir(path, 0755) on POSIX), since POSIX mkdir's mode argument doesn't exist in the Windows CRT. The POSIX path is behaviorally identical to the previous call sites.
• cpu_allocator.cpp (_aligned_malloc/_aligned_free), restart.cpp (_S_IREAD/_S_IWRITE + <io.h>), input_conv.h (<regex.h> → C++ , which MinGW provides) — all needed because the corresponding POSIX facilities are absent on the Windows CRT.
• source/source_base/module_fft/fft_base.h, fft_cpu.h — the FFT virtuals use attribute((weak)) so the ELF linker can null the unused FFT_CPU vtable slots when ENABLE_FLOAT_FFTW is off. MinGW/PE has no working equivalent (weak template members collide or null the slot). Introduced ABACUS_FFT_WEAK (= attribute((weak)) on non-Windows, empty on _WIN32); on Windows the build sets ENABLE_FLOAT_FFTW=ON so the real definitions exist, and the non-pure base virtuals get trivial bodies in a #if defined(_WIN32) block. Linux preprocesses to exactly the upstream headers.

Bug fixes

These are genuine correctness fixes (not Windows-only workarounds):

• structure_factor.cpp (bspline_sf) — in a serial build, zpiece_to_all() is MPI-only, leaving the real-space tmpr array uninitialized → garbage structure factor and a wrong total energy. Filled directly in the #else (non-MPI) branch using the same layout. Affects serial builds only; the MPI path is untouched. Fix Test case 01_PW/032_PW_15_CF_CS_bspline failed for serial version ABACUS. #7422.
• psi_initializer.cpp (random_t) — in a serial build, stick_to_pool() is MPI-only, so seeded (pw_seed>0) random wavefunctions came out all-zero and later tripped Gram-Schmidt (psi_norm <= 0). Copied the stick data directly in the #else branch. Serial only; MPI path untouched.
• esolver_ks_lcao.cpp — guarded a dereference of the DeePKS overlap_orb_alpha integrator, which is a null unique_ptr when DeePKS is disabled (undefined behavior). Harmless when DeePKS is on.
• binstream.cpp — Binstream is always a binary stream, but on Windows fopen mode "r"/"w" opens in text mode and corrupts binary wavefunction/charge files. Append "b" (a no-op on POSIX).
• input_conv.h (parse_expression) — initialize the accumulator and fail fast (WARNING_QUIT) on an unmatched token or a failed numeric conversion, instead of pushing an indeterminate value into the result vector.

Test harness

• tests/integrate/Autotest.sh — added a serial mode (-n 0) that runs the binary directly with no MPI launcher, so a serial build reuses the standard harness. Existing np > 0 (CI) behavior is unchanged.
• .gitattributes — force LF endings for .sh and CASES_.txt so they parse correctly under bash on Windows checkouts. No content change on Linux.

Scope / not included

The following remain disabled on Windows (excluded by design, not regressions): ELPA, PEXSI, hybrid functionals (LibRI/LibComm), DeePKS/ML-KEDF, LibXC (so meta-GGA/SCAN), GPU (CUDA/ROCm), DSP. Test cases that require them are expected to fail.

Known limitations

• Serial gamma-only LCAO converges to a wrong energy (a serial-only reduction gap in the gamma H/density assembly, not yet located). The MPI build is correct (matches references to ~1e-11 even on a single rank), so gamma-only LCAO should be run under MPI. Multi-k serial LCAO is unaffected.
• pw_seed is not bit-reproducible across platforms — the random initializer uses C std::rand, whose sequence is implementation-defined (RAND_MAX differs between the Windows CRT and glibc). Init-sensitive cases may converge to a different, equally valid near-degenerate state.

Testing

• Windows (MS-MPI, default harness): representative cases from 01_PW, 02_NAO_Gamma (gamma-only LCAO), and 03_NAO_multik pass. Across the full 01_PW suite, total energies match the Linux references to ~1e-8 relative; the residual harness "failures" are cross-platform/cross-BLAS float on forces/stresses exceeding the harness's strict absolute thresholds, excluded features (LibXC/etc.), gauge-dependent output-file dumps, and one stale reference (074, which is platform-independent) — not computational errors.
• Linux: the Windows-specific changes are all _WIN32-guarded or expand to the exact upstream token; verified the FFT headers preprocess to the upstream source with -U_WIN32, and the serial fixes live only in #else/#ifndef __MPI branches, so standard Linux MPI builds are unchanged.

[Copilot]

Pull request overview

Adds an experimental native Windows (MSYS2/MinGW-w64) build path for ABACUS (Phase 1: serial plane-wave only) while keeping Linux behavior unchanged, and extends the existing test harness to support running without an MPI launcher (-n 0).

Changes:

• Introduces a Windows toolchain variant (pacman-installed OpenBLAS/FFTW + Ninja/CMake) and build script to produce a real Windows executable.
• Improves portability across Windows/case-insensitive filesystems (CMake FindBLAS/LAPACK recursion fix, binary file I/O mode, mkdir compatibility, Windows CRT permission bits).
• Fixes serial-only correctness issues surfaced by running the PW test suite without MPI (seeded random wavefunction init + B-spline structure factor grid fill), and adds serial mode support to Autotest.sh.

Reviewed changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
toolchain/toolchain_windows.sh	Installs MSYS2/MinGW-w64 dependencies via pacman and writes an env setup file.
toolchain/build_abacus_windows.sh	Configures/builds a serial PW Windows executable and generates abacus_env.sh.
tests/integrate/Autotest.sh	Adds -n 0 serial mode (no mpirun) and adjusts OpenMP thread defaulting.
source/source_pw/module_pwdft/structure_factor.cpp	Initializes tmpr in serial builds to avoid garbage structure factors.
source/source_psi/psi_initializer.cpp	Fixes seeded random wavefunction initialization in serial (non-MPI) builds.
source/source_io/module_restart/restart.cpp	Adds Windows CRT compatibility for open() mode bits and includes <io.h>.
source/source_io/module_parameter/input_conv.h	Replaces POSIX <regex.h> parsing with portable std::regex.
source/source_io/module_output/binstream.cpp	Forces binary fopen mode by ensuring 'b' is present.
source/source_base/module_fft/fft_cpu.h	Removes __attribute__((weak)) from FFT_CPU virtuals (Windows/PE safety).
source/source_base/module_fft/fft_base.h	Provides non-null default virtual bodies to avoid PE null vtable slots.
source/source_base/module_container/base/core/cpu_allocator.cpp	Uses _aligned_malloc/_aligned_free on Windows for aligned allocations.
source/source_base/global_function.cpp	Switches directory creation to a new portable helper.
source/source_base/global_file.cpp	Switches directory creation to a new portable helper.
source/source_base/fs_compat.h	Adds portable ModuleBase::make_directory() wrapper.
docs/advanced/install_windows_native.md	Documents the experimental native Windows build and serial PW testing flow.
CMakeLists.txt	Adds Windows portability defines; gates ScaLAPACK on ENABLE_MPI; skips -lm and symlink install for Windows/MSVC.
cmake/FindLapack.cmake	Avoids infinite recursion on case-insensitive filesystems by temporarily adjusting CMAKE_MODULE_PATH.
cmake/FindBlas.cmake	Avoids infinite recursion on case-insensitive filesystems by temporarily adjusting CMAKE_MODULE_PATH.
.gitattributes	Forces LF endings for bash scripts and CASES_*.txt to avoid CRLF issues on Windows.

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