From 52960e00e62a7ad5ba7b3a945b1839c08257d520 Mon Sep 17 00:00:00 2001 From: Ludovic Henry Date: Sun, 6 Sep 2026 12:54:49 +0200 Subject: [PATCH 1/6] gemmi: add build-gemmi.yml for riscv64 wheels Mirrors upstream's cibuildwheel + scikit-build-core recipe as-is (no CIBW_ENVIRONMENT/CIBW_TEST_COMMAND overrides): pyproject.toml already sets SKBUILD_CMAKE_ARGS (FETCH_ZLIB_NG=ON among others) and the unittest-based test-command, so cibuildwheel picks both up unmodified from the checkout. zlib-ng (fetched via CMake FetchContent at build time) has confirmed riscv64 RVV dispatch support from the in-flight python-zlib-ng port. Co-Authored-By: Claude Sonnet 5 Claude-Session: https://claude.ai/code/session_01Az13NcXsVZzzxXmaxxUEy7 --- .github/workflows/build-gemmi.yml | 88 +++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 .github/workflows/build-gemmi.yml diff --git a/.github/workflows/build-gemmi.yml b/.github/workflows/build-gemmi.yml new file mode 100644 index 000000000..cea231c80 --- /dev/null +++ b/.github/workflows/build-gemmi.yml @@ -0,0 +1,88 @@ +# SPDX-FileCopyrightText: 2026 The RISE Project +# SPDX-License-Identifier: MIT +--- +# Based on the `build_wheels` job of +# https://github.com/project-gemmi/gemmi/blob/v0.7.5/.github/workflows/wheels2.yml +name: Build gemmi wheels (riscv64) + +on: + workflow_dispatch: + inputs: + version: + description: 'gemmi version/tag to build (git tag without leading v, e.g. 0.7.5)' + required: true + default: '0.7.5' + pull_request: + paths: + - '.github/workflows/build-gemmi.yml' + +concurrency: + group: ${{ github.workflow }}-${{ inputs.version || '0.7.5' }}-${{ github.head_ref || github.run_id }} + cancel-in-progress: true + +permissions: + contents: read # to fetch code (actions/checkout) + +env: + GEMMI_VERSION: ${{ inputs.version || '0.7.5' }} + MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64 + MUSLLINUX_RISCV64_IMAGE: quay.io/pypa/musllinux_1_2_riscv64 + +jobs: + setup: + uses: $/.github/workflows/_setup.yml + + build_wheels: + needs: [setup] + name: Build gemmi ${{ inputs.version || '0.7.5' }} ${{ matrix.python }}-${{ matrix.libc }}_riscv64 + runs-on: ubuntu-24.04-riscv + timeout-minutes: 120 + strategy: + fail-fast: false + matrix: + python: ["cp312", "cp313", "cp314", "cp314t"] + libc: [manylinux, musllinux] + + steps: + - name: Checkout gemmi v${{ env.GEMMI_VERSION }} + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + repository: project-gemmi/gemmi + ref: v${{ env.GEMMI_VERSION }} + persist-credentials: false + + - uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074 # v4.2.0 + env: + CIBW_ARCHS: riscv64 + CIBW_BUILD: ${{ matrix.python }}-${{ matrix.libc }}_riscv64 + CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }} + CIBW_MUSLLINUX_RISCV64_IMAGE: ${{ env.MUSLLINUX_RISCV64_IMAGE }} + + - name: Check wheel contents + run: | + python3 - wheelhouse/*.whl <<'EOF' + import sys, zipfile + path = sys.argv[1] + names = zipfile.ZipFile(path).namelist() + exts = [n for n in names if n.endswith(".so")] + assert exts and all("gemmi_ext" in n for n in exts), exts + licences = {n.split(".dist-info/licenses/", 1)[1] for n in names + if ".dist-info/licenses/" in n and not n.endswith("/")} + assert licences == {"LICENSE.txt"}, licences + EOF + + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + with: + name: gemmi-${{ env.GEMMI_VERSION }}-${{ matrix.python }}-${{ matrix.libc }}_riscv64 + path: ./wheelhouse/*.whl + if-no-files-found: error + + publish: + name: Publish gemmi ${{ inputs.version || '0.7.5' }} + needs: [setup, build_wheels] + permissions: + contents: write + pull-requests: write + uses: $/.github/workflows/_publish-wheel.yml + with: + artifact-pattern: gemmi-${{ inputs.version || '0.7.5' }}-*riscv64 From 2af6fd36c932825e9c2829fae967dab9dc737792 Mon Sep 17 00:00:00 2001 From: Ludovic Henry Date: Sun, 6 Sep 2026 13:14:43 +0200 Subject: [PATCH 2/6] gemmi: pin nanobind <3 for the CMake find_package(nanobind 2.4.0) check CMakeLists.txt's find_package(nanobind 2.4.0 CONFIG REQUIRED) rejects nanobind 3.x as a version mismatch, but pyproject.toml's build-system.requires carries no upper bound. nanobind 3.x requires Python >=3.10, so this reproduces on any architecture building cp310+ - it just never surfaced on upstream's own py3.9 leg. Constrain both the top-level and isolated build envs via CIBW_BEFORE_ALL + PIP_CONSTRAINT/PIP_BUILD_CONSTRAINT rather than disabling isolation. Co-Authored-By: Claude Sonnet 5 Claude-Session: https://claude.ai/code/session_01Az13NcXsVZzzxXmaxxUEy7 --- .github/workflows/build-gemmi.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/build-gemmi.yml b/.github/workflows/build-gemmi.yml index cea231c80..19a94d749 100644 --- a/.github/workflows/build-gemmi.yml +++ b/.github/workflows/build-gemmi.yml @@ -57,6 +57,13 @@ jobs: CIBW_BUILD: ${{ matrix.python }}-${{ matrix.libc }}_riscv64 CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }} CIBW_MUSLLINUX_RISCV64_IMAGE: ${{ env.MUSLLINUX_RISCV64_IMAGE }} + # find_package(nanobind 2.4.0) in CMakeLists.txt rejects nanobind 3.x as + # incompatible; pyproject.toml's build-system.requires has no upper bound. + CIBW_BEFORE_ALL: echo 'nanobind<3' > /nanobind-constraint.txt + CIBW_ENVIRONMENT: >- + SKBUILD_CMAKE_ARGS=-DBUILD_GEMMI_PROGRAM=OFF;-DINSTALL_DEV_FILES=OFF;-DBUILD_SHARED_LIBS=OFF;-DFETCH_ZLIB_NG=ON + PIP_CONSTRAINT=/nanobind-constraint.txt + PIP_BUILD_CONSTRAINT=/nanobind-constraint.txt - name: Check wheel contents run: | From dd56c68fa7483d5102555814e7ef6a55b46aa116 Mon Sep 17 00:00:00 2001 From: Ludovic Henry Date: Sun, 6 Sep 2026 13:31:53 +0200 Subject: [PATCH 3/6] gemmi: quote SKBUILD_CMAKE_ARGS in CIBW_ENVIRONMENT cibuildwheel parses CIBW_ENVIRONMENT with bashlex; the unquoted semicolon-separated CMake arg list was read as multiple shell statements instead of one assignment, so cibuildwheel rejected the whole option as malformed. Co-Authored-By: Claude Sonnet 5 Claude-Session: https://claude.ai/code/session_01Az13NcXsVZzzxXmaxxUEy7 --- .github/workflows/build-gemmi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-gemmi.yml b/.github/workflows/build-gemmi.yml index 19a94d749..771c3215b 100644 --- a/.github/workflows/build-gemmi.yml +++ b/.github/workflows/build-gemmi.yml @@ -61,7 +61,7 @@ jobs: # incompatible; pyproject.toml's build-system.requires has no upper bound. CIBW_BEFORE_ALL: echo 'nanobind<3' > /nanobind-constraint.txt CIBW_ENVIRONMENT: >- - SKBUILD_CMAKE_ARGS=-DBUILD_GEMMI_PROGRAM=OFF;-DINSTALL_DEV_FILES=OFF;-DBUILD_SHARED_LIBS=OFF;-DFETCH_ZLIB_NG=ON + SKBUILD_CMAKE_ARGS='-DBUILD_GEMMI_PROGRAM=OFF;-DINSTALL_DEV_FILES=OFF;-DBUILD_SHARED_LIBS=OFF;-DFETCH_ZLIB_NG=ON' PIP_CONSTRAINT=/nanobind-constraint.txt PIP_BUILD_CONSTRAINT=/nanobind-constraint.txt From e9258cbf412ae4129af8f0273a83fff9d2cfa149 Mon Sep 17 00:00:00 2001 From: Ludovic Henry Date: Sun, 6 Sep 2026 13:51:07 +0200 Subject: [PATCH 4/6] gemmi: patch riscv64 detection into vendored stb_sprintf.h stb_sprintf.h's stbsp__uintptr allowlist has no riscv64 entry, so it falls back to a 32-bit unsigned int on a 64-bit-pointer platform; every (stbsp__uintptr)ptr alignment check then narrows a pointer to 32 bits, which GCC 14 rejects as a hard error rather than a warning. Co-Authored-By: Claude Sonnet 5 Claude-Session: https://claude.ai/code/session_01Az13NcXsVZzzxXmaxxUEy7 --- .github/workflows/build-gemmi.yml | 11 ++++++ ...ect-riscv64-as-a-64-bit-pointer-arch.patch | 38 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 patches/gemmi/0.7.5/0001-third_party-detect-riscv64-as-a-64-bit-pointer-arch.patch diff --git a/.github/workflows/build-gemmi.yml b/.github/workflows/build-gemmi.yml index 771c3215b..089b65bbd 100644 --- a/.github/workflows/build-gemmi.yml +++ b/.github/workflows/build-gemmi.yml @@ -15,6 +15,7 @@ on: pull_request: paths: - '.github/workflows/build-gemmi.yml' + - 'patches/gemmi/**' concurrency: group: ${{ github.workflow }}-${{ inputs.version || '0.7.5' }}-${{ github.head_ref || github.run_id }} @@ -51,6 +52,16 @@ jobs: ref: v${{ env.GEMMI_VERSION }} persist-credentials: false + - name: Checkout python-wheels + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + path: python-wheels + persist-credentials: false + + # stb_sprintf.h has no riscv64 entry in its 64-bit-pointer-arch allowlist. + - name: Patch gemmi source + run: git apply python-wheels/patches/gemmi/${{ env.GEMMI_VERSION }}/00*.patch + - uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074 # v4.2.0 env: CIBW_ARCHS: riscv64 diff --git a/patches/gemmi/0.7.5/0001-third_party-detect-riscv64-as-a-64-bit-pointer-arch.patch b/patches/gemmi/0.7.5/0001-third_party-detect-riscv64-as-a-64-bit-pointer-arch.patch new file mode 100644 index 000000000..78044835c --- /dev/null +++ b/patches/gemmi/0.7.5/0001-third_party-detect-riscv64-as-a-64-bit-pointer-arch.patch @@ -0,0 +1,38 @@ +From dadacda267c6a3078c80576a103e970b4ed59ffc Mon Sep 17 00:00:00 2001 +From: Ludovic Henry +Date: Sun, 6 Sep 2026 13:48:56 +0200 +Subject: [PATCH] third_party: detect riscv64 as a 64-bit pointer arch in + stb_sprintf + +stb_sprintf.h's stbsp__uintptr allowlist (__ppc64__, __aarch64__, +__x86_64__, __s390x__, ...) has no riscv64 entry, so it falls back to +a 32-bit unsigned int on a platform with 64-bit pointers. Every +(stbsp__uintptr)ptr alignment check in the file then narrows a +pointer to 32 bits, which GCC 14 rejects as a hard error (cast ... +loses precision [-fpermissive]) rather than a warning. + +Add the same __riscv/__riscv_xlen==64 test glibc and the Linux kernel +use to detect riscv64, matching the pattern the file already uses for +every other LP64 architecture. + +Upstream-Status: Inappropriate [gemmi vendors stb_sprintf.h directly with no submodule; the actual gap is in nothings/stb's stb_sprintf.h itself, which has no riscv64 detection and no riscv64 CI] +--- + third_party/stb_sprintf.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/third_party/stb_sprintf.h b/third_party/stb_sprintf.h +index 28e9d64..4ce0ec9 100644 +--- a/third_party/stb_sprintf.h ++++ b/third_party/stb_sprintf.h +@@ -230,7 +230,7 @@ STBSP__PUBLICDEC void STB_SPRINTF_DECORATE(set_separators)(char comma, char peri + #define stbsp__uint16 unsigned short + + #ifndef stbsp__uintptr +-#if defined(__ppc64__) || defined(__powerpc64__) || defined(__aarch64__) || defined(_M_X64) || defined(__x86_64__) || defined(__x86_64) || defined(__s390x__) ++#if defined(__ppc64__) || defined(__powerpc64__) || defined(__aarch64__) || defined(_M_X64) || defined(__x86_64__) || defined(__x86_64) || defined(__s390x__) || (defined(__riscv) && __riscv_xlen == 64) + #define stbsp__uintptr stbsp__uint64 + #else + #define stbsp__uintptr stbsp__uint32 +-- +2.50.1 (Apple Git-155) + From fc47ee3884a505bcc4c89a810feaf13791e8bc37 Mon Sep 17 00:00:00 2001 From: Ludovic Henry Date: Sun, 6 Sep 2026 14:23:29 +0200 Subject: [PATCH 5/6] gemmi: disable project-wide LTO to fix a riscv64 SIGILL CMakeLists.txt enables CMAKE_INTERPROCEDURAL_OPTIMIZATION for Release builds by default, and already turns it off for the bundled zlib-ng because "IPO has been reported to mess it up leading to illegal-instruction crash" on some platforms. gemmi's own code hits that same crash on riscv64: the wheel builds and installs fine, but the very first unittest dies with SIGILL. Disable LTO globally rather than only where upstream anticipated the problem. Co-Authored-By: Claude Sonnet 5 Claude-Session: https://claude.ai/code/session_01Az13NcXsVZzzxXmaxxUEy7 --- .github/workflows/build-gemmi.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-gemmi.yml b/.github/workflows/build-gemmi.yml index 089b65bbd..4c6053d10 100644 --- a/.github/workflows/build-gemmi.yml +++ b/.github/workflows/build-gemmi.yml @@ -71,8 +71,11 @@ jobs: # find_package(nanobind 2.4.0) in CMakeLists.txt rejects nanobind 3.x as # incompatible; pyproject.toml's build-system.requires has no upper bound. CIBW_BEFORE_ALL: echo 'nanobind<3' > /nanobind-constraint.txt + # CMakeLists.txt enables LTO project-wide and already disables it for + # zlib-ng over a known illegal-instruction crash; gemmi's own code hits + # the same crash on riscv64, so disable LTO globally too. CIBW_ENVIRONMENT: >- - SKBUILD_CMAKE_ARGS='-DBUILD_GEMMI_PROGRAM=OFF;-DINSTALL_DEV_FILES=OFF;-DBUILD_SHARED_LIBS=OFF;-DFETCH_ZLIB_NG=ON' + SKBUILD_CMAKE_ARGS='-DBUILD_GEMMI_PROGRAM=OFF;-DINSTALL_DEV_FILES=OFF;-DBUILD_SHARED_LIBS=OFF;-DFETCH_ZLIB_NG=ON;-DCMAKE_INTERPROCEDURAL_OPTIMIZATION=OFF' PIP_CONSTRAINT=/nanobind-constraint.txt PIP_BUILD_CONSTRAINT=/nanobind-constraint.txt From f0b0f79ac1f2ecd5c63a22fee5248a1a8faf4660 Mon Sep 17 00:00:00 2001 From: Ludovic Henry Date: Sun, 6 Sep 2026 14:56:16 +0200 Subject: [PATCH 6/6] gemmi: disable zlib-ng's RVV kernels instead of LTO Disabling project-wide LTO did not fix the riscv64 SIGILL (identical crash, same test, same instruction pointer class) - so that was the wrong culprit. The crash is in test_align.py's very first test, which is also the first to read a real file through zlib (a .pdb.gz), pointing at the fetched zlib-ng's RVV-accelerated chunkset/inflate kernels instead. Pass -DWITH_RVV=OFF to fall back to zlib-ng's portable C implementation. Co-Authored-By: Claude Sonnet 5 Claude-Session: https://claude.ai/code/session_01Az13NcXsVZzzxXmaxxUEy7 --- .github/workflows/build-gemmi.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build-gemmi.yml b/.github/workflows/build-gemmi.yml index 4c6053d10..9f9114d2d 100644 --- a/.github/workflows/build-gemmi.yml +++ b/.github/workflows/build-gemmi.yml @@ -71,11 +71,10 @@ jobs: # find_package(nanobind 2.4.0) in CMakeLists.txt rejects nanobind 3.x as # incompatible; pyproject.toml's build-system.requires has no upper bound. CIBW_BEFORE_ALL: echo 'nanobind<3' > /nanobind-constraint.txt - # CMakeLists.txt enables LTO project-wide and already disables it for - # zlib-ng over a known illegal-instruction crash; gemmi's own code hits - # the same crash on riscv64, so disable LTO globally too. + # The fetched zlib-ng's RVV chunkset/inflate kernels SIGILL on the first + # gzipped file gemmi reads; fall back to its portable C implementation. CIBW_ENVIRONMENT: >- - SKBUILD_CMAKE_ARGS='-DBUILD_GEMMI_PROGRAM=OFF;-DINSTALL_DEV_FILES=OFF;-DBUILD_SHARED_LIBS=OFF;-DFETCH_ZLIB_NG=ON;-DCMAKE_INTERPROCEDURAL_OPTIMIZATION=OFF' + SKBUILD_CMAKE_ARGS='-DBUILD_GEMMI_PROGRAM=OFF;-DINSTALL_DEV_FILES=OFF;-DBUILD_SHARED_LIBS=OFF;-DFETCH_ZLIB_NG=ON;-DWITH_RVV=OFF' PIP_CONSTRAINT=/nanobind-constraint.txt PIP_BUILD_CONSTRAINT=/nanobind-constraint.txt