duan_j
ef1951d42a
- sysroot += libwebp, libdeflate, libtiff 4.6 (+libjpeg-turbo, jbigkit-libs, liblerc): from a NEEDED scan of every ELF object in the zip these are the libs RHEL8/9 lack at the required version (PIL _imaging, vendor libtiff.so.5, GUI binary libtiff.so.6). - install step 9: run olex2c once as the owner so Olex2 writes cctbx/cctbx_build/libtbx_env into the shared prefix (its first-start cold start; users cannot write there). The upstream fable/sdrive.f error on that run is expected and documented: libtbx_env is pickled before it. - install step 10: second start + refine of the sucrose sample; die if cctbx is still reported broken, warn on other errors. - launcher: PYTHONNOUSERSITE=1.
247 lines
14 KiB
Python
Executable File
247 lines
14 KiB
Python
Executable File
#!/usr/bin/env modbuild
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# Olex2 - official open-source (BSD) Linux x86_64 distribution from OlexSys.
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# https://www.olexsys.org/olex2/docs/getting-started/installing-olex2/
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#
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# Upstream ships NO installer and NOTHING to compile for Linux: a single
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# olex2-linux64.zip that already contains
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# olex2 GUI (wxWidgets) olex2c console/"headless" Olex2
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# unirun vendor auto-updater (NOT used here) start vendor launcher (NOT used here)
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# cctbx/ lib/ (private CPython 3.8 + libs) ilib/ util/ etc/ sample_data/ ...
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#
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# BUT: since 2026 OlexSys builds the Linux binaries on an Ubuntu 24.04-class
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# toolchain: olex2c/olex2/unirun/NoSpherA2/libopenblas/cctbx *.so need
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# GLIBC_2.38 + GLIBCXX_3.4.32, while RHEL9 has glibc 2.34 / GLIBCXX_3.4.29
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# (RHEL8: 2.28 / 3.4.25). A newer glibc cannot be supplied via LD_LIBRARY_PATH
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# (the dynamic loader is hard-wired into each ELF), so this recipe ships a
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# private glibc 2.39 + GCC 14 libstdc++/libgcc under $PREFIX/sysroot (frozen
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# Fedora 40 rpms from kojipkgs) and re-points the ELF executables at that
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# loader with patchelf (--set-interpreter + DT_RPATH). GTK2/X11/GL still come
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# from the host: older libs run fine on a newer glibc. The sysroot libc dir is
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# NEVER put on LD_LIBRARY_PATH - that would crash every system tool Olex2 spawns.
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#
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# Default pbuild::prep downloads every file (urls: in files/config.yaml),
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# checks the pinned sha256 (shasums:) and copies it into SRC_DIR (unpacker:
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# none). configure unpacks, install copies the vendor tree 1:1 into $PREFIX
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# (Olex2's BaseDir() is wherever the binaries sit) and adds $PREFIX/bin launchers.
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#
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# No errexit in modbuild hooks -> every critical step is die-guarded.
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# files fetched by prep (names must match urls:/shasums: in files/config.yaml)
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OLEX2_SYSROOT_RPMS=(
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glibc-2.39-37.fc40.x86_64.rpm
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libstdc++-14.2.1-3.fc40.x86_64.rpm
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libgcc-14.2.1-3.fc40.x86_64.rpm
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readline-8.2-8.fc40.x86_64.rpm # libreadline.so.8: RHEL8 has .so.7, vendor lib/ .so.6
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libwebp-1.3.2-5.fc40.x86_64.rpm # libwebp.so.7: PIL + libtiff
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libdeflate-1.19-2.fc40.x86_64.rpm # libdeflate.so.0: vendor libtiff.so.5 (absent on RHEL8)
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libtiff-4.6.0-2.fc40.x86_64.rpm # libtiff.so.6: GUI binary (RHEL ships .so.5) + its deps:
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libjpeg-turbo-3.0.2-1.fc40.x86_64.rpm
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jbigkit-libs-2.1-29.fc40.x86_64.rpm
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liblerc-4.0.0-6.fc40.x86_64.rpm
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)
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OLEX2_PATCHELF_TGZ="patchelf-0.18.0-x86_64.tar.gz"
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# ELF executables in the vendor tree that get the bundled loader (static ones,
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# e.g. hart, are detected and skipped)
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OLEX2_PATCH_EXES=(olex2c olex2 unirun NoSpherA2 hart_mpi)
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pbuild::configure() {
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local -r zip="${SRC_DIR}/olex2-${V}-linux64.zip"
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if [[ -f "${SRC_DIR}/olex2/olex2c" && -f "${SRC_DIR}/olex2/olex2" ]]; then
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# re-run after a failed configure/install: prep's stamp is set, the
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# tree is already unpacked - reuse it (the zip may be gone from SRC_DIR)
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echo "olex2: reusing unpacked tree in ${SRC_DIR}/olex2"
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else
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[[ -s "${zip}" ]] || std::die 42 "olex2: ${zip} not found - prep did not fetch it. \
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Pre-stage the archive by hand as <distdir>/olex2-${V}-linux64.zip (see README) and re-run (-f)."
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command -v unzip >/dev/null || std::die 42 "olex2: 'unzip' not on PATH on this build host"
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# partial downloads reused from distfiles are the classic failure: test the archive first
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unzip -tq "${zip}" >/dev/null || \
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std::die 42 "olex2: archive is corrupt/truncated - rm <distdir>/olex2-${V}-linux64.zip and re-run"
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# ~1 GB unpacked (cctbx + python + sample data); SRC_DIR is under --tmpdir
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unzip -q -o "${zip}" -d "${SRC_DIR}" || std::die 42 "olex2: unzip failed (disk/quota at --tmpdir?)"
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[[ -f "${SRC_DIR}/olex2/olex2c" && -f "${SRC_DIR}/olex2/olex2" ]] || \
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std::die 42 "olex2: unexpected archive layout - expected ${SRC_DIR}/olex2/{olex2,olex2c}"
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rm -f "${zip}" # 255 MB copy; the distfiles cache keeps the original
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fi
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# --- private glibc 2.39 + libstdc++ 14 sysroot (Fedora 40 rpms) ----------
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command -v rpm2cpio >/dev/null && command -v cpio >/dev/null || \
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std::die 42 "olex2: need rpm2cpio and cpio on the build host (dnf install rpm cpio)"
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local -r sysroot="${SRC_DIR}/sysroot"
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local rpm
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rm -rf "${sysroot}"
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mkdir -p "${sysroot}"
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for rpm in "${OLEX2_SYSROOT_RPMS[@]}"; do
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[[ -s "${SRC_DIR}/${rpm}" ]] || std::die 42 "olex2: ${rpm} missing in SRC_DIR - prep did not fetch it"
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( cd "${sysroot}" && rpm2cpio "${SRC_DIR}/${rpm}" | cpio -idm --quiet ) || \
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std::die 42 "olex2: extracting ${rpm} failed"
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done
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# Fedora's glibc + libstdc++ install to /usr/lib64 but libgcc still to
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# /lib64, which on a real system is the filesystem package's symlink to
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# usr/lib64 - we do not extract that package, so recreate the merge here.
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if [[ -d "${sysroot}/lib64" && ! -L "${sysroot}/lib64" ]]; then
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mkdir -p "${sysroot}/usr/lib64"
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cp -r --preserve=mode,timestamps,links "${sysroot}/lib64/." "${sysroot}/usr/lib64/" && \
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rm -rf "${sysroot}/lib64" && ln -s usr/lib64 "${sysroot}/lib64" || \
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std::die 42 "olex2: merging sysroot/lib64 into sysroot/usr/lib64 failed"
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fi
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local ld libc libdir
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ld="$(find "${sysroot}" -type f -name 'ld-linux-x86-64.so.2' -print -quit)"
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libc="$(find "${sysroot}" -type f -name 'libc.so.6' -print -quit)"
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[[ -n "${ld}" && -n "${libc}" ]] || std::die 42 "olex2: ld-linux-x86-64.so.2 / libc.so.6 not found in the extracted glibc rpm"
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libdir="$(dirname "${libc}")"
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[[ -e "${libdir}/libstdc++.so.6" && -e "${libdir}/libgcc_s.so.1" ]] || \
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std::die 42 "olex2: libstdc++.so.6 / libgcc_s.so.1 not next to libc.so.6 in ${libdir}"
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# the loader is static: it must run on any x86_64 host
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"${ld}" --version > "${SRC_DIR}/ldso.version" 2>&1 || \
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std::die 42 "olex2: the bundled ld.so does not run on this host"
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echo "olex2: bundled loader: $(head -n1 "${SRC_DIR}/ldso.version")"
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# --- patchelf (static release binary) --------------------------------------
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[[ -s "${SRC_DIR}/${OLEX2_PATCHELF_TGZ}" ]] || std::die 42 "olex2: ${OLEX2_PATCHELF_TGZ} missing in SRC_DIR - prep did not fetch it"
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mkdir -p "${SRC_DIR}/patchelf"
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tar -xzf "${SRC_DIR}/${OLEX2_PATCHELF_TGZ}" -C "${SRC_DIR}/patchelf" || std::die 42 "olex2: unpacking patchelf failed"
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"${SRC_DIR}/patchelf/bin/patchelf" --version >/dev/null || std::die 42 "olex2: patchelf binary does not run on this host"
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}
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pbuild::compile() {
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:
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}
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pbuild::install() {
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local -r src="${SRC_DIR}/olex2"
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local -r patchelf="${SRC_DIR}/patchelf/bin/patchelf"
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# 1. vendor tree, flat into $PREFIX (= BaseDir). Slow on /opt/psi: 12k files.
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# NOT `cp -a`: on /opt/psi chown is refused, so -a ends with thousands of
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# "failed to preserve ownership ... Permission denied" and a non-zero exit
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# (that killed the first build). Keep mode/timestamps/links only.
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cp -r --preserve=mode,timestamps,links "${src}/." "${PREFIX}/" || \
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std::die 42 "olex2: copying the vendor tree into ${PREFIX} failed"
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# 2. private glibc/libstdc++ sysroot
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rm -rf "${PREFIX}/sysroot"
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cp -r --preserve=mode,timestamps,links "${SRC_DIR}/sysroot" "${PREFIX}/sysroot" || \
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std::die 42 "olex2: copying the sysroot into ${PREFIX} failed"
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# 3. zip loses nothing, but make sure the ELF binaries are executable and
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# everything is world-readable on the shared install
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chmod 755 "${PREFIX}"/{olex2,olex2c,unirun,start,NoSpherA2,hart,hart_mpi} 2>/dev/null || true
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chmod -R a+rX "${PREFIX}" || true
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# 4. never auto-update a shared, read-only install (vendor default is
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# update=Always + ask_update=true, driven by unirun). Best effort - the
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# launchers never call unirun anyway.
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if [[ -f "${PREFIX}/usettings.dat" ]]; then
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sed -i -e 's/^update=.*/update=Never/' -e 's/^ask_update=.*/ask_update=false/' \
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"${PREFIX}/usettings.dat" || true
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fi
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# 5. re-point the ELF executables at the bundled loader. DT_RPATH (not
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# RUNPATH, hence --force-rpath) so that everything dlopen()ed later by the
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# embedded Python (cctbx *.so, lib-dynload, _ac7util) resolves libc,
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# libstdc++, libopenblas ... through the same list. Host dirs (/lib64)
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# follow via the loader's defaults + /etc/ld.so.cache.
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local ld libdir rpath exe
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ld="$(find "${PREFIX}/sysroot" -type f -name 'ld-linux-x86-64.so.2' -print -quit)"
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libdir="$(dirname "$(find "${PREFIX}/sysroot" -type f -name 'libc.so.6' -print -quit)")"
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[[ -x "${ld}" && -d "${libdir}" ]] || std::die 42 "olex2: sysroot loader/libdir not found under ${PREFIX}/sysroot"
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rpath="${libdir}:${PREFIX}/lib:${PREFIX}/ilib:${PREFIX}/cctbx/cctbx_build/lib:${PREFIX}:\$ORIGIN"
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for exe in "${OLEX2_PATCH_EXES[@]}"; do
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[[ -f "${PREFIX}/${exe}" ]] || continue
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if ! "${patchelf}" --print-interpreter "${PREFIX}/${exe}" >/dev/null 2>&1; then
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echo "olex2: ${exe} is statically linked - left untouched"
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continue
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fi
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"${patchelf}" --set-interpreter "${ld}" --force-rpath --set-rpath "${rpath}" "${PREFIX}/${exe}" || \
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std::die 42 "olex2: patchelf failed on ${exe}"
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echo "olex2: ${exe} -> interpreter ${ld}"
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done
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# 6. launchers: $PREFIX/bin/olex2 (GUI) and $PREFIX/bin/olex2c (console).
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# Two copies of one script (it dispatches on basename $0, so no symlinks).
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# Only $PREFIX/bin goes on PATH - the raw binaries and the vendor
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# 'start' (auto-updater) stay off it.
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mkdir -p "${PREFIX}/bin"
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install -m 755 "${BUILDBLOCK_DIR}/files/olex2-launcher" "${PREFIX}/bin/olex2" || \
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std::die 42 "olex2: installing bin/olex2 launcher failed"
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install -m 755 "${BUILDBLOCK_DIR}/files/olex2-launcher" "${PREFIX}/bin/olex2c" || \
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std::die 42 "olex2: installing bin/olex2c launcher failed"
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# 7. prove the patched olex2c resolves through the bundled glibc. The
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# build host (Ra, RHEL8) is not the execution host (RHEL9): a HOST lib
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# missing here ("=> not found", or a hard "cannot open shared object
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# file" that aborts the listing) is reported, not fatal. Anything else
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# (segfault, page alignment, GLIBC_PRIVATE ...) means patchelf/sysroot
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# is broken and the build must stop.
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local -r ldd="${SRC_DIR}/olex2c.ldd"
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local rc=0
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"${ld}" --list "${PREFIX}/olex2c" > "${ldd}" 2>&1 || rc=$?
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echo "olex2: --- ${ld} --list olex2c (rc=${rc}) ---"
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cat "${ldd}"
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echo "olex2: --- end of listing ---"
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if grep -q "${libdir}/libc.so.6" "${ldd}"; then
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if grep -q 'not found' "${ldd}"; then
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echo "olex2: WARNING - host libraries missing on THIS host; dnf install them on the execution hosts:"
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grep 'not found' "${ldd}"
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fi
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elif grep -q 'cannot open shared object file' "${ldd}"; then
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echo "olex2: WARNING - cannot verify the loader on THIS host, a host library is missing here:"
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grep 'cannot open shared object file' "${ldd}"
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echo "olex2: install it on the execution hosts (or bundle it in the sysroot) and re-check with"
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echo "olex2: ${ld} --list ${PREFIX}/olex2c"
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else
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std::die 42 "olex2: olex2c does not resolve through the bundled glibc (rc=${rc}, listing above) - patchelf/sysroot step broken"
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fi
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# 8. what the modulefile / launchers rely on
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local f
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for f in olex2 olex2c cctbx/cctbx_build/lib lib/libpython3.8.so.1.0 lib/python3.8 util/pyUtil/initpy.py bin/olex2c \
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sysroot/usr/lib64/libc.so.6 sysroot/usr/lib64/libstdc++.so.6 sysroot/usr/lib64/libgcc_s.so.1 \
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sysroot/usr/lib64/libreadline.so.8 sysroot/usr/lib64/libwebp.so.7 sysroot/usr/lib64/libdeflate.so.0 \
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sysroot/usr/lib64/libtiff.so.6 sysroot/usr/lib64/libLerc.so.4; do
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[[ -e "${PREFIX}/${f}" ]] || std::die 42 "olex2: ${PREFIX}/${f} missing after install - module would be broken"
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done
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# 9. cctbx first-run setup. On its FIRST start Olex2 regenerates
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# cctbx/cctbx_build/libtbx_env (+ dispatchers) by running libtbx's
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# configure.py into BaseDir (util/pyUtil/PyToolLib/path_utils.py,
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# cold_start). Users cannot write there, so do it now as the owner.
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# Upstream quirk: the vendor ships SCons in its site-packages, so
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# libtbx believes it can build and the scitbx refresh then fails on
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# Fortran sources that are not shipped ("[Errno 2] ... scitbx/lbfgs/
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# sdrive.f"). That happens AFTER libtbx_env is pickled (env_config.py),
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# so the first run printing "There is a problem with the cctbx" is
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# expected; what matters is that the second start is clean.
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local -r home="${SRC_DIR}/home" # keep ~/.olex2 of the build user out of it
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mkdir -p "${home}"
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printf 'exit\n' | HOME="${home}" timeout 900 "${PREFIX}/bin/olex2c" > "${SRC_DIR}/olex2c.firstrun.log" 2>&1 || true
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if [[ ! -f "${PREFIX}/cctbx/cctbx_build/libtbx_env" ]]; then
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cat "${SRC_DIR}/olex2c.firstrun.log"
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std::die 42 "olex2: first start did not create cctbx/cctbx_build/libtbx_env (log above) - host libs missing? see step 7"
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fi
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# 10. second start must be clean, and refine the shipped sucrose sample
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# (real cctbx/smtbx use: libgomp, openblas, PIL ... all exercised)
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local -r smoke="${SRC_DIR}/smoke"
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rm -rf "${smoke}"
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mkdir -p "${smoke}"
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cp "${PREFIX}/sample_data/sucrose/"* "${smoke}/"
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( cd "${smoke}" && printf 'reap sucrose.res\nrefine 2\nexit\n' | \
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HOME="${home}" timeout 900 "${PREFIX}/bin/olex2c" > "${SRC_DIR}/olex2c.smoke.log" 2>&1 ) || true
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echo "olex2: --- second start + refine smoke test, tail of ${SRC_DIR}/olex2c.smoke.log ---"
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tail -n 40 "${SRC_DIR}/olex2c.smoke.log"
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echo "olex2: --- end ---"
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grep -q 'problem with the cctbx' "${SRC_DIR}/olex2c.smoke.log" && \
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std::die 42 "olex2: cctbx still not usable on the second start - full log: ${SRC_DIR}/olex2c.smoke.log"
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if grep -qE 'ImportError|cannot open shared object|Traceback' "${SRC_DIR}/olex2c.smoke.log"; then
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echo "olex2: WARNING - errors during the smoke test on THIS host (full log: ${SRC_DIR}/olex2c.smoke.log):"
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grep -E 'ImportError|cannot open shared object|Error' "${SRC_DIR}/olex2c.smoke.log" | head -n 20
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fi
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# the first run wrote libtbx_env, dispatchers, .pyc files as the build user
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chmod -R a+rX "${PREFIX}" || true
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echo "olex2: installed upstream build '$(cat "${PREFIX}/version.txt" 2>/dev/null)' (tag $(cat "${PREFIX}/olex2.tag" 2>/dev/null))"
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}
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