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olex2: merge sysroot/lib64 (libgcc) into usr/lib64; make configure re-runnable

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duan_j committed 2026-10-16 17:55:10 +02:00
1 parent f6b63e740d
commit fffd36970c
2 files changed
+31 -12
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olex2/README.md
+5 -1
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@@ -79,7 +79,11 @@ executable and must match its libc. So the recipe:
- ships glibc 2.39 + GCC 14 `libstdc++`/`libgcc_s` under `$PREFIX/sysroot`
(frozen Fedora 40 rpms from kojipkgs, Fedora's permanent build archive;
same glibc generation as the upstream build host);
same glibc generation as the upstream build host). glibc and libstdc++
unpack to `usr/lib64`, libgcc to `/lib64` (Fedora relies on the
filesystem package's `lib64 -> usr/lib64` symlink, which we do not
extract), so `configure` merges `lib64` into `usr/lib64` and recreates
the symlink — one lib dir for the RPATH;
- runs `patchelf --set-interpreter <sysroot ld.so> --force-rpath --set-rpath
<sysroot libdir>:$PREFIX/lib:$PREFIX/ilib:$PREFIX/cctbx/cctbx_build/lib:$PREFIX:$ORIGIN`
on every dynamic executable (`hart`, `hart_mpi` are static and skipped).
olex2/build
+26 -11
View File
@@ -40,17 +40,23 @@ OLEX2_PATCH_EXES=(olex2c olex2 unirun NoSpherA2 hart_mpi)
pbuild::configure() {
local -r zip="${SRC_DIR}/olex2-${V}-linux64.zip"
[[ -s "${zip}" ]] || std::die 42 "olex2: ${zip} not found - prep did not fetch it. \
Pre-stage the archive by hand as <distdir>/olex2-${V}-linux64.zip (see README) and re-run."
command -v unzip >/dev/null || std::die 42 "olex2: 'unzip' not on PATH on this build host"
# partial downloads reused from distfiles are the classic failure: test the archive first
unzip -tq "${zip}" >/dev/null || \
std::die 42 "olex2: archive is corrupt/truncated - rm <distdir>/olex2-${V}-linux64.zip and re-run"
# ~1 GB unpacked (cctbx + python + sample data); SRC_DIR is under --tmpdir
unzip -q -o "${zip}" -d "${SRC_DIR}" || std::die 42 "olex2: unzip failed (disk/quota at --tmpdir?)"
[[ -f "${SRC_DIR}/olex2/olex2c" && -f "${SRC_DIR}/olex2/olex2" ]] || \
std::die 42 "olex2: unexpected archive layout - expected ${SRC_DIR}/olex2/{olex2,olex2c}"
rm -f "${zip}"
if [[ -f "${SRC_DIR}/olex2/olex2c" && -f "${SRC_DIR}/olex2/olex2" ]]; then
# re-run after a failed configure/install: prep's stamp is set, the
# tree is already unpacked - reuse it (the zip may be gone from SRC_DIR)
echo "olex2: reusing unpacked tree in ${SRC_DIR}/olex2"
else
[[ -s "${zip}" ]] || std::die 42 "olex2: ${zip} not found - prep did not fetch it. \
Pre-stage the archive by hand as <distdir>/olex2-${V}-linux64.zip (see README) and re-run (-f)."
command -v unzip >/dev/null || std::die 42 "olex2: 'unzip' not on PATH on this build host"
# partial downloads reused from distfiles are the classic failure: test the archive first
unzip -tq "${zip}" >/dev/null || \
std::die 42 "olex2: archive is corrupt/truncated - rm <distdir>/olex2-${V}-linux64.zip and re-run"
# ~1 GB unpacked (cctbx + python + sample data); SRC_DIR is under --tmpdir
unzip -q -o "${zip}" -d "${SRC_DIR}" || std::die 42 "olex2: unzip failed (disk/quota at --tmpdir?)"
[[ -f "${SRC_DIR}/olex2/olex2c" && -f "${SRC_DIR}/olex2/olex2" ]] || \
std::die 42 "olex2: unexpected archive layout - expected ${SRC_DIR}/olex2/{olex2,olex2c}"
rm -f "${zip}" # 255 MB copy; the distfiles cache keeps the original
fi
# --- private glibc 2.39 + libstdc++ 14 sysroot (Fedora 40 rpms) ----------
command -v rpm2cpio >/dev/null && command -v cpio >/dev/null || \
@@ -64,6 +70,15 @@ Pre-stage the archive by hand as <distdir>/olex2-${V}-linux64.zip (see README) a
( cd "${sysroot}" && rpm2cpio "${SRC_DIR}/${rpm}" | cpio -idm --quiet ) || \
std::die 42 "olex2: extracting ${rpm} failed"
done
# Fedora's glibc + libstdc++ install to /usr/lib64 but libgcc still to
# /lib64, which on a real system is the filesystem package's symlink to
# usr/lib64 - we do not extract that package, so recreate the merge here.
if [[ -d "${sysroot}/lib64" && ! -L "${sysroot}/lib64" ]]; then
mkdir -p "${sysroot}/usr/lib64"
cp -r --preserve=mode,timestamps,links "${sysroot}/lib64/." "${sysroot}/usr/lib64/" && \
rm -rf "${sysroot}/lib64" && ln -s usr/lib64 "${sysroot}/lib64" || \
std::die 42 "olex2: merging sysroot/lib64 into sysroot/usr/lib64 failed"
fi
local ld libc libdir
ld="$(find "${sysroot}" -type f -name 'ld-linux-x86-64.so.2' -print -quit)"
libc="$(find "${sysroot}" -type f -name 'libc.so.6' -print -quit)"