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.
59 lines
2.5 KiB
Bash
59 lines
2.5 KiB
Bash
#!/bin/bash
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# Olex2 launcher, installed by the MX Pmodule as BOTH
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# $PREFIX/bin/olex2 (GUI)
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# $PREFIX/bin/olex2c (console / "headless" Olex2)
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# One script, two copies: it dispatches on its own file name.
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#
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# It reproduces the environment of the vendor "start" script that ships in
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# olex2-linux64.zip, but deliberately does NOT run the "unirun" auto-updater:
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# /opt/psi/MX is shared and read-only for users, updates are done by
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# rebuilding the module (see README.md, "Adding a new version").
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set -u
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# $PREFIX/bin/<name> -> base = $PREFIX (= Olex2 BaseDir(): olex2, olex2c,
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# cctbx/, lib/, ilib/, util/, etc/ all live there, vendor layout untouched)
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here="$(cd -P "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")" && pwd)"
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base="${here%/bin}"
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exe="$(basename "$0")"
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case "$exe" in
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olex2|olex2c) ;;
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*) echo "olex2-launcher: must be invoked as 'olex2' or 'olex2c', not '$exe'" >&2; exit 2 ;;
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esac
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[[ -x "$base/$exe" ]] || { echo "olex2-launcher: $base/$exe is missing or not executable (broken install?)" >&2; exit 1; }
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# --- bundled glibc ---------------------------------------------------------
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# The executables were patchelf'ed at build time to use $base/sysroot's
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# ld.so + libc + libstdc++ via DT_RPATH. Nothing to export for that, and
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# NEVER add $base/sysroot/... to LD_LIBRARY_PATH: every system tool Olex2
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# spawns (sh, shelxl, editors) would then load the foreign libc and crash.
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# The bundled glibc has no locale archive -> use its built-in C.UTF-8.
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export LANG=C.UTF-8
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export LC_ALL=C.UTF-8
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# --- vendor 'start' environment ------------------------------------------
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export OLEX2_CCTBX_DIR="$base/cctbx"
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# cctbx sets signal handlers for FPE and does not handle them
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export BOOST_ADAPTBX_FPE_DEFAULT=1
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export BOOST_ADAPTBX_SIGNALS_DEFAULT=1
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export OLEX2_GL_STEREO=FALSE
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export OLEX2_GL_MULTISAMPLE=FALSE
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export OLEX2_GL_DEPTH_BITS=16
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export LD_LIBRARY_PATH="$base/lib:$base/ilib:$OLEX2_CCTBX_DIR/cctbx_build/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
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# embedded CPython 3.8 (lib/python3.8, lib/libpython3.8.so.1.0)
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export PYTHONHOME="$base"
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# a PYTHONPATH inherited from another module/conda env would be imported by
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# the embedded 3.8 interpreter and break it - never let it leak in; same for
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# the user's ~/.local/lib/python3.8/site-packages
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unset PYTHONPATH
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export PYTHONNOUSERSITE=1
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if [[ "$exe" == "olex2" ]]; then
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# GUI only: software OpenGL avoids "Vulkan drivers missing" / GLX errors
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# on display-less cluster nodes; users may override by pre-setting it to 0
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export LIBGL_ALWAYS_SOFTWARE="${LIBGL_ALWAYS_SOFTWARE:-1}"
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fi
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exec "$base/$exe" "$@"
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