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olex2: export OLEX2_ROOT from the modulefile, use it in the README checks

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duan_j committed 2026-10-16 17:49:09 +02:00
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commit f6b63e740d
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+16 -10
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olex2/README.md
+10 -9
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@@ -57,7 +57,9 @@ exports `OLEX2_CCTBX_DIR`, `BOOST_ADAPTBX_*`, `OLEX2_GL_*`,
inherited one would be imported by the embedded Python 3.8 and break it),
sets `LIBGL_ALWAYS_SOFTWARE=1` for the GUI only, then `exec`s the binary.
`unirun` is never run: `/opt/psi/MX` is shared and read-only, updates are
done by building a new module version.
done by building a new module version. The modulefile exports
`OLEX2_ROOT=$PREFIX` (our own name; the vendor's `OLEX2_DIR` re-targets the
updater and stays unset) and puts `$PREFIX/bin` on `PATH`.
### Bundled glibc 2.39 sysroot (why and how)
@@ -147,12 +149,11 @@ GTK2/X11/OpenGL — also `olex2c` (wx is linked in statically). Check once
per host type:
```sh
module load olex2/1.5-7665
P=/opt/psi/MX/olex2/1.5-7665
$P/sysroot/usr/lib64/ld-linux-x86-64.so.2 --list $P/olex2c | grep -E 'not found|libc.so.6|libstdc'
module load olex2/1.5-7665 # exports OLEX2_ROOT=/opt/psi/MX/olex2/1.5-7665
$OLEX2_ROOT/sysroot/usr/lib64/ld-linux-x86-64.so.2 --list $OLEX2_ROOT/olex2c | grep -E 'not found|libc.so.6|libstdc'
```
`libc.so.6`/`libstdc++.so.6` must resolve under `$P/sysroot`; every `not
`libc.so.6`/`libstdc++.so.6` must resolve under `$OLEX2_ROOT/sysroot`; every `not
found` line is a host package to `dnf install` (expected candidates on a
minimal RHEL9: `gtk2`, `mesa-libGL`, `mesa-libGLU`, `libSM`, `libXxf86vm`,
`libxkbcommon`). Plain `ldd` on the raw binary also works after the patch
@@ -161,13 +162,13 @@ minimal RHEL9: `gtk2`, `mesa-libGL`, `mesa-libGLU`, `libSM`, `libXxf86vm`,
## Verifying the install
```sh
which olex2c # -> /opt/psi/MX/olex2/1.5-7665/bin/olex2c
which olex2 # -> /opt/psi/MX/olex2/1.5-7665/bin/olex2
cat /opt/psi/MX/olex2/1.5-7665/version.txt # SVN Revision No. 7665
which olex2c # -> $OLEX2_ROOT/bin/olex2c (= /opt/psi/MX/olex2/1.5-7665/bin/olex2c)
which olex2 # -> $OLEX2_ROOT/bin/olex2
cat $OLEX2_ROOT/version.txt # SVN Revision No. 7665
# console: starts, loads a shipped sample, refines, exits (writes to ~/.olex2
# and to a scratch copy of the sample - run it in a scratch dir)
cd $(mktemp -d) && cp /opt/psi/MX/olex2/1.5-7665/sample_data/sucrose/* .
cd $(mktemp -d) && cp $OLEX2_ROOT/sample_data/sucrose/* .
olex2c # interactive prompt; then type:
# reap sucrose.res
# refine 4
olex2/modulefile
+6 -1
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@@ -22,6 +22,11 @@ Per-user data (DataDir) lives in ~/.olex2. The vendor Python API (olx, olex
modules) is only available from inside olex2/olex2c, not as a system python.
"
# Install root (= Olex2 BaseDir): sample_data, sysroot, version.txt live here.
# Our own name on purpose - OLEX2_DIR is a vendor variable that re-targets
# the auto-updater, so it must stay unset.
setenv OLEX2_ROOT $PREFIX
# Launchers only: the raw binaries, the vendor 'start' script (auto-updater)
# and the private python live under $PREFIX root and stay off PATH.
prepend-path PATH $PREFIX/bin
prepend-path PATH $PREFIX/bin