duan_jandClaude Fable 5
3bf22a4b7e
First Ra run "succeeded" while broken: modbuild has no errexit in hooks, so a truncated cached tarball (gzip EOF) and a wrong hardcoded top dir (tarball unpacks to ccp4-9, not ccp4-9.0) scrolled by and the modulefile got installed anyway. Every critical step now ends the build via std::die, the top dir is globbed, and install verifies ccp4.setup-sh exists before finishing. README documents the recovery (rm partial tarball from distfiles, --clean-install). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2.6 KiB
2.6 KiB
ccp4
CCP4 suite (binary distribution, bundled with SHELX and ARP/wARP) for macromolecular crystallography. https://www.ccp4.ac.uk/
- Vendor tarball install: default
prepdownloads the ~5 GB tarball (cached in$PMODULES_DISTFILESDIR),installuntars it into$PREFIXand runsBINARY.setup. - Non-interactive: the CCP4 licence is pre-agreed via
.agree2ccp4v6beforeBINARY.setupruns, so the build never prompts. - No
shasums:: the download link is session-gated (sid=expires), so the checksum cannot be pinned ahead of the first fetch. After the first successful build,sha256sumthe cached tarball and add it if wanted. - Module version is the series (
9.0); minor updates (9.0.xxx) come via the CCP4 update manager inside the installation.
Build on Ra
One-time per user: put the Pmodules build tmp and download cache on /das instead of /var/tmp and $HOME (the tarball alone would blow the home quota):
mkdir -p /das/work/p21/p21515/.cache/Pmodules/distfiles ~/.Pmodules
cat > ~/.Pmodules/Pmodules.yaml <<'EOF'
tmp_dir: /das/work/p21/p21515/.cache/Pmodules
download_dir: /das/work/p21/p21515/.cache/Pmodules/distfiles
EOF
Then:
module use unstable && module load modbuild/2.1.3
cd ccp4
modbuild build --prep 9.0 # download/cache only; also verifies tmp_dir took effect
modbuild build 9.0
If the download fails (expired sid), fetch a fresh link from
https://www.ccp4.ac.uk/download/ and update files/config.yaml, or drop a
hand-downloaded tarball into the distfiles dir under the name: given in
files/config.yaml.
Known failure modes
- "done" but broken install: modbuild has no errexit in hooks — errors in
pbuild::installused to scroll by and the build still reported done. The build script nowstd::dies on every critical step. - Truncated download reused silently: an interrupted
curlleaves a partial file in the distfiles dir, and prep reuses any file it finds there (no integrity check withoutshasums:). Symptom:gzip: stdin: unexpected end of file. Fix:rm ~/.cache/Pmodules/distfiles/ccp4-9.0-shelx-arp-x86_64.tar.gz modbuild build --clean-install 9.0 # or verify by hand before building: gzip -t ~/.cache/Pmodules/distfiles/ccp4-9.0-shelx-arp-x86_64.tar.gz - The tarball unpacks to
ccp4-9(notccp4-9.0as the CCP4 install doc implies); the build globsccp4-*/instead of assuming the name.
Verify
module use MX unstable && module load ccp4/9.0
which refmac5 ccp4i2
echo $CCP4 # should point into /opt/psi/MX/ccp4/9.0/ccp4 (-> ccp4-9)
Bundled SHELX and ARP/wARP still need their own academic registrations.