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>
72 lines
2.6 KiB
Markdown
72 lines
2.6 KiB
Markdown
# ccp4
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CCP4 suite (binary distribution, bundled with SHELX and ARP/wARP) for
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macromolecular crystallography. https://www.ccp4.ac.uk/
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- Vendor tarball install: default `prep` downloads the ~5 GB tarball
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(cached in `$PMODULES_DISTFILESDIR`), `install` untars it into `$PREFIX`
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and runs `BINARY.setup`.
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- Non-interactive: the CCP4 licence is pre-agreed via `.agree2ccp4v6`
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before `BINARY.setup` runs, so the build never prompts.
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- No `shasums:`: the download link is session-gated (`sid=` expires), so
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the checksum cannot be pinned ahead of the first fetch. After the first
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successful build, `sha256sum` the cached tarball and add it if wanted.
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- Module version is the series (`9.0`); minor updates (9.0.xxx) come via
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the CCP4 update manager inside the installation.
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## Build on Ra
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One-time per user: put the Pmodules build tmp and download cache on
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/das instead of /var/tmp and $HOME (the tarball alone would blow the
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home quota):
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```bash
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mkdir -p /das/work/p21/p21515/.cache/Pmodules/distfiles ~/.Pmodules
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cat > ~/.Pmodules/Pmodules.yaml <<'EOF'
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tmp_dir: /das/work/p21/p21515/.cache/Pmodules
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download_dir: /das/work/p21/p21515/.cache/Pmodules/distfiles
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EOF
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```
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Then:
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```bash
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module use unstable && module load modbuild/2.1.3
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cd ccp4
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modbuild build --prep 9.0 # download/cache only; also verifies tmp_dir took effect
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modbuild build 9.0
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```
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If the download fails (expired sid), fetch a fresh link from
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https://www.ccp4.ac.uk/download/ and update `files/config.yaml`, or drop a
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hand-downloaded tarball into the distfiles dir under the `name:` given in
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`files/config.yaml`.
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## Known failure modes
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- **"done" but broken install**: modbuild has no errexit in hooks — errors in
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`pbuild::install` used to scroll by and the build still reported done. The
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build script now `std::die`s on every critical step.
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- **Truncated download reused silently**: an interrupted `curl` leaves a
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partial file in the distfiles dir, and prep reuses any file it finds there
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(no integrity check without `shasums:`). Symptom:
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`gzip: stdin: unexpected end of file`. Fix:
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```bash
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rm ~/.cache/Pmodules/distfiles/ccp4-9.0-shelx-arp-x86_64.tar.gz
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modbuild build --clean-install 9.0
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# or verify by hand before building:
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gzip -t ~/.cache/Pmodules/distfiles/ccp4-9.0-shelx-arp-x86_64.tar.gz
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```
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- The tarball unpacks to `ccp4-9` (not `ccp4-9.0` as the CCP4 install doc
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implies); the build globs `ccp4-*/` instead of assuming the name.
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## Verify
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```bash
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module use MX unstable && module load ccp4/9.0
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which refmac5 ccp4i2
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echo $CCP4 # should point into /opt/psi/MX/ccp4/9.0/ccp4 (-> ccp4-9)
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```
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Bundled SHELX and ARP/wARP still need their own academic registrations.
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