MX_Pmodule/ccp4/README.md

ccp4

CCP4 suite (binary distribution, bundled with SHELX and ARP/wARP) for macromolecular crystallography. https://www.ccp4.ac.uk/

• Vendor tarball install: custom prep downloads the ~3.7 GB tarball with wget --continue (resumes partial downloads; the builtin curl can't) and verifies it with gzip -t; install untars it into $PREFIX and runs BINARY.setup.
• Non-interactive: the CCP4 licence is pre-agreed via .agree2ccp4v6 before BINARY.setup runs, 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, sha256sum the 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.

Install is SLOW — not stuck

The install step untars 3.7 GB into ~15-20 GB of small files on shared /opt/psi storage: the tar alone runs 10-30 min with no output (gzip is single-threaded, small-file creation on network storage is the bottleneck), and BINARY.setup afterwards walks the whole installation for several more minutes. Watch progress from a second shell:

watch -n 30 'du -sh /opt/psi/MX/ccp4/9.0/'

Growing du = working. Only investigate if it's frozen for 10+ min.

Known failure modes

• "done" but broken install: modbuild has no errexit in hooks — errors in pbuild::install used to scroll by and the build still reported done. The build script now std::dies on every critical step.
• Interrupted download: prep now detects a truncated tarball with gzip -t and resumes it with wget --continue — just re-run modbuild build 9.0. A download that dies with Failure writing output to destination means quota/disk full at the distfiles dir, not a network problem — free space or move download_dir: (see above) before retrying.
• The tarball unpacks to ccp4-9 (not ccp4-9.0 as the CCP4 install doc implies); the build globs ccp4-*/ 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.