# 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):

```bash
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:

```bash
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). `BINARY.setup` afterwards is just as bad — it walks the
whole installation patching paths and then **byte-compiles the bundled
Python environment** ("compiling py-files"), thousands of tiny .pyc
writes on network storage; expect another 15-30+ min. Budget roughly an
hour for the whole install on Ra. Watch progress from a second shell:

```bash
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::die`s 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

```bash
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.