Main README: clone/SSH/branching quickstart with full /das paths,
--tmpdir/--distdir as part of the standard build command (do not fill
/var/tmp or $HOME) with cleanup for defaults, tips deduplicated against
module READMEs, old-system references removed, resource links and
tutorial acknowledgements added.
Module READMEs: purge outdated recipes repo-wide — Pmodules/1.1.20 and
2.0.0 plus ./build replaced by modbuild/2.1.3 invocations; the cctbx
unbound-variable fix moved from the main README into phenix and DIALS
READMEs where it belongs.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Refresh to modbuild 2.1.3 (no build subcommand, real flag list, no
--dry-run/--check-mode), document the --tmpdir/--distdir /das recipe,
and collect the lessons from the ccp4 build: no errexit in hooks,
pipefail vs yes|, partial-download reuse, env contamination (module
purge + reload modbuild), slow shared-storage installs. The new-module
skill (SKILL.md + REFERENCE.md) now lives in .claude/skills/new-module
so Claude Code auto-discovers it and other agents can be pointed at the
same files.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The ~/.Pmodules/Pmodules.yaml route did not reliably set download_dir,
so the maintained recipe now passes both dirs on the command line;
readers must adapt the p-group path to their own.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Byte-compiling the bundled Python env writes thousands of .pyc files on
network storage; whole install budget on Ra is about an hour.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Untarring 3.7 GB into ~15-20 GB of small files on shared /opt/psi takes
10-30 min silently; documented so nobody kills a healthy build.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Builtin curl in default prep has no retry/resume: an interrupted 3.7 GB
download restarts from zero and leaves a partial file that prep reuses
silently. Custom pbuild::prep resumes with wget --continue and gates the
build on gzip -t, so a truncated tarball can neither be reused nor
require a full re-download. urls: dropped from config.yaml (unused with
custom prep); install untars straight from the distfiles cache instead
of a pointless 3.7 GB copy via SRC_DIR.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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>
No --check-mode exists; --prep is the real way to pre-fetch and check the
tmp_dir config. modbuild on Ra is 2.1.3 now.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Pre-agrees the CCP4 licence via .agree2ccp4v6 so BINARY.setup never
prompts. Download via urls: with unpacker: none (untar once into PREFIX,
BINARY.setup patches paths at final location). Build tmp and download
cache go to /das/work/p21/p21515/.cache/Pmodules through
~/.Pmodules/Pmodules.yaml (see README) since /var/tmp and the home quota
are too small for the ~5 GB tarball.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
XTRAPOL8_DIR and PATH were never set despite README referencing them;
upstream prerequisites require CCP4 alongside Phenix.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The installed careless/0.5.4 venv already contains the NVIDIA wheels
([cuda] extra), which need only the node driver and fall back to CPU,
so a separate GPU module and cuda module dep are unnecessary. Revert
careless/build to careless[cuda] to match the actual install.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
careless installs plain careless (CPU). careless-gpu also installs plain
careless but declares cuda/12.8.1 as build_requires/runtime_deps
(jfjoch_viewer pattern) instead of pip-bundling CUDA via the [cuda] extra.
Both builds honor UV_CACHE_DIR to share one download cache.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- main README: add Pmodules background from wiki, unx-mx_adm group
replaces -adm account for updating modules in /etc/psi/MX, and
how to propagate main to the build-* tutorial branches
- module READMEs: fix titles/paths to match module directories
(DIALS, jfjoch_viewer), replace -adm login steps with unx-mx_adm note
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Scaffold the standard 4-file Pmodule for autoPROC (Global Phasing Ltd.):
build, modulefile, files/config.yaml, README.md. The PSI licence token
(autoPROC/.licence) already existed and is installed into the software tree
at build time.
Follows the phenix archetype for the licence-gated install: the snapshot
tarball cannot be wget'd (download needs credentials), so it is staged by
hand in the module dir as autoPROC_snapshot_<date>.tar.gz and unpacked into
PREFIX with --strip-components=1 (xds pattern). Runtime is activated by
sourcing setup.sh via the modulefile.
CCP4 8.0 and XDS are wired as runtime_deps (xds from this repo; ccp4 is a
site module placeholder to confirm with `module avail ccp4`). Adds a
.gitignore guard so the proprietary snapshot is never committed.
Not built locally - to be tested on Ra.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
duan_jandClaude Fable 5