diff --git a/DIALS/README.md b/DIALS/README.md index 20b2d1e..e5826da 100644 --- a/DIALS/README.md +++ b/DIALS/README.md @@ -1,11 +1,6 @@ -XDS +# DIALS -Step 1: login with your -adm account - -``` -kinit xxxx_x-adm -aklog -``` +Step 1: make sure you are in the `unx-mx_adm` group -- no -adm account needed, members can update the modules in `/etc/psi/MX` directly (if you have problems, please let the admins know) Step 2: load the latest Pmodules package diff --git a/README.md b/README.md index a1a0290..bdae1f6 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,47 @@ # MX -This project includes all MX modules in use. +This project includes all MX modules in use. All modules are build with modbuild/2.1.2 Documentation for how-to-build modules can be found in: https://github.com/Pmodules/Pmodules/wiki +## Pmodules background (from the wiki) + +- Modules are organized in hierarchical groups; all modules in this repo belong to the `MX` group (`module use MX`). +- Filesystem layout: modulefile at `$PREFIX/GROUP/modulefiles/NAME/VERSION`, installation at `$PREFIX/GROUP/NAME/VERSION`, per-version config at `$PREFIX/GROUP/modulefiles/NAME/.config-VERSION` (YAML). +- Release stages: **unstable**, **stable**, **deprecated**. Newly built modules land in unstable; opt in with `module use unstable`. +- Pmodules automatically sets `$NAME_DIR`, `$NAME_HOME`, `$NAME_PREFIX`, `$NAME_VERSION` on load and prepends standard directories (`$PREFIX/bin` to `PATH`, `$PREFIX/lib` to `LD_LIBRARY_PATH`, ...) if they exist -- no explicit `setenv`/`prepend-path` needed in the modulefile. + +## Permissions + +No need to switch to an -adm account any more: members of the `unx-mx_adm` group can update the modules in `/etc/psi/MX` directly. If you run into permission problems, please let the admins know. + +## Tutorial branches (build-*) + +Each participant works on their own `build-` branch (e.g. `build-dials`). All of them start from `main`. + +To propagate new material from `main` to the `build-*` branches: + +While the branches are still identical to main (fast-forward, no force needed): + +``` +git push origin main:build-dials main:build-buster main:build-careless main:build-crystfel main:build-phenix main:build-pymol main:build-autoproc main:build-xtrapol8 + +for b in dials buster careless crystfel phenix pymol autoproc xtrapol8; do + git branch -f build-$b main +done +``` + +Once the branches have diverged (people committed on them), merge main into each instead: + +``` +for b in dials buster careless crystfel phenix pymol autoproc xtrapol8; do + git checkout build-$b && git merge main && git push +done +git checkout main +``` + +If `git push origin main:build-xxx` fails with "non-fast-forward", the branch has its own commits: switch to the merge loop, do not force-push over other people's work. ## Module tips 1. modules is name/version (not name/name-version) diff --git a/alphafold/README.md b/alphafold/README.md index 45c152f..7e82f71 100644 --- a/alphafold/README.md +++ b/alphafold/README.md @@ -94,9 +94,9 @@ flags.DEFINE_boolean('use_gpu_relax', True, 'Whether to relax on GPU. ' Add version to files/variants. The version number should match a github tag (e.g. `v2.0.1`) or else have the commit hash as `$V_RELEASE`. -As admin user: +As a member of the `unx-mx_adm` group (no -adm account needed; if you have problems, please let the admins know): ``` -cd MX/alphafold +cd alphafold ./build ``` diff --git a/autoPROC/README.md b/autoPROC/README.md index a9be6bb..d59fd57 100644 --- a/autoPROC/README.md +++ b/autoPROC/README.md @@ -8,12 +8,7 @@ dependencies. ## Build on Ra -Step 1: login with your `-adm` account - -``` -kinit xxxx_x-adm -aklog -``` +Step 1: make sure you are in the `unx-mx_adm` group -- no -adm account needed, members can update the modules in `/etc/psi/MX` directly (if you have problems, please let the admins know) Step 2: load the latest Pmodules package diff --git a/jfjoch_viewer/README.md b/jfjoch_viewer/README.md index 52802d0..27c7001 100644 --- a/jfjoch_viewer/README.md +++ b/jfjoch_viewer/README.md @@ -1,11 +1,6 @@ -jfjviewer +# jfjoch_viewer -Step 1: login with your -adm account - -``` -[smith_k@ra-l-005 xds]$ kinit smith_k-adm -[smith_k@ra-l-005 xds]$ aklog -``` +Step 1: make sure you are in the `unx-mx_adm` group -- no -adm account needed, members can update the modules in `/etc/psi/MX` directly (if you have problems, please let the admins know) Step 2: load the latest Pmodules package @@ -14,10 +9,10 @@ module use unstable module load Pmodules/1.1.20 ``` -Step 3: go into xds directory, update config.yaml to add newest release version and build module with that release name (e.g. below is for 20240724) +Step 3: go into jfjoch_viewer directory, update config.yaml to add newest release version and build module with that release name ``` -cd jfjviewer +cd jfjoch_viewer vi files/config.yaml ./build 1.0.0-rc.156 ``` diff --git a/xds/README.md b/xds/README.md index a6a87b4..30c9ee1 100644 --- a/xds/README.md +++ b/xds/README.md @@ -1,11 +1,6 @@ -XDS +# XDS -Step 1: login with your -adm account - -``` -[smith_k@ra-l-005 xds]$ kinit smith_k-adm -[smith_k@ra-l-005 xds]$ aklog -``` +Step 1: make sure you are in the `unx-mx_adm` group -- no -adm account needed, members can update the modules in `/etc/psi/MX` directly (if you have problems, please let the admins know) Step 2: load the latest Pmodules package