Add Alps section (#185)

* Add Alps section

* GitHub Action: Apply external link format

* Link to Alps section in news

* add: alps description, construction admonition

* GitHub Action: Apply external link format

* Small corrections & modify formatter script for download links

* GitHub Action: Apply external link format

* Modify date for blog post

* upd: uenv page

* upd: vClusters

* upd: Alps

* ref(alps): reintroduce listing

* Fix typos

---------

Co-authored-by: mjaehn <[email protected]>
Co-authored-by: Matthieu <[email protected]>
Co-authored-by: leclairm <[email protected]>

docs/.pages

@@ -9,6 +9,8 @@ nav:
     - tasks
   - User Support:
     - support
+  - Alps:
+    - alps
   - Models:
     - models
   - Tools:

docs/alps/.pages

@@ -0,0 +1,4 @@
+nav:
+  - Alps Infrastructure: index.md
+  - Supported vClusters: vclusters.md
+  - User Environments: uenvs.md

docs/alps/index.md

@@ -0,0 +1,40 @@
+!!! construction "Page under construction"
+
+    Information in this page is not yet complete nor final. It will be updated following the progress of
+
+    - the Alps system deployment at CSCS
+    - C2SM's adaptation to this new system
+
+# The Alps System
+
+Alps is a distributed HPC infrastructure managed by CSCS. Contrary to traditional HPC, it is composed of several logical units called vClusters (versatile clusters). From the users perspective, they play the role of a traditional HPC machine, each vCluster being tailored to the needs of a specific community. This setup also enables geographical distribution of vClusters which facilitates geo-redundancy. The main physical piece of Alps is hosted at CSCS in Lugano and a detailed description can be found at [their website :material-open-in-new:](https://www.cscs.ch/computers/alps){:target="_blank"}.
+
+## vClusters
+
+The following vClusters are hosted at CSCS:
+
+| vCluster | Activity          | Share            |
+|----------|-------------------|------------------|
+| Daint    | User Lab          | ~ 800 GH nodes   |
+| Clariden | Machine Learning  | ~ 800 GH nodes   |
+| Santis   | Weather & Climate | ~ 400 GH nodes   |
+| Tödi     | Testing           | few GH nodes     |
+| Eiger    |                   | multi-core nodes |
+
+*GH = Grace Hopper*
+
+## File Systems
+
+!!! note "TODO"
+
+    - [ ] `/users`, `/store` and `/scratch`
+    - [ ] reserved space per vClsuter vs shared space
+    - [ ] ...
+
+## Introductory Workshop Material
+
+As an introduction to the Alps infrastructure, the material of our [C2SM workshop "Switching to Alps"](../blog/posts/2024-07-02_switching_to_Alps.md) is available:
+
+- [Recording :material-download:](https://polybox.ethz.ch/index.php/s/oSxyJgTjyvJKX8B){:target="_blank"}<br>
+- [Slides presenting Alps, vClusters and Uenvs :material-download:](https://polybox.ethz.ch/index.php/s/jvtIYkBvHUSGZYD){:target="_blank"}<br>
+- [Slides for the integration of Uenvs in `spack-c2sm` :material-download:](https://polybox.ethz.ch/index.php/s/SWbYrOVRIprke60){:target="_blank"} 

docs/alps/uenvs.md

@@ -0,0 +1,82 @@
+!!! construction "Page under construction"
+
+    Information in this page is not yet complete nor final. It will be updated following the progress of
+
+    - the Alps system deployment at CSCS
+    - C2SM's adaptation to this new system
+
+# User Environments
+
+Software stacks at CSCS are now accessible through the so-called User Environments (uenv). They replace the previous monolithic software stack containing everything from which one could load any module, with all the infinite potential conflicts it involves. User environments contain the minimal software stack required for a certain activity, say, building and running ICON. They are generated by `spack`, packed into single `squashfs` file and then mounted by the user. In a way, they can be considered as poor man's containers.
+
+!!! success "Main Advantages of Uenvs"
+
+    To a large degree, we can consider that there is a separation of concerns between software stacks and the machine OS which enables the following:
+
+    - a much reduced maintenance of software stacks
+    - system-wide upgrades are limited to the low level OS, so should be way easier, when not transparent to the users
+    - upgrading to more recent software stacks or keeping old ones around (think compiler versions) is way easier
+    - users (for now C2SM) are able to build their own uenvs
+    - quicker access to software compared to classical multi-files directories
+
+## CSCS documentation
+
+A description of user environments and the `uenv` tool can be found in the [CSCS Knowledge Base :material-open-in-new:](https://confluence.cscs.ch/display/KB/UENV+user+environments){:target="_blank"}. 
+
+## Uenvs central Registry and C2SM uenvs
+
+The user environments provided by CSCS are registered in a central database. In the long run we should be able to operate only with those but, at least for the initial period, there is also the need for uenvs provided by C2SM. These are accessed by their absolute path. All supported uenvs are documented in the corresponding vClsuter section of the [dedicated page](../vclusters/). 
+
+## The `uenv` command line tool
+
+[Official documentation :material-open-in-new:](https://eth-cscs.github.io/uenv/){:target="_blank"}
+
+It can be used to
+
+- query images by metadata: tags, names, target architecture, etc ...
+- mount images and work interactively
+- run a single command with that uenv mounted
+- access uenv modules
+
+For now, `uenv` isn't available on Balfrin and requires (easy) [manual installation :material-open-in-new:](https://eth-cscs.github.io/uenv/#getting-uenv){:target="_blank"}.
+
+!!! note "TODO: Quick start"
+
+    - [ ] `uenv image repo create`
+    - [ ] `uenv image find`
+    - [ ] `uenv image pull`
+    - [ ] `uenv start`
+    - [ ] `uenv run`
+
+## `--uenv` SLURM plugin
+
+CSCS developped the `--uenv` slurm plugin in order to mount uenvs at runtime. Either use the name of a uenv in your local repo or the full absolute path to the uenv.
+
+```shell
+sbatch --uenv uenv_name:/mount/point
+sbatch --uenv /image/path:/mount/point
+```
+
+`:mount/point` can always be omitted and defaults to `:/user-environment`.
+
+On Balfrin, the installed plugin version doesn't allow access via uenv names but `uenv image inspect` can be used to query the corresponding absolute path:
+
+```shell
+uenv image inspect prgenv-gnu --format="{sqfs}"
+/bret/scratch/cscs/bcumming/.uenv-images/images/1736b4bb5ad9b3c5cae8878c71782a8bf2f2f739dbce8e039b629de418cb4dab/store.squashfs
+```
+
+## Mount points
+
+Uenvs cannot be mounted *anywhere*. They are generated with a predefined installation path contained in it, where the user is supposed to mount them, at least if they are used as a spack instance (don't know for other usage). By default, it is `/user-environment` and another `/user-tools` also exists for *side* environments that would potentially need to be mounted simultaneously to a *main* one.
+
+## `spack-c2sm` integration
+
+User environments are used as a spack upstream with
+```shell
+source spack-c2sm/setup-env.sh /user-environment
+``` 
+
+!!! note "TODO"
+
+    - [ ] Update official `spack-c2sm` documentation

docs/alps/vclusters.md

@@ -0,0 +1,74 @@
+!!! construction "Page under construction"
+
+    Information in this page is not yet complete nor final. It will be updated following the progress of
+
+    - the Alps system deployment at CSCS
+    - C2SM's adaptation to this new system
+
+# Supported vClusters
+
+This page is hosting information about C2SM supported vClusters. 
+
+## Access
+
+Connection to vClusters happens as for any other CSCS machine, e.g. `ssh santis.cscs.ch` with a `ProxyJump` on `ela.cscs.ch`.
+A section in the `~/.ssh/config` could look as follows:
+
+```config title="~/.ssh.config"
+Host ela
+  Hostname ela.cscs.ch
+  User cscsusername
+  IdentityFile ~/.ssh/cscs-key
+
+Host balfrin* daint* santis* todi*
+  Hostname %h.cscs.ch
+  User cscsusername
+  IdentityFile ~/.ssh/cscs-key
+  ProxyJump ela
+```
+
+This would allow standard connections like `ssh santis.cscs.ch` but also specifying the login node like `ssh santis-ln002.cscs.ch` if needed.
+
+## Daint
+
+Daint is the vCluster dedicated to the User Lab. It is deployed on ~800 Grace-Hopper nodes.
+
+Even though Weather and Climate also has the dedicated vCluster Santis (see [below](#santis)), traditional projects will be running on Daint.
+
+!!! warning "Hostname conflict"
+
+    For the duration of the overlap between the current expiring Piz Daint and its reincarnation as a vCluster, there will be two different host names. Most probably the current Piz Daint will continue being accessible at `daint.cscs.ch` while the vCluster hostname is not known yet.
+
+### Uenvs
+
+List of currently supported Uenvs on Daint:
+
+| uenv        | activity                      |
+|-------------|-------------------------------|
+| icon-vx:rcy | build and run icon            |
+| prepost-vx  | pre and post processing tools |
+|             |                               |
+
+### Storage
+
+!!! note "TODO"
+
+    - [ ] Storage
+
+## Santis
+
+Santis is dedicated to Weather and Climate and is deployed on ~400 Grace-Hopper nodes. At least at the beginning, it will be hosting only [EXCLAIM :material-open-in-new:](https://c2sm.ethz.ch/research/exclaim.html){:target="_blank"} and related projects.
+
+### Uenvs
+
+| uenv        | activity                      |
+|-------------|-------------------------------|
+| icon-vx:rcy | build and run icon            |
+| prepost-vx  | pre and post processing tools |
+|             |                               |
+
+### Storage
+
+!!! note "TODO"
+
+    - [ ] Storage

docs/blog/posts/2024-08-14_alps.md

@@ -0,0 +1,12 @@
+---
+date:
+  created: 2024-08-14
+---
+
+# New information about the Alps system available
+
+Since the transition from Piz Daint to the new Alps infrastructure is already taking place, 
+we have added a new navigation section [Alps](../../alps/index.md) to collect all necessary information there.
+
+Most importantly, C2SM users will find details about the new vClusters as well as how to
+use User Environments (uenvs) in order to access the software stacks.

docs/stylesheets/extra.css

@@ -11,3 +11,22 @@
 [data-md-color-scheme=c2sm-light] img[src$="#gh-dark-mode-only"] {
   display: none; /* Hide dark images in light mode */
 }
+
+/* Admonition for pages under construction */
+:root {
+  --md-admonition-icon--construction: url('data:image/svg+xml;charset=utf-8,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M22 20.59 20.59 22l-3.14-3.14c-.56.37-1.15.7-1.79.92-1.66.58-3.46.62-5.13.1-1.03-.3-1.97-.83-2.78-1.51l-3.19 3.19c-.56.59-1.53.59-2.12 0-.58-.56-.58-1.56 0-2.12l3.38-3.38 2.65-.52a6.1 6.1 0 0 0 2.81 1.96c1.16.35 2.44.34 3.59-.04.29-.09.57-.2.83-.34L7.6 9l-1.77 1.78L3 7.95 7.95 3l4.24 1.41L9 7.6l8.31 8.29c.19-.18.34-.36.49-.56 1.5-1.97 1.62-4.91.29-7.33C16.78 5.57 14.5 3.55 12 2c1.41.5 2.76 1.17 4 2.04 1.24.87 2.43 1.89 3.33 3.21.9 1.29 1.54 2.87 1.67 4.54.1 1.68-.34 3.44-1.3 4.86-.2.35-.46.63-.7.91l3 3.03Z"/></svg>')
+}
+.md-typeset .admonition.construction,
+.md-typeset details.construction {
+  border-color: rgb(255, 145, 0);
+}
+.md-typeset .construction > .admonition-title,
+.md-typeset .construction > summary {
+  background-color: rgba(255, 145, 0, 0.1);
+}
+.md-typeset .construction > .admonition-title::before,
+.md-typeset .construction > summary::before {
+  background-color: rgb(255, 145, 0);
+  -webkit-mask-image: var(--md-admonition-icon--construction);
+          mask-image: var(--md-admonition-icon--construction);
+}

scripts/format_external_links.py

@@ -3,12 +3,26 @@
 import argparse
 
 def modify_link(line):
-    pattern = r'\[([^\]]+)\]\((http[s]?://[^\s\)]+)\)'
-    replacement = r'[\1 :material-open-in-new:](\2){:target="_blank"}'
-    modified_line, num_subs = re.subn(pattern, replacement, line)
+    # Define patterns for general and download links
+    general_pattern = r'\[([^\]]+)\]\((http[s]?://[^\s\)]+)\)'
+    download_pattern = r'\[([^\]]+)\]\((https://polybox\.ethz\.ch/index\.php/s/[^\s\)]+)\)'
+
+    # Define replacements for general and download links
+    general_replacement = r'[\1 :material-open-in-new:](\2){:target="_blank"}'
+    download_replacement = r'[\1 :material-download:](\2){:target="_blank"}'
+
     # Check if the line was already modified or doesn't need modification
     if ':material-open-in-new:' in line and '{:target="_blank"}' in line:
         return line, False
+    if ':material-download:' in line and '{:target="_blank"}' in line:
+        return line, False
+
+    # Apply the appropriate replacement based on the URL pattern
+    if re.search(download_pattern, line):
+        modified_line, num_subs = re.subn(download_pattern, download_replacement, line)
+    else:
+        modified_line, num_subs = re.subn(general_pattern, general_replacement, line)
+
     return modified_line, num_subs > 0
 
 def process_markdown_file(file_path):