Merge branch 'main' into spellcheck

Author: bcumming

.github/CODEOWNERS

@@ -4,4 +4,5 @@ docs/software/communication @Madeeks @msimberg
 docs/software/devtools/linaro @jgphpc
 docs/software/prgenv/linalg.md @finkandreas @msimberg
 docs/software/sciapps/cp2k.md @abussy @RMeli
+docs/software/sciapps/gromacs.md @kanduri
 docs/software/ml @boeschf

docs/build-install/cpe.md

@@ -1,10 +1,111 @@
 # Cray Programming Environment (CPE)
 
-!!! warning
-    you don't want to use this
+The Cray Programming Environment (CPE) is a suite of software: programming environments, compilers, libraries and tools.
 
-!!! mlp
-    The CPE is not provided on the machine learning platform.
+The CPE is provided to users on Alps as containers.
 
-!!! cwp
-    The CPE is not provided on the climate and weather platform
+!!! info "CPE is the cray modules"
+    The familiar modules that provide the `Prgenv-gnu` and `Prgenv-cray`  programming environments, and packages like `cray-python` and `cray-fftw`, that will be familiar from the old Piz Daint system.
+
+!!! warning "CPE is not supported on Alps"
+    The Cray modules were provided on the old Daint system, and CSCS supported their use and provided software built on top of them.
+
+    **Alps is a big change - the CPE modules are not provide as officially supported software.**
+    They are provided _as is_ to users who still need to use them, however CSCS will not be able to provide detailed support for issues that arise when using them.
+
+    The recommended method for building and running software is to use [uenv][ref-uenv] or [containers][ref-container-engine].
+
+## CPE in a container
+
+[](){#ref-cpe-versions}
+### Available versions
+
+The `PrgEnv-gnu` and `PrgEnv-cray` programming environments are provided as separate containers, instead of having both in one container, named `gnu-$version` and `cray-$version` respectively.
+The `version` is the CPE version in the container.
+
+|                 | `zen2`   | `gh200` |
+|-----------------|----------|---------|
+| `cpe-gnu-24.7`  | ❌       | ✅      |
+| `cpe-cray-24.7` | ❌       | ✅      |
+
+!!! warning "only available on gh200"
+    The CPE container is only provided on systems with the "[container engine][ref-container-engine]" container runtime, which is currently the Grace-Hopper systems [Daint][ref-cluster-daint], [Clariden][ref-cluster-clariden] and [Santis][ref-cluster-santis].
+
+### How to use
+
+!!! info "Before you start"
+    To use the CPE containers as documented below, you need to set the `EDF_PATH` environment variable.
+    ```console
+    export EDF_PATH=/capstor/scratch/cscs/anfink/shared/cpe/edf:$EDF_PATH
+    ```
+    Note that the current location of the EDF files is temporary, to work around a file system bug.
+    The environment variable __will not be required__ once this issue is fixed.
+
+To start a session with the CPE (see [available-versions][ref-cpe-versions] above):
+```console
+$ srun --environment=cpe-cray-24.07 --pty bash
+```
+Once the container starts up you can directly use the programming environment, because there will be modules loaded by default at startup.
+
+```console
+$ srun -p debug --environment=cpe-cray-24.07 --pty bash
+$ module list
+
+Currently Loaded Modules:
+  1) craype-arm-grace     4) cce/18.0.0          7) cray-mpich/8.1.30
+  2) craype-network-ofi   5) craype/2.7.32       8) cuda/12.6
+  3) xpmem/2.9.6          6) PrgEnv-cray/8.5.0   9) craype-accel-nvidia90
+
+
+$ module avail
+
+---- /opt/cray/pe/lmod/modulefiles/mpi/crayclang/17.0/ofi/1.0/cray-mpich/8.0 ----
+   cray-hdf5-parallel/1.14.3.1    cray-parallel-netcdf/1.12.3.13
+
+---------- /opt/cray/pe/lmod/modulefiles/comnet/crayclang/17.0/ofi/1.0 ----------
+   cray-mpich-abi/8.1.30    cray-mpich/8.1.30 (L)
+
+------------- /opt/cray/pe/lmod/modulefiles/compiler/crayclang/17.0 -------------
+   cray-hdf5/1.14.3.1    cray-libsci/24.07.0
+
+------------------ /opt/cray/pe/lmod/modulefiles/mix_compilers ------------------
+   cce-mixed/18.0.0
+
+---------------- /opt/cray/pe/lmod/modulefiles/cpu/arm-grace/1.0 ----------------
+   cray-fftw/3.3.10.8
+
+------------- /opt/cray/pe/lmod/modulefiles/craype-targets/default --------------
+   craype-accel-amd-gfx908        craype-hugepages16M     craype-network-none
+   craype-accel-amd-gfx90a        craype-hugepages1G      craype-network-ofi  (L)
+   craype-accel-amd-gfx940        craype-hugepages256M    craype-network-ucx
+   craype-accel-amd-gfx942        craype-hugepages2G      craype-x86-genoa
+   craype-accel-host              craype-hugepages2M      craype-x86-milan-x
+   craype-accel-nvidia70          craype-hugepages32M     craype-x86-milan
+   craype-accel-nvidia80          craype-hugepages4M      craype-x86-rome
+   craype-accel-nvidia90   (L)    craype-hugepages512M    craype-x86-spr-hbm
+   craype-arm-grace        (L)    craype-hugepages64M     craype-x86-spr
+   craype-hugepages128M           craype-hugepages8M      craype-x86-trento
+
+---------------------- /opt/cray/pe/lmod/modulefiles/core -----------------------
+   PrgEnv-cray/8.5.0 (L)    cray-libsci_acc/24.07.0    cray-python/3.11.7
+   cce/18.0.0        (L)    cray-pmi/6.1.15.19         craype/2.7.32      (L)
+
+----------------------------- /opt/cray/modulefiles -----------------------------
+   xpmem/2.9.6 (L)
+
+----------------------------- /opt/cscs/modulefiles -----------------------------
+   cuda/12.6 (L)
+
+$ CC --version
+Cray clang version 18.0.0  (0e4696aa65fa9549bd5e19c216678cc98185b0f7)
+Target: aarch64-unknown-linux-gnu
+Thread model: posix
+InstalledDir: /opt/cray/pe/cce/18.0.0/cce-clang/aarch64/share/../bin
+```
+
+The recommended way of using CPE in a container is to start the container, and use `$SCRATCH` and `$STORE` to interact with persistent data. Please remember that any data that is written to a directory that is not mounted from the host system will be lost, after the container stops.
+
+!!! note
+    By default, the paths `/capstor`, `/iopsstor` are mounted to the same paths inside the container.
+
+Additionally `/users` will be mounted at `/users.host`, so you can access data in your home folder, but with a slightly different path. This is on purpose, and you can override this behaviour by writing your own [EDF file][ref-ce-edf-reference], especially using the key `base_environment`, referencing the predefined CPE environment files and override what you would like to change.

docs/index.md

@@ -40,11 +40,6 @@ The Alps Research infrastructure hosts multiple platforms and clusters targeting
 
     [:octicons-arrow-right-24: Alps Storage](alps/storage.md)
 
-</div>
-
-
-<div class="grid cards" markdown>
-
 -   :fontawesome-solid-layer-group: __Accounts and Projects__
 
     The first step is to get an account and a project

docs/services/firecrest.md

@@ -3,9 +3,9 @@
 
 FirecREST is a RESTful API for programmatically accessing High-Performance Computing resources, developed at CSCS.
 
-Users can make use of FirecREST to automate access to HPC, enabling [CI/CD pipelines](https://github.com/eth-cscs/firecrest/tree/master/examples/CI-pipeline), [workflow managers](https://github.com/eth-cscs/firecrest/tree/master/examples/airflow-operators), and other tools against HPC resources.
+Users can make use of FirecREST to automate access to HPC, enabling [CI/CD pipelines](https://eth-cscs.github.io/firecrest-v2/use_cases/CI-pipeline/), [workflow managers](https://github.com/eth-cscs/firecrest/tree/master/examples/airflow-operators), and other tools against HPC resources.
 
-Additionally, scientific platform developers can integrate FirecREST into [web-enabled portals](https://firecrest-ui-hpc.cscs.ch) and [applications](https://github.com/eth-cscs/firecrest/tree/master/examples/UI-client-credentials), allowing them to securely access authenticated and authorized CSCS services such as job submission and data transfer on HPC systems.
+Additionally, scientific platform developers can integrate FirecREST into [web-enabled portals](https://my.hpcp.cscs.ch) and [applications](https://github.com/eth-cscs/firecrest/tree/master/examples/UI-client-credentials), allowing them to securely access authenticated and authorized CSCS services such as job submission and data transfer on HPC systems.
 
 Users can make HTTP requests to perform the following operations:
 
@@ -17,18 +17,17 @@ Users can make HTTP requests to perform the following operations:
 
 Starting early 2025, CSCS has introduced a new version of the API: [FirecREST version 2](https://eth-cscs.github.io/firecrest-v2).
 
-Version 2 is faster, easier to use, and more efficient in resource management than its predecessor, therefore, if you are new to FirecREST start directly using **version 2** (if available for your platform).
+Version 2 is faster, easier to use, and more efficient in resource management than its predecessor, therefore, if you are new to FirecREST start directly using **version 2**.
 
-If you're using **version 1**, we recommend you to port your applications to use the new version.
+!!! warning "Deprecation notice"
+    If you're using **version 1**, we recommend you to port your applications to use the new version.
+    We will communicate soon the exact date of the decomission of version 1 (not before Quarter 4 of 2025).
 
 === "Version 2"
 
-    !!!Warning
-        Documentation for version 2 is still work in progress
-
     For a full feature set, have a look at the latest [FirecREST version 2 API specification](https://eth-cscs.github.io/firecrest-v2/openapi) deployed at CSCS.
 
-    Please refer to the [FirecREST-v2 documentation](https://eth-cscs.github.io/firecrest-v2/use) for detailed documentation.
+    Please refer to the [FirecREST-v2 documentation](https://eth-cscs.github.io/firecrest-v2/user_guide/) for detailed documentation.
 
 === "Version 1"
 
@@ -136,7 +135,7 @@ Back on the Subscription Management page, you can review your active subscriptio
 
 ![FirecREST subscription management](../images/firecrest/f7t-api-subscriptions-management.png)
 
-To use your Application to access FirecREST, follow the [API documentation](https://firecrest-docs.v1.svc.cscs.ch/).
+To use your Application to access FirecREST, follow the [API documentation](https://eth-cscs.github.io/firecrest-v2/openapi).
 
 ## Getting Started
 
@@ -444,14 +443,12 @@ A staging area is used for external transfers and downloading/uploading a file f
 
 ## Further Information
 
-* [FirecREST UI for HPC Platform](https://firecrest-ui-hpc.cscs.ch)
-* [FirecREST OpenAPI Specification Version 1](https://firecrest.readthedocs.io/en/latest/reference.html)
-* [FirecREST OpenAPI Specification Version 2](https://eth-cscs.github.io/firecrest-v2/openapi)
-* [FirecREST Docs Version 1](https://firecrest.readthedocs.io/)
-* [FirecREST Docs Version 2](https://eth-cscs.github.io/firecrest-v2)
-* [Documentation of pyFirecREST (v1/v2)](https://pyfirecrest.readthedocs.io/)
-* [FirecREST repository Version 1](https://github.com/eth-cscs/firecrest)
-* [FirecREST repository Version 2](https://github.com/eth-cscs/firecrest-v2)
+* [FirecREST UI for HPC Platform](https://my.hpcp.cscs.ch)
+* [FirecREST UI for ML Platform](https://my.mlp.cscs.ch)
+* [FirecREST OpenAPI Specification](https://eth-cscs.github.io/firecrest-v2/openapi)
+* [FirecREST Official Docs](https://eth-cscs.github.io/firecrest-v2)
+* [Documentation of pyFirecREST](https://pyfirecrest.readthedocs.io/)
+* [FirecREST repository](https://github.com/eth-cscs/firecrest-v2)
 * [What are JSON Web Tokens](https://jwt.io/introduction)
 * [Python Requests](https://requests.readthedocs.io/en/master/user/quickstart)
 * [Python Async API Calls](https://docs.aiohttp.org/en/stable/)