Update fontawesome icons names

Author: hcartiaux

docs/README.md

@@ -8,8 +8,8 @@
 **technical details** for users to make _effective_ use
 of the [Uni.lu High Performance Computing (ULHPC) Facility](https://hpc.uni.lu)'s resources.
 
-[:fontawesome-solid-sign-in-alt: ULHPC Supercomputers](systems/index.md){: .md-button .md-button--link }
-[:fontawesome-solid-sign-in-alt: Getting Started](getting-started.md){: .md-button .md-button--link }
+[:fontawesome-solid-right-to-bracket: ULHPC Supercomputers](systems/index.md){: .md-button .md-button--link }
+[:fontawesome-solid-right-to-bracket: Getting Started](getting-started.md){: .md-button .md-button--link }
 
 **New:** monthly HPC trainings for beginners, see [our dedicated page](hpc-schools.md).
 

docs/accounts/index.md

@@ -22,7 +22,7 @@ See [Acceptable Use Policy](../policies/aup.md) for more details.
 
 ### Resource allocation policies
 
-[:fontawesome-solid-sign-in-alt: ULHPC Usage Charging and Resource allocation policy](../policies/usage-charging.md){: .md-button .md-button--link }
+[:fontawesome-solid-right-to-bracket: ULHPC Usage Charging and Resource allocation policy](../policies/usage-charging.md){: .md-button .md-button--link }
 
 #### UL internal R&D and training
 

docs/data/encryption.md

@@ -19,7 +19,7 @@ $ gpg --decrypt <file>.gpg          # Decrypt PGP encrypted file
 
 One drawback is that files need to be completely decrypted for processing
 
-[:fontawesome-solid-sign-in-alt: Tutorial: Using GnuPG aka Gnu Privacy Guard aka GPG](https://varrette.gforge.uni.lu/tutorials/gpg.html){: .md-button .md-button--link }
+[:fontawesome-solid-right-to-bracket: Tutorial: Using GnuPG aka Gnu Privacy Guard aka GPG](https://varrette.gforge.uni.lu/tutorials/gpg.html){: .md-button .md-button--link }
 
 
 ## File Encryption Frameworks (EncFS, GoCryptFS...)

docs/data/gdpr.md

@@ -1,5 +1,5 @@
 
-[:fontawesome-solid-sign-in-alt: UL HPC Acceptable Use Policy (AUP) (pdf)](https://hpc-docs.uni.lu/policies/Uni.lu-HPC-Facilities_Acceptable-Use-Policy_v2.1.pdf){: .md-button .md-button--link }
+[:fontawesome-solid-right-to-bracket: UL HPC Acceptable Use Policy (AUP) (pdf)](https://hpc-docs.uni.lu/policies/Uni.lu-HPC-Facilities_Acceptable-Use-Policy_v2.1.pdf){: .md-button .md-button--link }
 
 !!! warning
     Personal data is/may be visible, accessible or handled:

docs/environment/easybuild.md

@@ -26,7 +26,7 @@ For several years now, Easybuild is used to [manage the ULHPC User Software Set]
 
 ## Easybuild Concepts and terminology
 
-[:fontawesome-solid-sign-in-alt: Official Easybuild Tutorial](https://easybuilders.github.io/easybuild-tutorial/){: .md-button .md-button--link}
+[:fontawesome-solid-right-to-bracket: Official Easybuild Tutorial](https://easybuilders.github.io/easybuild-tutorial/){: .md-button .md-button--link}
 
 EasyBuild relies on two main concepts, [toolchains](https://docs.easybuild.io/en/latest/Concepts_and_Terminology.html#toolchains) and [EasyConfig files](https://docs.easybuild.io/en/latest/Concepts_and_Terminology.html#easyconfig-files). A toolchain corresponds to a compiler and a set of libraries which are commonly used to build a software. The two main toolchains frequently used on the UL HPC platform are `foss` (Free and Open Source Software) and `intel` toolchains.
 

docs/environment/index.md

@@ -168,8 +168,8 @@ See [ULHPC Tutorial / Getting Started](https://ulhpc-tutorials.readthedocs.io/en
    end="<!--intro-end-->"
 %}
 
-[:fontawesome-solid-sign-in-alt: ULHPC Environment modules](modules.md){: .md-button .md-button--link }
-[:fontawesome-solid-sign-in-alt: Using Easybuild on ULHPC Clusters](../environment/easybuild.md){: .md-button .md-button--link }
+[:fontawesome-solid-right-to-bracket: ULHPC Environment modules](modules.md){: .md-button .md-button--link }
+[:fontawesome-solid-right-to-bracket: Using Easybuild on ULHPC Clusters](../environment/easybuild.md){: .md-button .md-button--link }
 
 ## Self management of work environments in UL HPC with Conda
 
@@ -179,4 +179,4 @@ See [ULHPC Tutorial / Getting Started](https://ulhpc-tutorials.readthedocs.io/en
    end="<!--intro-end-->"
 %}
 
-[:fontawesome-solid-sign-in-alt: Management of work environments with Conda](conda.md){: .md-button .md-button--link }
+[:fontawesome-solid-right-to-bracket: Management of work environments with Conda](conda.md){: .md-button .md-button--link }

docs/environment/spack.md

@@ -0,0 +1,289 @@
+# Spack: A Package Manager on the UL HPC Platform
+
+[<img width='400px' src='https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo-text.svg'/>](https://spack.readthedocs.io/en/latest/#)
+
+
+
+## Introduction to Spack
+
+
+A brief introduction to Spack will be added here.
+
+## Setting up Spack
+
+!!! note
+    The guide is also applicable to other HPC clusters where users need to manage components such as MPI libraries, compilers, and other software through the `module` system.
+
+
+### Connection to a compute node
+
+
+```{.sh .copy}
+si -N 1 -n 16 -c 1 -t 0-02:00:00 # on iris: -C broadwell or -C skylake
+```
+
+??? note "Allocation Details"
+
+    `si` is a shell function that wraps the `salloc` command to simplify interactive Slurm job allocation.  
+    It stands for:
+
+    ```bash
+    salloc -p interactive --qos debug -C batch ${options}
+    ```
+    - `${options}`: any additional arguments passed to `si` (e.g., `-N`, `-n`, `-c`, `-t`, etc.)
+
+    ```bash
+    si -N 1 -n 16 -c 1 -t 0-02:00:00
+    ```
+
+    This allocates:
+
+    - 1 node (`-N 1`)
+    - 16 MPI tasks (`-n 16`)
+    - 1 CPU per task (`-c 1`)
+    - for a wall time of 2 hours (`-t 0-02:00:00`) 
+
+    !!! info "Iris Cluster"
+
+        On the **Iris** cluster, 
+
+        - Use `-C broadwell` or  `-C skylake` 
+
+        **Examples:**
+        ```bash
+        si -N 1 -n 16 -c 1 -t 0-02:00:00 -C broadwell
+        ```
+
+
+### Clone & Setup Spack
+
+Clone and setup spack in `$HOME`  - it has better much better performance for 
+small files than `$SCRATCH`
+
+``` { .sh .copy }
+cd $HOME
+git clone --depth=2 https://github.com/spack/spack.git
+cd spack
+```
+To make Spack available in your shell session, source its environment setup script:
+
+``` { .sh .copy }
+source $HOME/spack/share/spack/setup-env.sh
+```
+For convenience, this line can be added to the .`bashrc` file to make Spack automatically available in every new shell session.
+
+### Define System-Provided Packages
+
+`packages.yaml` A spack configuration file used to tell Spack what tools and versions already exist on the cluster, so Spack can use those instead of building everything again.Create a packages.yaml file under: `$HOME/.spack/packages.yaml` 
+
+``` { .sh .copy }
+touch $HOME/.spack/packages.yaml
+```
+
+
+with the following contents:
+
+``` { .sh .copy }
+ packages:
+  gcc:
+    externals:
+    - spec: [email protected]+binutils languages:='c,c++,fortran'
+      modules:
+      - compiler/GCC/13.2.0
+      extra_attributes:
+        compilers:
+          c: /opt/apps/easybuild/systems/aion/rhel810-20250405/2023b/epyc/software/GCCcore/13.2.0/bin/gcc
+          cxx: /opt/apps/easybuild/systems/aion/rhel810-20250405/2023b/epyc/software/GCCcore/13.2.0/bin/g++
+          fortran: /opt/apps/easybuild/systems/aion/rhel810-20250405/2023b/epyc/software/GCCcore/13.2.0/bin/gfortran
+    buildable: false
+  binutils:
+    externals:
+    - spec: [email protected]
+      modules:
+      - tools/binutils/2.40-GCCcore-13.2.0
+    buildable: false
+  libevent:
+    externals:
+    - spec: [email protected]
+      modules:
+      - lib/libevent/2.1.12-GCCcore-13.2.0
+    buildable: false
+  libfabric:
+    externals:
+    - spec: [email protected]
+      modules:
+      - lib/libfabric/1.19.0-GCCcore-13.2.0
+    buildable: false
+  libpciaccess:
+    externals:
+    - spec: [email protected]
+      modules:
+      - system/libpciaccess/0.17-GCCcore-13.2.0
+    buildable: false
+  libxml2:
+    externals:
+    - spec: [email protected]
+      modules:
+      - lib/libxml2/2.11.5-GCCcore-13.2.0
+    buildable: false
+  hwloc:
+    externals:
+    - spec: [email protected]+libxml2
+      modules:
+      - system/hwloc/2.9.2-GCCcore-13.2.0
+    buildable: false
+  mpi:
+    buildable: false
+  munge:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+    buildable: false
+  numactl:
+    externals:
+    - spec: [email protected]
+      modules:
+      - tools/numactl/2.0.16-GCCcore-13.2.0
+    buildable: false
+  openmpi:
+    variants: fabrics=ofi,ucx schedulers=slurm
+    externals:
+    - spec: [email protected]
+      modules:
+      - mpi/OpenMPI/4.1.6-GCC-13.2.0
+    buildable: false
+  pmix:
+    externals:
+    - spec: [email protected]
+      modules:
+      - lib/PMIx/4.2.6-GCCcore-13.2.0
+    buildable: false
+  slurm:
+    externals:
+    - spec: [email protected] sysconfdir=/etc/slurm
+      prefix: /usr
+    buildable: false
+  ucx:
+    externals:
+    - spec: [email protected]
+      modules:
+      - lib/UCX/1.15.0-GCCcore-13.2.0
+    buildable: false
+  zlib:
+    externals:
+    - spec: [email protected]
+      modules:
+      - lib/zlib/1.2.13-GCCcore-13.2.0
+    buildable: false
+
+```
+This tells Spack to use the system available GCC, binutils and OpenMPI with the native fabrics.
+
+## Building FEniCS
+
+Create an environment and install FEniCS
+``` { .sh .copy }
+cd ~
+spack env create -d fenicsx-main-20230126/ 
+spack env activate fenicsx-main-20230126/
+spack add py-fenics-dolfinx@main fenics-dolfinx+adios2 adios2+python petsc+mumps
+# Change @main to e.g. @0.7.2 in the above if you want a fixed version.
+spack concretize
+spack install -j16
+``` 
+or the same directly in `spack.yaml` in `$SPACK_ENV`
+
+``` { .sh .copy }
+spack:
+  # add package specs to the `specs` list
+  specs:
+  - py-fenics-dolfinx@main
+  - fenics-dolfinx@main+adios2
+  - petsc+mumps
+  - adios2+python
+  view: true
+  concretizer:
+    unify: true
+```
+The following are also commonly used in FEniCS scripts and may be useful
+
+``` { .sh .copy }
+spack add gmsh+opencascade py-numba py-scipy py-matplotlib
+```
+It is possible to build a specific version (git ref) of DOLFINx. Note that the hash must be the full hash. It is best to specify appropriate git refs on all components.
+
+``` { .sh .copy }
+# This is a Spack Environment file.
+#
+# It describes a set of packages to be installed, along with
+# configuration settings.
+spack:
+  # add package specs to the `specs` list
+  specs:
+  - [email protected]=main+adios2
+  - [email protected]=main
+
+  - [email protected]=main
+  - [email protected]=main
+
+  - [email protected]=main
+
+  - [email protected]=main
+
+  - [email protected]=main
+
+  - petsc+mumps
+  - adios2+python
+  view: true
+  concretizer:
+    unify: true
+```
+
+It is also possible to build only the C++ layer using
+
+
+``` { .sh .copy }
+spack add fenics-dolfinx@main+adios2 py-fenics-ffcx@main petsc+mumps
+```
+To rebuild FEniCSx from main branches inside an existing environment
+
+
+``` { .sh .copy }
+spack install --overwrite -j16 fenics-basix py-fenics-basix py-fenics-ffcx fenics-ufcx py-fenics-ufl fenics-dolfinx py-fenics-dolfinx
+```
+
+
+## Testing the build
+
+Quickly test the build with
+``` { .sh .copy }
+srun python -c "from mpi4py import MPI; import dolfinx"
+```
+
+## Using the build
+
+See the uni.lu documentation for full details - using the environment should be as 
+simple as adding the following where `...` is the name/folder of your environment.
+
+``` { .sh .copy }
+#!/bin/bash -l
+source $HOME/spack/share/spack/setup-env.sh
+spack env activate ...
+```
+
+## Known issues
+
+Workaround for broken Python module find for gmsh on uni.lu cluster
+
+``` { .sh .copy }
+
+export PYTHONPATH=$SPACK_ENV/.spack-env/view/lib64/:$PYTHONPATH
+
+```
+Workaround for broken Python module find for adios2 (seems broken in Spack)
+
+``` { .sh .copy }
+
+export PYTHONPATH=$(find $SPACK_ENV/.spack-env -type d -name 'site-packages' | grep venv):$PYTHONPATH
+
+```