Installing-dolfinx-with-spack-on-Habrok.md

+Content:
+
 [[_TOC_]]
 
 [Spack](https://github.com/spack/spack) is a package management tool designed for HPC, allowing to easily build optimized software in multiple versions and configurations. Many packages are supported (see the [package list](https://spack.readthedocs.io/en/latest/package_list.html)), among them the fenicsx/dolfinx package [py-fenics-dolfinx](https://spack.readthedocs.io/en/latest/package_list.html#py-fenics-dolfinx).
@@ -64,39 +66,58 @@ Let Spack detect all additional system modules:
 spack external find
 ```
 
+To install newly released package versions, Spack has to be updated with a `git pull` in the Spack repository.
+
 ## dolfinx installation
 
+### Environment setup
+
 Create a new Spack environment, for instance with the name `fenicsx` and activate it:
 
 ```sh
 spack env create fenicsx
-spack env activate fenicsx
+spack env activate fenicsx -p
 ```
 Add the dolfinx package to the environment:
 ```sh
+spack add py-fenics-dolfinx@main arch=linux-rocky8-zen3 cflags="-O3" fflags="-O3"
+```
+This will select the latest development versions of the FEniCS ecosystem, corresponding to the `main` branches. To install the latest stable release (at the time of writing `v0.6.0`, see the list of tags [here](https://spack.readthedocs.io/en/latest/package_list.html#py-fenics-dolfinx)), use
+```sh
 spack add py-fenics-dolfinx arch=linux-rocky8-zen3 cflags="-O3" fflags="-O3"
 ```
-This will select the latest stable release (at the time of writing `v0.6.0`, see the list of tags [here](https://spack.readthedocs.io/en/latest/package_list.html#py-fenics-dolfinx)). To install the development version, use `py-fenics-dolfinx@main`.
+Our codes require the development version.
+
 The -O3 compiler flags optionally apply level 3 optimization (https://github.com/FEniCS/dolfinx#spack).
 The `arch` setting specifies the [microarchitecture](https://spack.readthedocs.io/en/latest/basic_usage.html#support-for-specific-microarchitectures) to determine the optimal compiler flags.
 Usually Spack will detect the correct settings automatically, if not compiling for a different machine.
-Because the login node and the compute nodes use different processors, in the command above we enforce the target archictecture for the compute nodes (`zen3`). (Confirm with `srun -n 1 spack arch`.)
+Because the login node and the compute nodes use different processors, in the command above we enforce the target architecture for the compute nodes (`zen3`). (Confirm with `srun -n 1 spack arch`.)
 This setting may not be necessary if we compile the packages on a compute node instead of the login node (strongly recommended).
 
-**NOTE** (31-05-2023): To install `dolfinx@main` with ADIOS2 support for visualization, the following works:
+**NOTE**: Optional dependencies
+
+To install dolfinx with ADIOS2 support for visualization, the optional `adios2` dependency must be activated in the `fenics-dolfinx` package (a dependency of `py-fenics-dolfinx`).
 ```sh
-spack add adios2@2.8.3 arch=linux-rocky8-zen3
 spack add fenics-dolfinx@main +adios2 arch=linux-rocky8-zen3 cflags="-O3" fflags="-O3"
 spack add py-fenics-dolfinx arch=linux-rocky8-zen3 cflags="-O3" fflags="-O3"
 ```
-(The default version `adios2@2.9.0` produces files that cannot be opened with ParaView 5.11.1.)
-In order to add MUMPS to petsc (not installed by default):
+In order to add MUMPS to PETSc (not installed by default), do:
 ```sh
-spack add petsc +mumps arch=linux-rocky8-zen3
+spack add petsc +mumps arch=linux-rocky8-zen3 cflags="-O3" fflags="-O3"
 ```
 Other options of interest are, e.g., choosing the partitioner, see `spack info fenics-dolfinx` and `spack info petsc`.
 
-Now the packages can be installed with `spack install`. This may take a while, so better create a job for a compute node:
+**Summary of the recommended environment for CHiMERA:**
+```sh
+spack add petsc +mumps arch=linux-rocky8-zen3 cflags="-O3" fflags="-O3"
+spack add fenics-dolfinx@main +adios2 arch=linux-rocky8-zen3 cflags="-O3" fflags="-O3"
+spack add py-fenics-dolfinx arch=linux-rocky8-zen3 cflags="-O3" fflags="-O3"
+spack add py-pip py-h5py arch=linux-rocky8-zen3
+```
+
+### Installation
+
+Now the packages can be installed with `spack install`. Create a job for a compute node:
 ```sh
 #!/bin/bash
 
@@ -110,8 +131,13 @@ source $HOME/spack/share/spack/setup-env.sh
 spack env activate fenicsx
 srun spack install
 ```
-and run the job with `sbatch job.sh`.
-dolfinx should now be installed. Check the logs if openmpi and openblas were correctly picked up from the system instead of compiling them from source.
+and run the job with 
+```sh
+sbatch job.sh
+```
+dolfinx should now be installed. Check the logs if OpenMPI and OpenBLAS were correctly picked up from the system instead of compiling them from source.
+
+### Test the installation
 
 Test your installation with, e.g.,
 ```sh