Fix more typos, whitelist more words

Author: msimberg

.github/actions/spelling/allow.txt

@@ -65,6 +65,8 @@ MFA
 MLP
 MNDO
 MPICH
+Makefile
+Makefiles
 Malvoisin
 MeteoSwiss
 NAMD
@@ -105,12 +107,17 @@ XDG
 Zumsteinspitz
 aarch
 aarch64
+acfdt
 acl
+admin
+admins
 artifactory
 autodetection
 aws
 baremetal
 biomolecular
+blaspp
+blt
 bristen
 bytecode
 capstor
@@ -121,49 +128,73 @@ concretizer
 containerised
 cpe
 cscs
+cshell
 cuda
 customised
+cyberduck
+dbcsr
 dcomex
+dftb
+dftd
 diagonalisation
+diffs
+diis
 dimms
 dockerhub
 dotenv
 dropbear
 edf
 edfs
+eigen
 eiger
+elpa
 epyc
 fftw
 filesystems
 fontawesome
+fpmd
 gcc
 gdrcopy
 github
 gitlab
+gmail
 gpt
 gpu
+gromos
 groundstate
 gsl
 hdf
+hotmail
 huggingface
 hwloc
 iframe
 ijulia
 inodes
 iopsstor
+ivo
 jfrog
 jobreport
 juhpc
 julia
 juliaup
 jupyter
+jwt
 kokkos
+lapackpp
 lexer
+lexers
 libfabric
+libint
+libtree
+libxc
 linalg
+linkx
 linux
+lts
 matlab
+metadynamics
 meteo
+mimalloc
 miniconda
 mkl
 mpi
@@ -173,22 +204,29 @@ nanotron
 nccl
 netlib
 netrc
+nql
 nsight
 numa
 nvcr
 nvdashboard
+nvhpc
 nvidia
 nwp
 octicons
 ofi
 omlin
 omp
 oom
+openblas
+opls
 osts
 osu
 papi
+parmetis
+petsc
 pme
 pmi
+pmix
 podman
 preinstalled
 prerelease
@@ -198,25 +236,40 @@ prioritisation
 prioritise
 prioritised
 proactively
+pseudopotentials
+pwscf
 pyfirecrest
+pygments
 pytorch
 quantumespresso
+quasiparticles
 quickstart
+rgw
+ripgrep
 rocm
+rowspan
+rpath
 runtime
 runtimes
 santis
 sbatch
+scalapack
 screenshot
+slepc
 slurm
 smartphone
 sourced
+spdlog
+spglib
 sphericart
+spla
 squashfs
 srun
 ssh
+sshservice
 stackinator
 stakeholders
+stdexec
 subfolders
 subtable
 subtables
@@ -226,6 +279,9 @@ sysadmin
 tarball
 tcl
 tcsh
+tds
+telematics
+terabyte
 testuser
 timeframe
 timelimit
@@ -234,14 +290,17 @@ todi
 toolbar
 toolset
 torchaudio
+torchrun
 torchvision
 treesitter
 trilinos
 trl
 uarch
+ucx
 uenv
 uenvs
 uids
+ultrasoft
 utkin
 vCluster
 vClusters
@@ -251,6 +310,7 @@ vboost
 venv
 versioned
 versioning
+vscode
 waldur
 wandb
 webhooks
@@ -265,6 +325,7 @@ workflows
 xattr
 xattrs
 xcb
+xeon
 xfer
 xname
 xpmem

.github/actions/spelling/patterns.txt

@@ -4,20 +4,25 @@ FirecREST
 RESTful
 IPyParallel
 \`ENV\`ironment
+HECBioSim
+GmbH
+hEGFR
+cuDNN
+Schrödinger
+GROningen
+Säntis
 
 # markdown figure
-^!\[.*\]\(.*\)$
+!\[.*\]\(.*\)
 
 # Most obvious URLs
-https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*)
+https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&\/=]*)
 
 # Markdown references and URLs (definition and use)
 ^\[\]\(\){#[a-z-]+}$
 \]\([^\s]+\)
 \]\[[a-z-]+\]
 
-# Markdown URLs
-
 # Inline code
 \`[^\`]+\`
 
@@ -27,3 +32,9 @@ https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0
 
 # versions
 [0-9]+\.[.0-9]+(\+[0-9a-z]+)?
+
+# software-name@version
+[A-Za-z-_]+@[0-9]+(\.[.0-9]+)?(\+[0-9a-z]+)?
+
+# img tag
+<img.*\/>

docs/clusters/bristen.md

@@ -16,7 +16,7 @@ Nodes are in the [`normal` Slurm partition][ref-slurm-partition-normal].
 
 ### Storage and file systems
 
-Bristen uses the [MLp filesystems and storage policies][ref-mlp-storage].
+Bristen uses the [MLP filesystems and storage policies][ref-mlp-storage].
 
 ## Getting started
 

docs/clusters/clariden.md

@@ -18,7 +18,7 @@ Most nodes are in the [`normal` Slurm partition][ref-slurm-partition-normal], wh
 
 ### Storage and file systems
 
-Clariden uses the [MLp filesystems and storage policies][ref-mlp-storage].
+Clariden uses the [MLP filesystems and storage policies][ref-mlp-storage].
 
 ## Getting started
 

docs/clusters/daint.md

@@ -115,10 +115,10 @@ There are four [Slurm partitions][ref-slurm-partitions] on the system:
 
 | name | nodes  | max nodes per job | time limit |
 | --   | --     | --                | -- |
-| `normal` | unlim        | -    | 24 hours |
+| `normal` | unlimited  | -    | 24 hours |
 | `debug`  | 24         | 2    | 30 minutes |
 | `xfer`   | 2          | 1    | 24 hours |
-| `low`    | unlim        | -    | 24 hours |
+| `low`    | unlimited  | -    | 24 hours |
 
 * nodes in the `normal` and `debug` (and `low`) partitions are not shared
 * nodes in the `xfer` partition can be shared

docs/running/index.md

@@ -0,0 +1,4 @@
+# Running Jobs
+
+[Slurm][ref-slurm] is used on CSCS systems to schedule jobs.
+The [job report tool][ref-jobreport] can be used in Slurm jobs to collect reports on how well an application uses the system.

docs/software/ml/index.md

@@ -50,7 +50,7 @@ To ensure optimal performance on CSCS systems, we recommend starting from an env
 This can be achieved either by:
 
 * building a [custom container image][ref-build-containers] based on a suitable ML-ready base image,
-* or starting from a provided uenv (e.g., [PrgEnv GNU][ref-uenv-prgenv-gnu] or [PyTorch uenv][ref-uenv-pytorch]),
+* or starting from a provided uenv (e.g., [`prgenv-gnu`][ref-uenv-prgenv-gnu] or [PyTorch uenv][ref-uenv-pytorch]),
 
 and extending it with a virtual environment.
 

docs/software/prgenv/prgenv-gnu.md

@@ -95,7 +95,7 @@ The environment is designed as a fairly minimal set of
 
 There are three ways to access the software provided by prgenv-gnu, once it has been started.
 
-=== "the default view"
+=== "the `default` view"
 
     The simplest way to get started is to use the `default` file system view, which automatically loads all of the packages when the uenv is started.
 

docs/software/prgenv/prgenv-nvfortran.md

@@ -67,9 +67,9 @@ uenv image find prgenv-nvfortran@*
 uenv image pull prgenv-nvfortran/24.11:v2
 ```
 
-=== "the nvfort view"
+=== "the `nvfort` view"
 
-    The nvfort view loads all of the packages into your environment (equivalent to loading all the modules at once):
+    The `nvfort` view loads all of the packages into your environment (equivalent to loading all the modules at once):
 
     ```bash
     uenv start prgenv-nvfortran/24.11:v1 --view=nvfort

docs/software/sciapps/gromacs.md

@@ -3,7 +3,7 @@
 
 [GROMACS] (GROningen Machine for Chemical Simulations) is a versatile and widely-used open source package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
 
-It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
+It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
 
 !!! note "uenvs"