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Fix more typos, whitelist more words
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‎.github/actions/spelling/allow.txt‎

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@@ -65,6 +65,8 @@ MFA
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MLP
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MNDO
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MPICH
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Makefile
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Makefiles
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Malvoisin
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MeteoSwiss
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NAMD
@@ -95,8 +97,10 @@ Roboto
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Roothaan
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SSHService
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STMV
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Schrödinger
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Scopi
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Signalkuppe
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Säntis
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TOTP
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UANs
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UserLab
@@ -105,12 +109,17 @@ XDG
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Zumsteinspitz
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aarch
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aarch64
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acfdt
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acl
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admin
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admins
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artifactory
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autodetection
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aws
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baremetal
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biomolecular
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blaspp
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blt
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bristen
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bytecode
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capstor
@@ -121,49 +130,73 @@ concretizer
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containerised
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cpe
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cscs
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cshell
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cuda
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customised
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cyberduck
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dbcsr
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dcomex
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dftb
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dftd
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diagonalisation
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diffs
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dimms
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dockerhub
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dotenv
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dropbear
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edf
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edfs
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eigen
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eiger
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elpa
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epyc
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fftw
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filesystems
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fontawesome
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fpmd
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gcc
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gdrcopy
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github
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gitlab
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gmail
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gpt
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gpu
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gromos
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groningen
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groundstate
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gsl
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hdf
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hotmail
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huggingface
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hwloc
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iframe
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ijulia
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inodes
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iopsstor
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ivo
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jfrog
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jobreport
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juhpc
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julia
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juliaup
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jupyter
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jwt
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kokkos
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lapackpp
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lexer
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lexers
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libfabric
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libint
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libtree
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libxc
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linalg
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linkx
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linux
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lts
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matlab
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metadynamics
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meteo
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mimalloc
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miniconda
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mkl
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mpi
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nccl
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netlib
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netrc
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nql
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nsight
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numa
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nvcr
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nvdashboard
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nvhpc
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nvidia
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nwp
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octicons
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ofi
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omlin
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omp
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oom
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openblas
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opls
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osts
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osu
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papi
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parmetis
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petsc
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pme
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pmi
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pmix
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podman
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preinstalled
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prerelease
@@ -198,25 +238,40 @@ prioritisation
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prioritise
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prioritised
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proactively
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pseudopotentials
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pwscf
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pyfirecrest
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pygments
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pytorch
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quantumespresso
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quasiparticles
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quickstart
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rgw
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ripgrep
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rocm
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rowspan
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rpath
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runtime
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runtimes
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santis
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sbatch
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scalapack
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screenshot
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slepc
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slurm
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smartphone
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sourced
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spdlog
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spglib
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sphericart
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spla
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squashfs
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srun
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ssh
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sshservice
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stackinator
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stakeholders
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stdexec
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subfolders
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subtable
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subtables
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tarball
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tcl
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tcsh
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tds
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telematics
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testuser
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timeframe
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timelimit
@@ -234,14 +291,17 @@ todi
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toolbar
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toolset
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torchaudio
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torchrun
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torchvision
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treesitter
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trilinos
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trl
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uarch
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ucx
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uenv
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uenvs
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uids
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ultrasoft
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utkin
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vCluster
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vClusters
@@ -251,6 +311,7 @@ vboost
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venv
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versioned
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versioning
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vscode
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waldur
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wandb
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webhooks
@@ -265,6 +326,7 @@ workflows
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xattr
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xattrs
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xcb
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xeon
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xfer
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xname
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xpmem

‎.github/actions/spelling/patterns.txt‎

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RESTful
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IPyParallel
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\`ENV\`ironment
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HECBioSim
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GmbH
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hEGFR
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cuDNN
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# markdown figure
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^!\[.*\]\(.*\)$
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!\[.*\]\(.*\)
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# Most obvious URLs
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https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*)
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https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&\/=]*)
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# Markdown references and URLs (definition and use)
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^\[\]\(\){#[a-z-]+}$
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\]\([^\s]+\)
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\]\[[a-z-]+\]
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# Markdown URLs
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# Inline code
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\`[^\`]+\`
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@@ -27,3 +29,9 @@ https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0
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# versions
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[0-9]+\.[.0-9]+(\+[0-9a-z]+)?
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# software-name@version
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[A-Za-z-_]+@[0-9]+(\.[.0-9]+)?(\+[0-9a-z]+)?
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# img tag
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<img.*\/>

‎docs/clusters/bristen.md‎

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### Storage and file systems
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Bristen uses the [MLp filesystems and storage policies][ref-mlp-storage].
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Bristen uses the [MLP filesystems and storage policies][ref-mlp-storage].
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## Getting started
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‎docs/clusters/clariden.md‎

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### Storage and file systems
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Clariden uses the [MLp filesystems and storage policies][ref-mlp-storage].
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Clariden uses the [MLP filesystems and storage policies][ref-mlp-storage].
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## Getting started
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‎docs/clusters/daint.md‎

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| name | nodes | max nodes per job | time limit |
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| -- | -- | -- | -- |
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| `normal` | unlim | - | 24 hours |
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| `normal` | unlimited | - | 24 hours |
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| `debug` | 24 | 2 | 30 minutes |
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| `xfer` | 2 | 1 | 24 hours |
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| `low` | unlim | - | 24 hours |
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| `low` | unlimited | - | 24 hours |
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* nodes in the `normal` and `debug` (and `low`) partitions are not shared
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* nodes in the `xfer` partition can be shared

‎docs/running/index.md‎

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# Running Jobs
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[Slurm][ref-slurm] is used on CSCS systems to schedule jobs.
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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

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This can be achieved either by:
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* building a [custom container image][ref-build-containers] based on a suitable ML-ready base image,
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* or starting from a provided uenv (e.g., [PrgEnv GNU][ref-uenv-prgenv-gnu] or [PyTorch uenv][ref-uenv-pytorch]),
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* or starting from a provided uenv (e.g., [`prgenv-gnu`][ref-uenv-prgenv-gnu] or [PyTorch uenv][ref-uenv-pytorch]),
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and extending it with a virtual environment.
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‎docs/software/prgenv/prgenv-gnu.md‎

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There are three ways to access the software provided by prgenv-gnu, once it has been started.
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=== "the default view"
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=== "the `default` view"
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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.
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‎docs/software/prgenv/prgenv-nvfortran.md‎

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

‎docs/software/sciapps/gromacs.md‎

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[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.
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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.
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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.
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!!! note "uenvs"
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