diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 26e4d59a..097af98f 100644 --- a/.github/actions/spelling/allow.txt +++ b/.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 @@ -173,10 +204,12 @@ nanotron nccl netlib netrc +nql nsight numa nvcr nvdashboard +nvhpc nvidia nwp octicons @@ -184,11 +217,16 @@ 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 diff --git a/.github/actions/spelling/patterns.txt b/.github/actions/spelling/patterns.txt index 5f85694c..658b88ce 100644 --- a/.github/actions/spelling/patterns.txt +++ b/.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 + diff --git a/docs/clusters/bristen.md b/docs/clusters/bristen.md index 86ed0f7a..6924ab6e 100644 --- a/docs/clusters/bristen.md +++ b/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 diff --git a/docs/clusters/clariden.md b/docs/clusters/clariden.md index 75f67cf7..62401236 100644 --- a/docs/clusters/clariden.md +++ b/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 diff --git a/docs/clusters/daint.md b/docs/clusters/daint.md index d450103b..15da5289 100644 --- a/docs/clusters/daint.md +++ b/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 diff --git a/docs/running/index.md b/docs/running/index.md index e69de29b..f4afa3b4 100644 --- a/docs/running/index.md +++ b/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. diff --git a/docs/software/ml/index.md b/docs/software/ml/index.md index 6544da90..ba101c0b 100644 --- a/docs/software/ml/index.md +++ b/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. diff --git a/docs/software/prgenv/prgenv-gnu.md b/docs/software/prgenv/prgenv-gnu.md index ad6c0225..a10d3892 100644 --- a/docs/software/prgenv/prgenv-gnu.md +++ b/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. diff --git a/docs/software/prgenv/prgenv-nvfortran.md b/docs/software/prgenv/prgenv-nvfortran.md index a6110e1e..b50eed37 100644 --- a/docs/software/prgenv/prgenv-nvfortran.md +++ b/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 diff --git a/docs/software/sciapps/gromacs.md b/docs/software/sciapps/gromacs.md index 6ab8ca92..47f86758 100644 --- a/docs/software/sciapps/gromacs.md +++ b/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" diff --git a/docs/software/sciapps/vasp.md b/docs/software/sciapps/vasp.md index 66f2c2d5..2c7a379d 100644 --- a/docs/software/sciapps/vasp.md +++ b/docs/software/sciapps/vasp.md @@ -111,9 +111,7 @@ Note that shared libraries might not be found when executing VASP, if the makefi Alternatively, since version 6.5.0, the build option `-DCRAY_MPICH` can be added to disable the check at compile time. The provided precompiled binaries of VASP are patched and do not require special settings. - -Examples for makefiles that set the necessary rpath and link options on GH200: - +Examples for Makefiles that set the necessary rpath and link options on GH200: ??? note "Makefile for v6.5.0" ```make diff --git a/docs/storage/longterm.md b/docs/storage/longterm.md index 6d42adc1..5f76ece4 100644 --- a/docs/storage/longterm.md +++ b/docs/storage/longterm.md @@ -36,7 +36,7 @@ The PID handles use for the LTS service are the one provided by the [CSCS PID se As of 2021: * Users from the free User Lab program are entitled to use 2 TB of LTS storage quota (for 10 years) free of charge per project -* Currently additional space can be purchased for CHF 600.- for each Terabyte (for 10 years) +* Currently additional space can be purchased for CHF 600.- for each terabyte (for 10 years) ## Prerequisites