From 7f40163b125a05c843e362e51cdb850d2ae950f8 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 24 Mar 2025 12:27:49 +0100 Subject: [PATCH 01/24] Add spellchecker action --- .github/workflows/spellcheck.yaml | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 .github/workflows/spellcheck.yaml diff --git a/.github/workflows/spellcheck.yaml b/.github/workflows/spellcheck.yaml new file mode 100644 index 00000000..92f44c4f --- /dev/null +++ b/.github/workflows/spellcheck.yaml @@ -0,0 +1,31 @@ +name: Check Spelling + +on: + push: + +jobs: + spelling: + name: Check Spelling + runs-on: ubuntu-latest + # if: ${{ contains(github.event_name, 'pull_request') || github.event_name == 'push' }} + # concurrency: + # group: spelling-${{ github.event.pull_request.number || github.ref }} + # # note: If you use only_check_changed_files, you do not want cancel-in-progress + # cancel-in-progress: true + steps: + - uses: actions/checkout@v3 + - name: Check spelling + id: spelling + uses: check-spelling/check-spelling@main + with: + check_file_names: 1 + post_comment: 0 + use_magic_file: 1 + warnings: bad-regex,binary-file,deprecated-feature,large-file,limited-references,no-newline-at-eof,noisy-file,non-alpha-in-dictionary,token-is-substring,unexpected-line-ending,whitespace-in-dictionary,minified-file,unsupported-configuration,no-files-to-check + use_sarif: ${{ (!github.event.pull_request || (github.event.pull_request.head.repo.full_name == github.repository)) && 1 }} + extra_dictionary_limit: 20 + extra_dictionaries: + cspell:software-terms/dict/softwareTerms.txt + cspell:bash/bash-words.txt + cspell:companies/companies.txt + cspell:filetypes/filetypes.txt From 5a22f22306c99b6d554056ce747f7fb560575c81 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 13:50:20 +0200 Subject: [PATCH 02/24] Fix some more typos --- docs/clusters/santis.md | 2 +- docs/software/sciapps/quantumespresso.md | 2 +- docs/software/uenv.md | 2 +- docs/storage/filesystems.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/clusters/santis.md b/docs/clusters/santis.md index 73aafddf..327f7691 100644 --- a/docs/clusters/santis.md +++ b/docs/clusters/santis.md @@ -102,7 +102,7 @@ See the SLURM documentation for instructions on how to run jobs on the [Grace-Ho | normal | 1266 | 1-infinite | 1-00:00:00 | 812/371 | | xfer | 2 | 1 | 1-00:00:00 | 1/1 | ``` - The last column shows the number of nodes that have been allocted in currently running jobs (`A`) and the number of jobs that are idle (`I`). + The last column shows the number of nodes that have been allocated in currently running jobs (`A`) and the number of jobs that are idle (`I`). ### FirecREST diff --git a/docs/software/sciapps/quantumespresso.md b/docs/software/sciapps/quantumespresso.md index 6697f0eb..871f1d22 100644 --- a/docs/software/sciapps/quantumespresso.md +++ b/docs/software/sciapps/quantumespresso.md @@ -134,7 +134,7 @@ spack -e $SCRATCH/qe-env config add packages:all:prefer:cuda_arch=90 spack -e $SCRATCH/qe-env develop -p /path/to/your/QE-src quantum-espresso@=develop spack -e $SCRATCH/qe-env concretize -f ``` -Check the output of `spack concretize -f`. All dependencies should have been picked up from spack upstream, marked eiter by a green `[^]` or `[e]`. +Check the output of `spack concretize -f`. All dependencies should have been picked up from spack upstream, marked either by a green `[^]` or `[e]`. Next we create a local filesystem view, this instructs spack to create symlinks for binaries and libraries in a local directory `view`. ```bash spack -e $SCRATCH/qe-env env view enable view diff --git a/docs/software/uenv.md b/docs/software/uenv.md index 05cc38e3..d717b2b2 100644 --- a/docs/software/uenv.md +++ b/docs/software/uenv.md @@ -308,7 +308,7 @@ The image can be a label, the hash/id of the uenv, or a file: # start the image using the name of the uenv $ uenv start netcdf-tools/2024:v1 - # or use the unqique id of the uenv + # or use the unique id of the uenv $ uenv start 499c886f2947538e # or provide the path to a squashfs file diff --git a/docs/storage/filesystems.md b/docs/storage/filesystems.md index b578d420..24b7c0bd 100644 --- a/docs/storage/filesystems.md +++ b/docs/storage/filesystems.md @@ -97,7 +97,7 @@ Expiration !!! warning All data will be deleted 3 months after the closure of the user account without further warning. -## Store on Capstore +## Store on Capstor The `/capstor/store` mount point of the Lustre file system `capstor` is intended for high-performance per-project storage on Alps. The mount point is accessible from the User Access Nodes (UANs) of Alps vClusters. From 160b75a2241002809de1049092247d8ac4cd5725 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 13:56:47 +0200 Subject: [PATCH 03/24] Add spellchecker whitelists --- .github/actions/spelling/allow.txt | 3 +++ .github/actions/spelling/only.txt | 0 2 files changed, 3 insertions(+) create mode 100644 .github/actions/spelling/allow.txt create mode 100644 .github/actions/spelling/only.txt diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt new file mode 100644 index 00000000..63baf7a3 --- /dev/null +++ b/.github/actions/spelling/allow.txt @@ -0,0 +1,3 @@ +blaspp +github +https diff --git a/.github/actions/spelling/only.txt b/.github/actions/spelling/only.txt new file mode 100644 index 00000000..e69de29b From 4076b0f657c96849da673eda0af02cd64e56cbca Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 13:59:07 +0200 Subject: [PATCH 04/24] Rename spellcheck action file --- .github/workflows/{spellcheck.yaml => spelling.yaml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{spellcheck.yaml => spelling.yaml} (100%) diff --git a/.github/workflows/spellcheck.yaml b/.github/workflows/spelling.yaml similarity index 100% rename from .github/workflows/spellcheck.yaml rename to .github/workflows/spelling.yaml From 1bcddd154c2620a0b89583cb9ab0f73c6e4b06d6 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 14:19:20 +0200 Subject: [PATCH 05/24] Fix more typos --- docs/build-install/cpe.md | 2 +- docs/build-install/uenv.md | 2 +- docs/clusters/santis.md | 2 +- docs/guides/terminal.md | 2 +- docs/platforms/cwp/index.md | 4 ++-- docs/platforms/mlp/index.md | 2 +- docs/services/cicd.md | 2 +- docs/software/sciapps/quantumespresso.md | 2 +- docs/software/uenv.md | 2 +- docs/storage/filesystems.md | 2 +- 10 files changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/build-install/cpe.md b/docs/build-install/cpe.md index 9e8e1876..823064d7 100644 --- a/docs/build-install/cpe.md +++ b/docs/build-install/cpe.md @@ -7,4 +7,4 @@ The CPE is not provided on the machine learning platform. !!! cwp - The CPE is not provided on the climage and weather platform + The CPE is not provided on the climate and weather platform diff --git a/docs/build-install/uenv.md b/docs/build-install/uenv.md index 6552b841..0f4166f3 100644 --- a/docs/build-install/uenv.md +++ b/docs/build-install/uenv.md @@ -131,7 +131,7 @@ The `uenv-spack` tool can be used to create a build directory with a template [S 1. Script to build the software stack. 2. `git` clone of the required version of Spack. -3. Spack onfiguration files for the software stack. +3. Spack configuration files for the software stack. 4. Information about the uenv that was used to run `uenv-spack`. 5. Description of the software to build. 6. Template [Spack environment file]. diff --git a/docs/clusters/santis.md b/docs/clusters/santis.md index 327f7691..6b0cf656 100644 --- a/docs/clusters/santis.md +++ b/docs/clusters/santis.md @@ -48,7 +48,7 @@ Currently, the following uenv are provided for the climate and weather community * `icon/25.1` * `climana/25.1` -In adition to the climate and weather uenv, all of the +In addition to the climate and weather uenv, all of the ??? example "using uenv provided for other clusters" You can run uenv that were built for other Alps clusters using the `@` notation. diff --git a/docs/guides/terminal.md b/docs/guides/terminal.md index b131fcf3..92660933 100644 --- a/docs/guides/terminal.md +++ b/docs/guides/terminal.md @@ -48,7 +48,7 @@ Binary applications are generally not portable, for example if you compile or in A common pattern for installing local software, for example some useful command line utilities like [ripgrep](https://github.com/BurntSushi/ripgrep), is to install them in `$HOME/.local/bin`. This approach won't work if the same home directory is mounted on two different clusters with different architectures: the version of ripgrep in our example would crash with `Exec format error` on one of the clusters. -Care needs to be taken to store executables, configuration and data for different architecures in separate locations, and automatically configure the login environment to use the correct location when you log into different systems. +Care needs to be taken to store executables, configuration and data for different architectures in separate locations, and automatically configure the login environment to use the correct location when you log into different systems. The following example: diff --git a/docs/platforms/cwp/index.md b/docs/platforms/cwp/index.md index f0745a71..79960e61 100644 --- a/docs/platforms/cwp/index.md +++ b/docs/platforms/cwp/index.md @@ -14,7 +14,7 @@ Project administrators (PIs and deputy PIs) of projects on the CWP can to invite This is performed using the [project management tool][ref-account-waldur] -Once invited to a project, you will receive an email, which you can need to create an account and configure [multi-factor authentification][ref-mfa] (MFA). +Once invited to a project, you will receive an email, which you can need to create an account and configure [multi-factor authentication][ref-mfa] (MFA). ## Systems @@ -62,7 +62,7 @@ Scratch is per user - each user gets separate scratch path and quota. !!! warning "scratch cleanup policy" Files that have not been accessed in 30 days are automatically deleted. - **Scratch is not intended for permanant storage**: transfer files back to the capstor project storage after job runs. + **Scratch is not intended for permanent storage**: transfer files back to the capstor project storage after job runs. ### Project diff --git a/docs/platforms/mlp/index.md b/docs/platforms/mlp/index.md index c657e65d..591ace75 100644 --- a/docs/platforms/mlp/index.md +++ b/docs/platforms/mlp/index.md @@ -55,7 +55,7 @@ Scratch is per user - each user gets separate scratch path and quota. !!! warning "scratch cleanup policy" Files that have not been accessed in 30 days are automatically deleted. - **Scratch is not intended for permanant storage**: transfer files back to the capstor project storage after job runs. + **Scratch is not intended for permanent storage**: transfer files back to the capstor project storage after job runs. !!! note There is an additional scratch path mounted on [Capstor][ref-alps-capstor] at `/capstor/scratch/cscs/$USER`, however this is not reccomended for ML workloads for performance reasons. diff --git a/docs/services/cicd.md b/docs/services/cicd.md index da531580..463190bc 100644 --- a/docs/services/cicd.md +++ b/docs/services/cicd.md @@ -94,7 +94,7 @@ If you don't already know how to obtain FirecREST credentials, you can find more 1. **Default trusted users and default CI-enabled branches**: Provide the default list of trusted users and CI-enabled branches. The global configuration will apply to all pipelines that do not overwrite it explicitly. -1. **Pipeline default**: Your first pipeline has the name `default`. Click on `Pipeline default` to see the pipeline setup details. The name can be chosen freely but it cannot contain whitespaces (a short descriptive name). Update the entry point, trusted users and CI-enabled branches. +1. **Pipeline default**: Your first pipeline has the name `default`. Click on `Pipeline default` to see the pipeline setup details. The name can be chosen freely but it cannot contain whitespace (a short descriptive name). Update the entry point, trusted users and CI-enabled branches. 1. **Submit your changes** diff --git a/docs/software/sciapps/quantumespresso.md b/docs/software/sciapps/quantumespresso.md index 871f1d22..80957ee7 100644 --- a/docs/software/sciapps/quantumespresso.md +++ b/docs/software/sciapps/quantumespresso.md @@ -35,7 +35,7 @@ The following sbatch script can be used as a template. srun -u --cpu-bind=socket /user-environment/env/default/bin/pw.x < pw.in ``` - Current observation is that best perfomance is achieved using [one MPI rank per GPU][ref-slurm-gh200-single-rank-per-gpu]. How to run multiple ranks per GPU is described [here][ref-slurm-gh200-multi-rank-per-gpu]. + Current observation is that best performance is achieved using [one MPI rank per GPU][ref-slurm-gh200-single-rank-per-gpu]. How to run multiple ranks per GPU is described [here][ref-slurm-gh200-multi-rank-per-gpu]. === "Eiger" diff --git a/docs/software/uenv.md b/docs/software/uenv.md index d717b2b2..c6ae64d3 100644 --- a/docs/software/uenv.md +++ b/docs/software/uenv.md @@ -2,7 +2,7 @@ # uenv Uenv are user environments that provide scientific applications, libraries and tools. -This page will explain how to find, dowload and use uenv on the command line, and how to enable them in SLURM jobs. +This page will explain how to find, download and use uenv on the command line, and how to enable them in SLURM jobs. Uenv are typically application-specific, domain-specific or tool-specific - each uenv contains only what is required for the application or tools that it provides. diff --git a/docs/storage/filesystems.md b/docs/storage/filesystems.md index 24b7c0bd..a61b3c7e 100644 --- a/docs/storage/filesystems.md +++ b/docs/storage/filesystems.md @@ -102,7 +102,7 @@ Expiration The `/capstor/store` mount point of the Lustre file system `capstor` is intended for high-performance per-project storage on Alps. The mount point is accessible from the User Access Nodes (UANs) of Alps vClusters. !!! note - Capstore store is not yet mounted on Eiger. + Capstor store is not yet mounted on Eiger. !!! info `/capstor/store` is equivalent to the `/project` and `/store` GPFS mounts on the old Daint system. From 034f9074978299ae49e5203097998d406e6ce601 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 14:19:32 +0200 Subject: [PATCH 06/24] Update spellcheck allow and only files --- .github/actions/spelling/allow.txt | 639 +++++++++++++++++++++++++++++ .github/actions/spelling/only.txt | 1 + 2 files changed, 640 insertions(+) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 63baf7a3..fd6eeaac 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -1,3 +1,642 @@ blaspp github https + +# ok +aarch +aarch64 + +# typos +# adition +# architecures +# authentification +# Capstore +# climage +# dowload +# onfiguration +# packae +# perfomance +# permanant +# whitespaces + +# ??? +# aafdca +# aafe +# aaff +# abf +# abfdadc +# ACFDT +# acm +# acr +# adb +# adf +# adfb +# afc +# alh +# Amz +# AOCNMKPDXQ +# bse +# ccd +# cef +# dfbd +# dfcaa + +accesstoken +acl +Admins # admins? +afterok +aiohttp +aistor +ALLFUNC +allowfullscreen +Alpstein +amadonna +amazonaws +amd +amdcpu +Andrease #? +apps +arithmatex +arpack +artifactory +artifactsreportsdotenv +asn +autoplay +autorefs +aws +azurecr +Balfrin +bbbbbb +bcumming +biomolecular +bitbucket +blt +bobsmith +bristen +Broyden +bytecode +capstor +ceph +CFLAGS +CHARMM +charmpp +chdir +CHF +chtml +cicd +CIvariables +clariden +climana +CODENAME +CODEOWNERS +compileall +concretise +concretizer +Containerfile +containerised +copyleft +COSMA +cpe +CPMD +cpunodebind +craype +creativecommons +cscs +cscsusername +cshell +csstaff +cublas +cublasmp +cudalib +cudnn +cufft +cusolver +cusolvermp +customised +cwp +cxi +cxil +cyberduck +czf +DACC +datacenter +Davoidalloc +dawidd +dbcsr +dblbuf +DBUILD +DCACHE +DCMAKE +DCom +dcomex +DCRAY +DCUBLASMP +DCUDA +DCUDPP +DCUSOLVERMP +debian +decf +deeplearning +devportal +DEXTERNAL +DFFTLIB +Dfock +DFTB +dftd +DHOST +diagonalisation +diffs +DIIS +DKokkos +dkr +dla +dlaf +dlib +DMPI +dns +DNVCUDA +Dockerfiles +doi +Dokumente +dotenv +DPKG +Dqd +DQE +dropbear +Dsca +Dsysv +dtags +Dtbdyn +DUSE +DUSENCCL +DUSENCCLP +dvasp +ebcc +ecr +edf +edu +eed +eee +Ehrenfest +eigen +eigensolvers +eiger +elpa +emacs +emoji +empa +endblock +Errigal +ethz +etotal +evaleev +executeable +fabe +Faws +Fawzi +fba +fcc +FCL +Fcscs +fdfdfd +ffff +ffffff +FFLAGS +fft +fftlib +fftmpi +fftmpiw +fftw +FILECHANGES +filesystems +finkandreas +Firc +Firec +Fock +fontawesome +Fonticons +FPMD +fptqzc +freedesktop +FSTYPE +FUFFIX +GAPW +gcc +gcloud +gcr +gencode +getent +GGA +githubusername +gitlab +gmail +Gmb +gmx +GNinja +gomp +google +GPFS +GPG +gpu +GPW +graphroot +gromacs +groundstate +gsl +GTH +gtl +Hartree +HCVo +HDD +hdf +hdl +helloworld +hilighting +HMAC +hotmail +hpc +hpcp +hpe +HPL +hsa +hsn +httpa +hwloc +hypre +iframe +imagestore +img +imgx +INCS +infrastructre +inodes +inp +INPLACE +iomaganaris +iopsstor +iopstor +ipify +javascripts +Jax +jfrog +jgphpc +jira +julia +jwt +Kbytes +Keycloak +keygen +koe +kokkos +KSPACE +lammps +lapack +lapackpp +LDA +ldconfig +ldd +ldl +lexer +lfftw +lhdf +Libc +libfabric +libint +libmpi +libtree +libxc +libxmm +libxsmm +lifecycle +linalg +linaro +linaroforge +linenums +linpack +linux +LLIBS +lmp +lnvhpcwrapcal +lnvpl +LOCALID +longterm +lov +lqd +lqdmod +lscalapack +ltcl +lts +LUMI +lwannier +madeeks +makefiles +MALLOC +manged +MANYBODY +mathjax +Mbackslash +Mbytes +membind +metadynamics +Meteo +meteoswiss +Mextend +mfa +Mfixed +Mfree +MGRID +mimalloc +mivl +mkdocs +mkl +mksquashfs +Mlarge +mlp +mml +MNDO +mpcdf +mpi +mpiargs +mpic +mpicc +mpich +mpicxx +MPIDI +mpif +mpifort +MPIR +Mpreprocess +mps +mpt +multiarch +multitenancy +Mwarperf +myapp +myenv +myexe +myexecutable +myimage +myregistry +mysub +nals +namd +nanoscale +naret +NBR +nccl +ncl +ncu +neoverse +nersc +netcdf +netlib +netrc +NICS +noappend +NODEID +nodev +nomultithread +nonlr +nosuid +nsight +ntasks +ntis +numa +numacontrol +numactl +numpy +nvc +nvcc +nvcr +nve +nvfort +nvfortran +nvhpc +nvidia +NVME +nvpl +NVROOT +NVTX +NVVERSION +nws +oauth +oauthtoken +octicons +octree +ODqo +ofi +ofiwg +OFL +OFLAG +omp +ompi +oneapi +onemkl +OPENACC +openapi +openblas +opencontainers +openmathlib +OPENMP +openmpi +osu +otp +pade +papi +parmetis +Parrinello +PASC +PBE +pdebug +PDUs +pead +petsc +pid +pidconsortium +pikacpp +Piz +Plesset +pmeps +pmi +PMPI +podman +posix +PRECONDITIONER +precsion +prgenv +Prioritisation +prioritised +prj +proactively +PROCID +procs +pseudopotentials +psmp +publickey +Pulay +PWscf +pyc +pyfirecrest +pygments +pymdownx +pytorch +quantumespresso +quasiparticles +quickstart +radosgw +rccl +RDMA +realpath +reccomended +rechtssammlung +recomended +referrerpolicy +relatime +repositorypid +rgb +rgba +rgw +ripgrep +Roboto +rocm +rocmdocs +Roothaan +rowspan +rpa +rpath +runroot +rwxr +rzyuleogzn +salloc +santis +sbatch +sca +scalapack +schedmd +Schr +sciapps +scontrol +Scopi +scp +screenshot +servlet +setcpuaffinity +shm +sinfo +slepc +sles +slurm +slurmstepd +smartphone +smi +smp +SMW +snx +sourcecode +spdlog +spglib +sphericart +spla +sqfs +sqsh +squashfs +squidfunk +srun +ssh +sshservice +stackinator +stakeholders +stdexec +STMV +subfolders +SUBSYS +subtable +sucessfully +supercomputing +superfences +superlu +swissai +sysadmin +taskset +tcl +TCLLIB +tcsh +tds +Telematics +tempfs +TEMPURL +Terabyte +testuser +Tful +Tgpus +THREADSAFE +Thu +timeframe +timelimit +tmpfs +toc +todi +toolbar +toolset +torchaudio +torchvision +TOTP +treesitter +trilinos +twemoji +UANs +uarch +ucc +uenv +uenvname +uids +uiuc +ultrasoft +Uncorr +unpkg +Unrecognised +upstreams +userlab +usingcurl +usr +utc +utf +vasp +vcluster +vcq +vectoradd +velan +venv +verlet +versioned +versioning +vhyy +viewname +vistools +vnd +Vyh +waldur +wannier +webhooks +webinar +webpage +website +WFC +wfn +whl +wikipedia +workaround +workdir +workflows +xattr +xcb +Xcompression +XDG +xdgbase +xfer +xvf +YNA +youtube +zonegroup +zstd +zulianp diff --git a/.github/actions/spelling/only.txt b/.github/actions/spelling/only.txt index e69de29b..b197bbd1 100644 --- a/.github/actions/spelling/only.txt +++ b/.github/actions/spelling/only.txt @@ -0,0 +1 @@ +docs/.*\.md$ From c539014a4984e9331e9db5b0c59cf4b9dc466d9c Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 14:32:19 +0200 Subject: [PATCH 07/24] Update extra dictionaries --- .github/workflows/spelling.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/spelling.yaml b/.github/workflows/spelling.yaml index 92f44c4f..d306fc49 100644 --- a/.github/workflows/spelling.yaml +++ b/.github/workflows/spelling.yaml @@ -26,6 +26,6 @@ jobs: extra_dictionary_limit: 20 extra_dictionaries: cspell:software-terms/dict/softwareTerms.txt - cspell:bash/bash-words.txt - cspell:companies/companies.txt + cspell:bash/dict/bash-words.txt + cspell:companies/dict/companies.txt cspell:filetypes/filetypes.txt From 983630c03ee69c6bc5d3aa9ffea7773d2c8625cc Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 14:33:21 +0200 Subject: [PATCH 08/24] Update allow.txt --- .github/actions/spelling/allow.txt | 365 ++++++++++++++--------------- 1 file changed, 173 insertions(+), 192 deletions(-) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index fd6eeaac..14b705db 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -1,60 +1,178 @@ -blaspp -github -https - -# ok +ACFDT +ALLFUNC +AOCNMKPDXQ +Admins +Alpstein +Amz +Andrease #? +Balfrin +Broyden +CFLAGS +CHARMM +CHF +CIvariables +CODENAME +CODEOWNERS +COSMA +CPMD +Containerfile +DACC +DBUILD +DCACHE +DCMAKE +DCRAY +DCUBLASMP +DCUDA +DCUDPP +DCUSOLVERMP +DCom +DEXTERNAL +DFFTLIB +DFTB +DHOST +DIIS +DKokkos +DMPI +DNVCUDA +DPKG +DQE +DUSE +DUSENCCL +DUSENCCLP +Davoidalloc +Dfock +Dockerfiles +Dokumente +Dqd +Dsca +Dsysv +Dtbdyn +Ehrenfest +Errigal +FCL +FFLAGS +FILECHANGES +FPMD +FSTYPE +FUFFIX +Faws +Fawzi +Fcscs +Firc +Firec +Fock +Fonticons +GAPW +GGA +GNinja +GPFS +GPG +GPW +GTH +Gmb +HCVo +HDD +HMAC +HPL +Hartree +INCS +INPLACE +Jax +KSPACE +Kbytes +Keycloak +LDA +LLIBS +LOCALID +LUMI +Libc +MALLOC +MANYBODY +MGRID +MNDO +MPIDI +MPIR +Mbackslash +Mbytes +Meteo +Mextend +Mfixed +Mfree +Mlarge +Mpreprocess +Mwarperf +NBR +NICS +NODEID +NVME +NVROOT +NVTX +NVVERSION +ODqo +OFL +OFLAG +OPENACC +OPENMP +PASC +PBE +PDUs +PMPI +PRECONDITIONER +PROCID +PWscf +Parrinello +Piz +Plesset +Prioritisation +Pulay +RDMA +Roboto +Roothaan +SMW +STMV +SUBSYS +Schr +Scopi +TCLLIB +TEMPURL +THREADSAFE +TOTP +Telematics +Terabyte +Tful +Tgpus +Thu +UANs +Uncorr +Unrecognised +Vyh +WFC +XDG +Xcompression +YNA +aafdca +aafe +aaff aarch aarch64 - -# typos -# adition -# architecures -# authentification -# Capstore -# climage -# dowload -# onfiguration -# packae -# perfomance -# permanant -# whitespaces - -# ??? -# aafdca -# aafe -# aaff -# abf -# abfdadc -# ACFDT -# acm -# acr -# adb -# adf -# adfb -# afc -# alh -# Amz -# AOCNMKPDXQ -# bse -# ccd -# cef -# dfbd -# dfcaa - +abf +abfdadc accesstoken acl -Admins # admins? +acm +acr +adb +adf +adfb +afc afterok aiohttp aistor -ALLFUNC +alh allowfullscreen -Alpstein -amadonna -amazonaws +amadonna amazonaws amd amdcpu -Andrease #? apps arithmatex arpack @@ -65,39 +183,32 @@ autoplay autorefs aws azurecr -Balfrin bbbbbb bcumming biomolecular bitbucket +blaspp blt bobsmith bristen -Broyden +bse bytecode capstor +ccd +cef ceph -CFLAGS -CHARMM charmpp chdir -CHF chtml cicd -CIvariables clariden climana -CODENAME -CODEOWNERS compileall concretise concretizer -Containerfile containerised copyleft -COSMA cpe -CPMD cpunodebind craype creativecommons @@ -118,58 +229,29 @@ cxi cxil cyberduck czf -DACC datacenter -Davoidalloc dawidd dbcsr dblbuf -DBUILD -DCACHE -DCMAKE -DCom dcomex -DCRAY -DCUBLASMP -DCUDA -DCUDPP -DCUSOLVERMP debian decf deeplearning devportal -DEXTERNAL -DFFTLIB -Dfock -DFTB +dfbd +dfcaa dftd -DHOST diagonalisation diffs -DIIS -DKokkos dkr dla dlaf dlib -DMPI dns -DNVCUDA -Dockerfiles doi -Dokumente dotenv -DPKG -Dqd -DQE dropbear -Dsca -Dsysv dtags -Dtbdyn -DUSE -DUSENCCL -DUSENCCLP dvasp ebcc ecr @@ -177,7 +259,6 @@ edf edu eed eee -Ehrenfest eigen eigensolvers eiger @@ -186,120 +267,87 @@ emacs emoji empa endblock -Errigal ethz etotal evaleev executeable fabe -Faws -Fawzi fba fcc -FCL -Fcscs fdfdfd ffff ffffff -FFLAGS fft fftlib fftmpi fftmpiw fftw -FILECHANGES filesystems finkandreas -Firc -Firec -Fock fontawesome -Fonticons -FPMD fptqzc freedesktop -FSTYPE -FUFFIX -GAPW gcc gcloud gcr gencode getent -GGA +github githubusername gitlab gmail -Gmb gmx -GNinja gomp google -GPFS -GPG gpu -GPW graphroot gromacs groundstate gsl -GTH gtl -Hartree -HCVo -HDD hdf hdl helloworld hilighting -HMAC hotmail hpc hpcp hpe -HPL hsa hsn httpa +https hwloc hypre iframe imagestore img imgx -INCS infrastructre inodes inp -INPLACE iomaganaris iopsstor iopstor ipify javascripts -Jax jfrog jgphpc jira julia jwt -Kbytes -Keycloak keygen koe kokkos -KSPACE lammps lapack lapackpp -LDA ldconfig ldd ldl lexer lfftw lhdf -Libc libfabric libint libmpi @@ -314,11 +362,9 @@ linaroforge linenums linpack linux -LLIBS lmp lnvhpcwrapcal lnvpl -LOCALID longterm lov lqd @@ -326,34 +372,22 @@ lqdmod lscalapack ltcl lts -LUMI lwannier madeeks makefiles -MALLOC manged -MANYBODY mathjax -Mbackslash -Mbytes membind metadynamics -Meteo meteoswiss -Mextend mfa -Mfixed -Mfree -MGRID mimalloc mivl mkdocs mkl mksquashfs -Mlarge mlp mml -MNDO mpcdf mpi mpiargs @@ -361,16 +395,12 @@ mpic mpicc mpich mpicxx -MPIDI mpif mpifort -MPIR -Mpreprocess mps mpt multiarch multitenancy -Mwarperf myapp myenv myexe @@ -382,7 +412,6 @@ nals namd nanoscale naret -NBR nccl ncl ncu @@ -391,9 +420,7 @@ nersc netcdf netlib netrc -NICS noappend -NODEID nodev nomultithread nonlr @@ -413,68 +440,47 @@ nvfort nvfortran nvhpc nvidia -NVME nvpl -NVROOT -NVTX -NVVERSION nws oauth oauthtoken octicons octree -ODqo ofi ofiwg -OFL -OFLAG omp ompi oneapi onemkl -OPENACC openapi openblas opencontainers openmathlib -OPENMP openmpi osu otp pade papi parmetis -Parrinello -PASC -PBE pdebug -PDUs pead petsc pid pidconsortium pikacpp -Piz -Plesset pmeps pmi -PMPI podman posix -PRECONDITIONER precsion prgenv -Prioritisation prioritised prj proactively -PROCID procs pseudopotentials psmp publickey -Pulay -PWscf pyc pyfirecrest pygments @@ -485,7 +491,6 @@ quasiparticles quickstart radosgw rccl -RDMA realpath reccomended rechtssammlung @@ -497,10 +502,8 @@ rgb rgba rgw ripgrep -Roboto rocm rocmdocs -Roothaan rowspan rpa rpath @@ -513,10 +516,8 @@ sbatch sca scalapack schedmd -Schr sciapps scontrol -Scopi scp screenshot servlet @@ -530,7 +531,6 @@ slurmstepd smartphone smi smp -SMW snx sourcecode spdlog @@ -547,9 +547,7 @@ sshservice stackinator stakeholders stdexec -STMV subfolders -SUBSYS subtable sucessfully supercomputing @@ -559,18 +557,10 @@ swissai sysadmin taskset tcl -TCLLIB tcsh tds -Telematics tempfs -TEMPURL -Terabyte testuser -Tful -Tgpus -THREADSAFE -Thu timeframe timelimit tmpfs @@ -580,11 +570,9 @@ toolbar toolset torchaudio torchvision -TOTP treesitter trilinos twemoji -UANs uarch ucc uenv @@ -592,9 +580,7 @@ uenvname uids uiuc ultrasoft -Uncorr unpkg -Unrecognised upstreams userlab usingcurl @@ -614,14 +600,12 @@ vhyy viewname vistools vnd -Vyh waldur wannier webhooks webinar webpage website -WFC wfn whl wikipedia @@ -630,12 +614,9 @@ workdir workflows xattr xcb -Xcompression -XDG xdgbase xfer xvf -YNA youtube zonegroup zstd From 259b7a120f46e3139fc05f62f20332b608d10a35 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 14:39:39 +0200 Subject: [PATCH 09/24] Update allow.txt --- .github/actions/spelling/allow.txt | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 14b705db..774300a3 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -1,4 +1,5 @@ ACFDT +ACLs ALLFUNC AOCNMKPDXQ Admins @@ -47,6 +48,7 @@ Dqd Dsca Dsysv Dtbdyn +EDFs Ehrenfest Errigal FCL @@ -113,6 +115,7 @@ OFL OFLAG OPENACC OPENMP +OTPs PASC PBE PDUs @@ -170,7 +173,9 @@ aiohttp aistor alh allowfullscreen +amadonna amadonna amazonaws +amazonaws amd amdcpu apps @@ -300,6 +305,7 @@ gmx gomp google gpu +gpus graphroot gromacs groundstate @@ -346,6 +352,7 @@ ldconfig ldd ldl lexer +lexers lfftw lhdf libfabric @@ -474,6 +481,7 @@ podman posix precsion prgenv +prgenvs prioritised prj proactively @@ -549,6 +557,7 @@ stakeholders stdexec subfolders subtable +subtables sucessfully supercomputing superfences @@ -577,6 +586,7 @@ uarch ucc uenv uenvname +uenvs uids uiuc ultrasoft @@ -589,6 +599,7 @@ utc utf vasp vcluster +vclusters vcq vectoradd velan @@ -613,6 +624,7 @@ workaround workdir workflows xattr +xattrs xcb xdgbase xfer From 0569f7396f7567603f3c5d72db5d53dd8e4bb7f4 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Mon, 14 Apr 2025 14:44:36 +0200 Subject: [PATCH 10/24] Introduce typo --- docs/software/uenv.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/software/uenv.md b/docs/software/uenv.md index c6ae64d3..aa22115e 100644 --- a/docs/software/uenv.md +++ b/docs/software/uenv.md @@ -1,7 +1,7 @@ [](){#ref-uenv} # uenv -Uenv are user environments that provide scientific applications, libraries and tools. +Uenv are user enviroments that provide scientific applications, libraries and tools. This page will explain how to find, download and use uenv on the command line, and how to enable them in SLURM jobs. Uenv are typically application-specific, domain-specific or tool-specific - each uenv contains only what is required for the application or tools that it provides. From 69848fd191ea17810741f15ae2fad996f12f461a Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 13:49:12 +0200 Subject: [PATCH 11/24] Trim spellchecker allow.txt --- .github/actions/spelling/allow.txt | 571 +++-------------------------- 1 file changed, 46 insertions(+), 525 deletions(-) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 774300a3..2eebfbaf 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -1,579 +1,132 @@ -ACFDT ACLs -ALLFUNC -AOCNMKPDXQ -Admins -Alpstein -Amz -Andrease #? +ACR +AMD +AWS Balfrin Broyden CFLAGS CHARMM CHF -CIvariables -CODENAME -CODEOWNERS COSMA +CPE CPMD +CSCS +CXI +Capstor +Ceph Containerfile -DACC -DBUILD -DCACHE -DCMAKE -DCRAY -DCUBLASMP -DCUDA -DCUDPP -DCUSOLVERMP -DCom -DEXTERNAL -DFFTLIB -DFTB -DHOST -DIIS -DKokkos -DMPI -DNVCUDA -DPKG -DQE -DUSE -DUSENCCL -DUSENCCLP -Davoidalloc -Dfock -Dockerfiles -Dokumente -Dqd -Dsca -Dsysv -Dtbdyn +DNS +EDF EDFs +EDFs +EMPA +ETHZ Ehrenfest Errigal -FCL -FFLAGS -FILECHANGES -FPMD -FSTYPE -FUFFIX -Faws -Fawzi -Fcscs -Firc -Firec -Fock -Fonticons +FFT GAPW +GCC GGA -GNinja GPFS GPG +GPU +GPUs GPW -GTH -Gmb -HCVo +GROMACS +GTL +Google HDD -HMAC -HPL +HPE +HSN Hartree -INCS -INPLACE +Iopstor Jax -KSPACE -Kbytes +Jira Keycloak +LAMMPS LDA -LLIBS LOCALID LUMI Libc -MALLOC -MANYBODY -MGRID +Linaro +Linux MNDO -MPIDI -MPIR -Mbackslash -Mbytes -Meteo -Mextend -Mfixed -Mfree -Mlarge -Mpreprocess -Mwarperf -NBR -NICS -NODEID -NVME -NVROOT -NVTX -NVVERSION -ODqo -OFL -OFLAG -OPENACC -OPENMP +MPICH +MPS +MeteoSwiss +NAMD +NVIDIA +OTP OTPs PASC PBE PDUs +PID PMPI -PRECONDITIONER -PROCID -PWscf +POSIX Parrinello Piz Plesset -Prioritisation Pulay +RCCL RDMA +RESTful +ROCm +RPA Roboto Roothaan -SMW +SSHService STMV -SUBSYS -Schr Scopi -TCLLIB -TEMPURL -THREADSAFE TOTP -Telematics -Terabyte -Tful -Tgpus -Thu UANs -Uncorr -Unrecognised -Vyh -WFC +UserLab +VASP +Waldur +Wannier XDG -Xcompression -YNA -aafdca -aafe -aaff aarch aarch64 -abf -abfdadc -accesstoken acl -acm -acr -adb -adf -adfb -afc -afterok -aiohttp -aistor -alh -allowfullscreen -amadonna -amadonna amazonaws -amazonaws -amd -amdcpu -apps -arithmatex -arpack -artifactory -artifactsreportsdotenv -asn -autoplay -autorefs -aws -azurecr -bbbbbb -bcumming biomolecular -bitbucket -blaspp -blt -bobsmith bristen -bse bytecode -capstor -ccd -cef -ceph -charmpp -chdir -chtml -cicd clariden -climana -compileall concretise concretizer containerised -copyleft -cpe -cpunodebind -craype -creativecommons -cscs -cscsusername -cshell -csstaff -cublas -cublasmp -cudalib -cudnn -cufft -cusolver -cusolvermp customised -cwp -cxi -cxil -cyberduck -czf -datacenter -dawidd -dbcsr -dblbuf -dcomex -debian -decf -deeplearning -devportal -dfbd -dfcaa -dftd diagonalisation -diffs -dkr -dla -dlaf -dlib -dns -doi -dotenv -dropbear -dtags -dvasp -ebcc -ecr -edf -edu -eed -eee -eigen -eigensolvers eiger -elpa -emacs -emoji -empa -endblock -ethz -etotal -evaleev -executeable -fabe -fba -fcc -fdfdfd -ffff -ffffff -fft -fftlib -fftmpi -fftmpiw -fftw filesystems -finkandreas -fontawesome -fptqzc -freedesktop -gcc -gcloud -gcr -gencode -getent -github -githubusername -gitlab -gmail -gmx -gomp -google -gpu -gpus -graphroot -gromacs groundstate -gsl -gtl -hdf -hdl -helloworld -hilighting -hotmail -hpc -hpcp -hpe -hsa -hsn -httpa -https -hwloc -hypre -iframe -imagestore -img -imgx -infrastructre inodes -inp -iomaganaris -iopsstor -iopstor -ipify -javascripts -jfrog -jgphpc -jira -julia -jwt -keygen -koe -kokkos -lammps -lapack -lapackpp -ldconfig -ldd -ldl -lexer -lexers -lfftw -lhdf libfabric -libint -libmpi -libtree -libxc -libxmm -libxsmm -lifecycle -linalg -linaro -linaroforge -linenums -linpack -linux -lmp -lnvhpcwrapcal -lnvpl -longterm -lov -lqd -lqdmod -lscalapack -ltcl -lts -lwannier -madeeks -makefiles -manged -mathjax -membind -metadynamics -meteoswiss -mfa -mimalloc -mivl -mkdocs -mkl -mksquashfs -mlp -mml -mpcdf -mpi -mpiargs -mpic -mpicc -mpich -mpicxx -mpif -mpifort -mps -mpt -multiarch -multitenancy -myapp -myenv -myexe -myexecutable -myimage -myregistry -mysub -nals -namd -nanoscale -naret -nccl -ncl -ncu -neoverse -nersc -netcdf -netlib -netrc -noappend -nodev -nomultithread -nonlr -nosuid -nsight -ntasks -ntis -numa -numacontrol -numactl -numpy -nvc -nvcc -nvcr -nve -nvfort -nvfortran -nvhpc -nvidia -nvpl -nws -oauth -oauthtoken -octicons -octree -ofi -ofiwg -omp -ompi -oneapi -onemkl -openapi -openblas -opencontainers -openmathlib -openmpi -osu -otp -pade -papi -parmetis -pdebug -pead -petsc -pid -pidconsortium -pikacpp -pmeps -pmi podman -posix -precsion -prgenv -prgenvs prioritised -prj proactively -procs -pseudopotentials -psmp -publickey -pyc -pyfirecrest -pygments -pymdownx -pytorch -quantumespresso -quasiparticles quickstart -radosgw -rccl -realpath -reccomended -rechtssammlung -recomended -referrerpolicy -relatime -repositorypid -rgb -rgba -rgw -ripgrep -rocm -rocmdocs -rowspan -rpa -rpath -runroot -rwxr -rzyuleogzn -salloc santis -sbatch -sca -scalapack -schedmd -sciapps -scontrol -scp screenshot -servlet -setcpuaffinity -shm -sinfo -slepc -sles slurm -slurmstepd smartphone -smi -smp -snx -sourcecode -spdlog -spglib -sphericart -spla -sqfs -sqsh squashfs -squidfunk srun ssh -sshservice stackinator stakeholders -stdexec subfolders subtable subtables -sucessfully supercomputing -superfences superlu -swissai sysadmin -taskset tcl tcsh -tds -tempfs testuser timeframe timelimit tmpfs -toc todi toolbar toolset @@ -581,55 +134,23 @@ torchaudio torchvision treesitter trilinos -twemoji uarch -ucc uenv -uenvname uenvs uids -uiuc -ultrasoft -unpkg -upstreams -userlab -usingcurl -usr -utc -utf -vasp -vcluster -vclusters -vcq -vectoradd -velan +vCluster +vClusters venv -verlet versioned versioning -vhyy -viewname -vistools -vnd -waldur -wannier webhooks webinar webpage website -wfn -whl wikipedia workaround -workdir workflows xattr xattrs -xcb -xdgbase -xfer -xvf youtube -zonegroup zstd -zulianp From ad3fc4bfab0400d8a1335ec8749a6d9caa1d4d81 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 13:49:54 +0200 Subject: [PATCH 12/24] Fix more typos --- docs/accounts/index.md | 2 +- docs/alps/hardware.md | 2 +- docs/alps/storage.md | 4 ++-- docs/build-install/uenv.md | 2 +- docs/index.md | 2 +- docs/platforms/mlp/index.md | 2 +- docs/software/sciapps/vasp.md | 4 ++-- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/accounts/index.md b/docs/accounts/index.md index da6c4cd5..5ba9ce80 100644 --- a/docs/accounts/index.md +++ b/docs/accounts/index.md @@ -9,7 +9,7 @@ To get an account you must be invited by a member of CSCS project adminstration CSCS issues calls for proposals that are announced via the CSCS website and e-mails. More information about upcoming calls is available on [the CSCS web site](https://www.cscs.ch/user-lab/allocation-schemes). -New PIs who have sucessfully applied for a preparatory project will receive an invitation from CSCS to get an account at CSCS. +New PIs who have successfully applied for a preparatory project will receive an invitation from CSCS to get an account at CSCS. PIs can then invite members of their groups to join their project. !!! info diff --git a/docs/alps/hardware.md b/docs/alps/hardware.md index f9ad3cce..c2bda378 100644 --- a/docs/alps/hardware.md +++ b/docs/alps/hardware.md @@ -28,7 +28,7 @@ This approach to cooling provides greater efficiency for the rack-level cooling, information about the network. * Details about SlingShot 11. - * how many NICS per node + * how many NICs per node * raw feeds and speeds * Some OSU benchmark results. * GPU-aware communication diff --git a/docs/alps/storage.md b/docs/alps/storage.md index 8d57b3f8..620e0f6c 100644 --- a/docs/alps/storage.md +++ b/docs/alps/storage.md @@ -2,7 +2,7 @@ # Alps Storage Alps has different storage attached, each with characteristics suited to different workloads and use cases. -HPC storage is manged in a separate cluster of nodes that host servers that manage the storage and the physical storage drives. +HPC storage is managed in a separate cluster of nodes that host servers that manage the storage and the physical storage drives. These separate clusters are on the same Slingshot 11 network as the Alps. | | Capstor | IOPStor | Vast | @@ -10,7 +10,7 @@ These separate clusters are on the same Slingshot 11 network as the Alps. | Model | HPE ClusterStor E1000D | HPE ClusterStor E1000F | Vast | | Type | Lustre | Lustre | NFS | | Capacity | 129 PB raw GridRAID | 7.2 PB raw RAID 10 | 1 PB | -| Number of Drives | 8,480 16 TB HDD | 240 * 30 TB NVME SSD | N/A | +| Number of Drives | 8,480 16 TB HDD | 240 * 30 TB NVMe SSD | N/A | | Read Speed | 1.19 TB/s | 782 GB/s | 38 GB/s | | Write Speed | 1.09 TB/s | 393 GB/s | 11 GB/s | | IOPs | 1.5M | 8.6M read, 24M write | 200k read, 768k write | diff --git a/docs/build-install/uenv.md b/docs/build-install/uenv.md index 0f4166f3..b4ce3054 100644 --- a/docs/build-install/uenv.md +++ b/docs/build-install/uenv.md @@ -72,7 +72,7 @@ uenv start prgenv-gnu/24.11:v1 --view=spack ??? warning "Upstream Spack version" - It is strongly recomended that your version of Spack and the version of Spack in the uenv match when building software on top of an uenv. + It is strongly recommended that your version of Spack and the version of Spack in the uenv match when building software on top of an uenv. !!! note "Advanced Spack users" diff --git a/docs/index.md b/docs/index.md index f34f3cf4..ee95d1fb 100644 --- a/docs/index.md +++ b/docs/index.md @@ -32,7 +32,7 @@ The Alps Research infrastructure hosts multiple platforms and clusters targeting [:octicons-arrow-right-24: Alps Overview](alps/index.md) - Get detailed information about the main components of the infrastructre + Get detailed information about the main components of the infrastructure [:octicons-arrow-right-24: Alps Clusters](alps/clusters.md) diff --git a/docs/platforms/mlp/index.md b/docs/platforms/mlp/index.md index 591ace75..b9b684f2 100644 --- a/docs/platforms/mlp/index.md +++ b/docs/platforms/mlp/index.md @@ -58,7 +58,7 @@ Scratch is per user - each user gets separate scratch path and quota. **Scratch is not intended for permanent storage**: transfer files back to the capstor project storage after job runs. !!! note - There is an additional scratch path mounted on [Capstor][ref-alps-capstor] at `/capstor/scratch/cscs/$USER`, however this is not reccomended for ML workloads for performance reasons. + There is an additional scratch path mounted on [Capstor][ref-alps-capstor] at `/capstor/scratch/cscs/$USER`, however this is not recommended for ML workloads for performance reasons. ### Project diff --git a/docs/software/sciapps/vasp.md b/docs/software/sciapps/vasp.md index d5fe1ad0..7f168e08 100644 --- a/docs/software/sciapps/vasp.md +++ b/docs/software/sciapps/vasp.md @@ -195,7 +195,7 @@ Examples for makefiles that set the necessary rpath and link options on GH200: #OFLAG_IN = -fast -Mwarperf #SOURCE_IN := nonlr.o - # Software emulation of quadruple precsion (mandatory) + # Software emulation of quadruple precision (mandatory) QD ?= $(NVROOT)/compilers/extras/qd LLIBS += -L$(QD)/lib -lqdmod -lqd -Wl,-rpath,$(QD)/lib INCS += -I$(QD)/include/qd @@ -322,7 +322,7 @@ Examples for makefiles that set the necessary rpath and link options on GH200: #OFLAG_IN = -fast -Mwarperf #SOURCE_IN := nonlr.o - # Software emulation of quadruple precsion (mandatory) + # Software emulation of quadruple precision (mandatory) QD ?= $(NVROOT)/compilers/extras/qd LLIBS += -L$(QD)/lib -lqdmod -lqd -Wl,-rpath,$(QD)/lib INCS += -I$(QD)/include/qd From b48540510c71d831053b0a01c10f0f52183e35b5 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 13:57:15 +0200 Subject: [PATCH 13/24] Add more whitelisted words --- .github/actions/spelling/allow.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 2eebfbaf..ae886d68 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -55,7 +55,9 @@ MPICH MPS MeteoSwiss NAMD +NICs NVIDIA +NVMe OTP OTPs PASC From 91554ad3df9c84744270e687fa7c9f0f5f903665 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 15:49:35 +0200 Subject: [PATCH 14/24] More spellchecker whitelist --- .github/actions/spelling/allow.txt | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index ae886d68..42fd506a 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -2,6 +2,7 @@ ACLs ACR AMD AWS +Alpstein Balfrin Broyden CFLAGS @@ -11,6 +12,7 @@ COSMA CPE CPMD CSCS +CWP CXI Capstor Ceph @@ -24,6 +26,8 @@ ETHZ Ehrenfest Errigal FFT +FirecREST +Fock GAPW GCC GGA @@ -34,12 +38,15 @@ GPUs GPW GROMACS GTL +Gaussian Google HDD +HPC +HPCP HPE HSN Hartree -Iopstor +Iopsstor Jax Jira Keycloak @@ -50,6 +57,8 @@ LUMI Libc Linaro Linux +MFA +MLP MNDO MPICH MPS @@ -103,7 +112,9 @@ eiger filesystems groundstate inodes +lexer libfabric +multitenancy podman prioritised proactively From ad8c71cd1b20c6598f51f1e513eddf48ca3cb84a Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 15:49:53 +0200 Subject: [PATCH 15/24] Fix firecrest typos --- .github/actions/spelling/allow.txt | 2 +- docs/clusters/bristen.md | 2 +- docs/clusters/clariden.md | 2 +- docs/clusters/santis.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 42fd506a..602c1a81 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -26,7 +26,7 @@ ETHZ Ehrenfest Errigal FFT -FirecREST +firecrest Fock GAPW GCC diff --git a/docs/clusters/bristen.md b/docs/clusters/bristen.md index c40bbab6..d03211a0 100644 --- a/docs/clusters/bristen.md +++ b/docs/clusters/bristen.md @@ -74,7 +74,7 @@ See the SLURM documentation for instructions on how to run jobs on the [Grace-Ho ### FirecREST -Bristen can also be accessed using [FircREST][ref-firecrest] at the `https://api.cscs.ch/ml/firecrest/v1` API endpoint. +Bristen can also be accessed using [FirecREST][ref-firecrest] at the `https://api.cscs.ch/ml/firecrest/v1` API endpoint. ### Scheduled Maintenance diff --git a/docs/clusters/clariden.md b/docs/clusters/clariden.md index 1afaf0e4..9fd73b13 100644 --- a/docs/clusters/clariden.md +++ b/docs/clusters/clariden.md @@ -102,7 +102,7 @@ See the SLURM documentation for instructions on how to run jobs on the [Grace-Ho ### FirecREST -Clariden can also be accessed using [FircREST][ref-firecrest] at the `https://api.cscs.ch/ml/firecrest/v1` API endpoint. +Clariden can also be accessed using [FirecREST][ref-firecrest] at the `https://api.cscs.ch/ml/firecrest/v1` API endpoint. ## Maintenance and status diff --git a/docs/clusters/santis.md b/docs/clusters/santis.md index 6b0cf656..b0366f0d 100644 --- a/docs/clusters/santis.md +++ b/docs/clusters/santis.md @@ -106,7 +106,7 @@ See the SLURM documentation for instructions on how to run jobs on the [Grace-Ho ### FirecREST -Santis can also be accessed using [FircREST][ref-firecrest] at the `https://api.cscs.ch/ml/firecrest/v1` API endpoint. +Santis can also be accessed using [FirecREST][ref-firecrest] at the `https://api.cscs.ch/ml/firecrest/v1` API endpoint. ## Maintenance and status From d9abe62ef5627d74f4abb3a4129a2b6595374821 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 15:59:09 +0200 Subject: [PATCH 16/24] Fix iopsstor typos --- .github/actions/spelling/allow.txt | 4 ++-- docs/alps/storage.md | 10 +++++----- docs/platforms/mlp/index.md | 4 ++-- docs/storage/transfer.md | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 602c1a81..2b3155c2 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -14,7 +14,7 @@ CPMD CSCS CWP CXI -Capstor +capstor Ceph Containerfile DNS @@ -46,7 +46,7 @@ HPCP HPE HSN Hartree -Iopsstor +iopsstor Jax Jira Keycloak diff --git a/docs/alps/storage.md b/docs/alps/storage.md index 620e0f6c..5681d445 100644 --- a/docs/alps/storage.md +++ b/docs/alps/storage.md @@ -5,7 +5,7 @@ Alps has different storage attached, each with characteristics suited to differe HPC storage is managed in a separate cluster of nodes that host servers that manage the storage and the physical storage drives. These separate clusters are on the same Slingshot 11 network as the Alps. -| | Capstor | IOPStor | Vast | +| | Capstor | Iopsstor | Vast | |--------------|------------------------|------------------------|---------------------| | Model | HPE ClusterStor E1000D | HPE ClusterStor E1000F | Vast | | Type | Lustre | Lustre | NFS | @@ -22,11 +22,11 @@ These separate clusters are on the same Slingshot 11 network as the Alps. Capstor is the largest file system, for storing large amounts of input and output data. It is used to provide SCRATCH and STORE for different clusters - the precise details are platform-specific. -[](){#ref-alps-iopstor} -## iopstor +[](){#ref-alps-iopsstor} +## iopsstor !!! todo - small text explaining what iopstor is designed to be used for. + small text explaining what iopsstor is designed to be used for. [](){#ref-alps-vast} ## vast @@ -34,7 +34,7 @@ It is used to provide SCRATCH and STORE for different clusters - the precise det The Vast storage is smaller capacity system that is designed for use as home folders. !!! todo - small text explaining what iopstor is designed to be used for. + small text explaining what iopsstor is designed to be used for. The mounts, and how they are used for SCRATCH, STORE, PROJECT, HOME would be in the [storage docs][ref-storage-fs] diff --git a/docs/platforms/mlp/index.md b/docs/platforms/mlp/index.md index b9b684f2..ad17f6eb 100644 --- a/docs/platforms/mlp/index.md +++ b/docs/platforms/mlp/index.md @@ -36,7 +36,7 @@ There are three main file systems mounted on the MLP clusters Clariden and Brist | type |mount | filesystem | | -- | -- | -- | | Home | /users/$USER | [VAST][ref-alps-vast] | -| Scratch | `/iopstor/scratch/cscs/$USER` | [Iopstor][ref-alps-iopstor] | +| Scratch | `/iopsstor/scratch/cscs/$USER` | [Iopsstor][ref-alps-iopsstor] | | Project | `/capstor/store/cscs/swissai/` | [Capstor][ref-alps-capstor] | ### Home @@ -50,7 +50,7 @@ Scratch filesystems provide temporary storage for high-performance I/O for execu Use scratch to store datasets that will be accessed by jobs, and for job output. Scratch is per user - each user gets separate scratch path and quota. -* The environment variable `SCRATCH=/iopstor/scratch/cscs/$USER` is set automatically when you log into the system, and can be used as a shortcut to access scratch. +* The environment variable `SCRATCH=/iopsstor/scratch/cscs/$USER` is set automatically when you log into the system, and can be used as a shortcut to access scratch. !!! warning "scratch cleanup policy" Files that have not been accessed in 30 days are automatically deleted. diff --git a/docs/storage/transfer.md b/docs/storage/transfer.md index a62c26a3..802b33c5 100644 --- a/docs/storage/transfer.md +++ b/docs/storage/transfer.md @@ -41,7 +41,7 @@ Currently Globus provide the following mount points at CSCS: ## Internal Transfer The Slurm queue `xfer` is available on Alps clusters to address data transfers between internal CSCS file systems. -The queue has been created to transfer files and folders from `/users`, `/capstor/store` or `/iopstor/store` to the `/capstor/scratch` and `/iopstor/scratch` file systems (stage-in) and vice versa (stage-out). +The queue has been created to transfer files and folders from `/users`, `/capstor/store` or `/iopsstor/store` to the `/capstor/scratch` and `/iopsstor/scratch` file systems (stage-in) and vice versa (stage-out). Currently the following commands are available on the cluster supporting the queue xfer: ``` From 350587f0005fd3c290c530e31d63fe1967340dff Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 16:47:26 +0200 Subject: [PATCH 17/24] Use fixed spellchecker action version --- .github/workflows/spelling.yaml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/.github/workflows/spelling.yaml b/.github/workflows/spelling.yaml index d306fc49..42e9d0ff 100644 --- a/.github/workflows/spelling.yaml +++ b/.github/workflows/spelling.yaml @@ -1,22 +1,17 @@ name: Check Spelling on: - push: + pull_request: jobs: spelling: name: Check Spelling runs-on: ubuntu-latest - # if: ${{ contains(github.event_name, 'pull_request') || github.event_name == 'push' }} - # concurrency: - # group: spelling-${{ github.event.pull_request.number || github.ref }} - # # note: If you use only_check_changed_files, you do not want cancel-in-progress - # cancel-in-progress: true steps: - uses: actions/checkout@v3 - name: Check spelling id: spelling - uses: check-spelling/check-spelling@main + uses: check-spelling/check-spelling@v0.0.24 with: check_file_names: 1 post_comment: 0 From 7d6148c0151455292be5059e7aa346e9913d4c08 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 17:06:25 +0200 Subject: [PATCH 18/24] Always enable SARIF reporting --- .github/workflows/spelling.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/spelling.yaml b/.github/workflows/spelling.yaml index 42e9d0ff..f2913cac 100644 --- a/.github/workflows/spelling.yaml +++ b/.github/workflows/spelling.yaml @@ -17,7 +17,7 @@ jobs: post_comment: 0 use_magic_file: 1 warnings: bad-regex,binary-file,deprecated-feature,large-file,limited-references,no-newline-at-eof,noisy-file,non-alpha-in-dictionary,token-is-substring,unexpected-line-ending,whitespace-in-dictionary,minified-file,unsupported-configuration,no-files-to-check - use_sarif: ${{ (!github.event.pull_request || (github.event.pull_request.head.repo.full_name == github.repository)) && 1 }} + use_sarif: 1 extra_dictionary_limit: 20 extra_dictionaries: cspell:software-terms/dict/softwareTerms.txt From 23ab7d1148a1442c6505fd7f9b9e19d40ecedf35 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 17:08:16 +0200 Subject: [PATCH 19/24] Update docs/software/uenv.md --- docs/software/uenv.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/software/uenv.md b/docs/software/uenv.md index aa22115e..c6ae64d3 100644 --- a/docs/software/uenv.md +++ b/docs/software/uenv.md @@ -1,7 +1,7 @@ [](){#ref-uenv} # uenv -Uenv are user enviroments that provide scientific applications, libraries and tools. +Uenv are user environments that provide scientific applications, libraries and tools. This page will explain how to find, download and use uenv on the command line, and how to enable them in SLURM jobs. Uenv are typically application-specific, domain-specific or tool-specific - each uenv contains only what is required for the application or tools that it provides. From 768f1cf4919dcba4cff5b94319ac95c41601d368 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Tue, 22 Apr 2025 17:11:16 +0200 Subject: [PATCH 20/24] Add FirecREST to patterns.txt --- .github/actions/spelling/allow.txt | 1 - .github/actions/spelling/patterns.txt | 1 + 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 .github/actions/spelling/patterns.txt diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 2b3155c2..a921012e 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -26,7 +26,6 @@ ETHZ Ehrenfest Errigal FFT -firecrest Fock GAPW GCC diff --git a/.github/actions/spelling/patterns.txt b/.github/actions/spelling/patterns.txt new file mode 100644 index 00000000..2f43272b --- /dev/null +++ b/.github/actions/spelling/patterns.txt @@ -0,0 +1 @@ +FirecREST From 690be92e22b3481ac6c6756554c488ec398cfd65 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Wed, 23 Apr 2025 09:55:52 +0200 Subject: [PATCH 21/24] Ignore markdown images --- .github/actions/spelling/patterns.txt | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/actions/spelling/patterns.txt b/.github/actions/spelling/patterns.txt index 2f43272b..e25ff222 100644 --- a/.github/actions/spelling/patterns.txt +++ b/.github/actions/spelling/patterns.txt @@ -1 +1,6 @@ +# Recognized as "Firec" and "REST" with the regular rules, so in patterns.txt +# instead of allow.txt FirecREST + +# markdown figure +^!\[.*\]\(.*\)$ From 0530fb8d9a73a530d34b35d3894eeeef1030a04d Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Wed, 23 Apr 2025 10:00:06 +0200 Subject: [PATCH 22/24] Ignore most obvious URLs from spell checking --- .github/actions/spelling/patterns.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/actions/spelling/patterns.txt b/.github/actions/spelling/patterns.txt index e25ff222..920afa7f 100644 --- a/.github/actions/spelling/patterns.txt +++ b/.github/actions/spelling/patterns.txt @@ -4,3 +4,6 @@ FirecREST # markdown figure ^!\[.*\]\(.*\)$ + +# Most obvious URLs +https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*) From 3f0cb18e451158670db5e35f8517aa1d40db4013 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Wed, 23 Apr 2025 10:00:59 +0200 Subject: [PATCH 23/24] Move RESTful to patterns.txt --- .github/actions/spelling/allow.txt | 1 - .github/actions/spelling/patterns.txt | 1 + 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index a921012e..6daa6780 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -80,7 +80,6 @@ Plesset Pulay RCCL RDMA -RESTful ROCm RPA Roboto diff --git a/.github/actions/spelling/patterns.txt b/.github/actions/spelling/patterns.txt index 920afa7f..ceb8203a 100644 --- a/.github/actions/spelling/patterns.txt +++ b/.github/actions/spelling/patterns.txt @@ -1,6 +1,7 @@ # Recognized as "Firec" and "REST" with the regular rules, so in patterns.txt # instead of allow.txt FirecREST +RESTful # markdown figure ^!\[.*\]\(.*\)$ From 3fc44d99f7c848eb32d10eb5cf77c1abcb01f8a5 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Wed, 23 Apr 2025 10:03:53 +0200 Subject: [PATCH 24/24] Ignore markdown references --- .github/actions/spelling/patterns.txt | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/actions/spelling/patterns.txt b/.github/actions/spelling/patterns.txt index ceb8203a..7ba7a54f 100644 --- a/.github/actions/spelling/patterns.txt +++ b/.github/actions/spelling/patterns.txt @@ -8,3 +8,8 @@ RESTful # Most obvious URLs https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*) + +# Markdown references (definition and use) +^\[\]\(\){#[a-z-]+}$ +\]\(#[a-z-]+\) +\]\[[a-z-]+\]