Merge branch 'main' into namd-eiger

Author: RMeli

.github/CODEOWNERS

@@ -4,3 +4,5 @@ docs/software/communication @Madeeks @msimberg
 docs/software/devtools/linaro @jgphpc
 docs/software/prgenv/linalg.md @finkandreas @msimberg
 docs/software/sciapps/cp2k.md @abussy @RMeli
+docs/software/sciapps/gromacs.md @kanduri
+docs/software/ml @boeschf

.github/actions/spelling/allow.txt

@@ -0,0 +1,169 @@
+ACLs
+ACR
+AMD
+AWS
+Alpstein
+Balfrin
+Broyden
+CFLAGS
+CHARMM
+CHF
+COSMA
+CPE
+cpe
+CPMD
+CSCS
+CWP
+CXI
+capstor
+Ceph
+Containerfile
+DNS
+EDF
+EDFs
+EDFs
+EMPA
+ETHZ
+Ehrenfest
+Errigal
+FFT
+Fock
+GAPW
+GCC
+GGA
+GPFS
+GPG
+GPU
+GPUs
+GPW
+GROMACS
+GTL
+Gaussian
+Google
+HDD
+HPC
+HPCP
+HPE
+HSN
+Hartree
+iopsstor
+Jax
+Jira
+Keycloak
+LAMMPS
+LDA
+LOCALID
+LUMI
+Libc
+Linaro
+Linux
+MFA
+MLP
+MNDO
+MPICH
+MPS
+MeteoSwiss
+NAMD
+NICs
+NVIDIA
+NVMe
+OTP
+OTPs
+PASC
+PBE
+PDUs
+PID
+PMPI
+POSIX
+Parrinello
+Piz
+Plesset
+Pulay
+RCCL
+RDMA
+ROCm
+RPA
+Roboto
+Roothaan
+SSHService
+STMV
+Scopi
+TOTP
+UANs
+UserLab
+VASP
+Waldur
+Wannier
+XDG
+aarch
+aarch64
+acl
+biomolecular
+bristen
+bytecode
+clariden
+concretise
+concretizer
+containerised
+customised
+diagonalisation
+eiger
+filesystems
+groundstate
+inodes
+lexer
+libfabric
+multitenancy
+podman
+prioritised
+prgenv
+proactively
+quickstart
+santis
+screenshot
+slurm
+smartphone
+squashfs
+srun
+ssh
+stackinator
+stakeholders
+subfolders
+subtable
+subtables
+supercomputing
+superlu
+sysadmin
+tcl
+tcsh
+testuser
+timeframe
+timelimit
+tmpfs
+todi
+toolbar
+toolset
+torchaudio
+torchvision
+treesitter
+trilinos
+uarch
+uenv
+uenvs
+uids
+vCluster
+vClusters
+venv
+versioned
+versioning
+webhooks
+webinar
+webpage
+website
+wikipedia
+workaround
+workflows
+xattr
+xattrs
+youtube
+zstd

.github/actions/spelling/only.txt

@@ -0,0 +1 @@
+docs/.*\.md$

.github/actions/spelling/patterns.txt

@@ -0,0 +1,15 @@
+# Recognized as "Firec" and "REST" with the regular rules, so in patterns.txt
+# instead of allow.txt
+FirecREST
+RESTful
+
+# markdown figure
+^!\[.*\]\(.*\)$
+
+# 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-]+}$
+\]\(#[a-z-]+\)
+\]\[[a-z-]+\]

.github/workflows/spelling.yaml

@@ -0,0 +1,26 @@
+name: Check Spelling
+
+on:
+  pull_request:
+
+jobs:
+  spelling:
+    name: Check Spelling
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Check spelling
+        id: spelling
+        uses: check-spelling/[email protected]
+        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: 1
+          extra_dictionary_limit: 20
+          extra_dictionaries:
+            cspell:software-terms/dict/softwareTerms.txt
+            cspell:bash/dict/bash-words.txt
+            cspell:companies/dict/companies.txt
+            cspell:filetypes/filetypes.txt

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

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

docs/alps/storage.md

@@ -2,15 +2,15 @@
 # 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                |
+|              | Capstor                | Iopsstor               | Vast                |
 |--------------|------------------------|------------------------|---------------------|
 | 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 |
@@ -22,19 +22,19 @@ 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
 
 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]
 

docs/build-install/cpe.md

@@ -8,14 +8,10 @@ Modern HPC applications and software stacks are often very complicated, and ther
 
 <div class="grid cards" markdown>
 
-- :fontawesome-solid-earth-americas: __[uenv]__ – uenv provide isolated software environments for applications and developers.
-- :fontawesome-solid-earth-americas: __[CPE]__ – the Cray Programming Environment is provided as-is on Alps.
+- :fontawesome-solid-earth-americas: __[uenv][ref-uenv]__ – uenv provide isolated software environments for applications and developers.
 
 </div>
 
-  [uenv]: uenv.md
-  [CPE]: cpe.md
-
 ## Python
 
 There are multiple ways to install Python software.
@@ -30,4 +26,4 @@ There are multiple ways to install Python software.
 
 ## Containers
 
-CSCS provides tools for building software in containers
+CSCS provides [Podman][ref-build-containers] for building software in containers