material/404.html

+{% extends "main.html" %}
+{% block content %}
+  <h1>404 - Not found</h1>
+{% endblock %}

mkdocs.yml

+site_name: IT4Innovations Documentation
+docs_dir: docs.it4i
+site_url: https://docs.it4i.cz/
+extra_css:
+   - src/css.css?id=2018100501
+   - https://unpkg.com/mermaid@10.1.0/dist/mermaid.css
+
+extra_javascript:
+   - https://unpkg.com/mermaid@10.1.0/dist/mermaid.min.js
+
+# Repository
+repo_name: sccs/docs.it4i.cz
+repo_url: https://code.it4i.cz/sccs/docs.it4i.cz
+edit_uri: -/edit/master/docs.it4i/
+
+# Copyright
+copyright: Copyright (c) 2013-__YEAR__ IT4Innovations__VERSION__
+
+theme:
+  name: material
+  custom_dir: material
+  language: 'en'
+
+  # 404 page
+  static_templates:
+    - 404.html
+
+  features:
+    - search.highlight
+    - search.share
+    - content.action.edit
+    - navigation.tabs
+    - navigation.tabs.sticky
+    - navigation.instant
+    - navigation.path
+    - navigation.prune
+    - navigation.indexes
+    - navigation.top
+
+  icon:
+    logo: fontawesome/solid/book-open
+    repo: fontawesome/brands/gitlab
+    edit: material/pencil 
+
+  # Don't include MkDocs' JavaScript
+  include_search_page: false
+  search_index_only: true
+
+  font:
+    text: 'Ubuntu'
+    #code: 'Ubuntu Mono' # Overwritten in css.css 
+  palette:
+    primary: 'indigo'
+    accent: 'indigo'
+
+  palette:
+
+    # Palette toggle for light mode
+    - scheme: default
+      toggle:
+        icon: material/brightness-7 
+        name: Switch to dark mode
+
+    # Palette toggle for dark mode
+    - scheme: slate
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+
+  favicon: img/favicon.ico
+
+nav:
+  - General:
+    - Introduction: index.md
+    - Get Access:
+      - Introduction: general/access/account-introduction.md
+      - Get Account:
+        - e-INFRA CZ Account: general/access/einfracz-account.md
+        - IT4I Account: general/obtaining-login-credentials/obtaining-login-credentials.md
+      - Get Project Membership: general/access/project-access.md
+    - Get Project: general/applying-for-resources.md
+    - Manage Your Profile:
+      - e-INFRA CZ Profile: general/management/einfracz-profile.md
+      - IT4I Profile: general/management/it4i-profile.md
+    - Access Services:
+      - Access the Clusters:
+        - SSH Access: general/shell-and-data-access.md
+        - SSH & Key Management: general/accessing-the-clusters/shell-access-and-data-transfer/ssh-key-management.md
+      - GUI:
+        - Open OnDemand: general/accessing-the-clusters/graphical-user-interface/ood.md
+        - VNC: general/accessing-the-clusters/graphical-user-interface/vnc.md
+        - X Window System: general/accessing-the-clusters/graphical-user-interface/x-window-system.md
+        - Xorg: general/accessing-the-clusters/graphical-user-interface/xorg.md
+      - Tmux: general/accessing-the-clusters/tmux.md
+      - Access the IS and Web Services: general/services-access.md
+      - VPN Access: general/accessing-the-clusters/vpn-access.md
+    - Run Jobs:
+      - Introduction: general/resource_allocation_and_job_execution.md
+      - Job Submission and Execution:
+        - General: general/job-submission-and-execution.md
+        - Karolina Specific: general/karolina-slurm.md
+        - Slurm Batch Examples: general/slurm-batch-examples.md
+      - Resources Allocation:
+        - Resource Allocation Policy: general/resources-allocation-policy.md
+        - Karolina Partitions: general/karolina-partitions.md
+        - Barbora Partitions: general/barbora-partitions.md
+        - Resource Accounting Policy: general/resource-accounting.md
+      - Job Priority: general/job-priority.md
+#      - Slurm Job Submission and Execution: general/slurm-job-submission-and-execution.md
+      - Capacity Computing:
+        - Introduction: general/capacity-computing.md
+        - Job Arrays: general/job-arrays.md
+        - HyperQueue: general/hyperqueue.md
+#      - Parallel Computing and MPI: general/karolina-mpi.md
+    - Tools:
+        - CodeIT4I: general/tools/codeit4i.md
+        - CI/CD: general/tools/cicd.md
+        - CLI Client Tools: general/tools/cli-client-tools.md
+        - Data Sharing Tools: general/tools/tools-list.md
+        - OpenCode: general/tools/opencode.md
+    - Technical Information:
+      - SSH Keys:
+        - OpenSSH Keys (UNIX): general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+        - PuTTY (Windows): general/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+      - Certificates FAQ: general/obtaining-login-credentials/certificates-faq.md
+      - API Documentation: apiv2.md
+    - Satisfaction and Feedback: general/feedback.md
+    - Energy Saving: general/energy.md
+    - DICE: dice.md
+    - Support: general/support.md
+    - Acceptable Use Policy (AUP): general/aup.md
+  - Clusters:
+    - VLQ: vlq/introduction.md
+    - Karolina:
+      - Introduction: karolina/introduction.md
+      - Hardware Overview: karolina/hardware-overview.md
+      - Compute Nodes: karolina/compute-nodes.md
+      - Storage: karolina/storage.md
+      - Network: karolina/network.md
+      - Visualization Servers: karolina/visualization.md
+    - Barbora:
+      - Introduction: barbora/introduction.md
+      - Hardware Overview: barbora/hardware-overview.md
+      - Compute Nodes: barbora/compute-nodes.md
+      - Storage: barbora/storage.md
+      - Network: barbora/network.md
+      - Visualization Servers: barbora/visualization.md
+    - Barbora NG:
+      - Introduction: barbora-ng/introduction.md
+      - Hardware Overview: barbora-ng/hardware-overview.md
+    - NVIDIA DGX-2:
+      - Introduction: dgx2/introduction.md
+      - Accessing DGX-2: dgx2/accessing.md
+      - Resource Allocation and Job Execution: dgx2/job_execution.md
+      - Software deployment: dgx2/software.md
+    - Complementary Systems:
+      - Introduction: cs/introduction.md
+      - Accessing CS: cs/accessing.md
+      - Specification: cs/specifications.md
+      - Complementary System Job Scheduling: cs/job-scheduling.md
+      - Guides:
+        - AMD Partition: cs/guides/amd.md
+        - ARM Partition: cs/guides/arm.md
+        - Heterogeneous Memory Management on Intel Platforms: cs/guides/hm_management.md
+        - IBM Power10 Partition: cs/guides/power10.md
+        - NVIDIA Grace Partition: cs/guides/grace.md
+        - VMware Horizon: cs/guides/horizon.md
+        - Xilinx Accelerator Platform: cs/guides/xilinx.md
+    - Archive:
+      - Introduction: archive/archive-intro.md
+      - Anselm:
+        - Introduction: anselm/introduction.md
+        - Hardware Overview: anselm/hardware-overview.md
+        - Compute Nodes: anselm/compute-nodes.md
+        - Storage: anselm/storage.md
+        - Network: anselm/network.md
+      - Salomon:
+        - Introduction: salomon/introduction.md
+        - Hardware Overview: salomon/hardware-overview.md
+        - Compute Nodes: salomon/compute-nodes.md
+        - Network:
+          - InfiniBand Network: salomon/network.md
+          - IB Single-Plane Topology: salomon/ib-single-plane-topology.md
+          - 7D Enhanced Hypercube: salomon/7d-enhanced-hypercube.md
+        - Storage: salomon/storage.md
+        - Visualization Servers: salomon/visualization.md
+      - PRACE: prace.md
+  - Storage:
+    - PROJECT: 
+      - Project storage: storage/project-storage.md
+      - Proj4 storage - S3: storage/proj4-storage.md
+    - CESNET:
+      - Storage: storage/cesnet-storage.md
+      - S3 Storage: 
+        - Introduction: storage/cesnet-s3.md
+        - S3cmd: storage/s3cmd.md
+        - AWS CLI: storage/awscli.md
+    - ARCHIVE:
+        - Introduction: storage/archive-storage.md
+    - Access Control List:
+      - Standard File ACL: storage/standard-file-acl.md
+      - NFSv4 File ACL: storage/nfs4-file-acl.md
+  - Software:
+    - Environment and Modules: environment-and-modules.md
+    - Modules:
+      - New Software Installation Request: software/modules/new-software.md
+      - Lmod Environment: software/modules/lmod.md
+      - Modules Matrix: modules-matrix.md
+      - Job Features: job-features.md
+      - Available Karolina Modules: modules-karolina.md
+      - Available Barbora Modules: modules-barbora.md
+      - Available DGX-2 Modules: modules-dgx.md
+      - Available CS AVX2 Modules: modules-cs-avx2.md
+      - Available CS AVX512 Modules: modules-cs-avx512.md
+      - Available CS AARCH64 Modules: modules-cs-aarch64.md
+      - Available CS PPC64LT Modules: modules-cs-ppc64lt.md
+      - Available CS EL9 AARCH64 Modules: modules-cs-el9-aarch64.md
+    - ISV Licenses: software/isv_licenses.md
+    - CAE:
+      - COMSOL:
+        - COMSOL: software/cae/comsol/comsol-multiphysics.md
+        - Licensing and Available Versions: software/cae/comsol/licensing-and-available-versions.md
+    - Chemistry:
+      - VASP: software/chemistry/vasp.md
+      - Gaussian: software/chemistry/gaussian.md
+      - Molpro: software/chemistry/molpro.md
+      - NWChem: software/chemistry/nwchem.md
+      - Orca: software/chemistry/orca.md
+      - Phono3py: software/chemistry/phono3py.md
+      - Phonopy: software/chemistry/phonopy.md
+    - Compilers:
+      - Overview: software/compilers.md
+      - Karolina Compilation: software/karolina-compilation.md
+    - Data Science:
+        - Dask: software/data-science/dask.md
+    - Debuggers:
+      - Introduction: software/debuggers/introduction.md
+      - Allinea Forge (DDT,MAP): software/debuggers/allinea-ddt.md
+      - Allinea Performance Reports: software/debuggers/allinea-performance-reports.md
+      - CUBE: software/debuggers/cube.md
+      - Intel VTune Amplifier XE: software/debuggers/intel-vtune-amplifier.md
+      - Intel VTune Profiler: software/debuggers/intel-vtune-profiler.md
+      - PAPI: software/debuggers/papi.md
+      - Scalasca: software/debuggers/scalasca.md
+      - Score-P: software/debuggers/score-p.md
+      - Total View: software/debuggers/total-view.md
+      - Valgrind: software/debuggers/valgrind.md
+      - Vampir: software/debuggers/vampir.md
+    - EESSI: software/eessi.md
+    - GPU:
+      - NVIDIA CUDA: software/nvidia-cuda.md
+      - NVIDIA CUDA Quantum: software/nvidia-cuda-q.md
+      - ROCm HIP: software/nvidia-hip.md
+    - Intel Suite:
+      - Introduction: software/intel/intel-suite/intel-parallel-studio-introduction.md
+      - Intel Advisor: software/intel/intel-suite/intel-advisor.md
+      - Intel Compilers: software/intel/intel-suite/intel-compilers.md
+      - Intel IPP: software/intel/intel-suite/intel-integrated-performance-primitives.md
+      - Intel Inspector: software/intel/intel-suite/intel-inspector.md
+      - Intel MKL: software/intel/intel-suite/intel-mkl.md
+      - Intel TBB: software/intel/intel-suite/intel-tbb.md
+      - Intel Trace Analyzer and Collector: software/intel/intel-suite/intel-trace-analyzer-and-collector.md
+    - Machine Learning:
+      - Introduction: software/machine-learning/introduction.md
+      - NetKet: software/machine-learning/netket.md
+      - TensorFlow: software/machine-learning/tensorflow.md
+      - Deep Learning:
+          - AlphaFold: software/machine-learning/alphafold.md
+          - DeepDock: software/machine-learning/deepdock.md
+    - LLM:
+      - vLLM with Deepseek: software/vllm_deepseek.md
+    - MPI:
+      - Introduction: software/mpi/mpi.md
+      - OpenMPI Examples: software/mpi/ompi-examples.md
+      - MPI4Py (MPI for Python): software/mpi/mpi4py-mpi-for-python.md
+      - Jupyter-lab MPI: software/mpi/jupyter_mpi.md
+    - Numerical Languages:
+      - Introduction: software/numerical-languages/introduction.md
+      - Clp: salomon/software/numerical-libraries/Clp.md
+      - R: software/numerical-languages/r.md
+      - Matlab: software/numerical-languages/matlab.md
+      - Octave: software/numerical-languages/octave.md
+      - OpenCoarrays: software/numerical-languages/opencoarrays.md
+    - Numerical Libraries:
+      - FFTW: software/numerical-libraries/fftw.md
+      - GSL: software/numerical-libraries/gsl.md
+      - HDF5: software/numerical-libraries/hdf5.md
+      - Intel Numerical Libraries: software/numerical-libraries/intel-numerical-libraries.md
+      - PETSc: software/numerical-libraries/petsc.md
+    - NVIDIA HPC SDK:
+      - Overview: software/sdk/nvhpc.md
+      - OpenAAC MPI Tutorial: software/sdk/openacc-mpi.md
+    - Languages:
+      - Java: software/lang/java.md
+      - C#: software/lang/csc.md
+      - Python: software/lang/python.md
+      - Python-Conda: software/lang/conda.md
+      - JuliaLang: software/lang/julialang.md
+    - Tools:
+      - Apptainer: software/tools/apptainer.md
+      - ANSYS:
+        - Introduction: software/tools/ansys/ansys.md
+        - ANSYS CFX: software/tools/ansys/ansys-cfx.md
+        - ANSYS Fluent: software/tools/ansys/ansys-fluent.md
+        - ANSYS LS-DYNA: software/tools/ansys/ansys-ls-dyna.md
+        - ANSYS MAPDL: software/tools/ansys/ansys-mechanical-apdl.md
+        - Workbench: software/tools/ansys/workbench.md
+        - Setting License Preferences: software/tools/ansys/licensing.md
+        - Licensing and Available Versions: software/tools/ansys/setting-license-preferences.md
+      - EasyBuild:
+        - Introduction: software/tools/easybuild.md
+        - Generating Container Recipes and Images: software/tools/easybuild-images.md
+      - Spack: software/tools/spack.md
+      - Virtualization: software/tools/virtualization.md
+    - Visualization:
+      - In situ: software/viz/insitu.md
+      - NICE DCV: software/viz/NICEDCVsoftware.md
+      - OpenFOAM: software/viz/openfoam.md
+      - OVITO: software/viz/ovito.md
+      - ParaView: software/viz/paraview.md
+      - QtiPlot: software/viz/qtiplot.md
+      - VirtualGL: software/viz/vgl.md
+      - VESTA: software/viz/vesta.md
+  - LUMI:
+      - About LUMI: lumi/about.md
+      - LUMI AI: lumi/lumiai.md
+      - LUMI Software:
+        - General: lumi/software.md
+        - OpenFoam: lumi/openfoam.md
+        - PyTorch: lumi/pytorch.md
+      - LUMI Support: lumi/support.md
+  - Clouds:
+    - e-INFRA CZ Cloud: cloud/einfracz-cloud.md
+    - IT4I Cloud:
+      - About IT4I Cloud: cloud/it4i-cloud.md
+      - IT4I Cloud Quotas: cloud/it4i-quotas.md
+
+extra:
+  disqus: 'test-3whnesz3gq'
+  social:
+    - icon: 'fontawesome/brands/gitlab'
+      link: 'https://code.it4i.cz/sccs/docs.it4i.cz'
+    - icon: 'fontawesome/solid/globe'
+      link: 'https://www.it4i.cz'
+
+plugins:
+  - search:
+      separator: '[\s\-,:!=\[\]()"/]+|(?!\b)(?=[A-Z][a-z])|\.(?!\d)|&[lg]t;'
+      lang:
+        - en
+  - exclude-search:
+      exclude:
+        - anselm/*.md
+        - archive/*.md
+        - prace.md
+        - salomon/*.md
+        - general/pbs-job-submission-and-execution.md
+        - general/job-arrays.md
+        - general/karolina-mpi.md
+        - software/viz/gpi2.md
+        - modules-karolina.md
+        - modules-barbora.md
+        - modules-dgx.md
+        - modules-cs-avx2.md
+        - modules-cs-avx512.md
+        - modules-cs-aarch64.md
+        - modules-cs-ppc64lt.md
+        - modules-cs-el9-aarch64.md
+        - software/bio/omics-master/*.md
+
+  - mkdocs-pdf
+#  - optimize
+
+markdown_extensions:
+  - codehilite
+  - markdown.extensions.admonition:
+  - pymdownx.arithmatex:
+  - markdown.extensions.toc:
+      permalink: true
+      slugify: !!python/name:pymdownx.slugs.uslugify
+  - pymdownx.snippets:
+      base_path: snippets
+  - pymdownx.tabbed:
+  - footnotes
+  - pymdownx.superfences
+  - attr_list

package.json

+{
+	"scripts": {
+		"lint-md": "remark ."
+	},
+
+	"remarkConfig": {
+		"presets": ["lint-recommended"]
+	}
+}

pathcheck.sh

+#!/bin/bash
+
+#the script controls links, only inside the whole directory, doesnt control outside pages
+
+for file in $@; do
+check=$(cat "$file" | grep -Po "\[.*?\]\([^ ]*?\)" | grep -v "#" | grep -vE "http|@|www|ftp|none" | sed 's/\[.*\]//g' | sed 's/[()]//g' | sed 's/\/$/.md/g')
+if [ ! -z "$check" ]; then
+
+wrong=0
+for line in $check; do
+
+pathtocheck=$(dirname "$file")/$line
+
+
+if [ -f $(dirname "$file")/"$line" ]; then
+	:
+	#echo "ok $pathtocheck"
+else
+	if [ $wrong -eq "0" ]; then
+		echo ""
+		echo "\n+++++ $file +++++\n"
+	fi
+	wrong=1
+	echo "wrong link in $pathtocheck"
+
+fi
+done
+fi
+done
+echo ""

requirements.txt

+backports-abc==0.5
+click==7.1.2
+EditorConfig==0.12.2
+future==0.18.2
+futures==3.1.1
+importlib-metadata==6.6.0
+Jinja2==3.1.2
+joblib==0.17.0
+jsbeautifier==1.13.0
+livereload==2.6.3
+lunr==0.5.8
+Markdown==3.4.3
+MarkupSafe==2.0.1
+mkdocs==1.4.3
+mkdocs-exclude-search==0.6.5
+mkdocs-git-committers-plugin-2==1.1.2
+mkdocs-git-revision-date-localized-plugin==1.2.0
+mkdocs-material==9.1.12
+mkdocs-material-extensions==1.1.1
+mkdocs-pdf==0.1.2
+nltk==3.5
+packaging==20.4
+Pygments==2.7.1
+pymdown-extensions==8.0.1
+pyparsing==2.4.7
+PyYAML==5.4.1
+regex==2023.5.5
+singledispatch==3.4.0.3
+six==1.16.0
+titlecase==1.1.1
+tornado==6.0.4
+tqdm==4.50.0

scripts/add_version.sh

+#!/bin/bash
+VER=$(git log --pretty=format:'/ ver. %h / %ai' -n 1)
+sed "s,__VERSION__, $VER," mkdocs.yml -i
+YEAR=$(date +"%Y")
+sed "s,__YEAR__, $YEAR," mkdocs.yml -i

scripts/check_version.rb

+require 'faraday'
+require 'json'
+
+#print ARGV[0].downcase
+puts "Checking the ver for #{ARGV[0]}"
+
+response = Faraday.get "https://release-monitoring.org/api/projects/?pattern=#{ARGV[0].downcase}"
+
+fedora_j = JSON.parse( response.body )['projects']
+fedora = fedora_j.select { |h| h['name'] == ARGV[0].downcase }.first['version']
+
+response = Faraday.get "https://docs.it4i.cz/modules-matrix.json"
+
+it4i = JSON.parse( response.body )['projects'][ARGV[0]]
+it4i_short = it4i.split('-')[0]
+puts "IT4Innovations: #{it4i_short} (#{it4i})"
+puts "Upstream      : #{fedora}"
+
+if it4i_short.eql? fedora
+  puts "Identical"
+else
+
+end

scripts/clean_json.sh

+#!/bin/bash
+sed 's/\\u00a0/ /g' -i "$@"
+sed 's,\\n\\n, ,g' -i "$@"
+sed 's,\\n , ,g' -i "$@"
+sed 's, \\n, ,g' -i "$@"
+sed -e 's/^[ \t]*//' -i "$@"

scripts/colors.sh

+#!/bin/bash
+for i in {"red","pink","purple","deep purple","indigo","blue","light blue","cyan","teal","green","light green","lime","yellow","amber","orange","deep orange","brown","grey","blue grey"}
+do
+  echo "Setting color to: $i, ${i/ /_}, color_${i/ /_}"
+  git checkout color_${i/ /_}
+  git pull --rebase origin colors
+  git pull --rebase 
+  sed -ri "s/(primary: ').*'/\1$i'/" mkdocs.yml
+  git commit -am "Setting color to: $i"
+  git push --set-upstream origin color_${i/ /_}
+  git checkout colors
+done

scripts/combinations.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+""" combinations """
+
+from __future__ import print_function
+
+import itertools
+import re
+
+CHARS = ['K', 'B', 'D']
+MASK = ''.join(reversed(CHARS))
+for i in range(1, len(CHARS)+1):
+    for comb in itertools.combinations(CHARS, i):
+        REG = "[^%s]" % ''.join(comb)
+        print(re.sub(REG, "-", MASK))

scripts/get_cvs.sh

+#!/bin/bash
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/dgx.csv -o dgx.csv
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/barbora.csv -o barbora.csv
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/karolina.csv -o karolina.csv

scripts/get_modules.sh

+#!/bin/bash
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/barbora.md -o docs.it4i/modules-barbora.md
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/dgx.md -o docs.it4i/modules-dgx.md
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/karolina.md -o docs.it4i/modules-karolina.md
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/cs_aarch64.md -o docs.it4i/modules-cs-aarch64.md
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/cs_all_avx2.md -o docs.it4i/modules-cs-avx2.md
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/cs_avx512.md -o docs.it4i/modules-cs-avx512.md
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/cs_ppc64le.md -o docs.it4i/modules-cs-ppc64lt.md
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/cs_el9_aarch64.md -o docs.it4i/modules-cs-el9-aarch64.md
+
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/dgx.csv -o scripts/dgx.csv
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/barbora.csv -o scripts/barbora.csv
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/karolina.csv -o scripts/karolina.csv

scripts/maketitle.py

+#!/usr/bin/python3
+
+"""
+Script to process Markdown files, convert them to MDX,
+and add frontmatter based on the first H1 heading.
+"""
+
+import os
+import re
+from pathlib import Path
+
+def process_md_file(md_path):
+    """
+    Converts a Markdown file (.md) to MDX format (.mdx),
+    adds frontmatter with title from H1 heading, and removes the original file.
+
+    Args:
+        md_path (Path): Path to the Markdown file.
+    """
+    try:
+        with open(md_path, 'r', encoding='utf-8') as file_handle:
+            content = file_handle.read()
+    except UnicodeDecodeError:
+        print(f"Skipping {md_path} - unable to decode as UTF-8")
+        return
+
+    # Remove existing hide-toc frontmatter
+    hide_toc_pattern = re.compile(
+        r'^---\s*\n\s*hide:\s*\n\s*-\s+toc\s*\n---\s*\n*',
+        flags=re.MULTILINE
+    )
+    content = hide_toc_pattern.sub('', content, count=1)
+
+    # Remove leading empty lines
+    content = re.sub(r'^\n+', '', content)
+
+    # Process H1 heading
+    h1_pattern = re.compile(r'^\s*#\s+(.*)$', re.MULTILINE)
+    match = h1_pattern.search(content)
+
+    if match:
+        title = match.group(1).strip()
+        frontmatter = f'---\ntitle: "{title}"\n---\n'
+
+        # Construct new content with frontmatter at beginning
+        before_h1 = content[:match.start()].lstrip('\n')
+        after_h1 = content[match.end():].lstrip('\n')
+        new_content = frontmatter + before_h1 + after_h1
+    else:
+        print(f"No H1 heading found in {md_path}, creating basic frontmatter")
+        frontmatter = '---\ntitle: ""\n---\n\n'
+        new_content = frontmatter + content.lstrip('\n')
+
+    # Ensure no empty lines after frontmatter
+    lines = new_content.split('\n')
+    if len(lines) >= 3 and lines[0] == '---' and lines[2] == '---':
+        remaining = lines[3:]
+        while remaining and not remaining[0].strip():
+            remaining.pop(0)
+        new_content = '\n'.join(lines[:3] + remaining)
+
+    # Create and write MDX file
+    mdx_path = md_path.with_suffix('.mdx')
+    with open(mdx_path, 'w', encoding='utf-8') as file_handle:
+        file_handle.write(new_content)
+
+    # Remove original MD file
+    md_path.unlink()
+    print(f"Converted {md_path} to {mdx_path}")
+
+def main():
+    """Walks through directories and processes all Markdown files."""
+    for root, dirs, files in os.walk('.'):
+        dirs[:] = [d for d in dirs if not d.startswith('.')]
+        for file in files:
+            if file.endswith('.md'):
+                md_path = Path(root) / file
+                process_md_file(md_path)
+
+if __name__ == '__main__':
+    main()

scripts/matrix.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+""" matrix """
+
+from __future__ import print_function
+
+import itertools
+
+CHARS = ['K', 'B', 'D']
+MASK = ''.join(reversed(CHARS))
+for bits in itertools.product([0, 1], repeat=len(CHARS)):
+    SBIT = "".join(str(bit) for bit in bits)
+    NST = ""
+    for i, _ in enumerate(SBIT):
+        if SBIT[i] == "1":
+            NST += MASK[i]
+        else:
+            NST += "-"
+    print(NST)

scripts/meta-json.sh

+#!/bin/bash
+
+find content/docs -type d -exec bash -c '
+cd "{}" || exit
+DIR=$(basename "$PWD")
+TITLE=$(echo "$DIR" | sed -E "s/^(.)/\U\1/")
+PAGES=$( (ls *.mdx 2>/dev/null | sed "s/\.mdx$//"; ls -d */ 2>/dev/null | sed "s#/##") | sort | jq -R . | jq -s . )
+jq -n --arg title "$TITLE" --argjson pages "$PAGES" "{title: \$title, pages: \$pages}" > meta.json
+' \;
+
+exit 0

scripts/modules_matrix.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+""" modules_matrix """
+
+import argparse
+import csv
+import itertools
+import json
+import os.path
+
+def arg_parse():
+    """
+    Argument parser
+    """
+    parser = argparse.ArgumentParser(
+        description="Module_matrix"
+    )
+    parser.add_argument('--json',
+                        action='store_true',
+                        help="get json")
+    return parser.parse_args()
+
+def get_data(filename):
+    """Function to read the data from the input CSV file to use in the analysis"""
+    reader = []  # Just in case the file open fails
+    with open(filename, 'r') as fdata:
+        reader = csv.reader(fdata, delimiter=',')
+        return list(reader)  # Only return the reader when you have finished.
+
+def get_datalist():
+    """Get data list"""
+    datalist = []
+    for name in ['karolina', 'dgx', 'barbora']:
+        path = os.path.join('scripts', f"{name}.csv")
+        datalist += get_data(path)
+    return datalist
+
+def get_counts(datalist):
+    """Get counts"""
+    counts = {}
+    for i in datalist:
+        counts[i[0]] = counts.get(i[0], 0) + int(i[1])
+    return counts
+
+def get_matrix():
+    """Get matrix"""
+    chars = ['K', 'B', 'D']
+    arr = []
+    mask = ''.join(reversed(chars))
+    for bits in itertools.product([0, 1], repeat=len(chars)):
+        sbit = "".join(str(bit) for bit in bits)
+        nst = ""
+        for i, _ in enumerate(sbit):
+            if sbit[i] == "1":
+                nst += mask[i]
+            else:
+                nst += "-"
+        arr.append(nst)
+    return arr
+
+def get_software(datalist):
+    """Get software"""
+    matrix = get_matrix()
+    counts = get_counts(datalist)
+    software = {}
+    prev = ''
+    for mat, i in sorted(counts.items()):
+        split = mat.split('/')
+        if len(split) > 1:
+            if split[0] != prev:
+                software[split[0]] = {}
+            software[split[0]][split[1]] = '`' + matrix[i] + '`'
+            prev = split[0]
+    return software
+
+def packages_json(software):
+    """Packages JSON"""
+    packages = {}
+    for module in sorted(software.items(), key=lambda i: i[0].lower()):
+        packages[module[0]] = sorted(module[1])[-1]
+    data = {'total': len(packages), 'projects': packages}
+    return data
+
+def print_software(software):
+    """Print software"""
+    for module in sorted(software.items(), key=lambda i: i[0].lower()):
+        software_name = module[0]
+        versions = []
+        clusters = []
+        for key in sorted(module[1].keys()):
+            versions.append(key)
+            clusters.append(module[1][key])
+        print(f"| {software_name} | {'<br>'.join(versions)} | {'<br>'.join(clusters)} |")
+    print()
+    print('---8<--- "modules_matrix_search.md"')
+
+def print_hint():
+    """Print hint"""
+    print('!!! Hint "Cluster Acronyms"')
+    print('    ```')
+    print('    D B K')
+    print('    | | |')
+    print('    | | +----> Karolina')
+    print('    | +------> Barbora')
+    print('    +--------> DGX')
+    print('    ```')
+    print()
+    print("| Module <br><form><input id=\"searchInput\" placeholder=\"🔍 Filter\""
+          " style=\"width: 8rem; border-radius: 0.2rem; color: black;"
+          " padding-left: .2rem;\"></form> | Versions | Clusters |")
+    print("| ------ | -------- | -------- |")
+
+def print_changelog():
+    """Print changelog"""
+    print('**Modules Changelog**<br>')
+    print('You can see the modules changelog for each supercomputer here:<br>')
+    print('[DGX modules changelog][1]<br>')
+    print('[Barbora modules changelog][2]<br>')
+    print('[Karolina modules changelog][3]<br>')
+
+def print_links():
+    """Print links"""
+    print('[1]: https://code.it4i.cz/sccs/it4i-modules/-/blob/master/dgx-changelog.md')
+    print('[2]: https://code.it4i.cz/sccs/it4i-modules/-/blob/master/barbora-changelog.md')
+    print('[3]: https://code.it4i.cz/sccs/it4i-modules/-/blob/master/karolina-changelog.md')
+
+def main():
+    """Main function"""
+    arg = arg_parse()
+    datalist = get_datalist()
+    software = get_software(datalist)
+
+    if arg.json:
+        print(json.dumps(packages_json(software)))
+    else:
+        print_changelog()
+        print_hint()
+        print_software(software)
+        print_links()
+
+if __name__ == "__main__":
+    main()

scripts/movefiles.sh

+#!/bin/bash
+
+find . -type f -not -name '*.md' -print0 | while IFS= read -r -d '' file; do
+    # Strip leading ./ from the file path
+    relative_path="${file#./}"
+    # Create target directory path
+    target_dir="../public/it4i/$(dirname "$relative_path")"
+    # Create directory structure if it doesn't exist
+    mkdir -p "$target_dir"
+    # Move the file
+    mv "$file" "$target_dir"
+done

scripts/movepublic.sh

+#!/bin/bash
+
+for i in $(find ../public/it4i -type f -printf "%P\n" | grep -v .gitkeep) ; do
+   short=$(echo $i | sed -e 's/.*\/\([^\/]*\)\/\([^\/]*\)$/\1\/\2/');
+   for f in $(grep -rl "$short)"); do
+      sh=$(echo $short | sed -e 's/\//\\\//g')
+      ie=$(echo $i | sed -e 's/\//\\\//g')
+      sed -i "s/(.*$sh)/(\/it4i\/$ie)/" $f
+   done
+done

scripts/titlemd.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# pylint: disable=C0301, R1710
+
+""" titlemd """
+
+import argparse
+import sys
+
+try:
+    from titlecase import titlecase
+except ImportError:
+    print("Please install titlecase")
+
+def arg_parse():
+    """
+    Argument parser
+    """
+    parser = argparse.ArgumentParser(
+        description="Titlemd"
+    )
+    parser.add_argument('-t', '--test',
+                        action='store_true',
+                        help="test")
+    parser.add_argument('location',
+                        nargs='?',
+                        default='.',
+                        help="location, default current directory")
+    return parser.parse_args()
+
+def mkdocs_available(location):
+    """ Is mkdocs.yml available? """
+    return "mkdocs.yml" in location
+
+def linestart(line, disabled, test, prev_line=None):
+    """ linestart """
+    if test:
+        if (line.startswith("``") or line.startswith("extra:")) and not disabled:
+            return True
+        if (line.startswith("``") or (prev_line and prev_line.startswith("pages:"))) and disabled:
+            return False
+    else:
+        if line.startswith("``") and not disabled:
+            return True
+        if line.startswith("``") and disabled:
+            return False
+    return disabled
+
+def testdata(arg):
+    """ test """
+    # Spelling exceptions
+    with open('.spelling', encoding='utf-8') as fdata:
+        spelling = fdata.readlines()
+
+    def abbreviations(word, **_):
+        """ abbreviations """
+        if word + "\n" in spelling:
+            return word
+
+    # Open the file and read the lines as a list
+    with open(arg.location, encoding='utf-8') as fdata:
+        lines = fdata.readlines()
+
+    # Loop through the list of lines and titlecase
+    # any line beginning with '#'.
+    return_value = 0
+    prev_line = lines[0] if lines else ""
+    echo_filename = False
+    disabled = mkdocs_available(arg.location)
+    for line in lines:
+        disabled = linestart(line, disabled, arg.test, prev_line)
+        if line.startswith('#') and not disabled and not mkdocs_available(arg.location):
+            title_line = titlecase(line[:line.find("]")], callback=abbreviations) + line[line.find("]"):]
+            if line != title_line:
+                if return_value == 0 and not echo_filename:
+                    print(f"{arg.location}")
+                    echo_filename = True
+                print(f"-{line}", end="")
+                print(f"+{title_line}", end="")
+                print()
+                return_value = 1
+        if (line.startswith('---') or line.startswith('===')) and not disabled:
+            title_prev_line = titlecase(prev_line[:prev_line.find("]")], callback=abbreviations) + prev_line[prev_line.find("]"):]
+            if prev_line != title_prev_line:
+                if return_value == 0 and not echo_filename:
+                    print(f"{arg.location}")
+                    echo_filename = True
+                print(f"-{prev_line}", end="")
+                print(f"+{title_prev_line}", end="")
+                print()
+                return_value = 1
+        if (mkdocs_available(arg.location) and not line.startswith('#') and not disabled):
+            title_line = titlecase(line[:line.find(":")], callback=abbreviations) + line[line.find(":"):]
+            if line != title_line:
+                if return_value == 0 and not echo_filename:
+                    print(f"{arg.location}")
+                    echo_filename = True
+                print(f"-{line}", end="")
+                print(f"+{title_line}", end="")
+                print()
+                return_value = 1
+        prev_line = line
+    return return_value
+
+def writedata(arg):
+    """ writedata """
+    # Spelling exceptions
+    with open('.spelling', encoding='utf-8') as fdata:
+        spelling = fdata.readlines()
+
+    def abbreviations(word, **_):
+        """ abbreviations """
+        if word + "\n" in spelling:
+            return word
+
+    # Open the file and read the lines as a list
+    with open(arg.location, encoding='utf-8') as fdata:
+        lines = fdata.readlines()
+
+    with open(arg.location, 'w', encoding='utf-8') as fdata:
+        prev_line = lines[0] if lines else ""
+        disabled = False
+        for line in lines:
+            disabled = linestart(line, disabled, arg.test)
+            if line.startswith('#') and not disabled:
+                line = titlecase(line[:line.find("]")], callback=abbreviations) + line[line.find("]"):]
+            if (line.startswith('---') or line.startswith('===')) and not disabled:
+                prev_line = titlecase(prev_line[:prev_line.find("]")], callback=abbreviations) + prev_line[prev_line.find("]"):]
+            fdata.write(prev_line)
+            prev_line = line
+        fdata.write(prev_line)
+
+def main():
+    """
+    main function
+    """
+
+    arg = arg_parse()
+
+    if arg.test:
+        sys.exit(testdata(arg))
+    else:
+        writedata(arg)
+
+if __name__ == "__main__":
+    main()

scripts/url_interni_test.py

+#!/usr/bin/python3
+
+"""
+Script to check internal links and section references in MDX files.
+"""
+
+import re
+from pathlib import Path
+
+def extract_links(content):
+    """
+    Extract all internal links from the file.
+
+    :param content: The content of the MDX file.
+    :return: A list of internal links.
+    """
+    link_pattern = re.compile(r'\[.*?\]\((?!http)(.*?)\)')  # Everything except http/https
+    return link_pattern.findall(content)
+
+def extract_headers(content):
+    """
+    Extract all H1-H6 headers for hash reference checks.
+
+    :param content: The content of the MDX file.
+    :return: A set of headers formatted as hash links.
+    """
+    header_pattern = re.compile(r'^(#+)\s*(.*)', re.MULTILINE)
+    return {f"#{match[1].lower().replace(' ', '-')}" for match in header_pattern.findall(content)}
+
+def check_internal_links(directory):
+    """
+    Check the existence of files and hash sections for internal links.
+
+    :param directory: The directory containing MDX files.
+    """
+    mdx_files = {f.relative_to(directory): f for f in Path(directory).rglob("*.mdx")}
+    file_headers = {}
+
+    # Extract headers from each file
+    for mdx_file, path in mdx_files.items():
+        with open(path, "r", encoding="utf-8") as file:
+            content = file.read()
+            file_headers[mdx_file] = extract_headers(content)
+
+    # Check internal links
+    for mdx_file, path in mdx_files.items():
+        with open(path, "r", encoding="utf-8") as file:
+            content = file.read()
+            links = extract_links(content)
+
+            for link in links:
+                parts = link.split("#")
+                file_part = parts[0] if parts[0] else mdx_file
+                hash_part = f"#{parts[1]}" if len(parts) > 1 else None
+
+                file_target = (Path(mdx_file).parent / file_part).resolve()
+
+                # Check if the file exists
+                if file_part and file_target not in mdx_files.values():
+                    print(f"❌ Broken file link in {mdx_file}: {link}")
+
+                # Check if the section exists
+                elif hash_part and hash_part not in file_headers.get(file_part, set()):
+                    print(f"⚠️ Broken section link in {mdx_file}: {link}")
+
+if __name__ == "__main__":
+    check_internal_links("content/docs")