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\ No newline at end of file

material/base.html

+{% import "partials/language.html" as lang %}
+<!DOCTYPE html>
+<html class="no-js">
+  <head>
+    {% block site_meta %}
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      {% if config.site_description %}
+        <meta name="description" content="{{ config.site_description }}">
+      {% endif %}
+      {% if page.canonical_url %}
+        <link rel="canonical" href="{{ page.canonical_url }}">
+      {% endif %}
+      {% if config.site_author %}
+        <meta name="author" content="{{ config.site_author }}">
+      {% endif %}
+      {% if config.site_favicon %}
+        <link rel="shortcut icon" href="{{ base_url }}/{{ config.site_favicon }}">
+      {% else %}
+        <link rel="shortcut icon" href="{{ base_url }}/assets/images/favicon.ico">
+      {% endif %}
+      <meta name="generator" content="mkdocs-{{ mkdocs_version }}, mkdocs-material-1.0.5">
+    {% endblock %}
+    {% block htmltitle %}
+      {% if page.title %}
+        <title>{{ page.title }} - {{ config.site_name }}</title>
+      {% elif config.site_description %}
+        <title>{{ config.site_name }} - {{ config.site_description }}</title>
+      {% else %}
+        <title>{{ config.site_name }}</title>
+      {% endif %}
+    {% endblock %}
+    {% block libs %}
+      <script src="{{ base_url }}/assets/javascripts/modernizr-56ade86843.js"></script>
+    {% endblock %}
+    {% block styles %}
+      <link rel="stylesheet" href="{{ base_url }}/assets/stylesheets/application-9c62e3c932.css">
+      {% if config.extra.palette %}
+        <link rel="stylesheet" href="{{ base_url }}/assets/stylesheets/application-02ce7adcc2.palette.css">
+      {% endif %}
+    {% endblock %}
+    {% block fonts %}
+      {% if config.extra.font != "none" %}
+        {% set text = config.extra.get("font", {}).text | default("Roboto") %}
+        {% set code = config.extra.get("font", {}).code
+                    | default("Roboto Mono") %}
+        {% set font = text + ':300,400,400i,700|' + code | replace(' ', '+') %}
+        <link rel="stylesheet" href="https://fonts.googleapis.com/css?family={{ font }}">
+        <style>body,input{font-family:"{{ text }}","Helvetica Neue",Helvetica,Arial,sans-serif}code,kbd,pre{font-family:"{{ code }}","Courier New",Courier,monospace}</style>
+      {% endif %}
+      <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
+    {% endblock %}
+    {% for path in extra_css %}
+      <link rel="stylesheet" href="{{ path }}">
+    {% endfor %}
+    {% block extrahead %}{% endblock %}
+  </head>
+  {% set palette = config.extra.get("palette", {}) %}
+  {% set primary = palette.primary | replace(" ", "-") | lower %}
+  {% set accent  = palette.accent  | replace(" ", "-") | lower %}
+  {% if primary or accent %}
+    <body data-md-color-primary="{{ primary }}" data-md-color-accent="{{ accent }}">
+  {% else %}
+    <body>
+  {% endif %}
+    <svg class="md-svg">
+      <defs>
+        {% set platform = config.extra.repo_icon or config.repo_url %}
+        {% if "github" in platform %}
+          {% include "assets/images/icons/github-1da075986e.svg" %}
+        {% elif "gitlab" in platform %}
+          {% include "assets/images/icons/gitlab-5ad3f9f9e5.svg" %}
+        {% elif "bitbucket" in platform %}
+          {% include "assets/images/icons/bitbucket-670608a71a.svg" %}
+        {% endif %}
+      </defs>
+    </svg>
+    <input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="drawer">
+    <input class="md-toggle" data-md-toggle="search" type="checkbox" id="search">
+    <label class="md-overlay" data-md-component="overlay" for="drawer"></label>
+    {% block header %}
+      {% include "partials/header.html" %}
+    {% endblock %}
+    <div class="md-container">
+      <main class="md-main">
+        <div class="md-main__inner md-grid" data-md-component="container">
+          {% block site_nav %}
+            {% if nav %}
+              <div class="md-sidebar md-sidebar--primary" data-md-component="navigation">
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    {% include "partials/nav.html" %}
+                  </div>
+                </div>
+              </div>
+            {% endif %}
+            {% if page.toc %}
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="toc">
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    {% include "partials/toc.html" %}
+                  </div>
+                </div>
+              </div>
+            {% endif %}
+          {% endblock %}
+          <div class="md-content">
+            <article class="md-content__inner md-typeset">
+               {% if config.edit_uri %}
+                 <a href="{{ page.edit_url }}" title="{{ lang.t('edit.link.title') }}" class="md-icon md-content__edit">edit</a>
+               {% endif %}
+              {% block content %}
+                {% if not "\x3ch1" in page.content %}
+                  <h1>{{ page.title | default(config.site_name, true)}}</h1>
+                {% endif %}
+                {{ page.content }}
+              {% endblock %}
+            </article>
+          </div>
+        </div>
+      </main>
+      {% block footer %}
+        {% include "partials/footer.html" %}
+      {% endblock %}
+    </div>
+    {% block scripts %}
+      <script src="{{ base_url }}/assets/javascripts/application-f7ac33b6fb.js"></script>
+      <script>app.initialize({url:{base:"{{ base_url }}"}})</script>
+      {% for path in extra_javascript %}
+        <script src="{{ path }}"></script>
+      {% endfor %}
+    {% endblock %}
+    {% block analytics %}
+      {% if config.google_analytics %}
+      <script>!function(e,t,a,n,o,c,i){e.GoogleAnalyticsObject=o,e[o]=e[o]||function(){(e[o].q=e[o].q||[]).push(arguments)},e[o].l=1*new Date,c=t.createElement(a),i=t.getElementsByTagName(a)[0],c.async=1,c.src=n,i.parentNode.insertBefore(c,i)}(window,document,"script","https://www.google-analytics.com/analytics.js","ga"),ga("create","{{ config.google_analytics[0] }}","{{ config.google_analytics[1] }}"),ga("set","anonymizeIp",!0),ga("send","pageview");var links=document.getElementsByTagName("a");Array.prototype.map.call(links,function(e){e.host!=document.location.host&&e.addEventListener("click",function(){var t=e.getAttribute("data-md-action")||"follow";ga("send","event","outbound",t,e.href)})});var query=document.forms.search.query;query.addEventListener("blur",function(){if(this.value){var e=document.location.pathname;ga("send","pageview",e+"?q="+this.value)}})</script>
+      {% endif %}
+    {% endblock %}
+  </body>
+</html>

material/main.html

+{% extends "base.html" %}

material/partials/footer.html

+{% import "partials/language.html" as lang %}
+<footer class="md-footer">
+  {% if page.previous_page or page.next_page %}
+    <div class="md-footer-nav">
+      <nav class="md-footer-nav__inner md-grid">
+        {% if page.previous_page %}
+          <a href="{{ page.previous_page.url }}" title="{{ page.previous_page.title }}" class="md-flex md-footer-nav__link md-footer-nav__link--prev" rel="prev">
+            <div class="md-flex__cell md-flex__cell--shrink">
+              <i class="md-icon md-icon--arrow-back md-footer-nav__button"></i>
+            </div>
+            <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title">
+              <span class="md-flex__ellipsis">
+                <span class="md-footer-nav__direction">
+                  {{ lang.t('footer.previous') }}
+                </span>
+                {{ page.previous_page.title }}
+              </span>
+            </div>
+          </a>
+        {% endif %}
+        {% if page.next_page %}
+          <a href="{{ page.next_page.url }}" title="{{ page.next_page.title }}" class="md-flex md-footer-nav__link md-footer-nav__link--next" rel="next">
+            <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title">
+              <span class="md-flex__ellipsis">
+                <span class="md-footer-nav__direction">
+                  {{ lang.t('footer.next') }}
+                </span>
+                {{ page.next_page.title }}
+              </span>
+            </div>
+            <div class="md-flex__cell md-flex__cell--shrink">
+              <i class="md-icon md-icon--arrow-forward md-footer-nav__button"></i>
+            </div>
+          </a>
+        {% endif %}
+      </nav>
+    </div>
+  {% endif %}
+  <div class="md-footer-meta md-typeset">
+    <div class="md-footer-meta__inner md-grid">
+      <div class="md-footer-copyright">
+        {% if config.copyright %}
+          <div class="md-footer-copyright__highlight">
+            {{ config.copyright }}
+          </div>
+        {% endif %}
+        powered by
+        <a href="http://www.mkdocs.org" title="MkDocs">MkDocs</a>
+        and
+        <a href="http://squidfunk.github.io/mkdocs-material/" title="Material for MkDocs">
+          Material for MkDocs</a>
+      </div>
+      {% block social %}
+        {% include "partials/social.html" %}
+      {% endblock %}
+    </div>
+  </div>
+</footer>

material/partials/header.html

+<header class="md-header">
+  <nav class="md-header-nav md-grid">
+    <div class="md-flex">
+      <div class="md-flex__cell md-flex__cell--shrink">
+        <a href="{{ nav.homepage.url }}" title="{{ config.site_name }}" class="{% if config.extra.logo %} md-logo {% else %} md-icon md-icon--home {% endif %} md-header-nav__button">
+          {% if config.extra.logo %}
+            <img src="{{ base_url }}/{{ config.extra.logo }}" width="24" height="24">
+          {% endif %}
+        </a>
+      </div>
+      <div class="md-flex__cell md-flex__cell--shrink">
+        <label class="md-icon md-icon--menu md-header-nav__button" for="drawer"></label>
+      </div>
+      <div class="md-flex__cell md-flex__cell--stretch">
+        <span class="md-flex__ellipsis md-header-nav__title">
+          {% block site_name %}
+            {% if page %}
+              {% for parent in page.ancestors %}
+                <span class="md-header-nav__parent">
+                  {{ parent.title }}
+                </span>
+              {% endfor %}
+            {% endif %}
+            {{ page.title | default(config.site_name, true) }}
+          {% endblock %}
+        </span>
+      </div>
+      <div class="md-flex__cell md-flex__cell--shrink">
+        {% block search_box %}
+          <label class="md-icon md-icon--search md-header-nav__button" for="search"></label>
+          {% include "partials/search.html" %}
+        {% endblock %}
+      </div>
+      <div class="md-flex__cell md-flex__cell--shrink">
+          <div class="md-header-nav__source">
+            {% if config.repo_url %}
+              {% include "partials/source.html" %}
+            {% endif %}
+          </div>
+      </div>
+    </div>
+  </nav>
+</header>

material/partials/language.html

+{% macro t(key) %}{{ {
+  "edit.link.title": "Edit this page",
+  "footer.previous": "Previous",
+  "footer.next": "Next",
+  "search.placeholder": "Search",
+  "source.link.title": "Go to repository",
+  "toc.title": "On this page"
+}[key] }}{% endmacro %}

material/partials/nav-item.html

+{% if nav_item.children %}
+  <li class="md-nav__item md-nav__item--nested">
+    {% if nav_item.active %}
+      <input class="md-toggle md-nav__toggle" data-md-toggle="{{ path }}" type="checkbox" id="{{ path }}" checked>
+    {% else %}
+      <input class="md-toggle md-nav__toggle" data-md-toggle="{{ path }}" type="checkbox" id="{{ path }}">
+    {% endif %}
+    <label class="md-nav__link" for="{{ path }}">
+      {{ nav_item.title }}
+    </label>
+    <nav class="md-nav" data-md-component="collapsible">
+      <label class="md-nav__title" for="{{ path }}">
+        {{ nav_item.title}}
+      </label>
+      <ul class="md-nav__list" data-md-scrollfix>
+        {% set base = path %}
+        {% for nav_item in nav_item.children %}
+          {% set path = base + "-" + loop.index | string %}
+          {% include "partials/nav-item.html"  %}
+        {% endfor %}
+      </ul>
+    </nav>
+  </li>
+{% elif nav_item == page %}
+  <li class="md-nav__item">
+    {% set toc_ = page.toc %}
+    <input class="md-toggle md-nav__toggle" data-md-toggle="toc" type="checkbox" id="toc">
+    {% if toc_ | first is defined %}
+      {% set toc_ = (toc_ | first).children %}
+    {% endif %}
+    {% if toc_ | first is defined %}
+      <label class="md-nav__link md-nav__link--active" for="toc">
+        {{ nav_item.title }}
+      </label>
+    {% endif %}
+    <a href="{{ nav_item.url }}" title="{{ nav_item.title }}" class="md-nav__link md-nav__link--active">
+      {{ nav_item.title }}
+    </a>
+    {% if toc_ | first is defined %}
+      {% include "partials/toc.html" %}
+    {% endif %}
+  </li>
+{% else %}
+  <li class="md-nav__item">
+    {% if nav_item.active %}
+      <a href="{{ nav_item.url }}" title="{{ nav_item.title }}" class="md-nav__link md-nav__link--active">
+        {{ nav_item.title }}
+      </a>
+    {% else %}
+      <a href="{{ nav_item.url }}" title="{{ nav_item.title }}" class="md-nav__link">
+        {{ nav_item.title }}
+      </a>
+    {% endif %}
+  </li>
+{% endif %}

material/partials/nav.html

+<nav class="md-nav md-nav--primary">
+  <label class="md-nav__title md-nav__title--site" for="drawer">
+    <i class="{% if config.extra.logo %} md-logo {% else %} md-icon md-icon--home {% endif %} md-nav__button">
+      {% if config.extra.logo %}
+        <img src="{{ base_url }}/{{ config.extra.logo }}">
+      {% endif %}
+    </i>
+    {{ config.site_name }}
+  </label>
+  {% if config.repo_url %}
+    <div class="md-nav__source">
+      {% include "partials/source.html" %}
+    </div>
+  {% endif %}
+  <ul class="md-nav__list" data-md-scrollfix>
+    {% for nav_item in nav %}
+      {% set path = "nav-" + loop.index | string %}
+      {% include "partials/nav-item.html" %}
+    {% endfor %}
+  </ul>
+</nav>

material/partials/search.html

+{% import "partials/language.html" as lang %}
+<div class="md-search" data-md-component="search">
+  <div class="md-search__overlay"></div>
+  <div class="md-search__inner">
+    <form class="md-search__form" name="search">
+      <input type="text" class="md-search__input" name="query" placeholder="{{ lang.t('search.placeholder') }}" accesskey="s" autocapitalize="off" autocorrect="off" autocomplete="off" spellcheck="false">
+      <label class="md-icon md-search__icon" for="search"></label>
+    </form>
+    <div class="md-search__output">
+      <div class="md-search__scrollwrap" data-md-scrollfix>
+        <div class="md-search-result" data-md-component="result"></div>
+      </div>
+    </div>
+  </div>
+</div>

material/partials/social.html

+{% if config.extra.social %}
+  <div class="md-footer-social">
+    {% set path = "ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" %}
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/{{ path }}">
+    {% for social in config.extra.social %}
+      <a href="{{ social.link }}" class="md-footer-social__link fa fa-{{ social.type }}"></a>
+    {% endfor %}
+  </div>
+{% endif %}

material/partials/source.html

+{% import "partials/language.html" as lang %}
+{% set platform = config.extra.repo_icon or config.repo_url %}
+{% if "github" in platform %}
+  {% set repo_type = "github" %}
+{% elif "gitlab" in platform %}
+  {% set repo_type = "gitlab" %}
+{% elif "bitbucket" in platform %}
+  {% set repo_type = "bitbucket" %}
+{% else %}
+  {% set repo_type = "" %}
+{% endif %}
+{% block repo %}
+  <a href="{{ config.repo_url }}" title="{{ lang.t('source.link.title') }}" class="md-source" data-md-source="{{ repo_type }}">
+    {% if repo_type %}
+      <div class="md-source__icon">
+        <svg viewBox="0 0 24 24" width="24" height="24">
+          <use xlink:href="#{{ repo_type }}" width="24" height="24"></use>
+        </svg>
+      </div>
+    {% endif %}
+    <div class="md-source__repository">
+      {{ config.repo_name }}
+    </div>
+  </a>
+{% endblock %}

material/partials/toc-item.html

+<li class="md-nav__item">
+  <a href="{{ toc_item.url }}" title="{{ toc_item.title }}" class="md-nav__link">
+    {{ toc_item.title }}
+  </a>
+  {% if toc_item.children %}
+    <nav class="md-nav">
+      <ul class="md-nav__list">
+        {% for toc_item in toc_item.children %}
+          {% include "partials/toc-item.html" %}
+        {% endfor %}
+      </ul>
+    </nav>
+  {% endif %}
+</li>

material/partials/toc.html

+{% import "partials/language.html" as lang %}
+<nav class="md-nav md-nav--secondary">
+  {% set toc_ = page.toc %}
+  {% if toc_ | first is defined and "\x3ch1 id=" in page.content %}
+    {% set toc_ = (toc_ | first).children %}
+  {% endif %}
+  {% set it4i_link = config.repo_url + '/edit/master/docs.it4i/index.md' %}
+  {% set it4i_page = '/index.md' %}
+  {% set it4i_url = 'https://docs.it4i.cz' %}
+  {% if toc_ | first is defined %}
+  <label class="md-nav__title" for="toc">{{ lang.t('toc.title') }}</label>
+  <ul class="md-nav__list" data-md-scrollfix>
+    <li class="md-nav__item">
+      <a href="{{ it4i_link }}" title="Edit This Page" class="md-nav__link_it4i" target="_blank">
+	<i class="md-icon md-icon--edit">
+	</i>
+	Edit This Page
+      </a>
+    </li>
+    <li class="md-nav__item">
+      <a href="https://code.it4i.cz/sccs/docs.it4i.cz/issues/new?issue%5Bdescription%5D=Requested change in page [{{ it4i_page }}]({{ it4i_url }}) /cc @hrb33 @kru0052" title="Request Change" class="md-nav__link_it4i" target="_blank">
+	<i class="md-icon md-icon--check">
+	</i>
+	Request Change
+      </a>
+    </li>
+    <li class="md-nav__item">
+      <a href="https://support.it4i.cz/rt" title="Get Support" class="md-nav__link_it4i" target="_blank">
+	<i class="md-icon md-icon--help">
+	</i>
+	Get Support
+      </a>
+    </li>
+    {% for toc_item in toc_ %}
+    {% include "partials/toc-item.html" %}
+    {% endfor %}
+  </ul>
+  {% endif %}
+</nav>

mkdocs.yml

+site_name: IT4Innovations Documentation
+docs_dir: docs.it4i
+site_url: https://docs.it4i.cz/
+extra_css:
+   - src/css.css
+   - https://unpkg.com/mermaid@7.0.5/dist/mermaid.css
+
+extra_javascript:
+   - https://unpkg.com/mermaid@7.0.5/dist/mermaid.min.js
+
+# Repository
+#repo_name: sccs/docs.it4i.cz
+#repo_url: https://code.it4i.cz/sccs/docs.it4i.cz
+
+# Copyright
+copyright: Copyright (c) 2013-2018 IT4Innovations / ver. 03ecba66 / 2018-10-16 10:21:23 +0200
+
+theme:
+  name: material
+  custom_dir: material-new
+
+  # 404 page
+  static_templates:
+    - 404.html
+
+  feature:
+    tabs: true
+
+  # Don't include MkDocs' JavaScript
+  include_search_page: false
+  search_index_only: true
+
+  font:
+    text: 'Ubuntu'
+    code: 'Ubuntu Mono'
+  palette:
+    primary: 'grey'
+    accent: 'yellow'
+
+  favicon: img/favicon.ico
+
+nav:
+  - General:
+    - Home: index.md
+    - Obtaining Login Credentials: general/obtaining-login-credentials/obtaining-login-credentials.md
+    - Applying for Resources: general/applying-for-resources.md
+    - Certificates FAQ: general/obtaining-login-credentials/certificates-faq.md
+    - Resource Allocation and Job Execution: general/resource_allocation_and_job_execution.md
+    - Connect to the Clusters:
+      - 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
+      - X Window System: general/accessing-the-clusters/graphical-user-interface/x-window-system.md
+      - VNC: general/accessing-the-clusters/graphical-user-interface/vnc.md
+      - VPN Access: general/accessing-the-clusters/vpn-access.md
+    - PRACE User Support: prace.md
+    - API Documentation: apiv1.md
+  - Salomon:
+    - Introduction: salomon/introduction.md
+    - Hardware Overview: salomon/hardware-overview.md
+    - Accessing the Cluster: salomon/shell-and-data-access.md
+    - Resource Allocation and Job Execution:
+      - Resources Allocation Policy: salomon/resources-allocation-policy.md
+      - Job Scheduling: salomon/job-priority.md
+      - Job Submission and Execution: salomon/job-submission-and-execution.md
+      - Capacity Computing: salomon/capacity-computing.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
+  - Anselm:
+    - Introduction: anselm/introduction.md
+    - Hardware Overview: anselm/hardware-overview.md
+    - Accessing the Cluster: anselm/shell-and-data-access.md
+    - Resource Allocation and Job Execution:
+      - Resource Allocation Policy: anselm/resources-allocation-policy.md
+      - Job Priority: anselm/job-priority.md
+      - Job Submission and Execution: anselm/job-submission-and-execution.md
+      - Capacity Computing: anselm/capacity-computing.md
+    - Compute Nodes: anselm/compute-nodes.md
+    - Storage: anselm/storage.md
+    - Network: anselm/network.md
+  - Software:
+    - Environment and Modules: environment-and-modules.md
+    - Modules:
+      - Lmod Environment: software/modules/lmod.md
+      - Intel Xeon Phi Environment: software/mic/mic_environment.md
+      - Modules Matrix: modules-matrix.md
+      - Job Features: job-features.md
+      - Available Salomon Modules: modules-salomon.md
+      - Available Salomon Modules on UV: modules-salomon-uv.md
+      - Available Salomon Modules on PHI Cards: modules-salomon-phi.md
+      - Available Anselm Modules: modules-anselm.md
+    - ISV Licenses: software/isv_licenses.md
+    - Bioinformatics:
+      - Bioinformatics Applications: software/bio/bioinformatics.md
+      - Omics Master:
+        - Overview: software/bio/omics-master/overview.md
+        - Diagnostic Component (TEAM): software/bio/omics-master/diagnostic-component-team.md
+        - Priorization Component (BiERApp): software/bio/omics-master/priorization-component-bierapp.md
+    - CAE:
+      - COMSOL:
+        - COMSOL: software/cae/comsol/comsol-multiphysics.md
+        - Licensing and Available Versions: software/cae/comsol/licensing-and-available-versions.md
+    - Chemistry:
+      - Molpro: software/chemistry/molpro.md
+      - Orca: software/chemistry/orca.md
+      - NWChem: software/chemistry/nwchem.md
+      - Phono3py: software/chemistry/phono3py.md
+    - Compilers: software/compilers.md
+    - Debuggers:
+      - Introduction: software/debuggers/Introduction.md
+      - Aislinn: software/debuggers/aislinn.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 Performance Counter Monitor: software/debuggers/intel-performance-counter-monitor.md
+      - Intel VTune Amplifier XE: software/debuggers/intel-vtune-amplifier.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
+    - GPU:
+      - NVIDIA CUDA: anselm/software/nvidia-cuda.md
+    - Intel:
+      - 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 Debugger: software/intel/intel-suite/intel-debugger.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
+      - Intel Xeon Phi:
+        - Intel Xeon Phi Salomon: software/intel/intel-xeon-phi-salomon.md
+        - Intel Xeon Phi Anselm: software/intel/intel-xeon-phi-anselm.md
+    - Machine Learning:
+      - Introduction: software/machine-learning/introduction.md
+      - TensorFlow: software/machine-learning/tensorflow.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
+      - Running Open MPI: software/mpi/Running_OpenMPI.md
+      - Running MPICH2: software/mpi/running-mpich2.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
+      - Matlab 2013-2014: software/numerical-languages/matlab_1314.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
+      - MAGMA for Intel Xeon Phi: software/numerical-libraries/magma-for-intel-xeon-phi.md
+      - PETSc: software/numerical-libraries/petsc.md
+      - Trilinos: software/numerical-libraries/trilinos.md
+    - Languages:
+      - Java: software/lang/java.md
+      - C#: software/lang/csc.md
+      - Python: software/lang/python.md
+      - Python-Conda: software/lang/conda.md
+    - Phys:
+      - LMGC90: salomon/software/phys/LMGC90.md
+      - PragTic: salomon/software/phys/PragTic.md
+    - Tools:
+      - 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
+        - LS-DYNA: software/tools/ansys/ls-dyna.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
+      - Singularity Container:
+        - Singularity: software/tools/singularity.md
+        - Singularity on IT4Innovations: software/tools/singularity-it4i.md
+      - Spack: software/tools/spack.md
+      - Virtualization: software/tools/virtualization.md
+    - Visualisation:
+      - GPI-2: software/viz/gpi2.md
+      - OpenFOAM: software/viz/openfoam.md
+      - ParaView: software/viz/paraview.md
+    - PBS Pro Documentation: pbspro.md
+
+extra:
+  repo_icon: gitlab
+  disqus: 'test-3whnesz3gq'
+  social:
+    - type: 'gitlab'
+      link: 'https://code.it4i.cz/sccs/docs.it4i.cz'
+    - type: globe
+      link: https://www.it4i.cz
+
+markdown_extensions:
+  - codehilite
+  - markdown.extensions.admonition:
+  - pymdownx.arithmatex:
+  - markdown.extensions.toc:
+      permalink: true
+      slugify: !!python/name:pymdownx.slugs.uslugify
+  - pymdownx.snippets:
+      base_path: docs.it4i/snippets
+  - pymdownx.superfences
+
+google_analytics:
+  - 'UA-90498826-1'
+  - 'auto'

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==7.0
+futures==3.2.0
+Jinja2==2.10
+livereload==2.5.2
+Markdown==3.0.1
+MarkupSafe==1.0
+mkdocs==1.0.4
+mkdocs-material==3.0.5
+Pygments==2.2.0
+pymdown-extensions==6.0
+PyYAML==3.13
+singledispatch==3.4.0.3
+six==1.11.0
+tornado==5.1.1

scripts/add_version.sh

+#!/bin/bash
+VER=$(git log --pretty=format:'/ ver. %h / %ai' -n 1)
+sed "s,__VERSION__, $VER," 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 "$@"