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{% 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 %}
{% 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 %}
<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>
{% import "partials/language.html" as lang %}
<nav class="md-nav md-nav--secondary">
{% set toc_ = page.toc %}
{% if "\x3ch1 id=" in page.content %}
{% set toc_ = (toc_ | first).children %}
{% endif %}
{% if toc_ and (toc_ | first) %}
<label class="md-nav__title" for="toc">{{ lang.t('toc.title') }}</label>
<ul class="md-nav__list" data-md-scrollfix>
{% for toc_item in toc_ %}
{% include "partials/toc-item.html" %}
{% endfor %}
</ul>
{% endif %}
</nav>
site_name: IT4Innovations Documentation
theme_dir: 'material'
docs_dir: docs.it4i
site_favicon: img/favicon.ico
extra_css:
- src/css.css
# Repository
#repo_name: it4i-admins/docs.it4i
#repo_url: https://gitlab.it4i.cz/it4i-admins/docs.it4i
# Copyright
copyright: Copyright (c) 2017 IT4Innovations__VERSION__
pages:
- Home: index.md
# - History of Downtimes: downtimes_history.md
- General:
- Applying for Resources: get-started-with-it4innovations/applying-for-resources.md
- Obtaining Login Credentials: get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
- Certificates FAQ: get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
- Accessing the Clusters:
#- Introduction: get-started-with-it4innovations/accessing-the-clusters/introduction.md
- OpenSSH Keys (UN*X): get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
- PuTTY (Windows): get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
- X Window System: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
- VNC: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
- VPN Access: get-started-with-it4innovations/accessing-the-clusters/vpn-access.md
# - VPN-Connection-Fail-in-Win-8.1: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
- Salomon Cluster:
- Introduction: salomon/introduction.md
- Hardware Overview: salomon/hardware-overview.md
- Accessing the Cluster: salomon/shell-and-data-access.md
- Environment and Modules: salomon/environment-and-modules.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
- PRACE User Support: salomon/prace.md
- Anselm Cluster:
- Introduction: anselm-cluster-documentation/introduction.md
- Hardware Overview: anselm-cluster-documentation/hardware-overview.md
- Accessing the Cluster: anselm-cluster-documentation/shell-and-data-access.md
- Environment and Modules: anselm-cluster-documentation/environment-and-modules.md
- Resource Allocation and Job Execution:
- Resource Allocation Policy: anselm-cluster-documentation/resources-allocation-policy.md
- Job Priority: anselm-cluster-documentation/job-priority.md
- Job Submission and Execution: anselm-cluster-documentation/job-submission-and-execution.md
- Capacity Computing: anselm-cluster-documentation/capacity-computing.md
- Compute Nodes: anselm-cluster-documentation/compute-nodes.md
- Storage: anselm-cluster-documentation/storage.md
- Network: anselm-cluster-documentation/network.md
- Remote Visualization: anselm-cluster-documentation/remote-visualization.md
- PRACE User Support: anselm-cluster-documentation/prace.md
- 'Software':
- Lmod Environment: software/lmod.md
- Modules Matrix: modules-matrix.md
- Salomon Software:
- Available Modules: modules-salomon.md
- Available Modules on UV: modules-salomon-uv.md
- 'ANSYS':
- Introduction: salomon/software/ansys/ansys.md
- ANSYS CFX: salomon/software/ansys/ansys-cfx.md
- ANSYS Fluent: salomon/software/ansys/ansys-fluent.md
- ANSYS LS-DYNA: salomon/software/ansys/ansys-ls-dyna.md
- ANSYS MAPDL: salomon/software/ansys/ansys-mechanical-apdl.md
- Workbench: salomon/software/ansys/workbench.md
- Setting License Preferences: salomon/software/ansys/licensing.md
- Licensing and Available Versions: salomon/software/ansys/setting-license-preferences.md
- 'Bioinformatics':
- Bioinformatics Applications: software/bioinformatics.md
- 'Chemistry':
- Molpro: salomon/software/chemistry/molpro.md
- NWChem: salomon/software/chemistry/nwchem.md
- Phono3py: salomon/software/chemistry/phono3py.md
- ORCA: software/orca.md
- Compilers: salomon/software/compilers.md
- 'COMSOL':
- COMSOL: salomon/software/comsol/comsol-multiphysics.md
- Licensing and Available Versions: salomon/software/comsol/licensing-and-available-versions.md
- 'Debuggers':
- Introduction: salomon/software/debuggers/Introduction.md
- Aislinn: salomon/software/debuggers/aislinn.md
- Allinea Forge (DDT,MAP): salomon/software/debuggers/allinea-ddt.md
- Allinea Performance Reports: salomon/software/debuggers/allinea-performance-reports.md
- Intel VTune Amplifier XE: salomon/software/debuggers/intel-vtune-amplifier.md
- Total View: salomon/software/debuggers/total-view.md
- Valgrind: salomon/software/debuggers/valgrind.md
- Vampir: salomon/software/debuggers/vampir.md
- 'Intel Suite':
- Introduction: salomon/software/intel-suite/intel-parallel-studio-introduction.md
- Intel Advisor: salomon/software/intel-suite/intel-advisor.md
- Intel Compilers: salomon/software/intel-suite/intel-compilers.md
- Intel Debugger: salomon/software/intel-suite/intel-debugger.md
- Intel IPP: salomon/software/intel-suite/intel-integrated-performance-primitives.md
- Intel Inspector: salomon/software/intel-suite/intel-inspector.md
- Intel MKL: salomon/software/intel-suite/intel-mkl.md
- Intel TBB: salomon/software/intel-suite/intel-tbb.md
- Intel Trace Analyzer and Collector: salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
- Intel Xeon Phi: salomon/software/intel-xeon-phi.md
- Java: salomon/software/java.md
- 'MPI':
- Introduction: salomon/software/mpi/mpi.md
- MPI4Py (MPI for Python): salomon/software/mpi/mpi4py-mpi-for-python.md
- Running Open MPI: salomon/software/mpi/Running_OpenMPI.md
- 'Numerical Languages':
- Introduction: salomon/software/numerical-languages/introduction.md
- Matlab: salomon/software/numerical-languages/matlab.md
- Octave: salomon/software/numerical-languages/octave.md
- R: salomon/software/numerical-languages/r.md
- Operating System: salomon/software/operating-system.md
- Anselm Software:
- Available Modules: modules-anselm.md
- 'ANSYS':
- Introduction: anselm-cluster-documentation/software/ansys/ansys.md
- ANSYS CFX: anselm-cluster-documentation/software/ansys/ansys-cfx.md
- ANSYS Fluent: anselm-cluster-documentation/software/ansys/ansys-fluent.md
- ANSYS LS-DYNA: anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
- ANSYS MAPDL: anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
- LS-DYNA: anselm-cluster-documentation/software/ansys/ls-dyna.md
- 'Bioinformatics':
- Bioinformatics Applications: software/bioinformatics.md
- 'Debuggers':
- Allinea Forge (DDT,MAP): anselm-cluster-documentation/software/debuggers/allinea-ddt.md
- Allinea Performance Reports: anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
- CUBE: anselm-cluster-documentation/software/debuggers/cube.md
- Intel Performance Counter Monitor: anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
- Intel VTune Amplifier: anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
- PAPI: anselm-cluster-documentation/software/debuggers/papi.md
- Scalasca: anselm-cluster-documentation/software/debuggers/scalasca.md
- Score-P: anselm-cluster-documentation/software/debuggers/score-p.md
- Total View: anselm-cluster-documentation/software/debuggers/total-view.md
- VNC: anselm-cluster-documentation/software/debuggers/debuggers.md
- Valgrind: anselm-cluster-documentation/software/debuggers/valgrind.md
- Vampir: anselm-cluster-documentation/software/debuggers/vampir.md
- 'Chemistry':
- Molpro: anselm-cluster-documentation/software/chemistry/molpro.md
- NWChem: anselm-cluster-documentation/software/chemistry/nwchem.md
- ORCA: software/orca.md
- COMSOL: anselm-cluster-documentation/software/comsol-multiphysics.md
- Compilers: anselm-cluster-documentation/software/compilers.md
- GPI-2: anselm-cluster-documentation/software/gpi2.md
- 'Intel Suite':
- Introduction: anselm-cluster-documentation/software/intel-suite/introduction.md
- Intel Compilers: anselm-cluster-documentation/software/intel-suite/intel-compilers.md
- Intel Debugger: anselm-cluster-documentation/software/intel-suite/intel-debugger.md
- Intel IPP: anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
- Intel MKL: anselm-cluster-documentation/software/intel-suite/intel-mkl.md
- Intel TBB: anselm-cluster-documentation/software/intel-suite/intel-tbb.md
- Intel Xeon Phi: anselm-cluster-documentation/software/intel-xeon-phi.md
- ISV Licenses: anselm-cluster-documentation/software/isv_licenses.md
- Java: anselm-cluster-documentation/software/java.md
- 'MPI':
- Introduction: anselm-cluster-documentation/software/mpi/mpi.md
- MPI4Py (MPI for Python): anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.md
- Running Open MPI: anselm-cluster-documentation/software/mpi/Running_OpenMPI.md
- Running MPICH2: anselm-cluster-documentation/software/mpi/running-mpich2.md
- 'Numerical Languages':
- Introduction: anselm-cluster-documentation/software/numerical-languages/introduction.md
- Matlab 2013-2014: anselm-cluster-documentation/software/numerical-languages/matlab_1314.md
- Matlab: anselm-cluster-documentation/software/numerical-languages/matlab.md
- Octave: anselm-cluster-documentation/software/numerical-languages/octave.md
- R: anselm-cluster-documentation/software/numerical-languages/r.md
- 'Numerical Libraries':
- FFTW: anselm-cluster-documentation/software/numerical-libraries/fftw.md
- GSL: anselm-cluster-documentation/software/numerical-libraries/gsl.md
- HDF5: anselm-cluster-documentation/software/numerical-libraries/hdf5.md
- Intel Numerical Libraries: anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
- MAGMA for Intel Xeon Phi: anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
- PETSc: anselm-cluster-documentation/software/numerical-libraries/petsc.md
- Trilinos: anselm-cluster-documentation/software/numerical-libraries/trilinos.md
- NVIDIA CUDA: anselm-cluster-documentation/software/nvidia-cuda.md
- 'Omics Master':
- Diagnostic Component (TEAM): anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
- Priorization Component (BiERApp): anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
- Overview: anselm-cluster-documentation/software/omics-master/overview.md
- OpenFOAM: anselm-cluster-documentation/software/openfoam.md
- Operating System: anselm-cluster-documentation/software/operating-system.md
- ParaView: anselm-cluster-documentation/software/paraview.md
- Virtualization: anselm-cluster-documentation/software/kvirtualization.md
# - Modules Matrix: modules-matrix.md
- PBS Pro Documentation: pbspro.md
# - Testing:
# - Colors: colors.md
extra:
#logo: img/logo2.png
palette:
primary: 'grey'
accent: 'yellow'
font:
text: 'Ubuntu'
code: 'Ubuntu Mono'
i18n:
prev: 'Previous'
next: 'Next'
social:
- type: 'gitlab'
link: 'https://code.it4i.cz'
markdown_extensions:
- codehilite
- admonition
- toc:
permalink: '(H)'
google_analytics:
- 'UA-90498826-1'
- 'auto'
{
"scripts": {
"lint-md": "remark ."
},
"remarkConfig": {
"presets": ["lint-recommended"]
}
}
#!/bin/bash
VER=$(git log --pretty=format:'/ ver. %h / %ai' -n 1)
sed "s,__VERSION__, $VER," mkdocs.yml -i
#!/bin/bash
sed 's/\\u00a0/ /g' -i "$@"
sed 's,\\n\\n, ,g' -i "$@"
sed 's,\\n , ,g' -i "$@"
sed 's, \\n, ,g' -i "$@"
sed -e 's/^[ \t]*//' -i "$@"
#!/usr/bin/python
import csv
import collections
def get_data(filename):
'''function to read the data form the input csv file to use in the analysis'''
reader = [] # Just in case the file open fails
with open(filename, 'rb') as f:
reader = csv.reader(f,delimiter=',')
#returns all the data from the csv file in list form
#f.close() # May need to close the file when done
return list(reader) # only return the reader when you have finished.
your_list = []
your_list += get_data('modules-anselm.csv')
your_list += get_data('modules-salomon.csv')
your_list += get_data('modules-salomon-uv.csv')
#print your_list
#a=[["python/2.8.1",1],["python/2.9.1",2],["python/2.8.1",4],["python/3.0.1",4]]
counts = dict()
for i in your_list:
#print i[0]
#print int(i[1])
counts[i[0]]=counts.get(i[0], 0) + int(i[1])
#print sorted(counts.items())
c=[
"---",
"--A",
"-S-",
"-SA",
"U--",
"U-A",
"US-",
"USA",
]
print "| Module | Versions | Clusters |"
print "| ------ | -------- | -------- |"
software = dict()
versions = ''
clusters = ''
prev = ''
for m,i in sorted(counts.items()):
#print m
split = m.split('/')
#print split
if len(split) > 1:
a = split[0]
b = split[1]
if split[0] <> prev:
software[a] = {}
software[a][b] = '`' + c[i] + '`'
prev = a
#print software.items()
for m in sorted(software.items(), key=lambda i: i[0].lower()):
software = m[0]
versions = ''
clusters = ''
#print '</br>'.join(m[1].keys())
#print '</br>'.join(m[1].values())
print "| %s | %s | %s |" % (software, '</br>'.join(m[1].keys()), '</br>'.join(m[1].values()))
#!/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 -b color_${i/ /_}
git checkout color_${i/ /_}
#rm -fr "/home/hrb33/Dokumenty/dev/it4i/docs.it4i.git/.git/rebase-apply"
git pull --rebase origin colors
git pull --rebase
sed -ri "s/(primary: ').*'/\1$i'/" mkdocs.yml
#git cherry-pick bd8e358
git commit -am "Setting color to: $i"
git push --set-upstream origin color_${i/ /_}
git checkout colors
done
#!/bin/bash
curl -s https://code.it4i.cz/hrb33/modules-anselm/raw/master/anselm.csv -o modules-anselm.csv
curl -s https://code.it4i.cz/hrb33/modules-salomon/raw/master/salomon.csv -o modules-salomon.csv
curl -s https://code.it4i.cz/hrb33/modules-salomon/raw/master/salomon-uv.csv -o modules-salomon-uv.csv
#!/bin/bash
curl -s https://code.it4i.cz/hrb33/modules-anselm/raw/master/anselm.md -o docs.it4i/modules-anselm.md
curl -s https://code.it4i.cz/hrb33/modules-salomon/raw/master/salomon.md -o docs.it4i/modules-salomon.md
curl -s https://code.it4i.cz/hrb33/modules-salomon/raw/master/salomon-uv.md -o docs.it4i/modules-salomon-uv.md
#!/bin/bash
### DOWNLOAD AND CONVERT DOCUMENTATION
# autor: kru0052
# version: 1.00
###
if [ "$1" = "-w" ]; then
# download html pages
rm -rf docs-old.it4i.cz
wget -X portal_css,portal_javascripts,++resource++jquery-ui-themes,anselm-cluster-documentation/icon.jpg -R favicon.ico,pdf.png,logo.png,background.png,application.png,search_icon.png,png.png,sh.png,touch_icon.png,anselm-cluster-documentation/icon.jpg,*js,robots.txt,*xml,RSS,download_icon.png,@@*,anselm-cluster-documentation/icon.jpg.1 --mirror --convert-links --adjust-extension --page-requisites --no-parent https://docs-old.it4i.cz;
fi
if [ "$1" = "-c" ]; then
# erasing the previous transfer
if [ -d ./docs.it4i ]; then
rm -rf ./docs.it4i
fi
if [ -d ./info ]; then
rm -rf ./info;
fi
# counter for html and md files
counter=1
count=$(find . -name "*.html" -type f | wc -l)
find . -name "*.ht*" |
while read i;
do
# filtering html files
echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$i";
counter=$((counter+1))
printf "\t\tFiltering html files...\n";
HEAD=$(grep -n -m1 '<h1' "$i" |cut -f1 -d: | tr --delete '\n')
END=$(grep -n -m1 '<!-- <div tal:content=' "$i" |cut -f1 -d: | tr --delete '\n')
LAST=$(wc -l "$i" | cut -f1 -d' ')
DOWN=$((LAST-END+2))
sed '1,'"$((HEAD-1))"'d' "$i" | sed -n -e :a -e '1,'"$DOWN"'!{P;N;D;};N;ba' > "${i%.*}TMP.html"
# converted .html to .md
printf "\t\t.html => .md\n"
pandoc -f html -t markdown+pipe_tables-grid_tables "${i%.*}TMP.html" -o "${i%.*}.md";
rm "${i%.*}TMP.html"
done
# delete empty files
find -type f -size -10c |
while read i;
do
rm "$i";
echo "$(tput setaf 9)$i deleted";
done
fi
#!/usr/bin/python
import fnmatch
import os
import sys
try:
from titlecase import titlecase
except ImportError:
print("Please install titlecase")
def main(location):
# Spelling exceptions
with open('.spelling') as f:
spelling = f.readlines()
def abbreviations(word, **kwargs):
if word+"\n" in spelling:
return word
# Open the file and read the lines as a list
with open(location) as f:
lines = f.readlines()
with open(location, 'w') as f:
# Loop through the list of lines and titlecase
# any line beginning with '#'.
prev_line = lines.pop(0)
disabled = 0
for line in lines:
if line.startswith("``") and disabled == 0:
disabled = 1
else:
if line.startswith("``") and disabled == 1:
disabled = 0
if line.startswith('#') and disabled == 0:
line = titlecase(line[:(line.find("]"))], callback=abbreviations)+line[(line.find("]")):]
if line.startswith('---') or line.startswith('==='):
prev_line = titlecase(prev_line[:(prev_line.find("]"))], callback=abbreviations)+prev_line[(prev_line.find("]")):]
f.write(prev_line)
prev_line = line
f.write(prev_line)
if __name__ == "__main__":
try:
main(sys.argv[1])
except IndexError:
main('.')
#!/usr/bin/env python
from __future__ import print_function
import fnmatch
import os
import sys
try:
from titlecase import titlecase
except ImportError:
print("Please install titlecase")
def main(location):
# Spelling exceptions
with open('.spelling') as f:
spelling = f.readlines()
def abbreviations(word, **kwargs):
if word+"\n" in spelling:
return word
# Open the file and read the lines as a list
with open(location) as f:
lines = f.readlines()
# Loop through the list of lines and titlecase
# any line beginning with '#'.
return_value = 0
prev_line = lines.pop(0)
disabled = 0
print(`location`)
for line in lines:
if line.startswith("``") and disabled == 0:
disabled = 1
else:
if line.startswith("``") and disabled == 1:
disabled = 0
if line.startswith('#') and disabled == 0:
if line != titlecase(line[:(line.find("]"))], callback=abbreviations)+line[(line.find("]")):]:
print()
print("-"+line,end="")
print("+"+titlecase(line[:(line.find("]"))], callback=abbreviations)+line[(line.find("]")):],end="")
return_value = 1
if line.startswith('---') or line.startswith('==='):
if prev_line != titlecase(prev_line[:(prev_line.find("]"))], callback=abbreviations)+prev_line[(prev_line.find("]")):]:
print()
print("-"+prev_line,end="")
print("+"+titlecase(prev_line[:(prev_line.find("]"))], callback=abbreviations)+prev_line[(prev_line.find("]")):],end="")
return_value = 1
prev_line = line
if return_value == 0:
print("==Ok==")
exit(return_value)
if __name__ == "__main__":
try:
main(sys.argv[1])
except IndexError:
main('.')