Merge branch 'clean_up' into 'master'

Clean up See merge request !13

Merge branch 'clean_up' into 'master'
565a8670 · Lukáš Krupčík · b72af5d0 · f8990216 · 565a8670 · 565a8670
Commit 565a8670 authored 8 years ago by Lukáš Krupčík
--- a/docs.it4i/index.md
+++ b/docs.it4i/index.md
@@ -3,19 +3,12 @@ Documentation

 Welcome to IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates supercomputers [Salomon](/salomon/introduction/) and [Anselm](/anselm-cluster-documentation/introduction/). The supercomputers are [available](get-started-with-it4innovations/applying-for-resources/) to academic community within the Czech Republic and Europe and industrial community worldwide. The purpose of these pages is to provide a comprehensive documentation on hardware, software and usage of the computers.

-!!! warning "Reminder"
-    [History of Downtimes](downtimes_history/)
-
 How to read the documentation
 ------------------------------

-1. Read the list in the left column. Select the subject of interest. Alternatively, use the Search box in the upper right corner.
-2. Read the CONTENTS in the upper right corner.
-3. Scan for all the yellow bulb call-outs on the page.
-4. Read the details if still more information is needed. **Look for examples** illustrating the concepts.
-
-!!! Note "Note"
-	The call-out.   Focus on the call-outs before reading full details.
+1. Read the list in the left column. Select the subject of interest. Alternatively, use the Search in the upper right corner.
+1. Scan for all the notes and reminders on the page.
+1. Read the details if still more information is needed. **Look for examples** illustrating the concepts.

 Getting Help and Support
 ------------------------
@@ -29,7 +22,7 @@ Required Proficiency
 !!! Note "Note"
 	You need basic proficiency in Linux environment.

-In order to use the system for your calculations, you need basic proficiency in Linux environment. To gain the proficiency, we recommend you reading the [introduction to Linux](http://www.tldp.org/LDP/intro-linux/html/) operating system environment and installing a Linux distribution on your personal computer. A good choice might be the [Fedora](http://fedoraproject.org/) distribution, as it is similar to systems on the clusters at IT4Innovations. It's easy to install and use. In fact, any distribution would do.
+In order to use the system for your calculations, you need basic proficiency in Linux environment. To gain the proficiency, we recommend you reading the [introduction to Linux](http://www.tldp.org/LDP/intro-linux/html/) operating system environment and installing a Linux distribution on your personal computer. A good choice might be the [CentOS](http://www.centos.org/) distribution, as it is similar to systems on the clusters at IT4Innovations. It's easy to install and use. In fact, any distribution would do.

 !!! Note "Note"
 	Learn how to parallelize your code!

--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -7,26 +7,23 @@ copyright: Copyright (c) 2016 IT4Innovations

 pages:
  - Home: index.md
-  - History of Downtimes: downtimes_history.md
-  - Get Started with IT4Innovations:
+#  - History of Downtimes: downtimes_history.md
+  - General:
    - Applying for Resources: get-started-with-it4innovations/applying-for-resources.md
-  - Get Started with IT4Innovations-Obtaining Login Credentials:
    - 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
-  - Get Started with IT4Innovations-Accessing the Clusters:
    - Accessing the Clusters: get-started-with-it4innovations/accessing-the-clusters/introduction.md
-  - Get Started with IT4Innovations-Accessing the Clusters-Shell access and data transfer:
-    - 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
+#    - 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
    - SSH keys: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
    - Pageant SSH agent: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
    - PuTTY key generator: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
    - PuTTY: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
-  - Get Started with IT4Innovations-Accessing the Clusters-Graphical User Interface:
+  - GUI Access:
    - Introduction: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.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
    - Cygwin and x11 Forwarding: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
-  - Anselm Cluster Documentation:
+  - Anselm Cluster:
    - Introduction: anselm-cluster-documentation/introduction.md
    - Hardware Overview: anselm-cluster-documentation/hardware-overview.md
    - Environment and Modules: anselm-cluster-documentation/environment-and-modules.md
@@ -34,20 +31,20 @@ pages:
    - Remote visualization: anselm-cluster-documentation/remote-visualization.md
    - Network: anselm-cluster-documentation/network.md
    - PRACE User Support: anselm-cluster-documentation/prace.md
-  - Anselm Cluster Documentation-Accessing the Cluster:
+  - Anselm Cluster Access:
    - Outgoing Connections: anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
    - VPN Access: anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
    - Shell and Data Access: anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.md
-  - Anselm Cluster Documentation-Resource Allocation and Job Execution:
+  - Anselm Cluster Resource Allocation and Job Execution:
    - Introduction: anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
    - Job Priority: anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
    - Job Submission and Execution: anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
    - Capacity computing: anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
    - Resource allocation policy: anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
-  - Anselm Cluster Documentation-Storage:
+  - Anselm Cluster Storage:
    - Cesnet Data Storage: anselm-cluster-documentation/storage/cesnet-data-storage.md
    - Storage: anselm-cluster-documentation/storage/storage.md
-  - Anselm Cluster Documentation-Software:
+  - Anselm Cluster Software:
    - COMSOL: anselm-cluster-documentation/software/comsol-multiphysics.md
    - ParaView: anselm-cluster-documentation/software/paraview.md
    - Compilers: anselm-cluster-documentation/software/compilers.md
@@ -59,19 +56,19 @@ pages:
    - Virtualization: anselm-cluster-documentation/software/kvirtualization.md
    - Java: anselm-cluster-documentation/software/java.md
    - Operating System: anselm-cluster-documentation/software/operating-system.md
-  - Anselm Cluster Documentation-Software-Intel Suite:
+  - Anselm Cluster Intel Suite:
    - Introduction: anselm-cluster-documentation/software/intel-suite/introduction.md
    - Intel MKL: anselm-cluster-documentation/software/intel-suite/intel-mkl.md
    - Intel Compilers: anselm-cluster-documentation/software/intel-suite/intel-compilers.md
    - Intel IPP: anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
    - Intel TBB: anselm-cluster-documentation/software/intel-suite/intel-tbb.md
    - Intel Debugger: anselm-cluster-documentation/software/intel-suite/intel-debugger.md
-  - Anselm Cluster Documentation-Software-MPI:
+  - Anselm Cluster MPI:
    - Introduction: anselm-cluster-documentation/software/mpi/mpi.md
    - MPI4Py (MPI for Python): anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.md
    - Running OpenMPI: anselm-cluster-documentation/software/mpi/Running_OpenMPI.md
    - Running MPICH2: anselm-cluster-documentation/software/mpi/running-mpich2.md
-  - Anselm Cluster Documentation-Software-Numerical Libraries:
+  - Anselm Cluster Numerical Libraries:
    - Intel numerical libraries: anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
    - PETSc: anselm-cluster-documentation/software/numerical-libraries/petsc.md
    - Trilinos: anselm-cluster-documentation/software/numerical-libraries/trilinos.md
@@ -79,11 +76,11 @@ pages:
    - GSL: anselm-cluster-documentation/software/numerical-libraries/gsl.md
    - MAGMA for Intel Xeon Phi: anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
    - HDF5: anselm-cluster-documentation/software/numerical-libraries/hdf5.md
-  - Anselm Cluster Documentation-Software-Omics Master:
+  - Anselm Cluster 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
-  - Anselm Cluster Documentation-Software-Debuggers:
+  - Anselm Cluster Debuggers:
    - Valgrind: anselm-cluster-documentation/software/debuggers/valgrind.md
    - PAPI: anselm-cluster-documentation/software/debuggers/papi.md
    - Allinea Forge (DDT,MAP): anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -96,16 +93,16 @@ pages:
    - Intel Performance Counter Monitor: anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
    - Allinea Performance Reports: anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
    - Vampir: anselm-cluster-documentation/software/debuggers/vampir.md
-  - Anselm Cluster Documentation-Software-Numerical Languages:
+  - Anselm Cluster Numerical Languages:
    - Introduction: anselm-cluster-documentation/software/numerical-languages/introduction.md
    - R: anselm-cluster-documentation/software/numerical-languages/r.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
-  - Anselm Cluster Documentation-Software-Chemistry:
+  - Anselm Cluster Chemistry:
    - Molpro: anselm-cluster-documentation/software/chemistry/molpro.md
    - NWChem: anselm-cluster-documentation/software/chemistry/nwchem.md
-  - Anselm Cluster Documentation-Software-Ansys:
+  - Anselm Cluster Ansys:
    - Introduction: anselm-cluster-documentation/software/ansys/ansys.md
    - ANSYS CFX: anselm-cluster-documentation/software/ansys/ansys-cfx.md
    - ANSYS LS-DYNA: anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
@@ -119,29 +116,29 @@ pages:
    - Hardware Overview: salomon/hardware-overview.md
    - Compute Nodes: salomon/compute-nodes.md
    - List of modules: salomon/list_of_modules.md
-  - Salomon Cluster Documentation-Accessing the Cluster:
+  - Salomon Cluster Access:
    - Outgoing connections: salomon/accessing-the-cluster/outgoing-connections.md
    - VPN Access: salomon/accessing-the-cluster/vpn-access.md
    - Accessing the Cluster: salomon/accessing-the-cluster/accessing-the-cluster.md
-  - Salomon Cluster Documentation-Network:
+  - Salomon Cluster Network:
    - Introduction: salomon/network/network.md
    - IB single-plane topology: salomon/network/ib-single-plane-topology.md
    - 7D Enhanced Hypercube: salomon/network/7d-enhanced-hypercube.md
-  - Salomon Cluster Documentation-Resource Allocation and Job Execution:
+  - Salomon Cluster Resource Allocation and Job Execution:
    - Introduction: salomon/resource-allocation-and-job-execution/introduction.md
    - Job scheduling: salomon/resource-allocation-and-job-execution/job-priority.md
    - Job submission and execution: salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
    - Capacity computing: salomon/resource-allocation-and-job-execution/capacity-computing.md
    - Resources Allocation Policy: salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
-  - Salomon Cluster Documentation-Storage:
+  - Salomon Cluster Storage:
    - CESNET Data Storage: salomon/storage/cesnet-data-storage.md
    - Storage: salomon/storage/storage.md
-  - Salomon Cluster Documentation-Software:
+  - Salomon Cluster Software:
    - Compilers: salomon/software/compilers.md
    - Intel Xeon Phi: salomon/software/intel-xeon-phi.md
    - Java: salomon/software/java.md
    - Operating System: salomon/software/operating-system.md
-  - Salomon Cluster Documentation-Software-Intel Suite:
+  - Salomon Cluster Intel Suite:
    - Introduction: salomon/software/intel-suite/intel-parallel-studio-introduction.md
    - Intel MKL: salomon/software/intel-suite/intel-mkl.md
    - Intel Compilers: salomon/software/intel-suite/intel-compilers.md
@@ -151,11 +148,11 @@ pages:
    - Intel Inspector: salomon/software/intel-suite/intel-inspector.md
    - Intel Trace Analyzer and Collector: salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
    - Intel Advisor: salomon/software/intel-suite/intel-advisor.md
-  - Salomon Cluster Documentation-Software-MPI:
+  - Salomon Cluster MPI:
    - Introduction: salomon/software/mpi/mpi.md
    - MPI4Py (MPI for Python): salomon/software/mpi/mpi4py-mpi-for-python.md
    - Running OpenMPI: salomon/software/mpi/Running_OpenMPI.md
-  - Salomon Cluster Documentation-Software-Debuggers:
+  - Salomon Cluster Debuggers:
    - Introduction: salomon/software/debuggers/Introduction.md
    - Valgrind: salomon/software/debuggers/valgrind.md
    - Allinea Forge (DDT,MAP): salomon/software/debuggers/allinea-ddt.md
@@ -164,19 +161,19 @@ pages:
    - Aislinn: salomon/software/debuggers/aislinn.md
    - Allinea Performance Reports: salomon/software/debuggers/allinea-performance-reports.md
    - Vampir: salomon/software/debuggers/vampir.md
-  - Salomon Cluster Documentation-Software-Numerical Languages:
+  - Salomon Cluster Numerical Languages:
    - Introduction: salomon/software/numerical-languages/introduction.md
    - R: salomon/software/numerical-languages/r.md
    - Matlab: salomon/software/numerical-languages/matlab.md
    - Octave: salomon/software/numerical-languages/octave.md
-  - Salomon Cluster Documentation-Software-Chemistry:
+  - Salomon Cluster Chemistry:
    - Molpro: salomon/software/chemistry/molpro.md
    - Phono3py: salomon/software/chemistry/phono3py.md
    - NWChem: salomon/software/chemistry/nwchem.md
-  - Salomon Cluster Documentation-Software-Comsol:
+  - Salomon Cluster Comsol:
    - COMSOL: salomon/software/comsol/comsol-multiphysics.md
    - Licensing and Available Versions: salomon/software/comsol/licensing-and-available-versions.md
-  - Salomon Cluster Documentation-Software-Ansys:
+  - Salomon Cluster Ansys:
    - Introduction: salomon/software/ansys/ansys.md
    - Workbench: salomon/software/ansys/workbench.md
    - ANSYS CFX: salomon/software/ansys/ansys-cfx.md