diff --git a/docs.it4i/index.md b/docs.it4i/index.md
index 1d5212ccc295b3eb7f3e349b3718738690e3e8b3..0b202d4a3625b8bbef09865cfab1edabb399a66e 100644
--- 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. Â 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!
diff --git a/mkdocs.yml b/mkdocs.yml
index c74a2cfce35991637ed20cb0697aa28ce1813515..9135d261eb22555c4885b4ef33349b5301860248 100644
--- 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