finale

.gitlab-ci.yml

@@ -9,7 +9,7 @@ docs:
   image: davidhrbac/docker-mdcheck:latest
   allow_failure: true
   script:
-  - mdl -r ~MD013,~MD033,~MD014 *.md docs.it4i/
+  - mdl -r ~MD013,~MD033,~MD014,~MD026 *.md docs.it4i/
 
 two spaces:
   stage: test

docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md

@@ -886,7 +886,7 @@ A possible output of the MPI "hello-world" example executed on two hosts and two
 !!! note
     At this point the MPI communication between MIC accelerators on different nodes uses 1Gb Ethernet only.
 
-**Using the PBS automatically generated node-files**
+### Using the PBS automatically generated node-files
 
 PBS also generates a set of node-files that can be used instead of manually creating a new one every time. Three node-files are genereated:
 

docs.it4i/anselm-cluster-documentation/software/kvirtualization.md

@@ -279,7 +279,7 @@ Optimized network setup with sharing and port forwarding
 
 ### Advanced Networking
 
-**Internet access**
+#### Internet access
 
 Sometime your virtual machine needs access to internet (install software, updates, software activation, etc). We suggest solution using Virtual Distributed Ethernet (VDE) enabled QEMU with SLIRP running on login node tunneled to compute node. Be aware, this setup has very low performance, the worst performance of all described solutions.
 
@@ -321,7 +321,7 @@ Optimized setup
     $ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev vde,id=net0,sock=/tmp/sw0
 ```
 
-**TAP interconnect**
+#### TAP interconnect
 
 Both user and vde network back-end have low performance. For fast interconnect (10 Gbit/s and more) of compute node (host) and virtual machine (guest) we suggest using Linux kernel TAP device.
 

docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md

@@ -42,7 +42,6 @@ $ matlab -nodesktop -nosplash
 
 Plots, images, etc... will be still available.
 
-
 ## Running Parallel Matlab Using Distributed Computing Toolbox / Engine
 
 Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is started on the first compute node assigned to job by PBS and workers are started on all remaining nodes. User can use both interactive and non-interactive PBS sessions. This mode guarantees that the data processing is not performed on login nodes, but all processing is on compute nodes.
@@ -54,6 +53,7 @@ For the performance reasons Matlab should use system MPI. On Anselm the supporte
 ```bash
 $ vim ~/matlab/mpiLibConf.m
 ```
+
 ```bash
 function [lib, extras] = mpiLibConf
 %MATLAB MPI Library overloading for Infiniband Networks
@@ -193,7 +193,7 @@ You can copy and paste the example in a .m file and execute. Note that the matla
 
 ### Non-Interactive Session and Licenses
 
-If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the "` -l __feature__matlab__MATLAB=1`" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../isv_licenses/).
+If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the ` -l __feature__matlab__MATLAB=1` for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../isv_licenses/).
 
 In case of non-interactive session please read the [following information](../isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
 

docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md

@@ -8,39 +8,39 @@ The GNU Scientific Library (GSL) provides a wide range of mathematical routines
 
 The library covers a wide range of topics in numerical computing. Routines are available for the following areas:
 
-                           Complex Numbers          	Roots of Polynomials
+                           Complex Numbers              Roots of Polynomials
 
-                           Special Functions        	Vectors and Matrices
+                           Special Functions            Vectors and Matrices
 
-                           Permutations            	Combinations
+                           Permutations                 Combinations
 
-                           Sorting                  	BLAS Support
+                           Sorting                      BLAS Support
 
-                           Linear Algebra           	CBLAS Library
+                           Linear Algebra               CBLAS Library
 
-                           Fast Fourier Transforms  	Eigensystems
+                           Fast Fourier Transforms      Eigensystems
 
-                           Random Numbers           	Quadrature
+                           Random Numbers               Quadrature
 
-                           Random Distributions     	Quasi-Random Sequences
+                           Random Distributions         Quasi-Random Sequences
 
-                           Histograms               	Statistics
+                           Histograms                   Statistics
 
-                           Monte Carlo Integration  	N-Tuples
+                           Monte Carlo Integration      N-Tuples
 
-                           Differential Equations   	Simulated Annealing
+                           Differential Equations       Simulated Annealing
 
                            Numerical Differentiation    Interpolation
 
-                           Series Acceleration      	Chebyshev Approximations
+                           Series Acceleration          Chebyshev Approximations
 
-                           Root-Finding             	Discrete Hankel Transforms
+                           Root-Finding                 Discrete Hankel Transforms
 
-                           Least-Squares Fitting    	Minimization
+                           Least-Squares Fitting        Minimization
 
-                           IEEE Floating-Point      	Physical Constants
+                           IEEE Floating-Point          Physical Constants
 
-                           Basis Splines            	Wavelets
+                           Basis Splines                Wavelets
 
 ## Modules
 

docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md

@@ -2,7 +2,7 @@
 
 Next generation dense algebra library for heterogeneous systems with accelerators
 
-### Compiling and Linking With MAGMA
+## Compiling and Linking With MAGMA
 
 To be able to compile and link code with MAGMA library user has to load following module:
 

docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md

@@ -2,11 +2,11 @@
 
 Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.
 
-### Introduction
+## Introduction
 
 Trilinos is a collection of software packages for the numerical solution of large scale scientific and engineering problems. It is based on C++ and features modern object-oriented design. Both serial as well as parallel computations based on MPI and hybrid parallelization are supported within Trilinos packages.
 
-### Installed Packages
+## Installed Packages
 
 Current Trilinos installation on ANSELM contains (among others) the following main packages
 
@@ -20,11 +20,11 @@ Current Trilinos installation on ANSELM contains (among others) the following ma
 
 For the full list of Trilinos packages, descriptions of their capabilities, and user manuals see [http://trilinos.sandia.gov.](http://trilinos.sandia.gov)
 
-### Installed Version
+## Installed Version
 
 Currently, Trilinos in version 11.2.3 compiled with Intel Compiler is installed on ANSELM.
 
-### Compiling Against Trilinos
+## Compiling Against Trilinos
 
 First, load the appropriate module: