From a2f14d2d288c6ed864f1af7e218780be5a92eab5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Fri, 27 Jan 2017 12:21:17 +0100
Subject: [PATCH] finale
---
.gitlab-ci.yml | 2 +-
.../software/intel-xeon-phi.md | 2 +-
.../software/kvirtualization.md | 4 +--
.../numerical-languages/matlab_1314.md | 4 +--
.../software/numerical-libraries/gsl.md | 32 +++++++++----------
.../magma-for-intel-xeon-phi.md | 2 +-
.../software/numerical-libraries/trilinos.md | 8 ++---
7 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d166f892a..05f5c3477 100644
--- a/.gitlab-ci.yml
+++ b/.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
diff --git a/docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md b/docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md
index 9d6700e30..baa0e6b53 100644
--- a/docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md
+++ b/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:
diff --git a/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md b/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
index 7febc9f8c..a5e8238c7 100644
--- a/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
+++ b/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.
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md
index b4d883071..8c1012531 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md
+++ b/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.
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md
index 0f21187f2..6b5308df3 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md
+++ b/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
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
index d0fccfede..8ce0b79e0 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
+++ b/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:
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
index bf2ffe6ec..42f8bc0dc 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
+++ b/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:
--
GitLab