From ddeb4d8a8d50414ef65a32058fe82cb0ebf75e80 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 11:54:24 +0100
Subject: [PATCH] update
---
docs.it4i/salomon/capacity-computing.md | 2 +-
docs.it4i/salomon/ib-single-plane-topology.md | 4 ++--
docs.it4i/salomon/software/chemistry/nwchem.md | 2 --
docs.it4i/salomon/software/debuggers/aislinn.md | 2 +-
docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md | 4 ++--
docs.it4i/salomon/software/debuggers/total-view.md | 4 +++-
6 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/docs.it4i/salomon/capacity-computing.md b/docs.it4i/salomon/capacity-computing.md
index 18b896440..aa947db01 100644
--- a/docs.it4i/salomon/capacity-computing.md
+++ b/docs.it4i/salomon/capacity-computing.md
@@ -292,7 +292,7 @@ When deciding this values, think about following guiding rules :
1. Number of tasks should be modulo 24.
1. These rules are valid only when all tasks have similar task walltimes T.
-### Submit the Job Array
+### Submit the Job Array (-J)
To submit the job array, use the qsub -J command. The 992 tasks' job of the [example above](capacity-computing/#combined_example) may be submitted like this:
diff --git a/docs.it4i/salomon/ib-single-plane-topology.md b/docs.it4i/salomon/ib-single-plane-topology.md
index 5ea655625..b1a5381e6 100644
--- a/docs.it4i/salomon/ib-single-plane-topology.md
+++ b/docs.it4i/salomon/ib-single-plane-topology.md
@@ -8,7 +8,7 @@ The SGI ICE X IB Premium Blade provides the first level of interconnection via d
* 3 ports on each chip provide connectivity between the chips
* 24 ports from each switch chip connect to the external bulkhead, for a total of 48
-### IB Single-Plane Topology - ICEX M-Cell
+## IB Single-Plane Topology - ICEX M-Cell
Each color in each physical IRU represents one dual-switch ASIC switch.
@@ -16,7 +16,7 @@ Each color in each physical IRU represents one dual-switch ASIC switch.
-### IB Single-Plane Topology - Accelerated Nodes
+## IB Single-Plane Topology - Accelerated Nodes
Each of the 3 inter-connected D racks are equivalent to one half of M-Cell rack. 18 x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 M-Cell racks as shown in a diagram [7D Enhanced Hypercube](7d-enhanced-hypercube/).
diff --git a/docs.it4i/salomon/software/chemistry/nwchem.md b/docs.it4i/salomon/software/chemistry/nwchem.md
index 00bebe9e1..a26fc701e 100644
--- a/docs.it4i/salomon/software/chemistry/nwchem.md
+++ b/docs.it4i/salomon/software/chemistry/nwchem.md
@@ -1,7 +1,5 @@
# NWChem
-**High-Performance Computational Chemistry**
-
## Introduction
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
diff --git a/docs.it4i/salomon/software/debuggers/aislinn.md b/docs.it4i/salomon/software/debuggers/aislinn.md
index 0b41542cf..e1dee28b8 100644
--- a/docs.it4i/salomon/software/debuggers/aislinn.md
+++ b/docs.it4i/salomon/software/debuggers/aislinn.md
@@ -8,7 +8,7 @@
!!! note
Aislinn is software developed at IT4Innovations and some parts are still considered experimental. If you have any questions or experienced any problems, please contact the author: <mailto:stanislav.bohm@vsb.cz>.
-### Usage
+## Usage
Let us have the following program that contains a bug that is not manifested in all runs:
diff --git a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
index 724e4e58a..2fdbd18e1 100644
--- a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -90,5 +90,5 @@ You can obtain this command line by pressing the "Command line..." button on Ana
## References
1. [Performance Tuning for Intel® Xeon Phi™ Coprocessors](https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf)
-2. [Intel® VTune™ Amplifier Support](https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation)
-3. [https://software.intel.com/en-us/amplifier_help_linux](https://software.intel.com/en-us/amplifier_help_linux)
+1. [Intel® VTune™ Amplifier Support](https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation)
+1. [https://software.intel.com/en-us/amplifier_help_linux](https://software.intel.com/en-us/amplifier_help_linux)
diff --git a/docs.it4i/salomon/software/debuggers/total-view.md b/docs.it4i/salomon/software/debuggers/total-view.md
index a7642fa19..f4f69278f 100644
--- a/docs.it4i/salomon/software/debuggers/total-view.md
+++ b/docs.it4i/salomon/software/debuggers/total-view.md
@@ -112,7 +112,9 @@ The source code of this function can be also found in
You can also add only following line to you ~/.tvdrc file instead of
the entire function:
-**source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl**
+```bash
+source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl
+```
You need to do this step only once. See also [OpenMPI FAQ entry](https://www.open-mpi.org/faq/?category=running#run-with-tv)
--
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