update

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:
 

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.
 
 ![../src/IB single-plane topology - ICEX Mcell.pdf](../img/IBsingleplanetopologyICEXMcellsmall.png)
 
-### 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/).
 

docs.it4i/salomon/software/chemistry/nwchem.md

 # 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.

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:
 

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)

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)