Links OK

docs.it4i/software/debuggers/score-p.md

@@ -2,16 +2,16 @@
 
 ## Introduction
 
-The [Score-P measurement infrastructure](http://www.vi-hps.org/projects/score-p/) is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
+The [Score-P measurement infrastructure][a] is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
 
-Score-P can be used as an instrumentation tool for [Scalasca](software/debuggers/scalasca/).
+Score-P can be used as an instrumentation tool for [Scalasca][1].
 
 ## Installed Versions
 
-There are currently two versions of Score-P version 1.2.6 [modules](modules-matrix/) installed on Anselm :
+There are currently two versions of Score-P version 1.2.6 [modules][2] installed on Anselm :
 
-* scorep/1.2.3-gcc-openmpi, for usage     with [GNU Compiler](software/compilers/) and [OpenMPI](software/mpi/Running_OpenMPI/)
-* scorep/1.2.3-icc-impi, for usage with [Intel Compiler](software/compilers/)> and [Intel MPI](software/mpi/running-mpich2/)>.
+* scorep/1.2.3-gcc-openmpi, for usage  with [GNU Compiler][3] and [OpenMPI][4]
+* scorep/1.2.3-icc-impi, for usage with [Intel Compiler][3] and [Intel MPI][5]
 
 ## Instrumentation
 
@@ -74,7 +74,7 @@ subroutine foo
 end subroutine foo
 ```
 
-Please refer to the [documentation for description of the API](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf).
+Please refer to the [documentation for description of the API][b].
 
 ### Manual Instrumentation Using Directives
 
@@ -114,4 +114,14 @@ subroutine foo(...)
 end subroutine foo
 ```
 
-The directives are ignored if the program is compiled without Score-P. Again, refer to the [documentation](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf) for a more elaborate description.
+The directives are ignored if the program is compiled without Score-P. Again, refer to the [documentation][c] for a more elaborate description.
+
+[1]: scalasca.md
+[2]: ../../modules-matrix.md
+[3]: ../compilers.md
+[4]: ../mpi/Running_OpenMPI.md
+[5]: ../mpi/running-mpich2.md
+
+[a]: http://www.vi-hps.org/projects/score-p/
+[b]: https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf
+[c]: (ttps://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf

docs.it4i/software/debuggers/total-view.md

@@ -13,7 +13,7 @@ On the cluster users can debug OpenMP or MPI code that runs up to 64 parallel pr
 
 Debugging of GPU accelerated codes is also supported.
 
-You can check the status of the licenses [here (Salomon)](https://extranet.it4i.cz/rsweb/anselm/license/Totalview) or type (Anselm):
+You can check the status of the licenses [Salomon][a] or [Anselm][b]:
 
 ```console
 $ cat /apps/user/licenses/totalview_features_state.txt
@@ -130,7 +130,7 @@ $ source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl #Salo
 $ source /apps/mpi/openmpi/intel/1.6.5/etc/openmpi-totalview.tcl #Anselm
 ```
 
-You need to do this step only once. See also [OpenMPI FAQ entry](https://www.open-mpi.org/faq/?category=running#run-with-tv)
+You need to do this step only once. See also [OpenMPI FAQ entry][c].
 
 Now you can run the parallel debugger using:
 
@@ -164,4 +164,9 @@ More information regarding the command line parameters of the TotalView can be f
 
 ## Documentation
 
-[1] The [TotalView documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview) web page is a good resource for learning more about some of the advanced TotalView features.
+[1] The [TotalView documentation][d] web page is a good resource for learning more about some of the advanced TotalView features.
+
+[a]: https://extranet.it4i.cz/rsweb/salomon/license/Totalview
+[b]: https://extranet.it4i.cz/rsweb/anselm/license/Totalview
+[c]: https://www.open-mpi.org/faq/?category=running#run-with-tv
+[d]: http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview

docs.it4i/software/debuggers/valgrind.md

@@ -6,7 +6,7 @@ Valgrind is a tool for memory debugging and profiling.
 
 Valgrind is an open-source tool, used mainly for debuggig memory-related problems, such as memory leaks, use of uninitalized memory etc. in C/C++ applications. The toolchain was however extended over time with more functionality, such as debugging of threaded applications, cache profiling, not limited only to C/C++.
 
-Valgind is an extremely useful tool for debugging memory errors such as [off-by-one](http://en.wikipedia.org/wiki/Off-by-one_error). Valgrind uses a virtual machine and dynamic recompilation of binary code, because of that, you can expect that programs being debugged by Valgrind run 5-100 times slower.
+Valgind is an extremely useful tool for debugging memory errors such as [off-by-one][a]. Valgrind uses a virtual machine and dynamic recompilation of binary code, because of that, you can expect that programs being debugged by Valgrind run 5-100 times slower.
 
 The main tools available in Valgrind are :
 
@@ -15,14 +15,14 @@ The main tools available in Valgrind are :
 * **Hellgrind** and **DRD** can detect race conditions in multi-threaded applications.
 * **Cachegrind**, a cache profiler.
 * **Callgrind**, a callgraph analyzer.
-* For a full list and detailed documentation, refer to the [official Valgrind documentation](http://valgrind.org/docs/).
+* For a full list and detailed documentation, refer to the [official Valgrind documentation][b].
 
 ## Installed Versions
 
 There are two versions of Valgrind available on Anselm.
 
 * Version 3.6.0, installed by operating system vendor in /usr/bin/valgrind. This version is available by default, without the need to load any module. This version however does not provide additional MPI support.
-* Version 3.9.0 with support for Intel MPI, available in [module](modules-matrix/) valgrind/3.9.0-impi. After loading the module, this version replaces the default valgrind.
+* Version 3.9.0 with support for Intel MPI, available in [module][1] valgrind/3.9.0-impi. After loading the module, this version replaces the default valgrind.
 
 There are two versions of Valgrind available on the Salomon.
 
@@ -271,3 +271,8 @@ Prints this output : (note that there is output printed for every launched MPI p
 ```
 
 We can see that Valgrind has reported use of uninitialized memory on the master process (which reads the array to be broadcast) and use of unaddressable memory on both processes.
+
+[1]: ../../modules-matrix.md
+
+[a]: http://en.wikipedia.org/wiki/Off-by-one_error
+[b]: http://valgrind.org/docs/

docs.it4i/software/debuggers/vampir.md

 # Vampir
 
-Vampir is a commercial trace analysis and visualization tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P](software/debuggers/score-p/)) first to collect the traces.
+Vampir is a commercial trace analysis and visualization tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P][1]) first to collect the traces.
 
 ![](../../img/Snmekobrazovky20160708v12.33.35.png)
 
@@ -21,4 +21,8 @@ You can find the detailed user manual in PDF format in $EBROOTVAMPIR/doc/vampir-
 
 ## References
 
-1. [https://www.vampir.eu](https://www.vampir.eu)
+1. [Web site][a]
+
+[1]: score-p.md
+
+[a]: https://www.vampir.eu

mkdocs.yml

@@ -34,8 +34,8 @@ theme:
     text: 'Ubuntu'
     code: 'Ubuntu Mono'
   palette:
-    primary: 'grey'
-    accent: 'yellow'
+    primary: 'red'
+    accent: 'deep orange'
 
   favicon: img/favicon.ico