Merge branch 'software_development_overview.md' into 'preview'

Review of software_development_overview.md

Closes #117

See merge request !280

doc.zih.tu-dresden.de/docs/software/software_development_overview.md

 # Software Development and Tools
 
-This section provides you with the basic knowledge and tools to get you out of trouble. It will tell
-you:
+This section provides you with the basic knowledge and tools for software development
+on the ZIH systems.
+It will tell you:
 
 - How to compile your code
-- Using mathematical libraries
-- Find caveats and hidden errors in application codes
-- Handle debuggers
-- Follow system calls and interrupts
-- Understand the relationship between correct code and performance
+    - [General advises for building software](building_software.md)
+    - [Using compilers](compilers.md)
+    - [GPU programming](gpu_programming.md)
+- How to use libraries
+    - [Using mathematical libraries](libraries.md)
+- How to deal with (or even prevent) bugs
+    - [Find caveats and hidden errors in MPI application codes](mpi_usage_error_detection.md)
+    - [Using debuggers](debuggers.md)
+- How to investigate the performance and efficiency of your code
+    - [Pika: monitoring of batch jobs](pika.md)
+    - [Perf: sampling-based performance analysis](perf_tools.md)
+    - [Score-P: event tracing of HPC applications](scorep.md)
+    - [Vampir: trace visualization](vampir.md)
 
 Some hints that are helpful:
 
-- Stick to standards wherever possible, e.g. use the **`-std`** flag
+- Stick to standards wherever possible, e.g. use the `-std` flag
   for GNU and Intel C/C++ compilers. Computers are short living
   creatures, migrating between platforms can be painful. In addition,
   running your code on different platforms greatly increases the
@@ -26,29 +35,10 @@ Some questions you should ask yourself:
 - Given that a code is parallel, are the results independent from the
   numbers of threads or processes?
 - Have you ever run your Fortran code with array bound and subroutine
-  argument checking (the **`-check all`** and **`-traceback`** flags
+  argument checking (the `-check all` and `-traceback` flags
   for the Intel compilers)?
 - Have you checked that your code is not causing floating point
   exceptions?
 - Does your code work with a different link order of objects?
 - Have you made any assumptions regarding storage of data objects in
   memory?
-
-Subsections:
-
-- [Compilers](compilers.md)
-- [Debugging](debuggers.md)
-- PerformanceTools.md: [Score-P](scorep.md), [Vampir](vampir.md)
-- [Libraries](libraries.md)
-
-Intel Tools Seminar \[Oct. 2013\]
-
-- [TU-Dresden_Intel_Multithreading_Methodologies.pdf]**todo** %ATTACHURL%/TU-Dresden_Intel_Multithreading_Methodologies.pdf:
-  Intel Multithreading Methodologies
-- [TU-Dresden_Advisor_XE.pdf] **todo** %ATTACHURL%/TU-Dresden_Advisor_XE.pdf):
-  Intel Advisor XE - Threading prototyping tool for software
-  architects
-- [TU-Dresden_Inspector_XE.pdf] **todo** %ATTACHURL%/TU-Dresden_Inspector_XE.pdf):
-  Inspector XE - Memory-, Thread-, Pointer-Checker, Debugger
-- [TU-Dresden_Intel_Composer_XE.pdf] **todo** %ATTACHURL%/TU-Dresden_Intel_Composer_XE.pdf):
-  Intel Composer - Compilers, Libraries

doc.zih.tu-dresden.de/mkdocs.yml

@@ -60,15 +60,14 @@ nav:
     - Software Development and Tools:
       - Overview: software/software_development_overview.md
       - Building Software: software/building_software.md
-      - GPU Programming: software/gpu_programming.md
       - Compilers: software/compilers.md
-      - Debugging:
-        - Overview: software/debuggers.md
-        - MPI Error Detection: software/mpi_usage_error_detection.md
+      - GPU Programming: software/gpu_programming.md
       - Libraries: software/libraries.md
-      - Score-P: software/scorep.md
+      - MPI Error Detection: software/mpi_usage_error_detection.md
+      - Debugging: software/debuggers.md
+      - Pika: software/pika.md
       - Perf Tools: software/perf_tools.md 
-      - PIKA: software/pika.md
+      - Score-P: software/scorep.md
       - Vampir: software/vampir.md
   - Data Life Cycle Management:
     - Overview: data_lifecycle/overview.md

doc.zih.tu-dresden.de/wordlist.aspell

@@ -66,6 +66,8 @@ OpenMPI
 Opteron
 PAPI
 pdf
+Perf
+Pika
 pipelining
 png
 rome