Merge branch 'mpiusageerrordetection' into 'preview'

Fix checks and move content to new wiki

See merge request zih/hpc-compendium/hpc-compendium!156

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

+# Introduction
+
+MPI as the de-facto standard for parallel applications of the the massage passing paradigm offers
+more than one hundred different API calls with complex restrictions. As a result, developing
+applications with this interface is error prone and often time consuming. Some usage errors of MPI
+may only manifest on some platforms or some application runs, which further complicates the
+detection of these errors. Thus, special debugging tools for MPI applications exist that
+automatically check whether an application conforms to the MPI standard and whether its MPI calls
+are safe. At ZIH, we maintain and support MUST for this task, though different types of these tools
+exist (see last section).
+
+## MUST
+
+MUST checks if your application conforms to the MPI standard and will issue warnings if there are
+errors or non-portable constructs. You can apply MUST without modifying your source code, though we
+suggest to add the debugging flag "-g" during compilation.
+
+- [MUST introduction slides]**todo** %ATTACHURL%/parallel_debugging_must.pdf
+
+### Setup and Modules
+
+You need to load a module file in order to use MUST. Each MUST installation uses a specific
+combination of a compiler and an MPI library, make sure to use a combination that fits your needs.
+Right now we only provide a single combination on each system, contact us if you need further
+combinations. You can query for the available modules with:
+
+```Bash
+module avail must
+```
+
+You can load a MUST module as follows:
+
+```Bash
+module load must
+```
+
+Besides loading a MUST module, no further changes are needed during compilation and linking.
+
+### Running with MUST
+
+In order to run with MUST you need to replace the mpirun/mpiexec command with mustrun:
+
+```Bash
+mustrun -np <NPROC> ./a.out
+```
+
+Besides replacing the mpiexec command you need to be aware that **MUST always allocates an extra
+process**. I.e. if you issue a `mustrun -np 4 ./a.out` then MUST will start 5 processes instead.
+This is usually not critical, however in batch jobs **make sure to allocate space for this extra
+task**.
+
+Finally, MUST assumes that your application may crash at any time. To still gather correctness
+results under this assumption is extremely expensive in terms of performance overheads. Thus, if
+your application does not crashs, you should add an "--must:nocrash" to the mustrun command to make
+MUST aware of this knowledge. Overhead is drastically reduced with this switch.
+
+### Result Files
+
+After running your application with MUST you will have its output in the working directory of your
+application. The output is named `MUST_Output.html`. Open this files in a browser to anlyze the
+results. The HTML file is color coded: Entries in green represent notes and useful information.
+Entries in yellow represent warnings, and entries in red represent errors.
+
+## Other MPI Correctness Tools
+
+Besides MUST, there exist further MPI correctness tools, these are:
+
+-   Marmot (predecessor of MUST)
+-   MPI checking library of the Intel Trace Collector
+-   ISP (From Utah)
+-   Umpire (predecessor of MUST)
+
+ISP provides a more thorough deadlock detection as it investigates alternative execution paths,
+however its overhead is drastically higher as a result. Contact our support if you have a specific
+use cases that needs one of these tools.

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

@@ -42,13 +42,17 @@ nav:
     - FAQs: software/modules-faq.md
     - Bio Informatics: software/Bioinformatics.md
     - SCS5 Migration Hints: software/SCS5Software.md
-    - GPU Programming: software/GPUProgramming.md
     - NanoscaleSimulations: software/NanoscaleSimulations.md
     - FEMSoftware: software/FEMSoftware.md
-    - Score-P: software/ScoreP.md
     - Cloud: software/Cloud.md
     - VM tools: software/VMTools.md
     - Virtual Desktops: software/VirtualDesktops.md
+    - Software Development and Tools:
+      - GPU Programming: software/GPUProgramming.md
+      - Compilers: software/Compilers.md
+      - Debuggers: software/Debuggers.md
+      - MPI Error Detection: software/MPIUsageErrorDetection.md
+      - Score-P: software/ScoreP.md
   - Data Management:
     - Overview: data_management/DataManagement.md
     - Announcement of Quotas: data_management/AnnouncementOfQuotas.md