Build.md

-\# Dependencies
+# Dependencies
 
 \* A standard compliant c++ compiller
 
-	\* The system, compiler and implementations must support silent NaN floating-point values.
+```plaintext
+\* The system, compiler and implementations must support silent NaN floating-point values.
+```
 
 \* An MPI implementation (ideally CUDA aware)
 
@@ -10,19 +12,25 @@
 
 \* If using NVLink (cuda), Omni-Path (psm2), UCX (ucp), or IBVerbs (ibverbs)
 
-	\* \`minipmi\`: <https://github.com/kraused/minipmi>
+```plaintext
+\* \`minipmi\`: <https://github.com/kraused/minipmi>
+```
 
 \* If using NVLink (cuda):
 
-    \* A standard compliant CUDA compiller
+```plaintext
+\* A standard compliant CUDA compiller
 
-    \* Python version 3.0.0 or a derivative
+\* Python version 3.0.0 or a derivative
+```
 
 \* If using linktest-report tool
 
-	\* Python 3.8.5 or above
+```plaintext
+\* Python 3.8.5 or above
 
-    \* numpy and matplotlib
+\* numpy and matplotlib
+```
 
 \# Build procedure
 
@@ -32,7 +40,7 @@ In general you have to do the following steps
 
 2\. Set-Up Environment, Pahs etc.
 
-3\. Install \`linktest\` with \`make\`, disable unavailable transportlayers 
+3\. Install \`linktest\` with \`make\`, disable unavailable transportlayers
 
 4\. Install \`linktest-report\` via pip (Update PYTHONPATH or use virtual environments)
 
@@ -44,25 +52,25 @@ Quick-Start Example installing only MPI and TCP support. (Might not work on your
 
 mkdir -p install
 
-ml GCC ParaStationMPI SIONlib SciPy-Stack             # 1 + 2
+ml GCC ParaStationMPI SIONlib SciPy-Stack # 1 + 2
 
-cd benchmark;                                         # 
+cd benchmark; #
 
-make HAVE_MINIPMI=0 PREFIX=../install clean install   # 3
+make HAVE_MINIPMI=0 PREFIX=../install clean install # 3
 
-python -m pip install ../python/setup.py --prefix=../install    # 4
+python -m pip install ../python/setup.py --prefix=../install # 4
 
 \`\`\`
 
-exampleBuild.sh showcases a more complicated build procedure. You can adapt it to your needs. 
+exampleBuild.sh showcases a more complicated build procedure. You can adapt it to your needs.
 
-A file named \`pingpong_results_bin.sion\` should be produced.  
+A file named \`pingpong_results_bin.sion\` should be produced.
 
-Some examples for JSC systems can also be found in chapter \[JSC Build Examples\](#JSC-Build-Examples)
+Some examples for JSC systems can also be found in chapter [JSC Build Examples](#JSC-Build-Examples)
 
 \## Transport Layers
 
-Transport Layers can be (de-)activated with \`make HAVE_<LAYER>=(0)1\`  
+Transport Layers can be (de-)activated with \`make HAVE_=(0)1\`
 
 The following transport layers and other variables may be used:
 
@@ -72,9 +80,9 @@ The following transport layers and other variables may be used:
 
 | \`mpi\` | \`HAVE_MPI\` | Enabled | MPI |
 
-| \`tcp\` | \`HAVE_TCP\` | Enabled | TCP sockets, if deactivated, layers below will crash at runtime (see chapter \[Execution\](Execution)) |
+| \`tcp\` | \`HAVE_TCP\` | Enabled | TCP sockets, if deactivated, layers below will crash at runtime (see chapter [Execution](/cstao-public/linktest/-/wikis/Execution)) |
 
-|  | \`HAVE_MINIPMI\` | Enabled | If deactivated, deactivates all layers below |
+| | \`HAVE_MINIPMI\` | Enabled | If deactivated, deactivates all layers below |
 
 | \`ibverbs\` | \`HAVE_IBVERBS\` | Enabled | Verbs-based implementation |
 
@@ -84,7 +92,7 @@ The following transport layers and other variables may be used:
 
 | \`cuda\` | \`HAVE_CUDA\` | Enabled | NVLink (node-internal) |
 
-|  | \`CUARCH\` |  | Needs to be set if \`cuda\` is enable |
+| | \`CUARCH\` | | Needs to be set if \`cuda\` is enable |
 
 For \`CUARCH\` values see <https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#virtual-architecture-feature-list>
 
@@ -96,7 +104,7 @@ For \`CUARCH\` values see <https://docs.nvidia.com/cuda/cuda-compiler-driver-nvc
 
 | ----------- | ------- |
 
-| Cluster | \`xenv -L GCC -L ParaStationMPI -L SIONlib make install HAVE_PSM2=0 PREFIX_DIR=<<<PREFIX_DIR>>>\`  (uses the \`generic\` system settings) |
+| Cluster | \`xenv -L GCC -L ParaStationMPI -L SIONlib make install HAVE_PSM2=0 PREFIX_DIR=<<<PREFIX_DIR>>>\` (uses the \`generic\` system settings) |
 
 | Booster | \`xenv -L CUDA -L GCC -L ParaStationMPI -L SIONlib make install HAVE_PSM2=0 PREFIX_DIR=<<<PREFIX_DIR>>> SYSTEM="JUWELS Booster"\` |
 
@@ -106,7 +114,7 @@ For \`CUARCH\` values see <https://docs.nvidia.com/cuda/cuda-compiler-driver-nvc
 
 | ----------- | ------- |
 
-| JURECA-DC CPU | \`xenv         -L GCC -L ParaStationMPI -L SIONlib make install HAVE_PSM2=0 HAVE_CUDA=0 PREFIX_DIR=<<<PREFIX_DIR>>>\`  (uses the \`generic\` system settings) |
+| JURECA-DC CPU | \`xenv -L GCC -L ParaStationMPI -L SIONlib make install HAVE_PSM2=0 HAVE_CUDA=0 PREFIX_DIR=<<<PREFIX_DIR>>>\` (uses the \`generic\` system settings) |
 
 | JURECA-DC CPU | \`xenv -L CUDA -L GCC -L ParaStationMPI -L SIONlib make install HAVE_PSM2=0 PREFIX_DIR=<<<PREFIX_DIR>>> SYSTEM="JURECA-DC GPU"\` |
 
@@ -126,51 +134,59 @@ The \`GenericSystem\` instance can be customized via the environment, via a wrap
 
 export LINKTEST_SYSTEM_NODENAME_SUFFIX="i"
 
-if \[\[ "0" == "$MPI_LOCALRANKID" \]\]
+["0" == "$MPI_LOCALRANKID"](/cstao-public/linktest/-/wikis/%220%22%20==%20%22%24MPI_LOCALRANKID%22)
 
 then
 
-	export LINKTEST_SYSTEM_HCA_NAME="mlx5_0"
+```plaintext
+export LINKTEST_SYSTEM_HCA_NAME="mlx5_0"
 
-	export LINKTEST_SYSTEM_HCA_PORT="1"
+export LINKTEST_SYSTEM_HCA_PORT="1"
 
-	export LINKTEST_SYSTEM_GPU="0"
+export LINKTEST_SYSTEM_GPU="0"
+```
 
 fi
 
-if \[\[ "1" == "$MPI_LOCALRANKID" \]\]
+["1" == "$MPI_LOCALRANKID"](/cstao-public/linktest/-/wikis/%221%22%20==%20%22%24MPI_LOCALRANKID%22)
 
 then
 
-	export LINKTEST_SYSTEM_HCA_NAME="mlx5_1"
+```plaintext
+export LINKTEST_SYSTEM_HCA_NAME="mlx5_1"
 
-	export LINKTEST_SYSTEM_HCA_PORT="1"
+export LINKTEST_SYSTEM_HCA_PORT="1"
 
-	export LINKTEST_SYSTEM_GPU="1"
+export LINKTEST_SYSTEM_GPU="1"
+```
 
 fi
 
-if \[\[ "2" == "$MPI_LOCALRANKID" \]\]
+["2" == "$MPI_LOCALRANKID"](/cstao-public/linktest/-/wikis/%222%22%20==%20%22%24MPI_LOCALRANKID%22)
 
 then
 
-	export LINKTEST_SYSTEM_HCA_NAME="mlx5_2"
+```plaintext
+export LINKTEST_SYSTEM_HCA_NAME="mlx5_2"
 
-	export LINKTEST_SYSTEM_HCA_PORT="1"
+export LINKTEST_SYSTEM_HCA_PORT="1"
 
-	export LINKTEST_SYSTEM_GPU="2"
+export LINKTEST_SYSTEM_GPU="2"
+```
 
 fi
 
-if \[\[ "3" == "$MPI_LOCALRANKID" \]\]
+["3" == "$MPI_LOCALRANKID"](/cstao-public/linktest/-/wikis/%223%22%20==%20%22%24MPI_LOCALRANKID%22)
 
 then
 
-	export LINKTEST_SYSTEM_HCA_NAME="mlx5_3"
+```plaintext
+export LINKTEST_SYSTEM_HCA_NAME="mlx5_3"
 
-	export LINKTEST_SYSTEM_HCA_PORT="1"
+export LINKTEST_SYSTEM_HCA_PORT="1"
 
-	export LINKTEST_SYSTEM_GPU="3"
+export LINKTEST_SYSTEM_GPU="3"
+```
 
 fi