profilage_code.md

@@ -4,9 +4,9 @@ In this Wiki, we will provide a methodology to install and run some code profile
 
 The tools that were tested are proposed:
 
--   [Score-P](https://www.vi-hps.org/projects/score-p/)
--   [TAU](https://www.cs.uoregon.edu/research/tau/home.php), which allows the profiling of `for` loops
--   [Scalasca](https://www.scalasca.org/)
+- [Score-P](https://www.vi-hps.org/projects/score-p/)
+- [TAU](https://www.cs.uoregon.edu/research/tau/home.php), which allows the profiling of `for` loops
+- [Scalasca](https://www.scalasca.org/)
 
 In order to be able to perform source instrumentation using Tau, the [PDT](https://www.cs.uoregon.edu/research/pdt/home.php) and [Salt](https://github.com/ParaToolsInc/salt) source instrumentation tool must be installed.
 
@@ -14,11 +14,11 @@ In order to be able to perform source instrumentation using Tau, the [PDT](https
 
 ### Download:
 
--   Salt: `git clone --recursive https://github.com/ParaToolsInc/salt.git`
--  PDT: [http://tau.uoregon.edu/pdt.tgz ](http://tau.uoregon.edu/pdt.tgz)
--   Score-P: [https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-8.4/scorep-8.4.tar.gz](https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-8.4/scorep-8.4.tar.gz)
--   Tau: `gh repo clone barriern/tau2`
--   Scalasca: [https://apps.fz-juelich.de/scalasca/releases/scalasca/2.6/dist/scalasca-2.6.1.tar.gz](https://apps.fz-juelich.de/scalasca/releases/scalasca/2.6/dist/scalasca-2.6.1.tar.gz)
+- Salt: `git clone --recursive https://github.com/ParaToolsInc/salt.git`
+- PDT: http://tau.uoregon.edu/pdt.tgz
+- Score-P: https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-8.4/scorep-8.4.tar.gz
+- Tau: `gh repo clone barriern/tau2`
+- Scalasca: https://apps.fz-juelich.de/scalasca/releases/scalasca/2.6/dist/scalasca-2.6.1.tar.gz
 
 ### Conda Environment
 
@@ -125,7 +125,6 @@ make
 make install
 ```
 
-
 #### Compilation Salt
 
 In order to install the Salt source instrumentation tool, go to the Salt folder and type the following:
@@ -161,8 +160,6 @@ make install
 
 > **CAUTION** In TAU, each set of compile options generate a specific Makefile that will be used for the profiling. In the above, the generated Makefile will include PDT, Score-P and MPI. To compile a non-MPI program, re-compile TAU without the `-mpi` option
 
-
-
 ### Compilation Scalasca
 
 Go to your Scalasca folder and type:
@@ -194,8 +191,7 @@ export PATH=$PROFILER_PATH_TAU/x86_64/bin/:$PATH
 
 #### Profiling with compiler instrumentation
 
-To profile with compiler instrumentation, you first need to define the `Makefile` that you will use and which has been generated by the
-compilation of TAU. For example:
+To profile with compiler instrumentation, you first need to define the `Makefile` that you will use and which has been generated by the compilation of TAU. For example:
 
 ```
 export TAU_MAKEFILE=$PROFILER_PATH/x86_64/lib/Makefile.tau-clang-mpi
@@ -209,8 +205,7 @@ export TAU_OPTIONS='-optKeepFiles -optVerbose -optCompInst'
 
 #### Profiling with source instrumentation
 
-To profile using source instrumentation with Tau, you need to specify the `Makefile` that you will use and which has been generated by the#
-compilation of TAU. For example:
+To profile using source instrumentation with Tau, you need to specify the `Makefile` that you will use and which has been generated by the# compilation of TAU. For example:
 
 ```
 export TAU_MAKEFILE=$PROFILER_PATH/x86_64/lib/Makefile.tau-clang-mpi
@@ -224,13 +219,11 @@ To compile a code by using the Salt parser, you also need to provide the followi
 export TAU_OPTIONS='-optKeepFiles -optVerbose -optTauSelectFile="select.tau" -optSaltParser="saltfm" -optSaltInst'
 ```
 
-
 In the above, the `-optKeepFiles` allows to keep intermediate files. The `-optTauSelectFile` specifies the file where additional profiling options are provided. These options are provided in a `select.tau` file (see below)
 
 ##### Using PDT parser
 
-To compile a code by using the PDT parser, you simply need to specify a Tau makefile that includes `pdt` and
-remove the `-optSaltParser` and `-optSaltInst` from the TAU_OPTIONS. For instance:
+To compile a code by using the PDT parser, you simply need to specify a Tau makefile that includes `pdt` and remove the `-optSaltParser` and `-optSaltInst` from the TAU_OPTIONS. For instance:
 
 ```
 export TAU_MAKEFILE=$PROFILER_PATH/x86_64/lib/Makefile.tau-clang-pdt
@@ -239,9 +232,7 @@ export TAU_OPTIONS='-optKeepFiles -optVerbose -optTauSelectFile="select.tau" -op
 
 In the above, the `-optKeepFiles` allows to keep intermediate files. The `-optTauSelectFile` specifies the file where additional profiling options are provided. These options are provided in a `select.tau` file (see below)
 
-> [!important]
-> The PDT parser will not work with resent C++ code. For example, it will fail with includes
-statements of the Boost library. You need to use Salt instead
+> \[!important\] The PDT parser will not work with resent C++ code. For example, it will fail with includes statements of the Boost library. You need to use Salt instead
 
 ##### Selecting profiled code
 
@@ -291,10 +282,10 @@ Here, we specify that loops will be instrumented in all the functions of the pro
 
 Now, to compile the program, replace the standard compile commands as follows:
 
--   `gcc` -\> `tau_cc.sh`
--   `g++` -\> `tau_cxx.sh`
--   `gfortran` -\> `tau_f90.sh`
--   `f77` -\> `tau_f70.sh`
+- `gcc` -\> `tau_cc.sh`
+- `g++` -\> `tau_cxx.sh`
+- `gfortran` -\> `tau_f90.sh`
+- `f77` -\> `tau_f70.sh`
 
 For example:
 
@@ -335,13 +326,13 @@ export PATH=$PROFILER_PATH_SCOREP/x86_64/bin/:$PATH
 
 To allow profiling with Score-P, replace the standard compile commands as follows:
 
--   `g++` -\> `scorep g++`
--   `gfortran` -\> `scorep gfortran`
--   `mpicxx` -\> `scorep mpicxx`
--   `mpif90` -\> `scorep mpif90`
--   `gcc` -\> `scorep gcc`
--   `mpicc` -\> `scorep mpicc`
--   `mpif77` -\> `scorep mpif77`
+- `g++` -\> `scorep g++`
+- `gfortran` -\> `scorep gfortran`
+- `mpicxx` -\> `scorep mpicxx`
+- `mpif90` -\> `scorep mpif90`
+- `gcc` -\> `scorep gcc`
+- `mpicc` -\> `scorep mpicc`
+- `mpif77` -\> `scorep mpif77`
 
 For example
 
@@ -425,7 +416,6 @@ void toto() {
 
     cout << "Sum = " << sum << endl;
 }
-
 ```
 
 To compile this instrumented code, you need to use the `--user` argument as follows:
@@ -445,13 +435,13 @@ scorep-g++ -DSCOREP -I$BOOST_ROOT test_cpp.cpp
 
 To profile a code with Scalasca, you need to compile the code by replacing:
 
--   `g++` -\> `skin g++`
--   `gfortran` -\> `skin gfortran`
--   `mpicxx` -\> `skin mpicxx`
--   `mpif90` -\> `skin mpif90`
--   `gcc` -\> `skin gcc`
--   `mpicc` -\> `skin mpicc`
--   `mpif77` -\> `skin mpif77`
+- `g++` -\> `skin g++`
+- `gfortran` -\> `skin gfortran`
+- `mpicxx` -\> `skin mpicxx`
+- `mpif90` -\> `skin mpif90`
+- `gcc` -\> `skin gcc`
+- `mpicc` -\> `skin mpicc`
+- `mpif77` -\> `skin mpif77`
 
 Once your code has been compiled, you can execute it as follows:
 
@@ -465,9 +455,9 @@ scan test.exe
 scan -t test.exe
 ```
 
-------------------------------------------------------------------------
+---
 
 Resources:
 
--   https://hpc.cea.fr/tgcc-public/en/html/toc/fulldoc/Profiling.html#
--   https://www.vi-hps.org/projects/score-p/
\ No newline at end of file
+- https://hpc.cea.fr/tgcc-public/en/html/toc/fulldoc/Profiling.html#
+- https://www.vi-hps.org/projects/score-p/
\ No newline at end of file