Build.md

@@ -7,25 +7,23 @@ As prerequisite, you must have verified that [git](Git), [a C++ compiler](C++ Co
 ```
 git clone git@gitlab.uliege.be:rboman/math0471.git
 ```
- * Open VS Code and load ("File / Open Folder...") the `math0471` folder. 
- * In the terminal of VS Code, go to the `lib` folder and install "gmsh-sdk" and "Eigen" using the scripts `get_gmsh.cmd` and `get_eigen.cmd` (this should be done only once per working copy of the repository):
+ * In the terminal of VS Code, open VS Code and load ("File / Open Folder...") the `math0471` folder. 
+ * Add the MinGW compiler (and the future zlib path) to your environment by running this script. This script assumes that the compiler has been installed in the default location proposed by the MinGW installer. Running this script should be done each time you re-open VS Code or a new terminal:
+```
+envs\windows.cmd
+```
+ * Then, go to the `lib` folder and install "zlib" using the scripts `get_zlib.cmd`. This should be done only once per working copy of the repository:
 ```
 cd math0471
 cd lib
-get_gmsh.cmd
-get_eigen.cmd
+get_zlib.cmd
 cd ..
 ```
-
- * Add MinGW, gmsh-sdk and Eigen to your environment by running this script (it should be done each time you re-open VS Code or a new terminal):
-```
-envs\windows.cmd
-```
- * Then, in the same terminal, go to the example folder:
+ * Next, in the same terminal, go to the `src` folder:
  ```
-cd examples\gmsh_api
+cd src
  ```  
- * Create a `build` folder in `examples\gmsh_api`:
+ * Create a `build` folder in `src`:
  ```
 mkdir build
  ```
@@ -33,21 +31,37 @@ mkdir build
  ```
 cd build
  ```
- * Run CMake (if an error occurs at this stage, it usually means that you forgot to run `envs\windows.cmd` or you  installed the programs at locations on your hard drive other than those recommended in this wiki):
+ * Run CMake (if an error occurs at this stage, it usually means that you forgot to run `envs\windows.cmd` or you installed the programs at locations on your hard drive other than those recommended in this wiki):
  ```
 cmake ..
  ```
  * Start the compilation (with 4 parallel processes):
  ```
-make -j 4
+make
  ```
- * Run a program:
+ * Run the program:
 ```
-code1_loadgeo.exe ..\rectangle.geo
+solver.exe ..\simulation.json
 ```
+ * Open Paraview from the start menu and open the `.vtp` files that have been created by the solver. 
 
+You can also build the OpenMP and MPI examples from the `examples` folder using the same method:
+```
+cd examples\openmp
+mkdir build
+cd build
+cmake .. && make
+set OMP_NUM_THREADS=4
+omp_hello.exe
+```
 
-
+```
+cd examples\mpi
+mkdir build
+cd build
+cmake .. && make
+mpiexec -np 4 mpi_hello.exe
+```
 
 
 ## CECI clusters / Linux / macOS
@@ -60,38 +74,35 @@ git clone git@gitlab.uliege.be:rboman/math0471.git
 ```
 cd math0471
 ```
- * Install gmsh-sdk and Eigen using the script `get_gmsh.sh` and `get_eigen.sh` in the `lib` folder:
-```
-cd lib
-./get_gmsh.sh
-./get_eigen.sh
-cd ..
-```
- * Set the environment variables for cmake:
-```
-source ./envs/linux-macos.sh
-```
- * Go to the `examples/gmsh_api` folder:
-```
-cd examples/gmsh_api
-```
- * Create a `build` folder and go into it:
+ * Build the source code:
 ```
+cd src
 mkdir build
 cd build
+cmake .. && make -j 4
+./solver ../simulation.json
 ```
- * Run CMake (if an error occurs at this stage, it usually means that you forgot to "source" `envs/linux-macos.sh`):
-```
-cmake ..
-```
- * Build the project (with 4 parallel processes):
+ * Display the results with Paraview
+
+You can also build the OpenMP and MPI examples from the `examples` folder using the same method:
 ```
-make -j 4
+cd examples/openmp
+mkdir build
+cd build
+cmake .. && make
+export OMP_NUM_THREADS=4
+./omp_hello
 ```
- * Run a program:
+
 ```
-./code1_loadgeo ../rectangle.geo
+cd examples/mpi
+mkdir build
+cd build
+cmake .. && make
+mpirun -np 4 ./mpi_hello
 ```
+
+
 # "Debug" mode vs "Release" mode
 
 The code is built in "*debug mode*" by default. It means that the compiler makes no optimisations at all. It also enables many runtime checks and makes debugging possible by embedding all the debug symbols (the name of your variables and functions) into the executable. 
@@ -113,16 +124,16 @@ which is equivalent to
 cmake -DCMAKE_BUILD_TYPE=Debug ..
 ```
 
-# Note about the environment scripts
+# Note about environment scripts
 
 The scripts in the `math0471/envs/` folder add several folders to 3 environment variables so that the system and CMake find the compiler and the libraries correctly:
-* `PATH`: this variable should contain the location of the folder of your `g++` compiler, of `gmsh.exe` and its shared library (`gmsh.dll/.so/.dylib`),
-* `LIB`: points to the path of the folder containing `gmsh.lib` (windows) or `gmsh.so` (linux) or `gmsh.dylib` (macOS),
-* `INCLUDE`: points to the path of the folder containing the `gmsh.h` header and the `Eigen` folder.
+* `PATH`: this variable should contain the location of the folder of your `g++` compiler, and the shared libraries you use in your program (`libzlib.dll/.so/.dylib`),
+* `LIB`: points to the path of the folder containing `zlib.lib` (windows),
+* `INCLUDE`: points to the path of the folder containing the `zlib.h` header.
 
 Instead of using these scripts which should be loaded each time you start a new terminal, these 3 variables can be defined in your global user environment once and for all.
 
 This is done by going to "Settings" on Windows, and typing "env" in the search bar. Then choose the appropriate menu ("modify environment variables").
 
-On Linux/macOS, you can add/modify environment variables by editing `~/.bashrc` or `~/.profile` (just copy & paste the contents of `envs/linux-macos.sh` at the end of the file).
+On Linux/macOS, you can add/modify environment variables by editing `~/.bashrc` or `~/.profile`.