[DO NOT MERGE] Assignment 5

.github/workflows/address-sanitizer.yml

@@ -23,7 +23,7 @@ jobs:
 
       - name: Install Dependencies
         # install libxerces
-        run: sudo apt install libxerces-c-dev
+        run: sudo apt install -y libxerces-c-dev libomp-dev
 
       - name: run asan
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.

.github/workflows/cmake-build.yml

@@ -31,14 +31,13 @@ jobs:
       run: sudo apt install libxerces-c-dev
 
     - name: Setup buildDir
-      run: mkdir buildDir && cd buildDir && mkdir Release && cd Release
+      run: mkdir buildDir && cd buildDir 
 
     - name: Configure CMake
-      run: cd buildDir/Release && cmake ../../CMakeLists.txt && cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTS=ON .
+      run: cd buildDir && cmake ../CMakeLists.txt && cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTS=ON .
 
     - name: Build
-      run: cd buildDir/Release && cmake --build . -- -"j$(nproc)"
+      run: cd buildDir && cmake --build . -- -"j$(nproc)"
 
     - name: Test
-      run: cd buildDir/Release/tests && ctest
-
+      run: cd buildDir/tests && ctest

CMakeLists.txt

@@ -9,7 +9,14 @@ set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
-add_compile_options(-O3 -ffast-math -march=native -std=c++17 -Wno-deprecated-declarations)
+if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    add_compile_options(-O3 -ffast-math -march=native -std=c++17 -Wno-deprecated-declarations)
+elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+    add_compile_options(-O3 -ffast-math -march=native -std=c++17 -Wno-deprecated-declarations)
+elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    message("Using intel compile options")
+    add_compile_options(-xHost -ipo -qopenmp -O3 -fp-model fast=2)
+endif ()
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules")
 include(googletest)
@@ -37,11 +44,12 @@ endif ()
 
 # Enable DEBUG macro
 if (CMAKE_BUILD_TYPE STREQUAL "Debug")
+    add_compile_options(-ggdb3)
     add_compile_definitions(DEBUG)
     message("Debug mode is enabled")
 endif ()
 
-option(ENABLE_BENCHMARK "Enable benchmark mode" ON)
+option(ENABLE_BENCHMARK "Enable benchmark mode" OFF)
 
 if (ENABLE_BENCHMARK)
     message("Benchmark mode is enabled")

Doxyfile

@@ -557,7 +557,7 @@ WARN_FORMAT            = "$file:$line: $text"
 # and error messages should be written. If left blank the output is written
 # to stderr.
 
-WARN_LOGFILE           =
+WARN_LOGFILE           = warnings.log
 
 #---------------------------------------------------------------------------
 # configuration options related to the input files
@@ -568,11 +568,11 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = ../../src \
-                          ../../README.md \
+INPUT                  = ./../src \
+                          ./../README.md \
 
 
-USE_MDFILE_AS_MAINPAGE = ../../README.md
+USE_MDFILE_AS_MAINPAGE = ./../README.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -649,7 +649,7 @@ EXAMPLE_RECURSIVE      = YES
 # directories that contain image that are included in the documentation (see
 # the \image command).
 
-IMAGE_PATH = ../../benchmark/graph.png
+IMAGE_PATH = ./../benchmark/graph.png
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program

README.md

@@ -1,45 +1,103 @@
 MolSim - Group A
 ===
 
+### Slides: 
+
+- **[Assignment 1](slides/assignment_1_slides.pdf):** Intro
+- **[Assignment 2](slides/assignment_2_slides.pdf):** Performance and Tests
+- **[Assignment 3](slides/assignment_3_slides.pdf):** Linked Cells Container
+- **[Assignment 4](slides/assignment_4_slides.pdf):** Boundary Conditions & SuperMUC
+- **[Assignment 5](slides/assignment_5_slides.pdf):** Parallelization Schemes
+
+
 ## Dependencies
 
-- Cmake 3.24
-- Doygen 1.9.8 (`sudo apt install doxygen`)
+- Cmake 3.28.3
+- Doxygen 1.9.8 (`sudo apt install doxygen`)
 - Libxerces (`sudo apt install libxerces-c-dev`)
 
 ## Build
 
 ### Configuration
 
 - Install
-  ```bash
+
+```bash
   git clone https://github.com/jkr11/MolSim.git
-  ```
+``` 
+
+- manual build (I would recommend using make with -j $(nproc) as this is pretty slow)
+
+```bash
+  mkdir build
+  cmake -S . -B build -<options>
+  cd build
+  make -j $(nproc)
+```
+
+- Testing:
+
+```bash
+  cmake -S . -B build -DBUILD_TESTS=ON 
+```
+
+To build with Intel's C++ compiler (```icx```/```icpx```), set the following options (currently this is on the [
+`coolmuc_test`](https://github.com/jkr11/MolSim/tree/coolmuc_test) branch, but it works locally)
+
+```bash
+  cmake -S . -B build -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx
+```
+
+for other compilers add the necessary compiler id to the options.
+
+```bash
+  cd build/tests
+  make -j $(nproc)
+  ctest
+```
+
+Using the build script in `/script/`
+
 - Build the project using the provided build script by using source, add `-t` to also build and run tests, add `-b` to
-  enable the BENCHMARK cmake macro
-  ```bash
+  enable the BENCHMARK cmake macro and `-p` to enable OpenMP.
+
+```bash
   cd MolSim/scripts
-  source build <CMAKE_BUILD_TYPE= Release (default) | Debug | asan | asan-quiet>  [-t|--test] [-b|--benchmark]
-  ```
+  source build <CMAKE_BUILD_TYPE= Release (default) | Debug | asan | asan-quiet>  [-t|--test] [-b|--benchmark] [-p|--parallel] 
+```
+
 - Set the Input file by selecting the corresponding number during the script execution
-  ```bash
+
+```bash
   source set-input
-  ```
+```
 
 - Creating documentation when doxygen is installed (has to be executed in the specific `buildDir/<CMAKE_BUILD_TYPE>`)
-  ```bash
+
+```bash
   (cd ../buildDir/<CMAKE_BUILD_TYPE> when starting from /scripts)
   make doc_doxygen 
-  ```
+```
+
 - Running the program
-  ```bash
+
+```bash
   $BUILD -f $INPUT <options>
-  ``` 
+ ``` 
+
 - `$BUILD` contains the location of the last compiled executable
 - `$INPUT` contains the location of the selected input file
 - Please note that `$BUILD` and `$INPUT` are only available if the scripts are executed via source.
 
-### Options
+### CMake Options
+
+```console
+  - ENABLE_BENCHMARK : enables benchmark mode with no printing of info and writing to files
+  - BUILD_TESTS : enables and builds the tests/ directory in the build directory
+  - ENABLE_OPENMP : enables OpenMP and support for multithreading
+```
+
+### Executable Options
 
   ```console
   Options:
@@ -48,22 +106,62 @@ MolSim - Group A
   [--step_size | -s <double>]     Specify how often the output will be written wrt. time(step_size), default=1
                                     Note that this is independent of the time resolution (t_delta) and dependent on the simulation time
   [--loglevel | -l <level>]       Specify the log level, default=info, valid=[off, error, warn, info, debug, trace]
-  [--checkpoint | -c ]            Specifies if the final particle state will be saved to a checkpoint file.
+  [--checkpoint | -c <path>]      Specifies the path the final state of the particles will be saved to.
   Example usage:
   $BUILD -f $INPUT -l <loglevel> -s <number>
   ```
 
 - Output is located in `./output/<current_time>`
-- Checkpoint is currently fixed to `checkpoint.xml` also in `./output/`
+- Checkpoints as an input have to be explicitely stated in the input ```.xml``` file. In order to verify against the
+  checkpoint schema, all checkpoint files must point to the valid schema. As this location is hardcoded, all checkpoints
+  work out of the box if they are in the `/input/` directory. If they are somewhere else, you have to adjust the schema
+  path in the header of the checkpoint file.
+
+- A quick example for checkpointing in Assignment 4 task 3: (in `build/src`)
+
+```bash
+  ./MolSim -f ../../input/week43checkpoint.xml -c ../../input/<name_of_your_choice.xml>
+  ..... This eventually writes the checkpoint after running ----------
+```
+
+the add the following to week43.xml:
+
+```xml
+
+<checkpoint>
+    <name>../../input/
+        <name_of_your_choice.xml>
+    </name>
+    ...
+</checkpoint>
+```
+
+and run
+
+```bash
+  ./MolSim -f ../../input/week43.xml
+```
+
 - `--step_size` is relative to the passed simulation time and not the number of iterations
 - `--loglevel debug` is only available if compiled with CMAKE_BUILD_TYPE=Debug
 - all other options are specified in the .xml input file
 - old inputs have been migrated to xml and support this pipeline
 
+## Parallelization strategies
+
+First, compile with `-DENABLE_OPENMP=ON` to support using OpenMP.
+
+Then, use the xml tag `<use_c18_strategy>` in `<metadata>`, write true to use the c18 travesal, false to use the force
+buffer
+method or remove the thing entirely to use no parallelization at all (even if this is active). If OpenMP is not used,
+this does nothing.
+
 ## LinkedCells vs DirectSum performance
 
 ### Running benchmark.py
 
+Note this is a remnant from week 3 and 4, but this technically could be rewritten to test 5
+
 For optimal performance run scripts/build with -b for benchmarking
 The python script uses the generated executable in buildDir/Release/src for execution.
 Ensure you have python 3.6 or later installed