MolSim - Group A

Final Assignment

• Cmake 3.24
• Doygen 1.9.8 (sudo apt install doxygen)
• Libxerces (sudo apt install libxerces-c-dev)

• Install

  git clone https://github.com/jkr11/MolSim.git

• manual build

  mkdir build
  cmake -S . -B build - <options>
  cd build
  make

• testing: use option -DBUILD_TESTS=ON

  cd build/tests
  make
  ctest

• 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

  cd MolSim/scripts
  source build <CMAKE_BUILD_TYPE= Release (default) | Debug | asan | asan-quiet>  [-t|--test] [-b|--benchmark]

• Set the Input file by selecting the corresponding number during the script execution

  source set-input

• Creating documentation when doxygen is installed (has to be executed in the specific buildDir/<CMAKE_BUILD_TYPE>)

  (cd ../buildDir/<CMAKE_BUILD_TYPE> when starting from /scripts)
  make doc_doxygen 

• Running the program

  $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:
--help | -h                     Show this help message
--file | -f <filename>          Specify the input file
[--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.
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/
• --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

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

cd benchmark
python -m vevn <name>
source <name>/bin/activate
pip3 install argparse matplotlib

python3 benchmark.py <options> 
options:
  -h, --help            show this help message and exit
  -a A_VALUES [A_VALUES ...], --a-values A_VALUES [A_VALUES ...]
                        List of 'a' values (multipliers of 1000 particles) to
                        simulate. Default: [1, 2, 4, 8].
  -o OUTPUT, --output OUTPUT
                        Path to save the output plot. Name it graph.png to
                        push it to git.
  -d, --cached-ds       Use default cached execution times for DirectSum
                        instead of running it.
  -s SAMPLES, --samples SAMPLES
                        Number of runs for each a value. Default = 1
  -c, --cubes           Compare three d files to two d files
  -n, --no-ds           Removes direct sum benchmarks from the plot

The LinkedCell implementation is more performant than the old DirectSum implementation.