denispaluca / psemoldyn

Molecular Dynamics Simulation

MolSim

Group B

Members:

• Trouvain, Mira
• Paluca, Denis
• Höbenreich, Jonas

Code

• Link: https://gitlab.lrz.de/denis/psemoldyn_groupb
• Branch: master
• commit: 5515b42b

Build and Run Instructions

Requirements

• log4cxx

MolSim program

• Compile with

  cmake -DDISABLE_DOXYGEN=ON -DCMAKE_BUILD_TYPE=Debug -G "CodeBlocks - Unix Makefiles" {PATH_TO_PROJECT}
  make MolSim -j <1.5 * number of cores>
  

• run main program with parameters specified in assignment:

  ./MolSim ./inputs/a4_task2_big.xml
  

• Compile on Cluster (Deactivate log4cxx)

  cmake -DCMAKE_BUILD_TYPE=Release -DCLUSTER=ON -G "CodeBlocks - Unix Makefiles" {PATH_TO_PROJECT}
  module load xerces-c
  cmake --build . --target MolSim -- -j 20
  

• Activate Parallelisation with -DOPENMP=ON

  cmake -DCMAKE_BUILD_TYPE=Release -DOPENMP=ON -G "CodeBlocks - Unix Makefiles" {PATH_TO_PROJECT}
  cmake --build . --target MolSim -- -j 20
  

General program call

./MolSim <PATH_TO_INPUT_FILE>

or for performance testing:

./MolSim <PATH_TO_INPUT_FILE> -pt

Tests

• Compile with

  cmake -DDISABLE_DOXYGEN=ON -DCMAKE_BUILD_TYPE=Debug  -G "CodeBlocks - Unix Makefiles" {PATH_TO_PROJECT}
  make Tests_run -j <1.5 * number of cores>
  

• run

  ctest
  

  or

  cd tests/
  ./Tests_run
  

Doxygen documentation

• Build with

  cmake -DCMAKE_BUILD_TYPE=Debug  -G "CodeBlocks - Unix Makefiles" {PATH_TO_PROJECT}
  make doc_doxygen
  

Input file format

see XSD file

Media

• a5_task2_video.avi

• Task 1 membrane

• as5_t4_color_velocityY.avi

• as5_t4_gravity5

• Additional Membrane Simulations:

• Membrane and cube

• Membrane lifted on three corners

• vertical membrane

Performance measurements

*The OS/hardware the measurements were made on Linux Cluster (COOL-MUC 2) *

Misc

• Compiler used: gcc 9.3.0
• CMake version: 3.16.3
• Google Tests version: 1.10.0
• modules used on cluster:

1. admin/1.0 4) spack/staging/20.2.2 7) intel-mpi/2019-intel
2. tempdir/1.0 5) intel/19.0.5 8) xerces-c/3.2.1
3. lrz/1.0 6) intel-mkl/2019 9) gcc/8.4.0