https://github.com/snapex2409/komd

Small MD framework
https://github.com/snapex2409/komd

kokkos md molecular-dynamics simulation

Last synced: about 1 month ago
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Small MD framework

• Host: GitHub
• URL: https://github.com/snapex2409/komd
• Owner: Snapex2409
• License: mit
• Created: 2024-08-04T20:46:24.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2024-11-12T10:40:16.000Z (about 1 month ago)
• Last Synced: 2024-11-12T11:32:59.459Z (about 1 month ago)
• Topics: kokkos, md, molecular-dynamics, simulation
• Language: C++
• Homepage:
• Size: 3.75 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# KoMD

Small MD framework

The intention is to provide a full MD framework for non-rigid multi-site molecular models. 

Portability is provided by using Kokkos. Currently, OpenMP and Cuda backends are supported.

## Prequisites

* vtk Library: ```sudo apt install libvtk-qt-dev``` minimum version: 7

* For CUDA support: Install CUDA Toolkit, follow the instructions on the official CUDA Toolkit page.

* For OpenMP support: Install OpenMP lib and runtime

## Compilation

* Create build directory ``` mkdir build && cd build``` 

* Configure CMake ``` cmake .. ``` or ```ccmake ..```

* CMake options:

  * ENABLE_VTK:BOOL=ON|OFF

  * CUDA options:

    * CUDA_TOOLKIT_ROOT_DIR:FILEPATH=``````

    * CUDAToolkit_INCLUDE_DIRECTORIES:FILEPATH=```/targets/x86_64-linux/include```

    * CUDA_CUDART:FILEPATH=```/targets/x86_64-linux/lib```

  * Kokkos options:

    * Kokkos_ENABLE_``````:BOOL=ON backend options are CUDA and OpenMP

    * Kokkos_ARCH_NATIVE:BOOL=ON

    * Kokkos_NVCC_WRAPPER:FILEPATH=``````/dependencies-external/kokkos-4.3.01/bin/nvcc_wrapper

    * Kokkos_ARCH_``````:BOOL=ON set arch to used GPU architecture

* Compile with ```make all```

## Troubleshooting

* When installing CUDA Toolkit, make sure it is fully installed and sourced. If it is not, then many CUDA tools and libs need to be symlinked into PATH directories.

* Recommendation: Use ccmake to configure CMake. There all options will be visible.

## Input File format

* see ```examples/inp.dat```

## Running KoMD

* ```KoMD ```

* When running with OpenMP, set these env variables: OMP_PROC_BIND=spread;OMP_NUM_THREADS=8