MCGPULite

A Lightweight version of MC-GPU v1.3 (A GPU-Accelerated Monte Carlo X-Ray Transport Simulation Tool).

What's Different

• Makefile is rewritten to support standalone zlib, CUDA, nvcc and openmpi so that sudo apt-get is no more needed.

  • Have CUDA installed correctly.

  • Download zlib and openmpi. Compile them.

    # zlib
    ./configure
    make
    make install prefix=/zlib/install/path
    # openmpi
    ./configure --prefix=/openmpi/install/path
    make
    make install

  • Modify paths in Makefile according to your machine.

    # You should modify these according to your machine.
    NVCC = /usr/local/cuda-10.1/bin/nvcc
    CUDA_INCLUDE = /usr/local/cuda-10.1/include/
    CUDA_LIB = /usr/local/cuda-10.1/lib64/
    CUDA_SDK_INCLUDE = /usr/local/cuda-10.0/samples/common/inc/
    CUDA_SDK_LIB = /usr/local/cuda-10.0/samples/common/lib/linux/x86_64/
    OPENMPI_INCLUDE = /home/zhuoxu/app/openmpi-4.1.1/install/include/
    OPENMPI_LIB = /home/zhuoxu/app/openmpi-4.1.1/install/lib/
    ZLIB_INCLUDE = /home/zhuoxu/app/zlib-1.2.11/install/include/
    ZLIB_LIB = /home/zhuoxu/app/zlib-1.2.11/install/lib/

  • Compile MCGPULite.

    make clean
    make

  • You can create a symbol link and add it to PATH if you want.

    ln -s MCGPULite_v1.3.x MCGPULite
    
    # vim ~/.bashrc
    export PATH="/path/to/MCGPULite/folder/:$PATH"
    # source ~/.bashrc

• Dose information is longer reported. And input file doesn't require [SECTION DOSE DEPOSITION] now.

  # [SECTION CT SCAN TRAJECTORY v.2011-10-25]
  ...
  
  - # [SECTION DOSE DEPOSITION v.2012-12-12]
  - ...
  
  # [SECTION VOXELIZED GEOMETRY FILE v.2009-11-30]
  ...

• The output raw file consists of only 3 slices: Total, Primary, Scatter. Individual scatters (Compton, Rayleigh, Multi Scatter) are no longer reported.

• The bug of multiple GPUs run when all GPUs are detected connected to one monitor is fixed.

  Now you can run it like this on one GPU:

  # .in file. Specify which CUDA GPU to run on here.
  3              # GPU NUMBER TO USE WHEN MPI IS NOT USED, OR TO BE AVOIDED IN MPI RUNS
  
  # Command line. Just as it should be.
  ./MCGPULite ./<input_file>.in

  Or like this on multiple GPUs:

  # .in file. Use -1 always here.
  -1              # GPU NUMBER TO USE WHEN MPI IS NOT USED, OR TO BE AVOIDED IN MPI RUNS
  
  # Command line. Use CUDA_VISIBLE_DEVICES to specify GPUs, and pass GPU counts to -np.
  mpirun -x CUDA_VISIBLE_DEVICES=0,1,2,3 -np 4 ./MCGPULite ./<input_file>.in

  Through experiments, I don't recommend you to use multiple GPUs if your TOTAL NUMBER OF HISTORIES is less than 1e10 because of the distribution overhead. Otherwise, I achieve a time cutdown by 66% with 1e11 histories.

• The terminal outputs talk less.

Known Issues

• If you terminate MCGPULite with ^Z or ^C, its child process and thread are not killed. You should manually use kill -9 <pid> to kill.