A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation

Algorithm 1

Algorithm for the stencil on a GPU.

for each color/parity do

  Load the potential Φ with opposite color/parity into a texture in the GPU.

  for all  𝑖∈[1,𝑛𝑧−1]  do

  Given a trace with given 𝑡𝑟𝑎𝑐𝑒𝐼𝑑.𝑥 and 𝑡𝑟𝑎𝑐𝑒𝐼𝑑.𝑦, calculate 𝑋,𝑌 and set 𝑍=𝑖:

    Fetch Φ_{(𝑋,𝑌,𝑍)} from the texture and put in shared memory.

   if  𝑖=1  then

   Fetch Φ_{(𝑋,𝑌,0)} from the texture.

   else

   Φ_{(𝑋,𝑌,𝑍−1)}=Φ_{(𝑋,𝑌,𝑍+1)}.

   end if

     Fetch Φ_{(𝑋,𝑌,𝑍+1)} from the texture.

     Calculate Laplace stencil and update the potential for the current color/parity.

  end for

end for