CUDA ProCell

CUDA version of ProCell software.

Installation

Software requirements:

• CUDA toolkit >= 8.0

• CMake >= 3.8

$ git clone https://github.com/ericniso/cuda-pro-cell.git

$ cd cuda-pro-cell

$ mkdir build

$ cd build

$ cmake -DCMAKE_CUDA_FLAGS="-arch=${GPU compute capability}" ..

$ make

The Compute Capability of your GPU can be found at this link CUDA GPU compute capabilities list.

It must be >= 3.5 in order to compile and execute the program.

For example, if you plan to use a GTX 970 with compute capability 5.2, the cmake command would look like the following:

$ cmake -DCMAKE_CUDA_FLAGS="-arch=sm_52" ..

Usage

The generated executable file is located under build/bin/ as procell

• -h or --histogram is the path of a file containing the histogram of the starting frequency values of the cell fluorescences:

  // histogram.txt
  
  <fluorescence value> <frequency>
  .
  .
  .
  <fluorescence value> <frequency>

  For example:

  1.0 0
  8.144 53
  .
  .
  .
  9823.85 274

• -c or --cell-types is the path of a file containing the list of subpopulation types properties:

  <ratio> <mean> <stddev>

  For example:

  // types.txt
  
  0.53 48.33 21.6
  0.29 86.3 26.8

  Quiescent type uses -1 as mean and stddev:

  // types-with-quiescent.txt
  
  0.18 -1 -1

• -t or --time-max is a double value >= 0 which specifies the max simulation time for cell divisions.

• -o or --output is the path of a file which will be used to store the resulting histogram values in the same format as the starting histogram.

• [OPTIONAL] -p or --phi is a double value > 0 which specifies the minimum fluorescence threshold for cell proliferation.

  If not provided, the minimum fluorescence value with frequency > 0 from the initial histogram will be used.

• [OPTIONAL] -r or --track-ratio tells the software to keep track of each input cell type frequency for each final fluorescence value.

  The ouput file is modified as follows:

  <fluorescence value> <total frequency> <cell type 1 frequency> ... <cell type nth frequency>
  .
  .
  .
  <fluorescence value> <total frequency> <cell type 1 frequency> ... <cell type nth frequency>

  The cell type frequencies are ordered as they are specified in the -c input file.