KrylovFspSsa

Fortran implementation of the Krylov-FSP-SSA algorithm.

Reference:

R.B.Sidje, H.D.Vo. "Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm". Mathematical Biosciences, Vol. 269, November 2015.

System requirements

This repository has been compiled successfully on ubuntu18.04 with the following libraries (installed with sudo apt-get install):

1. libblas
2. liblapack
3. gfortran

In addition, you need to build system CMake (version 3.17) that can be downloaded from https://cmake.org/download/.

If your computer uses a different operating system, I recommend trying first to compile this repository within a Docker container.

Compile the programs

You need the latest CMake (v 3.17) to properly generate the Makefile for this repository. Once you have installed CMake on your system, take the following steps to compile the modules and the example programs

1. Open a terminal; navigate to this repository folder; Then mkdir build
2. cd build; cmake ..
3. If things go well, you will see the following outputs from cmake:

-- Configuring done 
-- Generating done 
-- Build files have been written to: <repository_folder>/build

4. Type make
5. After compilation, all program files will be available in the directory build.

Example of solving a model from input file

Copy the compiled program TestSolverFromFile from build into the subfolder models of this repository. Navigate to models and execute the program. The program will parse a reaction network model from the file toggle_model.input and solve the CME defined from that model.