ParaCopasi

A Python Package for Parallel COPASI tasks.

Platform

ParaCopasi is written in Python 3. The development and test was on Python 3.7.6 and Python 3.8.3. It currently only support Linux OS. For windows users, Windows Subsystem for Linux (WSL) is recommended. Here is a documentation for WSL installation on Windows 10 https://docs.microsoft.com/en-us/windows/wsl/install-win10

Prerequisite

MPICH

Please refer to the download page on the official website of MPICH: https://www.mpich.org/downloads/

mpi4py

mpi4py can be installed with the pip command.

pip install mpi4py

Copasi

Download from http://copasi.org/Download/. In ParaCopasi, the executable of Copasi CLI interface CopasiSE is called. The location of executable file CopasiSE must be specified. This can be done by either explicitly providing the location to ParaCopasi interfaces (paracopasi class methods or paracopasi_cmd command line), or setting the COPASIDIR environment variable as specified in http://copasi.org/Support/Installation/Linux/.

Example

The following is an example of using ParaCopasi via command line:

python ~/projects/ParaCopasi/paracopasi_cmd.py pe --workspace . --result_dir ./results/ --max_workers 500 --task_batch pe_two_step_sGC_activation.py