bensutherland/install_colony_parallel_linux.md

## install_colony_parallel_linux.md

      
    Raw
  

              install_colony_parallel_linux.md
            
          
    Install colony on Linux

The following are instructions for installation of colony on linux, specifically for the user, with no guarantees of usefulness or correctness.
This allowed the current version of colony (downloaded 2019-05-21) to be installed with mpi for parallelization on Linux.
Installation instructions


Download colony from https://www.zsl.org/science/software/colony


Download mpich 3.2.1 source code here: https://www.mpich.org/downloads/


Move the downloaded mpich source code compressed folder to your programs folder.


Decompress, configure, and make the program:


tar -zxvf mpich-3.2.1.tar.gz
cd mpich-3.2.1
# make a directory within this folder for installation
mkdir mpi-install
./configure --prefix=/home/ben/Programs/mpich-3.2.1/mpi-install/ 
# Change the path to where you have saved your mpich folder
# If there is no prefix used, this will install into /usr/local/include

sudo make all install


Update your bashrc
Export LD library path by adding the following to your ~/.bashrc:

# Add the following to your $PATH variable in the ~/.bashrc
/home/ben/Programs/mpich-3.2.1/mpi-install/bin

# Add the following line to the bottom of your bashrc to give access to the libraries
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/ben/Programs/mpich-3.2.1/mpi-install/lib


Testing
Test it out from the COLONY directory, with the test dataset:
mpirun -np 8 ./colony2p.ifort.impi2015.out