Running amuse on the Cartesius supercomputer

Cartesius is a bullx system, a clustered SMP (Symmetric Multiprocessing) system built by Bull. For more information, visit  https://www.surfsara.nl/systems/cartesius/description.

Preparation

Make a directory for all work files etc.

mkdir amuse

cd amuse

Get the latest amuse release

wget http://www.amusecode.org/releases/amuse-8.1.tar.gz

To get an svn version of AMUSE (if you have an svn account):

module load subversion

svn co http://www.amusecode.org/svn/trunk amuse-svn

For a release download, unzip and untar the release

gzip -d amuse-8.1.tar.gz

tar -xvf amuse-8.1.tar

Create a file called 'setdev' and put this text in it:

#!/bin/sh

module load gsl
export PATH=$PATH:$SURFSARA_GSL_BIN
module load fftw3/gnu
module load hdf5

export AMUSEROOT=/home/<username>/<directory>

export PYTHONPATH=${PYTHONPATH}:${AMUSEROOT}/amuse-8.1/src
export PYTHONPATH=${AMUSEROOT}/prerequisites/lib/python2.6/site-packages/:${PYTHONPATH}

export PREFIX=${AMUSEROOT}/prerequisites/
export PATH=${PREFIX}/bin:${PATH}
export LD_LIBRARY_PATH=${PREFIX}/lib:${LD_LIBRARY_PATH}
export LIBRARY_PATH=${PREFIX}/lib:${LIBRARY_PATH}

export FC=gfortran
export F77=gfortran
export FORTRAN=gfortran
export CC=gcc
export CXX=g++

export MPIFC=mpif90
export MPICC=mpicc
export MPICXX=mpicxx

Take care to replace <username> with your name and <directory> with the directory containing the workfiles ('amuse' if you follow all steps to the letter). Also take car to replace amuse-8.1 with amuse-svn if you ran the svn checkout line.

Before installing any packages or building amuse do:

source setdev

mkdir $PREFIX

then, to install Python and the rest of the prerequisites:

cd <amuse-path>/doc/install
./install-python.sh
./install.py download
./install.py install

Install AMUSE

./configure --with-gsl-prefix=/hpc/sw/gsl-1.15-gnu

make clean

make

Run

You should be ready to go now. Run the nosetests to check whether AMUSE and all its community codes work properly. For information about how to run jobs on Cartesius, visit  https://www.surfsara.nl/systems/cartesius/usage.