Install notes for BRC HPC SAVIO cluster

Installing on the SAVIO cluster is pretty straightforward, as many things can be loaded via modules. First, load the following modules.

module purge
module load intel
module load openmpi
module load fftw/3.3.4-intel
module load python/3.2.3
module load nose
module load numpy/1.8.1
module load scipy/0.14.0
module load mpi4py
module load pip
module load virtualenv/1.7.2
module load mercurial/2.0.2
module load hdf5/1.8.13-intel-p

We next need to make a virtual environment in which to build the rest of the Dedalus depencencies.

virtualenv python_build
source python_build/bin/activate

The rest of the depencies will be pip-installed. However, because we are using intel compilers, we need to specify the compiler and some how to link things properly.

export CC=icc
export LDFLAGS="-lirc -limf"

Now we can use pip to install most of the remaining dependencies.

pip-3.2 install cython
pip-3.2 install h5py
pip-3.2 install matplotlib==1.3.1

Dedalus itself can be pulled down from Bitbucket.

hg clone https://bitbucket.org/dedalus-project/dedalus
cd dedalus
pip-3.2 install -r requirements.txt

To build Dedalus, you must specify the locations of FFTW and MPI.

export FFTW_PATH=/global/software/sl-6.x86_64/modules/intel/2013_sp1.4.211/fftw/3.3.4-intel
export MPI_PATH=/global/software/sl-6.x86_64/modules/intel/2013_sp1.2.144/openmpi/1.6.5-intel
python3 setup.py build_ext --inplace

Using Dedalus

To use Dedalus, put the following in your ~/.bashrc file:

module purge
module load intel
module load openmpi
module load fftw/3.3.4-intel
module load python/3.2.3
module load numpy/1.8.1
module load scipy/0.14.0
module load mpi4py
module load mercurial/2.0.2
module load hdf5/1.8.13-intel-p
source python_build/bin/activate
export PYTHONPATH=$PYTHONPATH:~/dedalus