Some extra notes on installation¶
If you followed the installation process detailed above, you shouldn’t need these notes, but they are provided for users who may be running on environments they do not manage themselves.
Installing eigen3 without conda¶
If eigen3 isn’t on your system, and installing it with conda didn’t work
For OS X do:
brew install eigen
or on a linux system with apt:
apt-get install libeigen3-dev
or compile it from source
Note that if you do install it in a custom location, you may have to compile celerite yourself.
pip install celerite --global-option=build_ext --global-option=-I/path/to/eigen3
Installing OpenMPI and mpi4py without conda¶
if no mpi is on your system, and installing it with conda didn’t work
For OS X do:
brew install [mpich|mpich2|open-mpi]
on a linux system with apt:
apt-get install openmpi-bin
and if you had to resort to brew or apt, then finish with:
pip install mpi4py
Notes from installing on the Odyssey cluster at Harvard¶
These may be of use to get the code up and running with MPI on some other cluster. Good luck.
Odyssey uses the lmod system for module management, like many other clusters
module spider openmpi to find what the openmpi modules.
The advantage to using this is distributing your computation over multiple nodes. The disadvantage is that you have to compile mpi4py yourself against the cluster mpi.
module load gcc/6.3.0-fasrc01 openmpi/126.96.36.199dc0399-fasrc01 wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-2.0.0.tar.gz tar xvzf mpi4py-2.0.0.tar.gz cd mpi4py-2.0.0 python setup.py build --mpicc=$(which mpicc) python setup.py build_exe --mpicc="$(which mpicc) --dynamic" python setup.py install