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Working with the HPC Server

Account Access and Setup

Request an account, if you haven't already, then ssh <ucinetid>@hpc.oit.uci.edu (this will only work from a uci.edu IP address, so go through darkmatter if you are offsite).

Add the following to the bottom of your .bashrc file:

module load enthought_python/7.3.2
module load gcc/4.8.2
module load cuda/6.0
module load hdf5/1.8.11
#module load gsl/1.16
export PYTHONUSERBASE=/share/dm/all/local
export PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python2.7/site-packages
export PATH=$PATH:/share/dm/all/local/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/dm/all/local/lib/

Note that we do not use the boost or fftw modules provided by HPC since we have our own builds of these under /share/dm/all/local/.

Installing Software

Use the top-level /share/dm/all/build and /share/dm/all/local directories to install shared software.

Python Modules

HPC provides a module for enthought_python/7.3.2 so we use that for all the modules it provides. Unlike anaconda (which is not available via a module on HPC), enthought does not include astropy but the HPC staff installed pyfits for us manually a while ago.

GalSim will use either pyfits or astropy.io.fits. However, bashes requires astropy.io.fits, so we install that in user mode:

pip install --user --no-deps astropy

Note that this installs into the shared $PYTHONUSERBASE/lib/python2.7/site-packages/astropy/ if you set PYTHONUSERBASE as described above. Otherwise, it would go into ~/.local/lib/python2.7/site-packages/astropy/ and require each user to install their own private copy.


Install GalSim into /share/dm/all/local/:

cd /share/dm/all/build
git clone git@github.com:GalSim-developers/GalSim.git
cd GalSim
scons EXTRA_LIB_PATH=/share/dm/all/local/lib EXTRA_INCLUDE_PATH=/share/dm/all/local/include
scons install PREFIX=/share/dm/all/local PYPREFIX=/share/dm/all/local/lib/python2.7/site-packages


module purge
module load gcc/4.2.1
module load boost/1.53.0_gcc-4.2.1


../configure --without-minuit2 --without-gsl --prefix=/dm/software


../configure LDFLAGS=-L/dm/software/lib CPPFLAGS=-I/dm/software/include --prefix=/dm/software --without-fftw3