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Installing NaMaster at NERSC

The following steps should be followed to install NaMaster at NERSC:

0 Python settings

First, pick your favourite python module at NERSC. NaMaster has been tested on both 2.7 and 3.6, so do either

module load python/2.7-anaconda-4.4

or

module load python/3.6-anaconda-5.2

You probably also want to have healpy installed:

pip install --user healpy

1 Install libsharp

libsharp is a C library for spherical harmonic transforms. Follow these steps to install it before moving on to NaMaster:

  1. Download libsharp from its github repository and unzip the file.
  2. From the libsharp folder run autoreconf -i, which will generate a configure file.
  3. Run ./configure --enable-pic and make
  4. Create three directories: bin, lib and include in your home directory (unless they're already there). E.g. mkdir $HOME/bin etc.
  5. Move the contents of auto/bin, auto/lib and auto/include to the corresponding folders you just created in your home directory.

Note that you should also have HEALPix installed. At NERSC, this is installed in /global/common/cori/contrib/hpcosmo/hpcports_gnu-4.0/healpix-3.30.1_62c0405b-4.0/ so just make sure this is included in your paths.

It's also useful to load anaconda 2.7 (e.g. module load python/2.7-anaconda).

2 Edit your .bashrc.ext

From your home directory, open the file .bashrc.ext with your favourite text editor and add the following lines at the end of it:

export PATH=$HOME/bin:$PATH
export LD_LIBRARY_PATH=$HOME/lib:/usr/common/software/gsl/2.1/intel/lib:/usr/common/software/cfitsio/3.370-reentrant/hsw/intel/lib:$LD_LIBRARY_PATH
export LDFLAGS="-L/usr/common/software/gsl/2.1/intel/lib -L/usr/common/software/cfitsio/3.370-reentrant/hsw/intel/lib -L$HOME/lib"
export CPPFLAGS="-I/usr/common/software/gsl/2.1/intel/include -I/usr/common/software/cfitsio/3.370-reentrant/hsw/intel/include -I$HOME/include"
export CC=cc

Note that, if you have previously editted either $LDFLAGS or $CPPFLAGS, the changes above should be appended to their already existing values to avoid messing up your environment.

3 Install NaMaster

Once libsharp has been installed, download or clone NaMaster from its github repository and follow these steps:

  1. Before anything else, run the following commands to avoid static linking of the final NaMaster library. Doing so just once would be enough (i.e. no need to include this in your .bashrc.ext):
export CRAYPE_LINK_TYPE=dynamic
export XTPE_LINK_TYPE=dynamic
  1. Run ./configure --prefix=$HOME, make and make install.
  2. Open the file setup.py with your favourite text editor and make sure that the variable use_icc is set to True.
  3. Run python setup.py install --user. This will install the python module, pymaster.
  4. To check that the installation worked, go to the test directory and run python check.py. If you see a bunch of small numbers and plots coming up after a while (and no errors occurred), you can congratulate yourself: you have a working version of NaMaster on NERSC!