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Installing pyPcazip on ARCHER

Step 1: Install or load the dependencies.

Most of pyPcazip's dependencies can be satisfied by loading the required ARCHER modules:

module load python-compute pc-numpy pc-scipy cray-hdf5 pc-netcdf4-python

Step 2: Set the installation directory.

For the pyPcazip tools (and any other user-installed Python packages) to be useable in batch jobs, they must be installed under the user's $WORK directory, not under the $HOME directory. The simplest way to do this is to edit your .bashrc file to include the following lines (AFTER the lines where the modules python-compute, etc., are loaded):

# PYTHONUSERBASE defines where pip with '--user' puts packages.
export PYTHONUSERBASE=$(readlink -f /work/e280/e280/username/.local)
# Ensure the local package directories get searched first
export PATH=$PYTHONUSERBASE/bin:$PATH
export PYTHONPATH=$PYTHONUSERBASE/lib/python2.7/site-packages:$PYTHONPATH

##Step 3: Install pyPcazip.

Before installing pyPcazip, it may be necessary to install a newer version of the cython package:

module swap PrgEnv-cray PrgEnv-gnu
pip install --user --ignore-installed cython

Now pyPcazip should install without problems:

pip install --user pyPcazip

Example of a submission script on ARCHER to run a pyPcazip job

(this assumes that all required modules and paths (see above) are specified in your .bashrc file)

#!shell

#!/bin/bash --login 
#PBS -N pczArch
#PBS -l select=1
#PBS -l walltime=0:01:00
#PBS -A code_of_project_to_be_charged

export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
cd $PBS_O_WORKDIR

aprun -n 2 pyPcazip -i trajectory1.dcd  trajectory2.dcd -p topology.pdb -s 'name CA' -o pczfile.pcz

Installing pyPcazip on ARCHER with virtualenv

By using virtualenv it is possible to install pyPcazip in a manner that insulates it from other aspects of the user's environment on ARCHER:

export MYENV="/work/e290/e290/username/pyPcazipenv"
virtualenv $MYENV
. $MYENV/bin/activate
module swap PrgEnv-cray PrgEnv-gnu
easy_install cython
git clone https://bitbucket.org/ramonbsc/pyPcazip.git
cd pyPcazip
module load python-compute pc-numpy pc-scipy cray-hdf5 pc-netcdf4-python
easy_install --upgrade .

Afterwards, set the environment variables PATH and PYTHONPATH as follows:

export PATH=$MYENV/bin:$PATH
export PYTHONPATH=$MYENV/lib/python2.7/site-packages:$PYTHONPATH

Uninstalling pyPcazip

To uninstall pyPcazip that has previously been installed through pip/easy_install on ARCHER type:

pip uninstall pyPcazip

Who do I talk to?

• charles.laughton@nottingham.ac.uk
• ardita.shkurti@nottingham.ac.uk (Repo admin)
• rgoni@mmb.pcb.ub.es (Repo owner/admin)
• e.breitmoser@epcc.ed.ac.uk
• ibethune@epcc.ed.ac.uk