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Prerequisites
Basic installation
Optional: adding capabilities to read AMBER .ncdf format trajectory files.

#Installing the pyPcazip package on an Amazon ec2 instance

This document walks through the process of installing pyPcazip on a fresh micro instance on AWS ec2 (i.e., the sort of resource available for free trials).

Prerequisites

We assume you have got to the stage of creating your fresh instance, and have just logged into it for the first time.

Basic installation

Step 1: get up-to-date:

$ sudo yum update

Step 2: install development tools (compilers):

$ sudo yum groupinstall “Development Tools”
$ sudo yum install python-devel
$ sudo yum install lapack-devel

Step 3: increase virtual memory to allow for future compilation, see: http://stackoverflow.com/questions/17173972/how-do-you-add-swap-to-an-ec2-instance

Step 4: edit .bashrc to add ~/.local/bin to PATH and reload.

Step 5: install numpy, scipy, cython and mdtraj:

$ pip install --user numpy
$ pip install --user scipy
$ pip install --user cython
$ pip install --user mdtraj

Step 6: install pyPcazip:

$ pip install --user pyPcazip

Step 7 (Optional): download and run the tests:

$ pyPcazip --tests

Optional: adding capabilities to read AMBER .ncdf format trajectory files.

Step 1: install zlib-devel:

$ sudo yum install zlib-devel

Step 2: now follow instructions at: https://code.google.com/p/mdanalysis/wiki/netcdf

Specifically:

$ wget ftp://ftp.hdfgroup.org/HDF5/current18/src/hdf5-1.8.18.tar.bz2
$ tar -jxvf hdf5-1.8.18.tar.bz2
$ cd hdf5-1.8.18
$ HDF5_DIR=/usr/local
$ ./configure --prefix=$HDF5_DIR --enable-hl --enable-shared
$ make
$ sudo make install

$ wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz
$ tar –zxvf netcdf-4.3.3.tar.gz
$ cd netcdf-4.3.3
$ ./configure --prefix=/usr/local --enable-netcdf-4 --enable-shared ¬¬--enable-dap --disable-doxygen CPPFLAGS="-I$HDF5_DIR/include" LDFLAGS="-L$HDF5_DIR/lib"
$ make
$ sudo make install

Step 3: install Python netCDF4:

$ pip install --user netCDF4

Step 4: run the tests to check:

$ pyPcazip --tests