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#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
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
Updated