GBNCC-search: A complete python data reduction pipeline for the GBNCC pulsar survey.

Authors: Kevin Stovall (Univeristy of New Mexico) and Ryan S. Lynch (McGill University)

Repository Maintained by: Ryan S. Lynch ([email protected])

This file last modified on: 2013-11-04

This pipeline is used for downloading data from the GBNCC data archive (located at NRAO in Charlottesvile, VA), searching the data using a standalone script or through the use of HPC clusters, and tracking search jobs and verifying output. Logistics are handled through communication with a MySQL database that stores up-to-date information about the raw data files and their status regarding searches. The pipeline currently supports usage on the Guillimin HPC cluster.

The main executables used for data reduction are:

download.py : Communicate with the MySQL database to download raw data submit.py : Submit jobs to a supported HPC cluster search.py : Search data with the use of an HPC cluster trackjobs.py: Track the status of jobs in progress, verify results, and update the MySQL database

In addition to standard python packages, the following packages are required:

• PRESTO (www.cv.nrao.edu/~sransom/presto)
• MySQLdb
• numpy
• scipy
• pylab
• matplotlib
• mpfit
• pyfits
• pyslalib

Before using this pipeline, you should edit pipeline/lib/python/config.py, run setup.py, and update your PATH and PYTHONPATH. Then find pulsars!

Contents:

setup.py : Verify packages, test database connection, and set up directories pipeline/ : Top level pipeline directory pipeline/bin/ : Executables pipeline/bin/addObservations.py : Add raw data files to database pipeline/bin/download.py : Download raw data pipeline/bin/search.py : Search GBNCC data pipeline/bin/submit.py : Submit jobs to a supported HPC cluster pipeline/bin/trackjobs.py : Track HPC cluster jobs pipeline/lib/ : Libraries pipeline/lib/db_schema.txt : MySQL database description pipeline/lib/for_tarball/ : Packages for Guillimin python tarball pipeline/lib/GBNCC.zaplist : Standard Fourier zap list pipeline/lib/make_python_tarball.py : Make tarball of python packages pipeline/lib/python : Python modules pipeline/lib/python/analyse_sp.py : Single pulse searching algorithm pipeline/lib/python/clans2batch1.py : Script for running CLAS2 jobs pipeline/lib/python/config.py : Pipeline configuration variables pipeline/lib/python/database.py : Methods for communicating with MySQL database pipeline/lib/python/diagnostics.py : Methods for calculating job diagnostics pipeline/lib/python/group_sp.py : Methods for analyse_sp.py pipeline/lib/python/handle_exit.py : Clean-up during unexpected exits pipeline/lib/python/msub.py : Methods for communicating with moab que pipeline/lib/python/profile_tools.py : Methods for analyzing pulsar profiles pipeline/lib/python/ratings.py : Methods for calculating candidate ratings pipeline/lib/python/sp_utils.py : Methods for analyse_sp.py pipeline/lib/python/utils.py : General pipeline utilities pipeline/lib/python-2.6.8-packages-base.tar.gz : Base tarball of common python packages for use on Guillimn