Computing signal-to-noise ratio of dedispersed and folded time series.
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README.md

README.md

SNR

Some signal to noise computation kernels for many-core accelerators, with classes to use them in C++.

Publications

  • Alessio Sclocco, Joeri van Leeuwen, Henri E. Bal, Rob V. van Nieuwpoort. A Real-Time Radio Transient Pipeline for ARTS. 3rd IEEE Global Conference on Signal & Information Processing, December 14-16, 2015, Orlando (Florida), USA. (print) (preprint) (slides)
  • Alessio Sclocco, Henri E. Bal, Rob V. van Nieuwpoort. Finding Pulsars in Real-Time. IEEE International Conference on eScience, 31 August - 4 September, 2015, Munic, Germany. (print) (preprint) (slides)

Installation

Set the INSTALL_ROOT environment variable to the location of the pipeline sourcode. If this package is installed in $HOME/Code/APERTIF/Dedispersion this would be:

 $ export INSTALL_ROOT=$HOME/Code/APERTIF

Then build and test as follows:

 $ make install

Dependencies

Included programs

The integration step is typically compiled as part of a larger pipeline, but this repo contains two example programs in the bin/ directory to test and autotune an integration kernel.

SNRTest

Checks if the output of the CPU is the same for the GPU. The CPU is assumed to be always correct. Takes platform, layout, and kernel arguments, and has the following extra parameters:

  • print_code Print kernel source code
  • print_results Prints the integrated data

TODO: samples_dms and dms_samples options?

SNRTuning

Tune the SNR kernel's parameters by doing a complete sampling of the parameter space. Kernel configuration and runtime statistics are written to stdout. Takes platform, layout, and tuning arguments.

The output can be analyzed using the python scripts in in the analysis directory.

printCode

Prints the code for a specific integration kernel to stdout. Takes platform, data layout, and kernel arguments.

Commandline arguments

Description of common commandline arguments for the separate binaries.

Compute platform specific arguments

  • opencl_platform OpenCL platform
  • opencl_device OpenCL device number
  • padding number of elements in the cacheline of the platform

Data layout arguments

  • samples Number of samples; ie length of time dimension
  • dms Number of dispersion measures; ie length second dimension
  • dms_samples Ordering of the two dimensions: samples is fastest
  • samples_dms Ordering of the two dimensions: dms is fastest

Tuning parameters

  • iterations Number of times to run a specific kernel to improve statistics.
  • min_threads Minimum number of threads
  • max_threads Maximum number of threads
  • max_items Maximum number of variables that the automated code is allowed to use.

Kernel Configuration arguments

  • threads0 TODO
  • items0 TODO

Dependencies

Analyzing tuning output

Kernel statistics can be saved to a database, and analyzed to find the optimal configuration.

Setup

MariaDB

Install mariadb, fi. via your package manager. Then:

  1. log in to the database: $ mysql
  2. create a database to hold our tuning data: create database AAALERT
  3. make sure we can use it (replace USER with your username): grant all privileges on AAALERT.* to 'USER'@'localhost';
  4. copy the template configuration file: cp analysis/config.py.orig analysis/config.py and enter your configuration.

Python

The analysis scripts use some python3 packages. An easy way to set this up is using virtualenv:

$ cd $INSTALL_ROOT/SNR/analysis`
$ virtualenv --system-site-packages --python=python3 env`
$ . env/bin/activate`

And then install the missing packages:

$ pip install pymysql

Run Analysis

The analysis is controlled by the analysis/dedispersin.py script. It prints data as space-separated data to stdout, where you can plot it with fi. gnuplot, or copy-paste it in your favorite spreadsheet. You can also write it to a file, that can then be read by the SNR code.

  1. List current tables: ./snr.py list
  2. Create a table: ./snr.py create <table name>
  3. Enter a file create with SNRTuning into the database: ./snr.py load <table name> <file name>
  4. Find optimal kernel configuration: ./snr.py tune <table name> max <channels> <samples>

The tune subcommand also takes a number of different parameters: ./snr.py tune <table> <operator> <channels> <samples>

  • operator: max, min, avg, std (SQL aggergation commands)
  • channels: number of channels
  • samples: number of samples

License

Licensed under the Apache License, Version 2.0.