IMP::benchmark Namespace Reference

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Detailed Description

This module provides benchmarks of a variety of aspects of IMP.

The benchmarks modules provides support for developing and analyzing benchmarks of IMP code. In addition, it include a number of actual benchmarks of functionality from various modules (these may be moved to their respective modules later).

When the Google PerfTools are found, that profiler is linked in and its functionality exposed to python. This allows profiling of IMP C++ code on non-Mac OS enviroments (Mac OS users should use the Instruments program that comes as part of the developer tools for a much simpler and friendlier solution).

See the Benchmark Results page for historical benchmark results.

Author(s): Daniel Russel, Dina Schneidman

Version: SVN.r12662

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

• Daniel Russel, Keren Lasker, Ben Webb, Dina Schneidman, Javier Velázquez-Muriel, Andrej Sali, “Putting the pieces together: integrative structure determination of macromolecular assemblies”, PLoS Biology, 2012. This paper provides an overview of the key concepts in IMP and how to apply them to biological problems.
• Frank Alber, Friedrich Foerster, Dmitry Korkin, Maya Topf, Andrej Sali, “Integrating diverse data for structure determination of macromolecular assemblies”, Annual Review of Biochemistry, 2008. This paper provides a review of the integrative structure determination methodology and various data sources that can be used.

Profiling
One can use the google perftools profiler to profile code. On a mac, you should use the Instruments program instead (part of the mac os developer tools).
void	set_profile_name (std::string name)
void	set_is_profiling (bool tf)
Functions
int	get_return_value ()
void	report (std::string name, double value, double check)
	Report a benchmark result in a standard way.

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Function Documentation

void IMP::benchmark::report	(	std::string	name,
		double	value,
		double	check
	)

Report a benchmark result in a standard way.

void IMP::benchmark::set_is_profiling

(

bool

tf

)

Turn on or off profiling.

void IMP::benchmark::set_profile_name

(

std::string

name

)

Set the name of the file to use for profiling results.