Memory Leak (David Estes-Smargiassi) Mac OS

Mac OS 8.0 introduces the most visible changes in the line-up, including the Platinum interface and a native PowerPC multithreaded Finder. Mac OS 8.1 introduces a new, more efficient file system named HFS Plus. Mac OS 8.5 is the first version of the Mac OS to require a PowerPC processor. Wired memory is used by the OS and is pretty much untouchable. Another application can't 'borrow' wired memory. Active memory is what is currently in use by running applications. Note that thanks to the splendors of virtual memory, all of the memory needed by an application isn't necessarily contained here. In computer science, a memory leak is a type of resource leak that occurs when a computer program incorrectly manages memory allocations in a way that memory which is no longer needed is not released. A memory leak may also happen when an object is stored.

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GARLI - by Derrick J. Zwickl (zwickl@nescent.org)

(Genetic Algorithm for Rapid Likelihood Inference)

May 2008: A new GARLI version has been released (version 0.96 beta) and the download page has moved to: http://garli.nescent.org

This is a major revision that adds many new features and improvements (listed at the new download page), and users should migrate from the previous version 0.951.

A GARLI information and support page has been created at: http://www.nescent.org/wg/garli

Note that the OS X graphical version of the program has not yet been updated, but the old graphical version 0.951 may still be downloaded below.

The old (pre-May 2008) download page:

version 0.951 (posted 10/26/06, page updated 10/31/06)

• GARLI performs heuristic phylogenetic searches under the General Time Reversible (GTR) model of nucleotide substitution and its submodels, with or without gamma distributed rate heterogeneity and a proportion of invariant sites.
• The implementation of this model is exactly equivalent to that in PAUP* (by David Swofford), so that likelihood scores obtained by each program are directly comparable.
• Besides the OS X GUI version, GARLI is not interactive. All program settings are specified in a configuration file. Examples come with the program, and the manual describes all of the options.
• The program reads non-interleaved phylip and nexus datafiles. In reality it is not currently very nexus compliant, and can be confused in various ways. It should have no problem with nexus datasets exported directly from PAUP, however.
• GARLI also implements a parallel MPI based algorithm for use on parallel computing clusters (note that the parallel version seeks to perform a more thorough tree search and does NOT reduce runtimes. It typically is only helpful on datasets with greater than about 500 sequences)
• The program is not yet published, but has been used for published analyses. A publication presenting the program and investigating its performance is forthcoming. For the moment, please mention the download URL: www.bio.utexas.edu/faculty/antisense/garli/Garli.html and cite:
  

  Zwickl, D. J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin.

• PLEASE contact me with any problems, errors or questions you might about the program. The manual contains an FAQ, and I would be happy to add to it.
• If you would like to be notified by email about future GARLI news and updates, email me.(zwickl@nescent.org)

NEWS:

(10/16/06):-At long last, version 0.95 is released!
• This version includes constrained searches, flexible model specification, checkpointing a number of other important enhancements. It is highly recommended that all previous users upgrade to this version. See the manual for details.
• PLEASE review the differences in the config file from previous versions!! A number of new settings have been added and default settings changed. See the sample garli.conf file that comes with the program.
• The MPI parallel version of 0.95 requires more testing and is not yet available (expected release date unknown).
(10/19/06) - Mac OS X graphical version 0.95 is now available
(10/26/06) - Updated version 0.951 available
• All versions: Fixed a few minor issues that are unlikely to have any noticeable effect (small memory leak, constrained bootstrap now allowed, certain branch swaps were being avoided, minor output changes)
• Mac OSX GUI: Corrected problem when specifying model without rate heterogeneity, clarified interface for specification of starting topology, added ability to specify topological constraints, changes to default options
(10/31/06) - New postings
• Recompiled Windows executable (solves the 'application failed to start because the application configuration is incorrect' problem that some users were having)
• Multithreaded Windows executable (allows GARLI to use multiple processors on multi-core or multi-processor systems)

Known issues: PLEASE let me know of any issues that you encounter! (zwickl@nescent.org)

• Version 0.951 - (10/30/06) Changing the distanceswapbias option is not currently working as intended. Please leave it at its default value of 1.0, which effectively turns this feature off. This will be fixed in the next release.

Download GARLI version 0.951 (sample dataset and configuration file included):

Memory Leak (david Estes-smargiassi) Mac Os Download

GARLI version 0.95 manual: GARLIv0.95manual.pdf

Windows versions:

Windows executable: GARLIv0.951.win.zip

Multithreaded Windows executable: GARLIv0.951.winMultithread.zip (for Windows machines with multiple processors or multiple cores. May require installation of the 'Microsoft Visual C++ 2005 Redistributable Package', which is available here.)

Mac OS X versions:

Graphical Mac OS X application: (universal binary, requires OS 10.3 or later, interface designed by Jim Balhoff): GARLIv0.951.osX-GUI.tar.gz

Memory Leak (david Estes-smargiassi) Mac Os Full

Command-line Mac OS X application (universal binary): GARLIv0.951.osX.tar.gz (this must be run from the terminal, and cannot be double clicked)

Source code

Memory Leak (david Estes-smargiassi) Mac Os File

Source for serial unix compilation: GARLIv0.951.src.tar.gz

Source for most recent parallel MPI version: GARLIv0.942.src.tar.gz