beagle-lib - Project Hosting on Google Code

Last 7 days Dec 04, 2009 r638 (added 4-state optimized CPU version of calcRoot for mixed mo...) committed by daniel.ayres - added 4-state optimized CPU version of calcRoot for mixed models added 4-state optimized CPU version of calcRoot for mixed models Dec 04, 2009 r637 (fixed bug with second derivative in calcEdge; added empirica...) committed by daniel.ayres - fixed bug with second derivative in calcEdge; added empirical derivative testing to fourtaxon; refactored calcRoot in CPU implementation to allow optimized versions (SSE, 4State) of mixed models fixed bug with second derivative in calcEdge; added empirical derivative testing to fourtaxon; refactored calcRoot in CPU implementation to allow optimized versions (SSE, 4State) of mixed models Dec 03, 2009 r636 (added support for derivative calculation to CPU implementati...) committed by daniel.ayres - added support for derivative calculation to CPU implementation; added option to fourtaxon to calculate and print derivatives added support for derivative calculation to CPU implementation; added option to fourtaxon to calculate and print derivatives Last 30 days Nov 30, 2009 r635 (reference to platform.h move from libhmsbeagle_la_SOURCES to...) committed by mtholder - reference to platform.h move from libhmsbeagle_la_SOURCES to library_include_HEADERS. beagle.h includes platform.h so we have to make sure that platform.h is installed when a user installs the library (or just inline the content of platform.h into beagle.h) reference to platform.h move from libhmsbeagle_la_SOURCES to library_include_HEADERS. beagle.h includes platform.h so we have to make sure that platform.h is installed when a user installs the library (or just inline the content of platform.h into beagle.h) Nov 29, 2009 r634 (Fixed bug in setTransitionMatrix; Ian would like this functi...) committed by msuchard - Fixed bug in setTransitionMatrix; Ian would like this functionality for porting BEAGLE into xrate Fixed bug in setTransitionMatrix; Ian would like this functionality for porting BEAGLE into xrate Nov 27, 2009 issue 8 (A typo about EAGLE_FLAGS_COMPLEX) reported by xiepenguin - libhmsbeagle\GPU\BeagleGPUImpl.cpp(601): if (kFlags & EAGLE_FLAGS_COMPLEX) "EAGLE_FLAGS_COMPLEX" should be "EAGLE_FLAG_COMPLEX" libhmsbeagle\GPU\BeagleGPUImpl.cpp(601): if (kFlags & EAGLE_FLAGS_COMPLEX) "EAGLE_FLAGS_COMPLEX" should be "EAGLE_FLAG_COMPLEX" Nov 25, 2009 r633 (Removed a hard coded preferences for SSE that was overriding...) committed by rambaut - Removed a hard coded preferences for SSE that was overriding other preferences. Sorry for putting it there. Removed a hard coded preferences for SSE that was overriding other preferences. Sorry for putting it there. Nov 23, 2009 r632 (implemented rescaling support for GPU version of calcRootLog...) committed by daniel.ayres - implemented rescaling support for GPU version of calcRootLogLikelihood when count is > 1 implemented rescaling support for GPU version of calcRootLogLikelihood when count is > 1 Nov 19, 2009 r631 (implemented GPU version of calcRootLogLikelihood when count ...) committed by daniel.ayres - implemented GPU version of calcRootLogLikelihood when count is > 1 (though no rescaling support yet) implemented GPU version of calcRootLogLikelihood when count is > 1 (though no rescaling support yet) Nov 17, 2009 r630 (fixed CPU rescaling for calcRootLogLikelihood when count is ...) committed by daniel.ayres - fixed CPU rescaling for calcRootLogLikelihood when count is > 1 fixed CPU rescaling for calcRootLogLikelihood when count is > 1 Nov 17, 2009 r629 (added code in tinyTest to test calcRootLogLikelihood when co...) committed by daniel.ayres - added code in tinyTest to test calcRootLogLikelihood when count is > 1 (works but need to fix scaling) added code in tinyTest to test calcRootLogLikelihood when count is > 1 (works but need to fix scaling) Nov 12, 2009 r628 (updated xcode project and removed a couple of minor warnings) committed by daniel.ayres - updated xcode project and removed a couple of minor warnings updated xcode project and removed a couple of minor warnings Earlier this year Oct 31, 2009 r627 (Fixed issue with pattern padding in CPU implementations) committed by msuchard - Fixed issue with pattern padding in CPU implementations Fixed issue with pattern padding in CPU implementations Oct 31, 2009 r626 (In process of debugging pattern padding) committed by dave.swofford - In process of debugging pattern padding In process of debugging pattern padding Oct 31, 2009 r625 (Changed cpp to hpp in Xcode) committed by msuchard - Changed cpp to hpp in Xcode Changed cpp to hpp in Xcode Oct 30, 2009 r624 (need to make the pesky config dir ) committed by aaron.darling - need to make the pesky config dir need to make the pesky config dir Oct 23, 2009 r623 (simplify optimization flags for profile-guided optimization,...) committed by aaron.darling - simplify optimization flags for profile-guided optimization, reduce requirement to sse2 simplify optimization flags for profile-guided optimization, reduce requirement to sse2 Oct 23, 2009 r622 (SSE now returns the SSE flag in its instance description.) committed by rambaut - SSE now returns the SSE flag in its instance description. SSE now returns the SSE flag in its instance description. Oct 23, 2009 r621 (Added a few more beagle options to BEAST main.) committed by rambaut - Added a few more beagle options to BEAST main. Added a few more beagle options to BEAST main. Oct 23, 2009 r620 (Possible fix for bug on GTX295) committed by msuchard - Possible fix for bug on GTX295 Possible fix for bug on GTX295 Oct 22, 2009 r619 (Started to convert 4StateSSEImpl into a template to easily a...) committed by msuchard - Started to convert 4StateSSEImpl into a template to easily allow for a singe-precision version Started to convert 4StateSSEImpl into a template to easily allow for a singe-precision version Oct 22, 2009 r618 (Fixed getPartials and getTransitionMatrix to handle padding ...) committed by msuchard - Fixed getPartials and getTransitionMatrix to handle padding (always for matrices and sometimes for partials) Fixed getPartials and getTransitionMatrix to handle padding (always for matrices and sometimes for partials) Oct 22, 2009 r617 (Stage 2 of adding beagleGetTransitionMatrix to JNI interface) committed by msuchard - Stage 2 of adding beagleGetTransitionMatrix to JNI interface Stage 2 of adding beagleGetTransitionMatrix to JNI interface Oct 22, 2009 r616 (Stage 1 is adding beagleGetTransitionMatrix to the API) committed by msuchard - Stage 1 is adding beagleGetTransitionMatrix to the API Stage 1 is adding beagleGetTransitionMatrix to the API Oct 22, 2009 r615 (Added pattern padding in CPU implementations for vectorizati...) committed by msuchard - Added pattern padding in CPU implementations for vectorization across patterns Added pattern padding in CPU implementations for vectorization across patterns Oct 22, 2009 r614 (Removed duplicated implementation names) committed by msuchard - Removed duplicated implementation names Removed duplicated implementation names Oct 22, 2009 r613 (Added some more BEAGLE options to the main dialog box.) committed by rambaut - Added some more BEAGLE options to the main dialog box. Added some more BEAGLE options to the main dialog box. Oct 22, 2009 r612 (Added some BEAST command-line options to control the BEAGLE ...) committed by rambaut - Added some BEAST command-line options to control the BEAGLE preference flags. For example -beagle_single to ask for single precision. These actually set a system preference beagle.preferred.flags so this can be set by the JVM. Cleaned up the presentation of information about what resource is being used - now the 'instance flags' are shown to show info about the implementation actually being used. Added some BEAST command-line options to control the BEAGLE preference flags. For example -beagle_single to ask for single precision. These actually set a system preference beagle.preferred.flags so this can be set by the JVM. Cleaned up the presentation of information about what resource is being used - now the 'instance flags' are shown to show info about the implementation actually being used. Oct 21, 2009 r611 (trying inline to avoid duplicate symbols in link ) committed by aaron.darling - trying inline to avoid duplicate symbols in link trying inline to avoid duplicate symbols in link Oct 21, 2009 r610 (Refactored MEMCNV to beagleMemCpy to avoid conflict with mac...) committed by msuchard - Refactored MEMCNV to beagleMemCpy to avoid conflict with macro defined in GPU Refactored MEMCNV to beagleMemCpy to avoid conflict with macro defined in GPU Oct 21, 2009 r609 (adding OpenMP for generic likelihood calc ) committed by aaron.darling - adding OpenMP for generic likelihood calc adding OpenMP for generic likelihood calc Oct 21, 2009 r608 (adding vis studio installer project to make dist ) committed by aaron.darling - adding vis studio installer project to make dist adding vis studio installer project to make dist Oct 21, 2009 r607 (removing extraneous #include ) committed by aaron.darling - removing extraneous #include removing extraneous #include Oct 21, 2009 r606 (removing extraneous #include ) committed by aaron.darling - removing extraneous #include removing extraneous #include Oct 21, 2009 r605 (templating MEMCNV to eliminate some of the if(DOUBLE_PRECISI...) committed by aaron.darling - templating MEMCNV to eliminate some of the if(DOUBLE_PRECISION) statements templating MEMCNV to eliminate some of the if(DOUBLE_PRECISION) statements Oct 21, 2009 r604 (Implement a different template-based naming function ) committed by aaron.darling - Implement a different template-based naming function Implement a different template-based naming function Oct 21, 2009 r603 (fix for dependency tracking, at least on linux ) committed by aaron.darling - fix for dependency tracking, at least on linux fix for dependency tracking, at least on linux Oct 21, 2009 r602 (Implemented getPartials with rescaling for the CPU) committed by msuchard - Implemented getPartials with rescaling for the CPU Implemented getPartials with rescaling for the CPU Oct 21, 2009 r601 (Some not-so-good compilation instructions; as INSTALL does n...) committed by msuchard - Some not-so-good compilation instructions; as INSTALL does not mention autogen.sh Some not-so-good compilation instructions; as INSTALL does not mention autogen.sh Oct 21, 2009 r600 (give appropriate visibility to base-class members ) committed by aaron.darling - give appropriate visibility to base-class members give appropriate visibility to base-class members Oct 20, 2009 r599 (Reduced memory footprint of GPU-complex implementation) committed by msuchard - Reduced memory footprint of GPU-complex implementation Reduced memory footprint of GPU-complex implementation Oct 20, 2009 r598 (Removing unnecessary kernels and related code) committed by msuchard - Removing unnecessary kernels and related code Removing unnecessary kernels and related code Oct 20, 2009 r597 (Complex GPU algorithm now works for stateCount == 4 under bo...) committed by msuchard - Complex GPU algorithm now works for stateCount == 4 under both MULTIPLY_BLOCK_SIZE = 16 and = 2, so it should work for any arbitrary stateCount as well Complex GPU algorithm now works for stateCount == 4 under both MULTIPLY_BLOCK_SIZE = 16 and = 2, so it should work for any arbitrary stateCount as well Oct 20, 2009 r596 (don't change the PATH env variable because MSI installer wil...) committed by aaron.darling - don't change the PATH env variable because MSI installer will then delete it on uninstall! don't change the PATH env variable because MSI installer will then delete it on uninstall! Oct 20, 2009 r595 (fix for wrong project name in installer build) committed by aaron.darling - fix for wrong project name in installer build fix for wrong project name in installer build Oct 20, 2009 r594 (New algorithm for complex GPU calculations; should be more s...) committed by msuchard - New algorithm for complex GPU calculations; should be more scalabe for large stateCounts New algorithm for complex GPU calculations; should be more scalabe for large stateCounts Oct 20, 2009 r593 (adding a script that will build all targets and create an in...) committed by aaron.darling - adding a script that will build all targets and create an installer using viz studio 2008 adding a script that will build all targets and create an installer using viz studio 2008 Oct 20, 2009 r592 (adding a windows installer project for viz studio 2008. cou...) committed by aaron.darling - adding a windows installer project for viz studio 2008. could use some testing. adding a windows installer project for viz studio 2008. could use some testing. Oct 20, 2009 r591 (Complex GPU works for stateCount == 4; further work is neede...) committed by msuchard - Complex GPU works for stateCount == 4; further work is needed general stateCounts Complex GPU works for stateCount == 4; further work is needed general stateCounts Oct 19, 2009 r590 (Added R script to generate test values for complex diagonali...) committed by msuchard - Added R script to generate test values for complex diagonalization Added R script to generate test values for complex diagonalization

r612 (Added some BEAST command-line options to control the BEAGLE ...) committed by rambaut - Added some BEAST command-line options to control the BEAGLE preference flags. For example -beagle_single to ask for single precision. These actually set a system preference beagle.preferred.flags so this can be set by the JVM. Cleaned up the presentation of information about what resource is being used - now the 'instance flags' are shown to show info about the implementation actually being used.

Added some BEAST command-line options to control the BEAGLE preference flags. For example -beagle_single to ask for single precision. These actually set a system preference beagle.preferred.flags so this can be set by the JVM. Cleaned up the presentation of information about what resource is being used - now the 'instance flags' are shown to show info about the implementation actually being used.

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