ReleaseNotes

BEAGLE release notes

version 3.1.2

• Further fixes to pthread linking problems for Linux compilation under GCC;
• Fixed issue with odd state counts and CPU SSE;
• Fixed issue with non nucleotide state counts on AMD GPUs;
• Adjustments to CPU auto-threading heuristics.

version 3.1.1

• Fixed pthread linking issue on Linux which prevented some programs from loading CPU plugin;
• Fixed issue with multi-partition mode and unrooted trees on CPU implementation (multi-partition on CPU typically only used for debugging)

version 3.1.0

• Automatic resource selection via beagleGetBenchmarkedResourceList;
• Control of CPU threading with beagleSetCPUThreadCount;
• CPU implementation now defaults to non-threaded implementation to replicate behaviour of previous versions;
• Improved CPU auto-threading to use fewer threads for better performance in some scenarios;
• Improved performance for CUDA implementation when rescaling (improved synchonization of streams).

version 3.0.2

• Fixed macOS installer to place BEAGLE JNI library in correct location;
• Removed OpenCL implementation from macOS build and installer, as OpenCL is being deprecated by Apple.

version 3.0.1

• Fixed issue with GPU implementation (undersized array allocation).

version 3.0.0

• Improved performance for partitioned data sets;
• Improved performance for large trees with short alignments;
• Improved performance for default CPU implementation, via use of threading;
• Several bug fixes.

version 2.1.2

• Fixed OS X binary release issue with GNU libtool shared library dependency.

version 2.1.1

• Fixed OS X binary release compatibility with system versions 10.6, 10.7, and 10.8.

version 2.1

• Support for OpenCL on CPU for Apple devices;
• SSE and CUDA plugins for Windows reintroduced;
• Windows installer detects previous versions and removes them automatically;
• Other bug fixes, including ones that affected OpenCL performance.

version 2.0

• OpenCL support for GPUs, including AMD, and CPUs (multicore and vectorisation);
• Multi-epoch substitution models;
• Bug fixes and performance improvements.

version 1.0

• Initial release.