diff --git a/README.md b/README.md index ff9fbc07..d2335027 100644 --- a/README.md +++ b/README.md @@ -21,12 +21,15 @@ The paper describing the algorithms used for calculating likelihoods of sequence ### Binary installers -* [BEAGLE v3.0.0 pre-release for Mac OS X 10.6 and later](https://github.com/beagle-dev/beagle-lib/releases/download/v3.0.0-pre20180420/BEAGLE.v3.0.0pre.pkg) -* [BEAGLE v2.1 for Windows XP and later](https://www.dropbox.com/s/61z48jvruzkwkku/BEAGLE-2.1.msi) (v3.0.0 for Windows coming soon) +* [BEAGLE v3.0.0 for macOS](https://github.com/beagle-dev/beagle-lib/releases/download/v3.0.0/BEAGLE.v3.0.0.pkg) +* [BEAGLE v3.0.0 for Windows 64-bit](https://github.com/beagle-dev/beagle-lib/releases/download/v3.0.0/BEAGLE.v3.0.0.msi) + +- [BEAGLE v2.1.2 for Mac OS X 10.6 and later](https://www.dropbox.com/s/11kgt2jlq3lzln3/BEAGLE-2.1.2.pkg) +- [BEAGLE v2.1.0 for Windows XP and later](https://www.dropbox.com/s/61z48jvruzkwkku/BEAGLE-2.1.msi) ### Installation instructions -* [Instructions for installing BEAGLE on Mac OS X](https://github.com/beagle-dev/beagle-lib/wiki/MacInstallInstructions) +* [Instructions for installing BEAGLE on macOS](https://github.com/beagle-dev/beagle-lib/wiki/MacInstallInstructions) * [Instructions for installing BEAGLE on Windows](https://github.com/beagle-dev/beagle-lib/wiki/WindowsInstallInstructions) * [Instructions for installing BEAGLE on Linux](https://github.com/beagle-dev/beagle-lib/wiki/LinuxInstallInstructions) diff --git a/configure.ac b/configure.ac index b9dcc4fb..5663030f 100644 --- a/configure.ac +++ b/configure.ac @@ -1,6 +1,6 @@ dnl Process this file with autoconf to produce a configure script. AC_PREREQ([2.59]) -AC_INIT(libhmsbeagle, 3.0.0, beagle-dev@googlegroups.com) +AC_INIT(libhmsbeagle, 3.0.1, beagle-dev@googlegroups.com) : ${CXXFLAGS=" -std=c++11 -O3"} @@ -13,7 +13,7 @@ GENERIC_LIBRARY_NAME=libhmsbeagle #release versioning GENERIC_MAJOR_VERSION=3 GENERIC_MINOR_VERSION=0 -GENERIC_MICRO_VERSION=0 +GENERIC_MICRO_VERSION=1 #API version GENERIC_API_VERSION=1 diff --git a/libhmsbeagle/GPU/BeagleGPUImpl.hpp b/libhmsbeagle/GPU/BeagleGPUImpl.hpp index e85255b0..87bbe418 100644 --- a/libhmsbeagle/GPU/BeagleGPUImpl.hpp +++ b/libhmsbeagle/GPU/BeagleGPUImpl.hpp @@ -1942,13 +1942,19 @@ int BeagleGPUImpl::upPartials(bool byPartition, } int gridLaunches = 0; - std::vector gridStartOp(operationCount); - std::vector gridOpType(operationCount); - std::vector gridOpBlocks(operationCount); + int* gridStartOp; + int* gridOpType; + int* gridOpBlocks; int parentMinIndex = 0; int lastStreamIndex = 0; int gridOpIndex = 0; + if (kUsingMultiGrid) { + gridStartOp = (int*) malloc(sizeof(int) * (operationCount + 1)); + gridOpType = (int*) malloc(sizeof(int) * (operationCount + 1)); + gridOpBlocks = (int*) malloc(sizeof(int) * (operationCount + 1)); + } + int anyRescale = BEAGLE_OP_NONE; if (kUsingMultiGrid && (kFlags & BEAGLE_FLAG_SCALING_MANUAL)) { for (int op = 0; op < operationCount; op++) { @@ -2380,6 +2386,12 @@ int BeagleGPUImpl::upPartials(bool byPartition, gpu->SynchronizeDevice(); } + if (kUsingMultiGrid) { + free(gridStartOp); + free(gridOpType); + free(gridOpBlocks); + } + #ifdef BEAGLE_DEBUG_SYNCH gpu->SynchronizeHost(); #endif diff --git a/project/beagle-macos-packages/BEAGLE.pkgproj b/project/beagle-macos-packages/BEAGLE.pkgproj index 5b0f33dd..bbc309f1 100644 --- a/project/beagle-macos-packages/BEAGLE.pkgproj +++ b/project/beagle-macos-packages/BEAGLE.pkgproj @@ -786,7 +786,7 @@ USE_HFS+_COMPRESSION VERSION - 3.0.0 + 3.0.1 PROJECT_COMMENTS diff --git a/project/beagle-vs-2017/libhmsbeagle/PropertySheet.props b/project/beagle-vs-2017/libhmsbeagle/PropertySheet.props index 8afe98c0..9739e9dc 100644 --- a/project/beagle-vs-2017/libhmsbeagle/PropertySheet.props +++ b/project/beagle-vs-2017/libhmsbeagle/PropertySheet.props @@ -2,7 +2,7 @@ - 3.0 + 3.0.1 30