Merge branch 'master' of https://github.com/beagle-dev/beagle-lib

beagle-dev · May 11, 2018 · c2b4229 · c2b4229
2 parents a40b868 + bdca732
commit c2b4229
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Showing 5 changed files with 25 additions and 10 deletions.
diff --git 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
@@ -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, [email protected])
+AC_INIT(libhmsbeagle, 3.0.1, [email protected])
 
 : ${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
@@ -1942,13 +1942,19 @@ int BeagleGPUImpl<BEAGLE_GPU_GENERIC>::upPartials(bool byPartition,
     }
 
     int gridLaunches = 0;
-	std::vector<int> gridStartOp(operationCount);
-	std::vector<int> gridOpType(operationCount);
-	std::vector<int> 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<BEAGLE_GPU_GENERIC>::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
@@ -786,7 +786,7 @@
 			<key>USE_HFS+_COMPRESSION</key>
 			<false/>
 			<key>VERSION</key>
-			<string>3.0.0</string>
+			<string>3.0.1</string>
 		</dict>
 		<key>PROJECT_COMMENTS</key>
 		<dict>

diff --git a/project/beagle-vs-2017/libhmsbeagle/PropertySheet.props b/project/beagle-vs-2017/libhmsbeagle/PropertySheet.props
@@ -2,7 +2,7 @@
 <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <ImportGroup Label="PropertySheets" />
   <PropertyGroup Label="UserMacros">
-    <BeaglePackageVersion>3.0</BeaglePackageVersion>
+    <BeaglePackageVersion>3.0.1</BeaglePackageVersion>
     <BeaglePluginVersion>30</BeaglePluginVersion>
   </PropertyGroup>
   <PropertyGroup />