Merge pull request #826 from veg/2.3.14-rc

2.3.14
veg · Aug 8, 2018 · e142045 · e142045
2 parents 3cade25 + 1d4ca26
commit e142045
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Showing 60 changed files with 7,538 additions and 4,254 deletions.
diff --git a/.gitignore b/.gitignore
@@ -36,3 +36,4 @@ gmon.out
 messages.log
 errors.log
 tests/hbltests/libv3/data/CD2.nex.*.json
+tests/hbltests/libv3/data/CD2.prot.BGM.json
diff --git a/.travis.yml b/.travis.yml
@@ -27,10 +27,13 @@ env:
   - METHOD_TEST=tests/hbltests/libv3/aBSREL.wbf
   - METHOD_TEST=tests/hbltests/libv3/BUSTED.wbf
   - METHOD_TEST=tests/hbltests/libv3/LEISR.wbf
+  - METHOD_TEST=tests/hbltests/libv3/BGM.wbf
 
 language: c++
+
 compiler: 
   - gcc
+  - clang
 
 addons:
   apt:
@@ -39,17 +42,18 @@ addons:
         - ubuntu-toolchain-r-test
         - george-edison55-precise-backports
     packages:
-        - g++-6
-        - gcc-6
+        - g++-7
+        - gcc-7
 
 install:
-  - if [ "$CXX" = "g++" ]; then export CXX="g++-6" CC="gcc-6"; fi
+  - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
   - cmake . 
   - make HYPHYMP
   - make HYPHYGTEST
 
 script: 
-  - export OMP_NUM_THREADS=4
+  - export OMP_NUM_THREADS=8
+  - export LD_LIBRARY_PATH=/usr/local/clang/lib:$LD_LIBRARY_PATH
   - ./HYPHYGTEST
   - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/math.bf
   - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/iofunctions.bf

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -20,9 +20,9 @@ macro(PCL_CHECK_FOR_SSE3)
   include(CheckCXXSourceRuns)
   set(CMAKE_REQUIRED_FLAGS)
 
-  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
+  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
       set(CMAKE_REQUIRED_FLAGS "-msse3")
-  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
+  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
 
   check_cxx_source_runs("
       #include <pmmintrin.h>
@@ -46,9 +46,9 @@ macro(PCL_CHECK_FOR_AVX)
   include(CheckCXXSourceRuns)
   set(CMAKE_REQUIRED_FLAGS)
 
-  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
+  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
       set(CMAKE_REQUIRED_FLAGS "-march=corei7-avx -mtune=corei7-avx")
-  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
+  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
 
   check_cxx_source_runs("
       #include <immintrin.h>
@@ -71,6 +71,7 @@ endmacro(PCL_CHECK_FOR_AVX)
 set(CMAKE_MODULE_PATH cmake)
 set(HYPHY_VERSION 2.1)
 
+
 #-------------------------------------------------------------------------------
 # setup the files we'll be using
 #-------------------------------------------------------------------------------
@@ -94,7 +95,6 @@ set(DEFAULT_WARNING_FLAGS "-w")
 set(DEFAULT_DEBUG_WARNING_FLAGS "-Wall -Wno-int-to-pointer-cast -Wno-conversion-null -Wno-sign-compare -Wno-maybe-uninitialized")
 
 
-
 if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
     execute_process(
         COMMAND ${CMAKE_CXX_COMPILER} -dumpversion
@@ -144,13 +144,13 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
     set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3")
     PCL_CHECK_FOR_AVX()
     if(${HAVE_AVX_EXTENSIONS})
-        set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=corei7-avx -mtune=corei7-avx")
+        set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=corei7-avx -mtune=corei7-avx ")
         add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
     else(${HAVE_AVX_EXTENSIONS})
         PCL_CHECK_FOR_SSE3()
         if(${HAVE_SSE3_EXTENSIONS})
             add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
-            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse3 ")
+            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse3")
         endif(${HAVE_SSE3_EXTENSIONS})
     endif (${HAVE_AVX_EXTENSIONS})
 
@@ -175,6 +175,14 @@ if(NOT DEFINED DEFAULT_WARNING_FLAGS)
     set(DEFAULT_WARNING_FLAGS "")
 endif(NOT DEFINED DEFAULT_WARNING_FLAGS)
 
+include (CheckLibraryExists)
+
+CHECK_LIBRARY_EXISTS( "libamdlibm.so" "amd_log" "" HAS_AMD_LIBM)
+if(HAS_AMD_LIBM)
+    set(DEFAULT_LINK_FLAGS "${DEFAULT_LINK_FLAGS} -lamdlibm")
+    add_definitions(-D__USEAMDLOG__)
+endif(HAS_AMD_LIBM)
+
 
 #-------------------------------------------------------------------------------
 # OpenMP support

diff --git a/res/TemplateBatchFiles/AnalyzeCodonData.bf b/res/TemplateBatchFiles/AnalyzeCodonData.bf
@@ -23,12 +23,12 @@ if (modelType)
 	ChoiceList (branchLengths, "Branch Lengths", 1, SKIP_NONE,
 							   "Estimate", "Estimate branch lengths by ML",
 							   "Proportional to input tree", "Branch lengths are proportional to those in input tree");
-				 				  
+
 	if (branchLengths < 0)
 	{
 		return;
 	}
-	
+
 	if (branchLengths == 1)
 	{
 		global treeScaler = 1;