Merge remote-tracking branch 'origin/kernel-concurrency'

app-benchmarks/v3-app-note/mcmc-dengue.nex

@@ -0,0 +1,50 @@
+#NEXUS
+
+begin mrbayes;
+
+set autoclose=yes nowarn=yes seed=1 swapseed=1;
+
+exe Dengue997.nex;
+
+
+
+charset capsid = 1-342;
+charset glycoprotein = 343-834;
+charset envelope = 835-2325;
+charset NS1 = 2325-3381;
+charset NS2A = 3382-4038;
+charset NS2B = 4039-4428;
+charset NS3 = 4429-6285;
+charset NS4A = 6286-6735;
+charset NS4B = 6736-7482;
+charset NS5 = 7483-.;
+
+[partition by_codon = 3:1st_pos,2nd_pos,3rd_pos;]
+partition by_gene = 10:capsid,glycoprotein,envelope,NS1,NS2A,NS2B,NS3,NS4A,NS4B,NS5;
+
+set partition=by_gene;
+
+lset nst=6 rates=invgamma;
+
+[lset rates=propinv;]
+
+[prset brlenspr=clock:uni;]
+[prset applyto=(all) brlenspr=clock:uni;]
+
+prset applyto=(all) ratepr=variable;
+
+unlink  shape=(all);
+unlink  pinvar=(all);
+unlink  statefreq=(all);
+unlink  revmat=(all);
+unlink  ratemultiplier=(all);
+[unlink  brlens=(all);]
+[unlink  clockrate=(all);]
+
+set seed=1 swapseed=1;
+
+[mcmc ngen=50000 nruns=1 nchains=1;]
+[mcmc ngen=1 nruns=1 nchains=1;]
+mcmc ngen=1000 nruns=1 nchains=1 printfreq=1000;
+
+end;

configure.ac

@@ -1,8 +1,8 @@
 dnl Process this file with autoconf to produce a configure script.
 AC_PREREQ([2.59])
-AC_INIT(libhmsbeagle, 2.1.2, beagle-dev@googlegroups.com)
+AC_INIT(libhmsbeagle, 3.0.0, beagle-dev@googlegroups.com)
 
-: ${CXXFLAGS=" -O3"}
+: ${CXXFLAGS=" -std=c++11 -O3"}
 
 dnl -----------------------------------------------
 dnl Package name and version number (user defined)
@@ -11,9 +11,9 @@ dnl -----------------------------------------------
 GENERIC_LIBRARY_NAME=libhmsbeagle
 
 #release versioning
-GENERIC_MAJOR_VERSION=2
-GENERIC_MINOR_VERSION=1
-GENERIC_MICRO_VERSION=2
+GENERIC_MAJOR_VERSION=3
+GENERIC_MINOR_VERSION=0
+GENERIC_MICRO_VERSION=0
 
 #API version
 GENERIC_API_VERSION=1
@@ -23,7 +23,7 @@ AC_SUBST(GENERIC_API_VERSION)
 GENERIC_REVISION_VERSION=$GENERIC_MINOR_VERSION
 
 #shared library versioning
-GENERIC_LIBRARY_VERSION=2:$GENERIC_REVISION_VERSION:1
+GENERIC_LIBRARY_VERSION=3:$GENERIC_REVISION_VERSION:2
 #
 #             current:revision:age
 #                |        |     |
@@ -126,6 +126,18 @@ dnl OpenMP checker only defines for C when compiling both C and C++
 OPENMP_CXXFLAGS=$OPENMP_CFLAGS
 AC_SUBST(OPENMP_CXXFLAGS)
 
+# ------------------------------------------------------------------------------
+# Setup C++11 threads 
+# ------------------------------------------------------------------------------
+dnl Check for gcc
+case $host_os in
+*linux*)
+  if test x$GCC = xyes
+  then
+    AM_CXXFLAGS="$AM_CXXFLAGS -pthread"
+  fi
+esac
+
 # ------------------------------------------------------------------------------
 # Setup OpenCL
 # ------------------------------------------------------------------------------
@@ -214,13 +226,16 @@ if test x$DEBUG = xtrue
 then
    NVCCFLAGS="-g"
 else
-   NVCCFLAGS="-O3"
+   NVCCFLAGS="-O3 -arch compute_32"
 fi
 if test x$EMULATION = xtrue
 then
    NVCCFLAGS+=" -deviceemu"
 fi
 
+# do not warn about deprecated GPU architectures
+NVCCFLAGS+=" -Wno-deprecated-gpu-targets"
+
 # ------------------------------------------------------------------------------
 # Setup SSE
 # ------------------------------------------------------------------------------