@@ -12,6 +12,7 @@ env:

   global:

     - TMPDIR=$HOME

+# make sure configure is executable

 before_install:

   - chmod +x configure

@@ -1,6 +1,6 @@

 #! /bin/sh

 # Guess values for system-dependent variables and create Makefiles.

-# Generated by GNU Autoconf 2.69 for CoGAPS 3.3.1.

+# Generated by GNU Autoconf 2.69 for CoGAPS 3.3.2.

 #

 #

 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.

@@ -577,8 +577,8 @@ MAKEFLAGS=

 # Identity of this package.

 PACKAGE_NAME='CoGAPS'

 PACKAGE_TARNAME='cogaps'

-PACKAGE_VERSION='3.3.1'

-PACKAGE_STRING='CoGAPS 3.3.1'

+PACKAGE_VERSION='3.3.2'

+PACKAGE_STRING='CoGAPS 3.3.2'

 PACKAGE_BUGREPORT=''

 PACKAGE_URL=''

@@ -698,6 +698,7 @@ enable_dependency_tracking

 enable_debug

 enable_warnings

 enable_simd

+enable_openmp

 '

       ac_precious_vars='build_alias

 host_alias

@@ -1261,7 +1262,7 @@ if test "$ac_init_help" = "long"; then

   # Omit some internal or obsolete options to make the list less imposing.

   # This message is too long to be a string in the A/UX 3.1 sh.

   cat <<_ACEOF

-\`configure' configures CoGAPS 3.3.1 to adapt to many kinds of systems.

+\`configure' configures CoGAPS 3.3.2 to adapt to many kinds of systems.

 Usage: $0 [OPTION]... [VAR=VALUE]...

@@ -1332,7 +1333,7 @@ fi

 if test -n "$ac_init_help"; then

   case $ac_init_help in

-     short | recursive ) echo "Configuration of CoGAPS 3.3.1:";;

+     short | recursive ) echo "Configuration of CoGAPS 3.3.2:";;

    esac

   cat <<\_ACEOF

@@ -1349,6 +1350,7 @@ Optional Features:

   --enable-debug          build debug version of CoGAPS

   --enable-warnings       compile CoGAPS with warning messages

   --enable-simd           specify simd instruction set (sse, avx)

+  --enable-openmp         compile with openMP support if available

 Some influential environment variables:

   CXX         C++ compiler command

@@ -1428,7 +1430,7 @@ fi

 test -n "$ac_init_help" && exit $ac_status

 if $ac_init_version; then

   cat <<\_ACEOF

-CoGAPS configure 3.3.1

+CoGAPS configure 3.3.2

 generated by GNU Autoconf 2.69

 Copyright (C) 2012 Free Software Foundation, Inc.

@@ -1871,7 +1873,7 @@ cat >config.log <<_ACEOF

 This file contains any messages produced by compilers while

 running configure, to aid debugging if configure makes a mistake.

-It was created by CoGAPS $as_me 3.3.1, which was

+It was created by CoGAPS $as_me 3.3.2, which was

 generated by GNU Autoconf 2.69.  Invocation command line was

   $ $0 $@

@@ -2734,7 +2736,7 @@ fi

 # Define the identity of the package.

  PACKAGE='cogaps'

- VERSION='3.3.1'

+ VERSION='3.3.2'

 cat >>confdefs.h <<_ACEOF

@@ -5129,7 +5131,16 @@ fi

 $as_echo "$ax_cv_cxx_compiler_version" >&6; }

-# set openmp flags

+# set openmp flags, disable only if requested

+# Check whether --enable-openmp was given.

+if test "${enable_openmp+set}" = set; then :

+  enableval=$enable_openmp; use_openmp=$enableval

+else

+  use_openmp=yes

+fi

+

+

+if test "x$use_openmp" != "xno" ; then

 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for OpenMP flag of C++ compiler" >&5

@@ -5196,8 +5207,9 @@ $as_echo "#define HAVE_OPENMP 1" >>confdefs.h

 fi

-GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

-GAPS_LIBS+=" $OPENMP_CXXFLAGS "

+    GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

+    GAPS_LIBS+=" $OPENMP_CXXFLAGS "

+fi

 # detect SIMD support

 # Make sure we can run config.sub.

@@ -7460,7 +7472,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1

 # report actual input values of CONFIG_FILES etc. instead of their

 # values after options handling.

 ac_log="

-This file was extended by CoGAPS $as_me 3.3.1, which was

+This file was extended by CoGAPS $as_me 3.3.2, which was

 generated by GNU Autoconf 2.69.  Invocation command line was

   CONFIG_FILES    = $CONFIG_FILES

@@ -7517,7 +7529,7 @@ _ACEOF

 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1

 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"

 ac_cs_version="\\

-CoGAPS config.status 3.3.1

+CoGAPS config.status 3.3.2

 configured by $0, generated by GNU Autoconf 2.69,

   with options \\"\$ac_cs_config\\"

@@ -32,10 +32,16 @@ GAPS_LIBS=

 AX_COMPILER_VENDOR

 AX_COMPILER_VERSION

-# set openmp flags

+# set openmp flags, disable only if requested

+AC_ARG_ENABLE(openmp, [AC_HELP_STRING([--enable-openmp],

+    [compile with openMP support if available])],

+    [use_openmp=$enableval], [use_openmp=yes])

+

 AX_OPENMP

-GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

-GAPS_LIBS+=" $OPENMP_CXXFLAGS "

+if test "x$use_openmp" != "xno" ; then

+    GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

+    GAPS_LIBS+=" $OPENMP_CXXFLAGS "

+fi

 # detect SIMD support

 AX_EXT

@@ -520,11 +520,16 @@ template <class T, class MatA, class MatB>

 void GibbsSampler<T, MatA, MatB>::exchange(uint64_t p1, float m1, uint64_t p2,

 float m2, unsigned r1, unsigned c1, unsigned r2, unsigned c2)

 {

-    float pUpper = gaps::random::p_gamma(m1 + m2, 2.f, 1.f / mLambda);

-    float newMass = gaps::random::inverseGammaSample(0.f, pUpper, 2.f, 1.f / mLambda);

     if (r1 != r2 || c1 != c2) // automatically reject if change in same bin

     {

-        if ((m1 > m2 && newMass - m1 < 0) || (m2 > m1 && m2 - newMass < 0))

+        float pUpper = gaps::random::p_gamma(m1 + m2, 2.f, 1.f / mLambda);

+        float newMass = gaps::random::inverseGammaSample(0.f, pUpper, 2.f, 1.f / mLambda);

+

+        // swapping only effects alpha parameters - only effects gibbs

+        // flips the sign of alpha parameters (only su)

+        // flips sign in gibbs mass

+        // can we swap after gibbsMass calculation?

+        if ((m1 > m2 && m1 > newMass) || (m2 > m1 && m2 < newMass))

         {

             std::swap(r1, r2);

             std::swap(c1, c2);

@@ -105,6 +105,8 @@ public:

     void load(const float *ptr) { mData = LOAD_PACKED(ptr); }

     void store(float *ptr) { STORE_PACKED(ptr, mData); }

+// RTTI may be expensive

+

 #if defined( __GAPS_AVX__ )

     float scalar()

     {