Merge branch 'hotfix-0.56.1'

libqueso · Dec 15, 2016 · e10fa41 · e10fa41
2 parents f390dee + 01724cf
commit e10fa41
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Showing 31 changed files with 109 additions and 85 deletions.
diff --git a/CHANGES b/CHANGES
@@ -3,6 +3,14 @@ QUESO: Quantification of Uncertainty for Estimation,
 Simulation, and Optimization.
 -----------------------------------------------------
 
+Version 0.56.1 (Dec 15, 2016)
+  * queso.h and config_queso.h had some duplicate #defines.  These have been
+    consodlidated and queso.h has been deprecated.
+  * Fix for gcc 4.4, change < ...<T>> to < ...<T> >
+  * Fix for gcc 4.4, remove `typename' for non-dependent types
+  * Updating documentation for m_normalizationStyle
+  * Fix sample-based normalisation computation in LogNormalJointPdf
+
 Version 0.56.0 (Nov 18, 2016)
   * Multivariate GPMSA implementation (experimental)
   * Multivariate GPMSA examples

diff --git a/configure.ac b/configure.ac
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.65)
-AC_INIT([queso], [0.56.0], [[email protected]])
+AC_INIT([queso], [0.56.1], [[email protected]])
 PACKAGE_DESCRIPTION="The parallel C++ statistical library QUESO: Quantification of uncertainty for estimation, simulation and optimization"
 AC_SUBST([PACKAGE_DESCRIPTION])
 PACKAGE_URL="https://github.com/libqueso/queso"
@@ -26,6 +26,12 @@ GENERIC_MAJOR_VERSION=$AX_MAJOR_VERSION
 GENERIC_MINOR_VERSION=$AX_MINOR_VERSION
 GENERIC_MICRO_VERSION=$AX_POINT_VERSION
 
+# Defines needed by Environment.C (formerly in queso.h)
+# The values are not quoted strings per queso.h history (Environment.C uses for arithmetic)
+AC_DEFINE_UNQUOTED([MAJOR_VERSION], ${GENERIC_MAJOR_VERSION}, "Major version")
+AC_DEFINE_UNQUOTED([MINOR_VERSION], ${GENERIC_MINOR_VERSION}, "Minor version")
+AC_DEFINE_UNQUOTED([MICRO_VERSION], ${GENERIC_MICRO_VERSION}, "Micro version")
+
 # Generating a libtool library
 
 GENERIC_RELEASE=$GENERIC_MAJOR_VERSION.$GENERIC_MINOR_VERSION
@@ -257,7 +263,6 @@ AC_CONFIG_FILES([
   src/Makefile
   src/contrib/ANN/Makefile
   src/contrib/ANN/test/Makefile
-  src/core/inc/queso.h
   examples/Makefile
   test/Makefile
   test/t01_valid_cycle/Makefile

diff --git a/examples/simpleStatisticalInverseProblem/src/Makefile.am b/examples/simpleStatisticalInverseProblem/src/Makefile.am
@@ -2,7 +2,6 @@
 
 AM_CPPFLAGS =
 AM_CPPFLAGS += -I$(top_builddir)/inc
-AM_CPPFLAGS += -I$(top_builddir)/src/core/inc  # For queso.h
 AM_CPPFLAGS += $(BOOST_CPPFLAGS)
 AM_CPPFLAGS += $(GSL_CFLAGS)
 AM_CPPFLAGS += $(GRVY_CFLAGS)
@@ -30,6 +29,6 @@ exStatisticalInverseProblem_gsl_SOURCES += example_compute.C
 exStatisticalInverseProblem_gsl_SOURCES += example_likelihood.C
 exStatisticalInverseProblem_gsl_SOURCES += example_compute.h
 exStatisticalInverseProblem_gsl_SOURCES += example_likelihood.h
-	       
+
 # Required for AX_AM_MACROS
 @INC_AMINCLUDE@
diff --git a/examples/statisticalForwardProblem/src/Makefile.am b/examples/statisticalForwardProblem/src/Makefile.am
@@ -2,7 +2,6 @@
 
 AM_CPPFLAGS =
 AM_CPPFLAGS += -I$(top_builddir)/inc
-AM_CPPFLAGS += -I$(top_builddir)/src/core/inc  # For queso.h
 AM_CPPFLAGS += $(BOOST_CPPFLAGS)
 AM_CPPFLAGS += $(GSL_CFLAGS)
 AM_CPPFLAGS += $(GRVY_CFLAGS)

diff --git a/examples/statisticalInverseProblem/src/Makefile.am b/examples/statisticalInverseProblem/src/Makefile.am
@@ -2,7 +2,6 @@
 
 AM_CPPFLAGS =
 AM_CPPFLAGS += -I$(top_builddir)/inc
-AM_CPPFLAGS += -I$(top_builddir)/src/core/inc  # For queso.h
 AM_CPPFLAGS += $(BOOST_CPPFLAGS)
 AM_CPPFLAGS += $(GSL_CFLAGS)
 AM_CPPFLAGS += $(GRVY_CFLAGS)

diff --git a/examples/validationPyramid/src/Makefile.am b/examples/validationPyramid/src/Makefile.am
@@ -8,7 +8,6 @@ AM_CPPFLAGS += -I$(top_srcdir)/examples/validationPyramid/src/physics_1
 AM_CPPFLAGS += -I$(top_srcdir)/examples/validationPyramid/src/physics_2
 AM_CPPFLAGS += -I$(top_srcdir)/examples/validationPyramid/src/physics_1_2
 AM_CPPFLAGS += -I$(top_builddir)/inc
-AM_CPPFLAGS += -I$(top_builddir)/src/core/inc  # For queso.h
 AM_CPPFLAGS += $(BOOST_CPPFLAGS)
 AM_CPPFLAGS += $(GSL_CFLAGS)
 AM_CPPFLAGS += $(GRVY_CFLAGS)

diff --git a/generate_queso_headers.sh b/generate_queso_headers.sh
@@ -2,7 +2,7 @@
 set -e
 
 # Find all teh headers
-headers=`find src -name "*.h" -a -not -name queso.h -a -not -name all.h -type f | grep -v 'ANN'`
+headers=`find src -name "*.h" -a -not -name all.h -type f | grep -v 'ANN'`
 
 # Find the thing we want to conduct wizardry on
 quesoh=`find src -name "all.h"`

diff --git a/inc/queso/Makefile.am b/inc/queso/Makefile.am
@@ -75,6 +75,7 @@ BUILT_SOURCES += TransitionKernelFactory.h
 BUILT_SOURCES += Vector.h
 BUILT_SOURCES += asserts.h
 BUILT_SOURCES += exceptions.h
+BUILT_SOURCES += queso.h
 BUILT_SOURCES += ExperimentModel.h
 BUILT_SOURCES += ExperimentModelOptions.h
 BUILT_SOURCES += ExperimentStorage.h
@@ -205,7 +206,6 @@ BUILT_SOURCES += LinearLagrangeInterpolationSurrogate.h
 BUILT_SOURCES += SurrogateBase.h
 BUILT_SOURCES += SurrogateBuilderBase.h
 BUILT_SOURCES += config_queso.h
-BUILT_SOURCES += queso.h
 
 DISTCLEANFILES = $(BUILT_SOURCES)
 
@@ -349,6 +349,8 @@ asserts.h: $(top_srcdir)/src/core/inc/asserts.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 exceptions.h: $(top_srcdir)/src/core/inc/exceptions.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
+queso.h: $(top_srcdir)/src/core/inc/queso.h
+	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 ExperimentModel.h: $(top_srcdir)/src/gp/inc/ExperimentModel.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 ExperimentModelOptions.h: $(top_srcdir)/src/gp/inc/ExperimentModelOptions.h
@@ -609,5 +611,3 @@ SurrogateBuilderBase.h: $(top_srcdir)/src/surrogates/inc/SurrogateBuilderBase.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 config_queso.h: $(top_builddir)/config_queso.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
-queso.h: $(top_builddir)/src/core/inc/queso.h
-	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
diff --git a/inc/queso/rebuild_makefile.sh b/inc/queso/rebuild_makefile.sh
@@ -3,7 +3,7 @@
 # This file was shamelessly stolen from the libmesh source tree
 # See https://github.com/libMesh/libmesh
 
-headers=`find ../../src -name "*.h" -a -not -name queso.h -a -not -name all.h -type f | grep -v 'ANN' | grep -v 'interface' | LC_COLLATE=POSIX sort`
+headers=`find ../../src -name "*.h" -a -not -name all.h -type f | grep -v 'ANN' | grep -v 'interface' | LC_COLLATE=POSIX sort`
 
 cat <<EOF > Makefile.am
 # Note - this file is automatically generated by $0 
@@ -26,7 +26,6 @@ done
 # Manually handle the auto-generated headers
 cat <<EOF >> Makefile.am
 BUILT_SOURCES += config_queso.h
-BUILT_SOURCES += queso.h
 EOF
 
 cat <<EOF >> Makefile.am
@@ -56,6 +55,4 @@ done
 cat <<EOF >> Makefile.am
 config_queso.h: \$(top_builddir)/config_queso.h
 	\$(AM_V_GEN)rm -f \$@ && \$(LN_S) \$< \$@
-queso.h: \$(top_builddir)/src/core/inc/queso.h
-	\$(AM_V_GEN)rm -f \$@ && \$(LN_S) \$< \$@
 EOF
diff --git a/m4/common/config_environment.m4 b/m4/common/config_environment.m4
@@ -56,10 +56,25 @@ AC_DEFINE_UNQUOTED([BUILD_VERSION],  "${BUILD_VERSION}",  [git revision])
 AC_DEFINE_UNQUOTED([BUILD_DEVSTATUS],"${BUILD_DEVSTATUS}",[Dev/Release build])
 AC_DEFINE(         [BUILD_DATE],     __DATE__ " " __TIME__, [Build date])
 
+# Defines needed by Environment.C (formerly in queso.h)
+AC_DEFINE_UNQUOTED([CXX],          "${CXX}",           [C++ compiler])
+AC_DEFINE_UNQUOTED([CXXFLAGS],     "${CXXFLAGS}",      [C++ compiler flags])
+# The following must be unconditionally defined per Environment.C
+# TODO: Should these go in the respective <tpl>.m4?
+AC_DEFINE_UNQUOTED([TRILINOS_DIR], "${TRILINOS_HOME}", [Trilinos home directory])
+AC_DEFINE_UNQUOTED([GSL_DIR],      "${GSL_LIBS}",      [GSL libraries])
+AC_DEFINE_UNQUOTED([GRVY_DIR],     "${GRVY_PREFIX}",   [GRVY directory])
+AC_DEFINE_UNQUOTED([GLPK_DIR],     "${GLPK_PREFIX}",   [GLPK directory])
+AC_DEFINE_UNQUOTED([HDF5_DIR],     "${HDF5_PREFIX}",   [HDF directory])
+
 AC_SUBST(BUILD_USER)
 AC_SUBST(BUILD_ARCH)
 AC_SUBST(BUILD_HOST)
 AC_SUBST(BUILD_DATE)
 AC_SUBST(BUILD_VERSION)
 
+# Defines needed by Environment.C (formerly in queso.h)
+AC_SUBST(CXX)
+AC_SUBST(CXX_FLAGS)
+
 ])
diff --git a/m4/common/queso_new.m4 b/m4/common/queso_new.m4
@@ -82,7 +82,7 @@ HAVE_QUESO=0
 
     AC_LANG_PUSH([C++])
 
-    AC_CHECK_HEADER([queso/queso.h], [found_header=yes], [found_header=no])
+    AC_CHECK_HEADER([queso/config_queso.h], [found_header=yes], [found_header=no])
 
     #-----------------------
     # Minimum version check
@@ -115,7 +115,7 @@ HAVE_QUESO=0
         version_succeeded=no
 
         AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
-        @%:@include <queso/queso.h>
+        @%:@include <queso/config_queso.h>
             ]], [[
             #if QUESO_MAJOR_VERSION > $MAJOR_VER
             /* Sweet nibblets */
@@ -136,7 +136,7 @@ HAVE_QUESO=0
     fi   dnl end test if header if available
 
 
-#####     AC_COMPILE_IFELSE([#include "queso/queso.h"],[found_header=yes],[found_header=no])
+#####     AC_COMPILE_IFELSE([#include "queso/config_queso.h"],[found_header=yes],[found_header=no])
 ##### 
 #####     ac_QUESO_BOOST_PROGRAM_OPTIONS_LDFLAGS_COMPILER=''
 #####     

diff --git a/src/Makefile.am b/src/Makefile.am
@@ -1,6 +1,5 @@
 AM_CPPFLAGS = $(QUESO_CPPFLAGS)
 AM_CPPFLAGS += -I$(top_builddir)/inc
-AM_CPPFLAGS += -I$(top_builddir)/src/core/inc  # For queso.h
 AM_CPPFLAGS += $(BOOST_CPPFLAGS)
 AM_CPPFLAGS += $(GSL_CFLAGS)
 AM_CPPFLAGS += $(ANN_CFLAGS)
@@ -289,7 +288,7 @@ libqueso_la_SOURCES += gp/src/GPMSAOptions.C
 # Headers to install from core/inc
 
 libqueso_include_HEADERS =
-libqueso_include_HEADERS += $(top_builddir)/src/core/inc/queso.h
+libqueso_include_HEADERS += core/inc/queso.h
 libqueso_include_HEADERS += core/inc/Defines.h
 libqueso_include_HEADERS += core/inc/Environment.h
 libqueso_include_HEADERS += core/inc/EnvironmentOptions.h
@@ -512,7 +511,6 @@ libqueso_include_HEADERS += contrib/getpot/getpot.h
 
 nodist_libqueso_include_HEADERS =
 nodist_libqueso_include_HEADERS += $(top_builddir)/config_queso.h
-nodist_libqueso_include_HEADERS += $(top_builddir)/src/core/inc/queso.h
 
 # Standalone binaries
 

diff --git a/src/core/inc/AlgorithmFactory.h b/src/core/inc/AlgorithmFactory.h
@@ -75,11 +75,11 @@ class AlgorithmFactory : public Factory<Algorithm<GslVector, GslMatrix> >
    * Create a Base class.  Force this to be implemented
    * later.
    */
-  virtual typename SharedPtr<Algorithm<GslVector, GslMatrix> >::Type create();
+  virtual SharedPtr<Algorithm<GslVector, GslMatrix> >::Type create();
 };
 
 inline
-typename SharedPtr<Algorithm<GslVector, GslMatrix> >::Type
+SharedPtr<Algorithm<GslVector, GslMatrix> >::Type
 AlgorithmFactory::create()
 {
   queso_require_msg(m_env, "ERROR: must call set_environment() before building alg!");

diff --git a/src/core/inc/FunctionBase.h b/src/core/inc/FunctionBase.h
@@ -77,7 +77,7 @@ class FunctionBase {
    * identically zero (by copying \c this) everywhere and return a boost shared
    * pointer to it
    */
-  virtual typename SharedPtr<FunctionBase>::Type zero_clone() const = 0;
+  virtual SharedPtr<FunctionBase>::Type zero_clone() const = 0;
 
   //! Save the current function to an Exodus file called \c filename.  \c time is the time to attach to the function and is usually the iteration number
   virtual void save_function(const std::string & filename, double time) const = 0;

diff --git a/src/core/inc/InfiniteDimensionalGaussian.h b/src/core/inc/InfiniteDimensionalGaussian.h
@@ -65,7 +65,7 @@ class InfiniteDimensionalGaussian : public InfiniteDimensionalMeasureBase {
   //@}
 
   //! Draw from the measure, and then return a shared pointer to the draw
-  virtual typename SharedPtr<FunctionBase>::Type draw();
+  virtual SharedPtr<FunctionBase>::Type draw();
 
   //! Return coefficient \c i of the KL expansion of the current draw.  Must be called after draw()
   virtual double get_kl_coefficient(unsigned int i) const;

diff --git a/src/core/inc/InfiniteDimensionalMCMCSampler.h b/src/core/inc/InfiniteDimensionalMCMCSampler.h
@@ -80,7 +80,7 @@ class InfiniteDimensionalMCMCSampler
   unsigned int iteration() const;
 
   //! Returns a pointer to new sampler, with all the moments reset.
-  typename SharedPtr<InfiniteDimensionalMCMCSampler>::Type clone_and_reset() const;
+  SharedPtr<InfiniteDimensionalMCMCSampler>::Type clone_and_reset() const;
 
 private:
   // Current iteration
@@ -109,22 +109,22 @@ class InfiniteDimensionalMCMCSampler
   const BaseEnvironment& m_env;
 
   // Pointer to the current physical state
-  typename SharedPtr<FunctionBase>::Type current_physical_state;
+  SharedPtr<FunctionBase>::Type current_physical_state;
 
   // Pointer to the current proposed state
-  typename SharedPtr<FunctionBase>::Type proposed_physical_state;
+  SharedPtr<FunctionBase>::Type proposed_physical_state;
 
   // Pointer to the current physical mean
-  typename SharedPtr<FunctionBase>::Type current_physical_mean;
+  SharedPtr<FunctionBase>::Type current_physical_mean;
 
   // Pointer to the current physical variance
-  typename SharedPtr<FunctionBase>::Type current_physical_var;
+  SharedPtr<FunctionBase>::Type current_physical_var;
 
   // Stores the differences from the mean
-  typename SharedPtr<FunctionBase>::Type _delta;
+  SharedPtr<FunctionBase>::Type _delta;
 
   // Stores a running sum-of-squares (kinda)
-  typename SharedPtr<FunctionBase>::Type _M2;
+  SharedPtr<FunctionBase>::Type _M2;
 
   // A pointer to the random number generator to use.
   // Should probably use the one in the queso environment.

diff --git a/src/core/inc/InfiniteDimensionalMeasureBase.h b/src/core/inc/InfiniteDimensionalMeasureBase.h
@@ -52,7 +52,7 @@ class InfiniteDimensionalMeasureBase {
   //@}
 
   //! Draw from the measure, and then return a shared pointer to the draw
-  virtual typename SharedPtr<FunctionBase>::Type draw() = 0;
+  virtual SharedPtr<FunctionBase>::Type draw() = 0;
 
   //! Return coefficient \c i of the KL expansion of the current draw.  Must be called after draw()
   virtual double get_kl_coefficient(unsigned int i) const = 0;

diff --git a/src/core/inc/LibMeshFunction.h b/src/core/inc/LibMeshFunction.h
@@ -98,15 +98,15 @@ class LibMeshFunction : public FunctionBase {
    * identically zero (by copying \c this) everywhere and return a boost shared
    * pointer to it
    */
-  virtual typename SharedPtr<FunctionBase>::Type zero_clone() const;
+  virtual SharedPtr<FunctionBase>::Type zero_clone() const;
 
   //! Return the internal libmesh equation systems object
-  virtual typename SharedPtr<libMesh::EquationSystems>::Type get_equation_systems() const;
+  virtual SharedPtr<libMesh::EquationSystems>::Type get_equation_systems() const;
 
 private:
   const FunctionOperatorBuilder & builder;
 
-  typename SharedPtr<libMesh::EquationSystems>::Type equation_systems;
+  SharedPtr<libMesh::EquationSystems>::Type equation_systems;
 };
 
 }  // End namespace QUESO

diff --git a/src/core/inc/LibMeshOperatorBase.h b/src/core/inc/LibMeshOperatorBase.h
@@ -112,11 +112,11 @@ class LibMeshOperatorBase : public OperatorBase,
    *  where the lambda are eigenvalues of the precision operator, \c this, and
    *  the \phi(x) are eigenfunctions of the precision operator, \c this
    */
-  virtual typename SharedPtr<FunctionBase>::Type
+  virtual SharedPtr<FunctionBase>::Type
   inverse_kl_transform(std::vector<double> & xi, double alpha) const;
 
 protected:
-  typename SharedPtr<libMesh::EquationSystems>::Type equation_systems;
+  SharedPtr<libMesh::EquationSystems>::Type equation_systems;
 
   const FunctionOperatorBuilder & builder;
 

diff --git a/src/core/inc/OperatorBase.h b/src/core/inc/OperatorBase.h
@@ -74,7 +74,7 @@ class OperatorBase {
    *  where the lambda are eigenvalues of the precision operator, \c this, and
    *  the \phi(x) are eigenfunctions of the precision operator, \c this
    */
-  virtual typename SharedPtr<FunctionBase>::Type
+  virtual SharedPtr<FunctionBase>::Type
   inverse_kl_transform(std::vector<double>& xi, double alpha) const = 0;
 };
 

diff --git a/src/core/inc/TransitionKernelFactory.h b/src/core/inc/TransitionKernelFactory.h
@@ -118,11 +118,11 @@ class TransitionKernelFactory : public Factory<BaseTKGroup<GslVector, GslMatrix>
    * Create a Base class.  Force this to be implemented
    * later.
    */
-  virtual typename SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type create();
+  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type create();
 };
 
 inline
-typename SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type TransitionKernelFactory::create()
+SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type TransitionKernelFactory::create()
 {
   queso_require_msg(m_vectorSpace, "ERROR: must call set_vectorspace() before building tk!");
   queso_require_msg(m_dr_scales, "ERROR: must call set_dr_scales() before building tk!");