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Merge branch 'hotfix-0.56.1'
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dmcdougall committed Dec 15, 2016
2 parents f390dee + 01724cf commit e10fa41
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8 changes: 8 additions & 0 deletions CHANGES
Original file line number Diff line number Diff line change
Expand Up @@ -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
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9 changes: 7 additions & 2 deletions configure.ac
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Expand Up @@ -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"
Expand All @@ -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
Expand Down Expand Up @@ -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
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3 changes: 1 addition & 2 deletions examples/simpleStatisticalInverseProblem/src/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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@
1 change: 0 additions & 1 deletion examples/statisticalForwardProblem/src/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -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)
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1 change: 0 additions & 1 deletion examples/statisticalInverseProblem/src/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -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 += $(GRVY_CFLAGS)
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1 change: 0 additions & 1 deletion examples/validationPyramid/src/Makefile.am
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Expand Up @@ -8,7 +8,6 @@ AM_CPPFLAGS += -I$(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)
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2 changes: 1 addition & 1 deletion generate_queso_headers.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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"`
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6 changes: 3 additions & 3 deletions inc/queso/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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) $< $@
5 changes: 1 addition & 4 deletions inc/queso/rebuild_makefile.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
15 changes: 15 additions & 0 deletions m4/common/config_environment.m4
Original file line number Diff line number Diff line change
Expand Up @@ -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)
])
6 changes: 3 additions & 3 deletions m4/common/queso_new.m4
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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 */
Expand All @@ -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=''
#####
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4 changes: 1 addition & 3 deletions src/Makefile.am
Original file line number Diff line number Diff line change
@@ -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)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

Expand Down
4 changes: 2 additions & 2 deletions src/core/inc/AlgorithmFactory.h
Original file line number Diff line number Diff line change
Expand Up @@ -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!");
Expand Down
2 changes: 1 addition & 1 deletion src/core/inc/FunctionBase.h
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down
2 changes: 1 addition & 1 deletion src/core/inc/InfiniteDimensionalGaussian.h
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down
14 changes: 7 additions & 7 deletions src/core/inc/InfiniteDimensionalMCMCSampler.h
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion src/core/inc/InfiniteDimensionalMeasureBase.h
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down
6 changes: 3 additions & 3 deletions src/core/inc/LibMeshFunction.h
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions src/core/inc/LibMeshOperatorBase.h
Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand Down
2 changes: 1 addition & 1 deletion src/core/inc/OperatorBase.h
Original file line number Diff line number Diff line change
Expand Up @@ -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;
};

Expand Down
4 changes: 2 additions & 2 deletions src/core/inc/TransitionKernelFactory.h
Original file line number Diff line number Diff line change
Expand Up @@ -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!");
Expand Down
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