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dmcdougalldmcdougall
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Merge branch 'hotfix-0.56.1'
2 parents f390dee + 01724cf commit e10fa41

31 files changed

+109
-85
lines changed

‎CHANGES

+8
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,14 @@ QUESO: Quantification of Uncertainty for Estimation,
33
Simulation, and Optimization.
44
-----------------------------------------------------
55

6+
Version 0.56.1 (Dec 15, 2016)
7+
* queso.h and config_queso.h had some duplicate #defines. These have been
8+
consodlidated and queso.h has been deprecated.
9+
* Fix for gcc 4.4, change < ...<T>> to < ...<T> >
10+
* Fix for gcc 4.4, remove `typename' for non-dependent types
11+
* Updating documentation for m_normalizationStyle
12+
* Fix sample-based normalisation computation in LogNormalJointPdf
13+
614
Version 0.56.0 (Nov 18, 2016)
715
* Multivariate GPMSA implementation (experimental)
816
* Multivariate GPMSA examples

‎configure.ac

+7-2
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
# Process this file with autoconf to produce a configure script.
33

44
AC_PREREQ(2.65)
5-
AC_INIT([queso], [0.56.0], [[email protected]])
5+
AC_INIT([queso], [0.56.1], [[email protected]])
66
PACKAGE_DESCRIPTION="The parallel C++ statistical library QUESO: Quantification of uncertainty for estimation, simulation and optimization"
77
AC_SUBST([PACKAGE_DESCRIPTION])
88
PACKAGE_URL="https://github.com/libqueso/queso"
@@ -26,6 +26,12 @@ GENERIC_MAJOR_VERSION=$AX_MAJOR_VERSION
2626
GENERIC_MINOR_VERSION=$AX_MINOR_VERSION
2727
GENERIC_MICRO_VERSION=$AX_POINT_VERSION
2828

29+
# Defines needed by Environment.C (formerly in queso.h)
30+
# The values are not quoted strings per queso.h history (Environment.C uses for arithmetic)
31+
AC_DEFINE_UNQUOTED([MAJOR_VERSION], ${GENERIC_MAJOR_VERSION}, "Major version")
32+
AC_DEFINE_UNQUOTED([MINOR_VERSION], ${GENERIC_MINOR_VERSION}, "Minor version")
33+
AC_DEFINE_UNQUOTED([MICRO_VERSION], ${GENERIC_MICRO_VERSION}, "Micro version")
34+
2935
# Generating a libtool library
3036

3137
GENERIC_RELEASE=$GENERIC_MAJOR_VERSION.$GENERIC_MINOR_VERSION
@@ -257,7 +263,6 @@ AC_CONFIG_FILES([
257263
src/Makefile
258264
src/contrib/ANN/Makefile
259265
src/contrib/ANN/test/Makefile
260-
src/core/inc/queso.h
261266
examples/Makefile
262267
test/Makefile
263268
test/t01_valid_cycle/Makefile

‎examples/simpleStatisticalInverseProblem/src/Makefile.am

+1-2
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,6 @@
22

33
AM_CPPFLAGS =
44
AM_CPPFLAGS += -I$(top_builddir)/inc
5-
AM_CPPFLAGS += -I$(top_builddir)/src/core/inc # For queso.h
65
AM_CPPFLAGS += $(BOOST_CPPFLAGS)
76
AM_CPPFLAGS += $(GSL_CFLAGS)
87
AM_CPPFLAGS += $(GRVY_CFLAGS)
@@ -30,6 +29,6 @@ exStatisticalInverseProblem_gsl_SOURCES += example_compute.C
3029
exStatisticalInverseProblem_gsl_SOURCES += example_likelihood.C
3130
exStatisticalInverseProblem_gsl_SOURCES += example_compute.h
3231
exStatisticalInverseProblem_gsl_SOURCES += example_likelihood.h
33-
32+
3433
# Required for AX_AM_MACROS
3534
@INC_AMINCLUDE@

‎examples/statisticalForwardProblem/src/Makefile.am

-1
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,6 @@
22

33
AM_CPPFLAGS =
44
AM_CPPFLAGS += -I$(top_builddir)/inc
5-
AM_CPPFLAGS += -I$(top_builddir)/src/core/inc # For queso.h
65
AM_CPPFLAGS += $(BOOST_CPPFLAGS)
76
AM_CPPFLAGS += $(GSL_CFLAGS)
87
AM_CPPFLAGS += $(GRVY_CFLAGS)

‎examples/statisticalInverseProblem/src/Makefile.am

-1
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,6 @@
22

33
AM_CPPFLAGS =
44
AM_CPPFLAGS += -I$(top_builddir)/inc
5-
AM_CPPFLAGS += -I$(top_builddir)/src/core/inc # For queso.h
65
AM_CPPFLAGS += $(BOOST_CPPFLAGS)
76
AM_CPPFLAGS += $(GSL_CFLAGS)
87
AM_CPPFLAGS += $(GRVY_CFLAGS)

‎examples/validationPyramid/src/Makefile.am

-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,6 @@ AM_CPPFLAGS += -I$(top_srcdir)/examples/validationPyramid/src/physics_1
88
AM_CPPFLAGS += -I$(top_srcdir)/examples/validationPyramid/src/physics_2
99
AM_CPPFLAGS += -I$(top_srcdir)/examples/validationPyramid/src/physics_1_2
1010
AM_CPPFLAGS += -I$(top_builddir)/inc
11-
AM_CPPFLAGS += -I$(top_builddir)/src/core/inc # For queso.h
1211
AM_CPPFLAGS += $(BOOST_CPPFLAGS)
1312
AM_CPPFLAGS += $(GSL_CFLAGS)
1413
AM_CPPFLAGS += $(GRVY_CFLAGS)

‎generate_queso_headers.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
set -e
33

44
# Find all teh headers
5-
headers=`find src -name "*.h" -a -not -name queso.h -a -not -name all.h -type f | grep -v 'ANN'`
5+
headers=`find src -name "*.h" -a -not -name all.h -type f | grep -v 'ANN'`
66

77
# Find the thing we want to conduct wizardry on
88
quesoh=`find src -name "all.h"`

‎inc/queso/Makefile.am

+3-3
Original file line numberDiff line numberDiff line change
@@ -75,6 +75,7 @@ BUILT_SOURCES += TransitionKernelFactory.h
7575
BUILT_SOURCES += Vector.h
7676
BUILT_SOURCES += asserts.h
7777
BUILT_SOURCES += exceptions.h
78+
BUILT_SOURCES += queso.h
7879
BUILT_SOURCES += ExperimentModel.h
7980
BUILT_SOURCES += ExperimentModelOptions.h
8081
BUILT_SOURCES += ExperimentStorage.h
@@ -205,7 +206,6 @@ BUILT_SOURCES += LinearLagrangeInterpolationSurrogate.h
205206
BUILT_SOURCES += SurrogateBase.h
206207
BUILT_SOURCES += SurrogateBuilderBase.h
207208
BUILT_SOURCES += config_queso.h
208-
BUILT_SOURCES += queso.h
209209

210210
DISTCLEANFILES = $(BUILT_SOURCES)
211211

@@ -349,6 +349,8 @@ asserts.h: $(top_srcdir)/src/core/inc/asserts.h
349349
$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
350350
exceptions.h: $(top_srcdir)/src/core/inc/exceptions.h
351351
$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
352+
queso.h: $(top_srcdir)/src/core/inc/queso.h
353+
$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
352354
ExperimentModel.h: $(top_srcdir)/src/gp/inc/ExperimentModel.h
353355
$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
354356
ExperimentModelOptions.h: $(top_srcdir)/src/gp/inc/ExperimentModelOptions.h
@@ -609,5 +611,3 @@ SurrogateBuilderBase.h: $(top_srcdir)/src/surrogates/inc/SurrogateBuilderBase.h
609611
$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
610612
config_queso.h: $(top_builddir)/config_queso.h
611613
$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
612-
queso.h: $(top_builddir)/src/core/inc/queso.h
613-
$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@

‎inc/queso/rebuild_makefile.sh

+1-4
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
# This file was shamelessly stolen from the libmesh source tree
44
# See https://github.com/libMesh/libmesh
55

6-
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`
6+
headers=`find ../../src -name "*.h" -a -not -name all.h -type f | grep -v 'ANN' | grep -v 'interface' | LC_COLLATE=POSIX sort`
77

88
cat <<EOF > Makefile.am
99
# Note - this file is automatically generated by $0
@@ -26,7 +26,6 @@ done
2626
# Manually handle the auto-generated headers
2727
cat <<EOF >> Makefile.am
2828
BUILT_SOURCES += config_queso.h
29-
BUILT_SOURCES += queso.h
3029
EOF
3130

3231
cat <<EOF >> Makefile.am
@@ -56,6 +55,4 @@ done
5655
cat <<EOF >> Makefile.am
5756
config_queso.h: \$(top_builddir)/config_queso.h
5857
\$(AM_V_GEN)rm -f \$@ && \$(LN_S) \$< \$@
59-
queso.h: \$(top_builddir)/src/core/inc/queso.h
60-
\$(AM_V_GEN)rm -f \$@ && \$(LN_S) \$< \$@
6158
EOF

‎m4/common/config_environment.m4

+15
Original file line numberDiff line numberDiff line change
@@ -56,10 +56,25 @@ AC_DEFINE_UNQUOTED([BUILD_VERSION], "${BUILD_VERSION}", [git revision])
5656
AC_DEFINE_UNQUOTED([BUILD_DEVSTATUS],"${BUILD_DEVSTATUS}",[Dev/Release build])
5757
AC_DEFINE( [BUILD_DATE], __DATE__ " " __TIME__, [Build date])
5858
59+
# Defines needed by Environment.C (formerly in queso.h)
60+
AC_DEFINE_UNQUOTED([CXX], "${CXX}", [C++ compiler])
61+
AC_DEFINE_UNQUOTED([CXXFLAGS], "${CXXFLAGS}", [C++ compiler flags])
62+
# The following must be unconditionally defined per Environment.C
63+
# TODO: Should these go in the respective <tpl>.m4?
64+
AC_DEFINE_UNQUOTED([TRILINOS_DIR], "${TRILINOS_HOME}", [Trilinos home directory])
65+
AC_DEFINE_UNQUOTED([GSL_DIR], "${GSL_LIBS}", [GSL libraries])
66+
AC_DEFINE_UNQUOTED([GRVY_DIR], "${GRVY_PREFIX}", [GRVY directory])
67+
AC_DEFINE_UNQUOTED([GLPK_DIR], "${GLPK_PREFIX}", [GLPK directory])
68+
AC_DEFINE_UNQUOTED([HDF5_DIR], "${HDF5_PREFIX}", [HDF directory])
69+
5970
AC_SUBST(BUILD_USER)
6071
AC_SUBST(BUILD_ARCH)
6172
AC_SUBST(BUILD_HOST)
6273
AC_SUBST(BUILD_DATE)
6374
AC_SUBST(BUILD_VERSION)
6475
76+
# Defines needed by Environment.C (formerly in queso.h)
77+
AC_SUBST(CXX)
78+
AC_SUBST(CXX_FLAGS)
79+
6580
])

‎m4/common/queso_new.m4

+3-3
Original file line numberDiff line numberDiff line change
@@ -82,7 +82,7 @@ HAVE_QUESO=0
8282
8383
AC_LANG_PUSH([C++])
8484
85-
AC_CHECK_HEADER([queso/queso.h], [found_header=yes], [found_header=no])
85+
AC_CHECK_HEADER([queso/config_queso.h], [found_header=yes], [found_header=no])
8686
8787
#-----------------------
8888
# Minimum version check
@@ -115,7 +115,7 @@ HAVE_QUESO=0
115115
version_succeeded=no
116116
117117
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
118-
@%:@include <queso/queso.h>
118+
@%:@include <queso/config_queso.h>
119119
]], [[
120120
#if QUESO_MAJOR_VERSION > $MAJOR_VER
121121
/* Sweet nibblets */
@@ -136,7 +136,7 @@ HAVE_QUESO=0
136136
fi dnl end test if header if available
137137
138138
139-
##### AC_COMPILE_IFELSE([#include "queso/queso.h"],[found_header=yes],[found_header=no])
139+
##### AC_COMPILE_IFELSE([#include "queso/config_queso.h"],[found_header=yes],[found_header=no])
140140
#####
141141
##### ac_QUESO_BOOST_PROGRAM_OPTIONS_LDFLAGS_COMPILER=''
142142
#####

‎src/Makefile.am

+1-3
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,5 @@
11
AM_CPPFLAGS = $(QUESO_CPPFLAGS)
22
AM_CPPFLAGS += -I$(top_builddir)/inc
3-
AM_CPPFLAGS += -I$(top_builddir)/src/core/inc # For queso.h
43
AM_CPPFLAGS += $(BOOST_CPPFLAGS)
54
AM_CPPFLAGS += $(GSL_CFLAGS)
65
AM_CPPFLAGS += $(ANN_CFLAGS)
@@ -289,7 +288,7 @@ libqueso_la_SOURCES += gp/src/GPMSAOptions.C
289288
# Headers to install from core/inc
290289

291290
libqueso_include_HEADERS =
292-
libqueso_include_HEADERS += $(top_builddir)/src/core/inc/queso.h
291+
libqueso_include_HEADERS += core/inc/queso.h
293292
libqueso_include_HEADERS += core/inc/Defines.h
294293
libqueso_include_HEADERS += core/inc/Environment.h
295294
libqueso_include_HEADERS += core/inc/EnvironmentOptions.h
@@ -512,7 +511,6 @@ libqueso_include_HEADERS += contrib/getpot/getpot.h
512511

513512
nodist_libqueso_include_HEADERS =
514513
nodist_libqueso_include_HEADERS += $(top_builddir)/config_queso.h
515-
nodist_libqueso_include_HEADERS += $(top_builddir)/src/core/inc/queso.h
516514

517515
# Standalone binaries
518516

‎src/core/inc/AlgorithmFactory.h

+2-2
Original file line numberDiff line numberDiff line change
@@ -75,11 +75,11 @@ class AlgorithmFactory : public Factory<Algorithm<GslVector, GslMatrix> >
7575
* Create a Base class. Force this to be implemented
7676
* later.
7777
*/
78-
virtual typename SharedPtr<Algorithm<GslVector, GslMatrix> >::Type create();
78+
virtual SharedPtr<Algorithm<GslVector, GslMatrix> >::Type create();
7979
};
8080

8181
inline
82-
typename SharedPtr<Algorithm<GslVector, GslMatrix> >::Type
82+
SharedPtr<Algorithm<GslVector, GslMatrix> >::Type
8383
AlgorithmFactory::create()
8484
{
8585
queso_require_msg(m_env, "ERROR: must call set_environment() before building alg!");

‎src/core/inc/FunctionBase.h

+1-1
Original file line numberDiff line numberDiff line change
@@ -77,7 +77,7 @@ class FunctionBase {
7777
* identically zero (by copying \c this) everywhere and return a boost shared
7878
* pointer to it
7979
*/
80-
virtual typename SharedPtr<FunctionBase>::Type zero_clone() const = 0;
80+
virtual SharedPtr<FunctionBase>::Type zero_clone() const = 0;
8181

8282
//! 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
8383
virtual void save_function(const std::string & filename, double time) const = 0;

‎src/core/inc/InfiniteDimensionalGaussian.h

+1-1
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,7 @@ class InfiniteDimensionalGaussian : public InfiniteDimensionalMeasureBase {
6565
//@}
6666

6767
//! Draw from the measure, and then return a shared pointer to the draw
68-
virtual typename SharedPtr<FunctionBase>::Type draw();
68+
virtual SharedPtr<FunctionBase>::Type draw();
6969

7070
//! Return coefficient \c i of the KL expansion of the current draw. Must be called after draw()
7171
virtual double get_kl_coefficient(unsigned int i) const;

‎src/core/inc/InfiniteDimensionalMCMCSampler.h

+7-7
Original file line numberDiff line numberDiff line change
@@ -80,7 +80,7 @@ class InfiniteDimensionalMCMCSampler
8080
unsigned int iteration() const;
8181

8282
//! Returns a pointer to new sampler, with all the moments reset.
83-
typename SharedPtr<InfiniteDimensionalMCMCSampler>::Type clone_and_reset() const;
83+
SharedPtr<InfiniteDimensionalMCMCSampler>::Type clone_and_reset() const;
8484

8585
private:
8686
// Current iteration
@@ -109,22 +109,22 @@ class InfiniteDimensionalMCMCSampler
109109
const BaseEnvironment& m_env;
110110

111111
// Pointer to the current physical state
112-
typename SharedPtr<FunctionBase>::Type current_physical_state;
112+
SharedPtr<FunctionBase>::Type current_physical_state;
113113

114114
// Pointer to the current proposed state
115-
typename SharedPtr<FunctionBase>::Type proposed_physical_state;
115+
SharedPtr<FunctionBase>::Type proposed_physical_state;
116116

117117
// Pointer to the current physical mean
118-
typename SharedPtr<FunctionBase>::Type current_physical_mean;
118+
SharedPtr<FunctionBase>::Type current_physical_mean;
119119

120120
// Pointer to the current physical variance
121-
typename SharedPtr<FunctionBase>::Type current_physical_var;
121+
SharedPtr<FunctionBase>::Type current_physical_var;
122122

123123
// Stores the differences from the mean
124-
typename SharedPtr<FunctionBase>::Type _delta;
124+
SharedPtr<FunctionBase>::Type _delta;
125125

126126
// Stores a running sum-of-squares (kinda)
127-
typename SharedPtr<FunctionBase>::Type _M2;
127+
SharedPtr<FunctionBase>::Type _M2;
128128

129129
// A pointer to the random number generator to use.
130130
// Should probably use the one in the queso environment.

‎src/core/inc/InfiniteDimensionalMeasureBase.h

+1-1
Original file line numberDiff line numberDiff line change
@@ -52,7 +52,7 @@ class InfiniteDimensionalMeasureBase {
5252
//@}
5353

5454
//! Draw from the measure, and then return a shared pointer to the draw
55-
virtual typename SharedPtr<FunctionBase>::Type draw() = 0;
55+
virtual SharedPtr<FunctionBase>::Type draw() = 0;
5656

5757
//! Return coefficient \c i of the KL expansion of the current draw. Must be called after draw()
5858
virtual double get_kl_coefficient(unsigned int i) const = 0;

‎src/core/inc/LibMeshFunction.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -98,15 +98,15 @@ class LibMeshFunction : public FunctionBase {
9898
* identically zero (by copying \c this) everywhere and return a boost shared
9999
* pointer to it
100100
*/
101-
virtual typename SharedPtr<FunctionBase>::Type zero_clone() const;
101+
virtual SharedPtr<FunctionBase>::Type zero_clone() const;
102102

103103
//! Return the internal libmesh equation systems object
104-
virtual typename SharedPtr<libMesh::EquationSystems>::Type get_equation_systems() const;
104+
virtual SharedPtr<libMesh::EquationSystems>::Type get_equation_systems() const;
105105

106106
private:
107107
const FunctionOperatorBuilder & builder;
108108

109-
typename SharedPtr<libMesh::EquationSystems>::Type equation_systems;
109+
SharedPtr<libMesh::EquationSystems>::Type equation_systems;
110110
};
111111

112112
} // End namespace QUESO

‎src/core/inc/LibMeshOperatorBase.h

+2-2
Original file line numberDiff line numberDiff line change
@@ -112,11 +112,11 @@ class LibMeshOperatorBase : public OperatorBase,
112112
* where the lambda are eigenvalues of the precision operator, \c this, and
113113
* the \phi(x) are eigenfunctions of the precision operator, \c this
114114
*/
115-
virtual typename SharedPtr<FunctionBase>::Type
115+
virtual SharedPtr<FunctionBase>::Type
116116
inverse_kl_transform(std::vector<double> & xi, double alpha) const;
117117

118118
protected:
119-
typename SharedPtr<libMesh::EquationSystems>::Type equation_systems;
119+
SharedPtr<libMesh::EquationSystems>::Type equation_systems;
120120

121121
const FunctionOperatorBuilder & builder;
122122

‎src/core/inc/OperatorBase.h

+1-1
Original file line numberDiff line numberDiff line change
@@ -74,7 +74,7 @@ class OperatorBase {
7474
* where the lambda are eigenvalues of the precision operator, \c this, and
7575
* the \phi(x) are eigenfunctions of the precision operator, \c this
7676
*/
77-
virtual typename SharedPtr<FunctionBase>::Type
77+
virtual SharedPtr<FunctionBase>::Type
7878
inverse_kl_transform(std::vector<double>& xi, double alpha) const = 0;
7979
};
8080

‎src/core/inc/TransitionKernelFactory.h

+2-2
Original file line numberDiff line numberDiff line change
@@ -118,11 +118,11 @@ class TransitionKernelFactory : public Factory<BaseTKGroup<GslVector, GslMatrix>
118118
* Create a Base class. Force this to be implemented
119119
* later.
120120
*/
121-
virtual typename SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type create();
121+
virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type create();
122122
};
123123

124124
inline
125-
typename SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type TransitionKernelFactory::create()
125+
SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type TransitionKernelFactory::create()
126126
{
127127
queso_require_msg(m_vectorSpace, "ERROR: must call set_vectorspace() before building tk!");
128128
queso_require_msg(m_dr_scales, "ERROR: must call set_dr_scales() before building tk!");

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