Merge branch 'hotfix-0.56.2'

CHANGES

@@ -3,6 +3,9 @@ QUESO: Quantification of Uncertainty for Estimation,
 Simulation, and Optimization.
 -----------------------------------------------------
 
+Version 0.56.2 (Feb 2, 2017)
+  * Fixed missing factory symbols when linking statically
+
 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.

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.65)
-AC_INIT([queso], [0.56.1], [queso-users@googlegroups.com])
+AC_INIT([queso], [0.56.2], [queso-users@googlegroups.com])
 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"

inc/queso/Makefile.am

@@ -29,6 +29,7 @@ BUILT_SOURCES += VectorSpace.h
 BUILT_SOURCES += VectorSubset.h
 BUILT_SOURCES += getpot.h
 BUILT_SOURCES += AlgorithmFactory.h
+BUILT_SOURCES += AlgorithmFactoryInitializer.h
 BUILT_SOURCES += BaseInputOptionsParser.h
 BUILT_SOURCES += BasicPdfsBase.h
 BUILT_SOURCES += BasicPdfsBoost.h
@@ -65,6 +66,7 @@ BUILT_SOURCES += RngBoost.h
 BUILT_SOURCES += RngGsl.h
 BUILT_SOURCES += ScopedPtr.h
 BUILT_SOURCES += SharedPtr.h
+BUILT_SOURCES += TKFactoryInitializer.h
 BUILT_SOURCES += TKFactoryLogitRandomWalk.h
 BUILT_SOURCES += TKFactoryMALA.h
 BUILT_SOURCES += TKFactoryRandomWalk.h
@@ -257,6 +259,8 @@ getpot.h: $(top_srcdir)/src/contrib/getpot/getpot.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 AlgorithmFactory.h: $(top_srcdir)/src/core/inc/AlgorithmFactory.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
+AlgorithmFactoryInitializer.h: $(top_srcdir)/src/core/inc/AlgorithmFactoryInitializer.h
+	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 BaseInputOptionsParser.h: $(top_srcdir)/src/core/inc/BaseInputOptionsParser.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 BasicPdfsBase.h: $(top_srcdir)/src/core/inc/BasicPdfsBase.h
@@ -329,6 +333,8 @@ ScopedPtr.h: $(top_srcdir)/src/core/inc/ScopedPtr.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 SharedPtr.h: $(top_srcdir)/src/core/inc/SharedPtr.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
+TKFactoryInitializer.h: $(top_srcdir)/src/core/inc/TKFactoryInitializer.h
+	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 TKFactoryLogitRandomWalk.h: $(top_srcdir)/src/core/inc/TKFactoryLogitRandomWalk.h
 	$(AM_V_GEN)rm -f $@ && $(LN_S) $< $@
 TKFactoryMALA.h: $(top_srcdir)/src/core/inc/TKFactoryMALA.h

src/Makefile.am

@@ -79,11 +79,9 @@ libqueso_la_SOURCES += core/src/OptimizerOptions.C
 libqueso_la_SOURCES += core/src/BaseInputOptionsParser.C
 libqueso_la_SOURCES += core/src/BoostInputOptionsParser.C
 libqueso_la_SOURCES += core/src/TransitionKernelFactory.C
-libqueso_la_SOURCES += core/src/TKFactoryStochasticNewton.C
-libqueso_la_SOURCES += core/src/TKFactoryRandomWalk.C
-libqueso_la_SOURCES += core/src/TKFactoryLogitRandomWalk.C
 libqueso_la_SOURCES += core/src/AlgorithmFactory.C
-libqueso_la_SOURCES += core/src/TKFactoryMALA.C
+libqueso_la_SOURCES += core/src/TKFactoryInitializer.C
+libqueso_la_SOURCES += core/src/AlgorithmFactoryInitializer.C
 
 
 # Sources that need libmesh
@@ -322,6 +320,8 @@ libqueso_include_HEADERS += core/inc/TKFactoryRandomWalk.h
 libqueso_include_HEADERS += core/inc/TKFactoryLogitRandomWalk.h
 libqueso_include_HEADERS += core/inc/AlgorithmFactory.h
 libqueso_include_HEADERS += core/inc/TKFactoryMALA.h
+libqueso_include_HEADERS += core/inc/TKFactoryInitializer.h
+libqueso_include_HEADERS += core/inc/AlgorithmFactoryInitializer.h
 
 # Headers that need libmesh
 libqueso_include_HEADERS += core/inc/FunctionBase.h

src/core/inc/AlgorithmFactory.h

@@ -108,7 +108,13 @@ class AlgorithmFactoryImp : public AlgorithmFactory
   virtual ~AlgorithmFactoryImp() {}
 
 private:
-  virtual SharedPtr<Algorithm<GslVector, GslMatrix> >::Type build_algorithm();
+  virtual SharedPtr<Algorithm<GslVector, GslMatrix> >::Type build_algorithm()
+  {
+    SharedPtr<Algorithm<GslVector, GslMatrix> >::Type new_alg;
+    new_alg.reset(new DerivedAlgorithm(*(this->m_env), *(this->m_tk)));
+    return new_alg;
+  }
+
 };
 
 } // namespace QUESO

src/core/src/TKFactoryRandomWalk.C → src/core/inc/AlgorithmFactoryInitializer.h

@@ -22,27 +22,19 @@
 //
 //-----------------------------------------------------------------------el-
 
-#include <queso/TKFactoryRandomWalk.h>
-#include <queso/ScaledCovMatrixTKGroup.h>
+#ifndef QUESO_ALGORITHM_FACTORY_INITIALIZER_H
+#define QUESO_ALGORITHM_FACTORY_INITIALIZER_H
 
 namespace QUESO
 {
 
-template <class DerivedTK>
-SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type
-TKFactoryRandomWalk<DerivedTK>::build_tk()
+class AlgorithmFactoryInitializer
 {
-  SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type new_tk;
+public:
+  AlgorithmFactoryInitializer();
+  virtual ~AlgorithmFactoryInitializer();
+};
 
-  new_tk.reset(new DerivedTK(this->m_options->m_prefix.c_str(),
-                             *(this->m_vectorSpace),
-                             *(this->m_dr_scales),
-                             *(this->m_initial_cov_matrix)));
+} // namespace QUESO
 
-  return new_tk;
-}
-
-// Instantiate all the transition kernel factories
-TKFactoryRandomWalk<ScaledCovMatrixTKGroup<GslVector, GslMatrix> > tk_factory_random_walk("random_walk");
-
-}  // namespace QUESO
+#endif  // QUESO_ALGORITHM_FACTORY_INITIALIZER_H

src/core/src/TKFactoryMALA.C → src/core/inc/TKFactoryInitializer.h

@@ -22,33 +22,19 @@
 //
 //-----------------------------------------------------------------------el-
 
-#include <queso/TKFactoryMALA.h>
-#include <queso/MetropolisAdjustedLangevinTK.h>
-#include <queso/BayesianJointPdf.h>
+#ifndef QUESO_TK_FACTORY_INITIALIZER_H
+#define QUESO_TK_FACTORY_INITIALIZER_H
 
 namespace QUESO
 {
 
-template <class DerivedTK>
-SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type
-TKFactoryMALA<DerivedTK>::build_tk()
+class TKFactoryInitializer
 {
-  SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type new_tk;
-
-  // Assume the problem is Bayesian
-  const BayesianJointPdf<GslVector, GslMatrix> * target_bayesian_pdf =
-    dynamic_cast<const BayesianJointPdf<GslVector, GslMatrix> *>(
-        this->m_target_pdf);
-
-  new_tk.reset(new DerivedTK(this->m_options->m_prefix.c_str(),
-                             *target_bayesian_pdf,
-                             *(this->m_dr_scales),
-                             *(this->m_initial_cov_matrix)));
-
-  return new_tk;
-}
-
-// Instantiate all the transition kernel factories
-TKFactoryMALA<MetropolisAdjustedLangevinTK<GslVector, GslMatrix> > tk_factory_mala("mala");
+public:
+  TKFactoryInitializer();
+  virtual ~TKFactoryInitializer();
+};
 
 } // namespace QUESO
+
+#endif  // QUESO_TK_FACTORY_INITIALIZER_H

src/core/inc/TKFactoryLogitRandomWalk.h

@@ -54,7 +54,23 @@ class TKFactoryLogitRandomWalk : public TransitionKernelFactory
   virtual ~TKFactoryLogitRandomWalk() {}
 
 protected:
-  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type build_tk();
+  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type build_tk()
+  {
+    SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type new_tk;
+
+    // Cast the domain to a box.  Might this cast fail?
+    const BoxSubset<GslVector, GslMatrix> & boxSubset =
+      dynamic_cast<const BoxSubset<GslVector, GslMatrix> & >(
+          this->m_target_pdf->domainSet());
+
+    new_tk.reset(new DerivedTK(this->m_options->m_prefix.c_str(),
+                               boxSubset,
+                               *(this->m_dr_scales),
+                               *(this->m_initial_cov_matrix)));
+
+    return new_tk;
+  }
+
 };
 
 } // namespace QUESO

src/core/inc/TKFactoryMALA.h

@@ -27,6 +27,7 @@
 
 #include <queso/TransitionKernelFactory.h>
 #include <queso/TKGroup.h>
+#include <queso/BayesianJointPdf.h>
 
 namespace QUESO
 {
@@ -52,7 +53,23 @@ class TKFactoryMALA : public TransitionKernelFactory
   virtual ~TKFactoryMALA() {}
 
 protected:
-  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type build_tk();
+  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type build_tk()
+  {
+    SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type new_tk;
+
+    // Assume the problem is Bayesian
+    const BayesianJointPdf<GslVector, GslMatrix> * target_bayesian_pdf =
+      dynamic_cast<const BayesianJointPdf<GslVector, GslMatrix> *>(
+          this->m_target_pdf);
+
+    new_tk.reset(new DerivedTK(this->m_options->m_prefix.c_str(),
+                               *target_bayesian_pdf,
+                               *(this->m_dr_scales),
+                               *(this->m_initial_cov_matrix)));
+
+    return new_tk;
+  }
+
 };
 
 } // namespace QUESO

src/core/inc/TKFactoryRandomWalk.h

@@ -52,7 +52,18 @@ class TKFactoryRandomWalk : public TransitionKernelFactory
   virtual ~TKFactoryRandomWalk() {}
 
 protected:
-  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type build_tk();
+  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type build_tk()
+  {
+    SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type new_tk;
+
+    new_tk.reset(new DerivedTK(this->m_options->m_prefix.c_str(),
+                               *(this->m_vectorSpace),
+                               *(this->m_dr_scales),
+                               *(this->m_initial_cov_matrix)));
+
+    return new_tk;
+  }
+
 };
 
 } // namespace QUESO

src/core/inc/TKFactoryStochasticNewton.h

@@ -52,7 +52,18 @@ class TKFactoryStochasticNewton : public TransitionKernelFactory
   virtual ~TKFactoryStochasticNewton() {}
 
 protected:
-  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type build_tk();
+  virtual SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type build_tk()
+  {
+    SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type new_tk;
+
+    new_tk.reset(new DerivedTK(this->m_options->m_prefix.c_str(),
+                               *(this->m_vectorSpace),
+                               *(this->m_dr_scales),
+                               *(this->m_pdf_synchronizer)));
+
+    return new_tk;
+  }
+
 };
 
 } // namespace QUESO

src/core/src/AlgorithmFactory.C

@@ -38,21 +38,7 @@ Factory<Algorithm<GslVector, GslMatrix> >::factory_map()
   return _factory_map;
 }
 
-// AlgorithmFactoryImp implementation
-template <class DerivedAlgorithm>
-SharedPtr<Algorithm<GslVector, GslMatrix> >::Type
-AlgorithmFactoryImp<DerivedAlgorithm>::build_algorithm()
-{
-  SharedPtr<Algorithm<GslVector, GslMatrix> >::Type new_alg;
-  new_alg.reset(new DerivedAlgorithm(*(this->m_env), *(this->m_tk)));
-  return new_alg;
-}
-
 const BaseEnvironment * AlgorithmFactory::m_env = NULL;
 const BaseTKGroup<GslVector, GslMatrix> * AlgorithmFactory::m_tk = NULL;
 
-// Register with the factory
-AlgorithmFactoryImp<Algorithm<GslVector, GslMatrix> > random_walk_alg("random_walk");
-AlgorithmFactoryImp<Algorithm<GslVector, GslMatrix> > logit_random_walk_alg("logit_random_walk");
-
 } // namespace QUESO

src/core/src/TKFactoryStochasticNewton.C → src/core/src/AlgorithmFactoryInitializer.C

@@ -22,27 +22,23 @@
 //
 //-----------------------------------------------------------------------el-
 
-#include <queso/TKFactoryStochasticNewton.h>
-#include <queso/HessianCovMatricesTKGroup.h>
+#include <queso/AlgorithmFactory.h>
+#include <queso/AlgorithmFactoryInitializer.h>
 
 namespace QUESO
 {
 
-template <class DerivedTK>
-SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type
-TKFactoryStochasticNewton<DerivedTK>::build_tk()
+AlgorithmFactoryInitializer::AlgorithmFactoryInitializer()
 {
-  SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type new_tk;
+  // Instantiate all the algorithm factories
+  static AlgorithmFactoryImp<Algorithm<GslVector, GslMatrix> > random_walk_alg("random_walk");
+  static AlgorithmFactoryImp<Algorithm<GslVector, GslMatrix> > logit_random_walk_alg("logit_random_walk");
 
-  new_tk.reset(new DerivedTK(this->m_options->m_prefix.c_str(),
-                             *(this->m_vectorSpace),
-                             *(this->m_dr_scales),
-                             *(this->m_pdf_synchronizer)));
-
-  return new_tk;
 }
 
-// Instantiate all the transition kernel factories
-TKFactoryStochasticNewton<HessianCovMatricesTKGroup<GslVector, GslMatrix> > tk_factory_stochastic_newton("stochastic_newton");
+AlgorithmFactoryInitializer::~AlgorithmFactoryInitializer()
+{
+  // Do nothing
+}
 
 } // namespace QUESO

src/core/src/TKFactoryLogitRandomWalk.C → src/core/src/TKFactoryInitializer.C

@@ -22,32 +22,32 @@
 //
 //-----------------------------------------------------------------------el-
 
+#include <queso/TKFactoryInitializer.h>
+
+#include <queso/TKFactoryRandomWalk.h>
+#include <queso/TKFactoryMALA.h>
 #include <queso/TKFactoryLogitRandomWalk.h>
+#include <queso/TKFactoryStochasticNewton.h>
+#include <queso/ScaledCovMatrixTKGroup.h>
 #include <queso/TransformedScaledCovMatrixTKGroup.h>
+#include <queso/MetropolisAdjustedLangevinTK.h>
+#include <queso/HessianCovMatricesTKGroup.h>
 
 namespace QUESO
 {
 
-template <class DerivedTK>
-SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type
-TKFactoryLogitRandomWalk<DerivedTK>::build_tk()
+TKFactoryInitializer::TKFactoryInitializer()
 {
-  SharedPtr<BaseTKGroup<GslVector, GslMatrix> >::Type new_tk;
-
-  // Cast the domain to a box.  Might this cast fail?
-  const BoxSubset<GslVector, GslMatrix> & boxSubset =
-    dynamic_cast<const BoxSubset<GslVector, GslMatrix> & >(
-        this->m_target_pdf->domainSet());
-
-  new_tk.reset(new DerivedTK(this->m_options->m_prefix.c_str(),
-                             boxSubset,
-                             *(this->m_dr_scales),
-                             *(this->m_initial_cov_matrix)));
-
-  return new_tk;
+  // Instantiate all the transition kernel factories
+  static TKFactoryRandomWalk<ScaledCovMatrixTKGroup<GslVector, GslMatrix> > tk_factory_random_walk("random_walk");
+  static TKFactoryLogitRandomWalk<TransformedScaledCovMatrixTKGroup<GslVector, GslMatrix> > tk_factory_logit_random_walk("logit_random_walk");
+  static TKFactoryStochasticNewton<HessianCovMatricesTKGroup<GslVector, GslMatrix> > tk_factory_stochastic_newton("stochastic_newton");
+  static TKFactoryMALA<MetropolisAdjustedLangevinTK<GslVector, GslMatrix> > tk_factory_mala("mala");
 }
 
-// Instantiate all the transition kernel factories
-TKFactoryLogitRandomWalk<TransformedScaledCovMatrixTKGroup<GslVector, GslMatrix> > tk_factory_logit_random_walk("logit_random_walk");
+TKFactoryInitializer::~TKFactoryInitializer()
+{
+  // Do nothing
+}
 
-}  // namespace QUESO
+} // namespace QUESO