Merge remote-tracking branch 'upstream/v0.53.0-release'

.gitignore

@@ -89,6 +89,8 @@ examples/fullCovariance
 examples/blockDiagonalCovariance
 examples/fullCovarianceRandomCoefficient
 examples/blockDiagonalCovarianceRandomCoefficients
+examples/4d_interp
+examples/4d_interp_read
 
 src/core/inc/queso.h
 src/libqueso.la
@@ -115,7 +117,6 @@ test/test_uqEnvironment
 test/test_uqEnvironmentCopy
 test/test_uqEnvironmentEquals
 test/test_uqEnvironmentNonFatal
-test/test_uqEnvironmentOptionsPrint
 test/test_uqGaussianVectorRVClass
 test/test_uqGslMatrix
 test/test_uqGslMatrixConstructorFatal
@@ -188,3 +189,20 @@ test/test_fullCovarianceChain
 test/test_diagonalCovarianceChain
 test/test_scalarCovarianceChain
 test/test_blockDiagonalCovarianceChain
+test/test_BoostInputOptionsParser
+test/test_InputOptionsParser/test_options_good.txt
+test/test_InputOptionsParser/test_options_bad.txt
+test/test_InputOptionsParser/test_options_default.txt
+test/test_NoInputFile
+test/test_InterpolationSurrogate/queso_input.txt
+test/test_output_interp_surrogates
+test/test_write_InterpolationSurrogateBuilder.dat
+test/test_outputNoInputFile
+test/test_1D_LinearLagrangeInterpolationSurrogate
+test/test_2D_LinearLagrangeInterpolationSurrogate
+test/test_3D_LinearLagrangeInterpolationSurrogate
+test/test_4D_LinearLagrangeInterpolationSurrogate
+test/test_InterpolationSurrogateHelper
+test/test_build_InterpolationSurrogateBuilder
+test/test_write_InterpolationSurrogateBuilder_1.dat
+test/test_write_InterpolationSurrogateBuilder_2.dat

CHANGES

@@ -3,8 +3,17 @@ QUESO: Quantification of Uncertainty for Estimation,
 Simulation, and Optimization.
 -----------------------------------------------------
 
+Version 0.53.0
+  * Add linear interpolation surrogates
+  * Refactor input options processing
+  * Refactor existing queso errors and asserts
+  * Add new error checking macros
+  * Add basic scoped pointer wrappers
+  * Better error message reporting for bad sample covariance matrices
+
 Version 0.52.0
   * Add canned Gaussian likelihoods
+  * Fix bug in logit transform logic
 
 Version 0.51.0
   * Add canned likelihood for scalar GPMSA use-case a la Higdon et al

README.md

@@ -1,5 +1,5 @@
-The `QUESO` Library
-=================
+The `QUESO` Library [![Build Status](https://travis-ci.org/libqueso/queso.svg?branch=dev)](https://travis-ci.org/libqueso/queso)
+===================
 
 `QUESO` stands for Quantification of Uncertainty for Estimation,
 Simulation and Optimization.
@@ -18,15 +18,18 @@ uniprocessor or multiprocessor environments.
 Installation
 ------------
 
+You can obtain `QUESO` tarballs
+[here](https://github.com/libqueso/queso/releases).
+
 If you do not have a `configure` script in the top level directory,
-run `bootstrap` to generate a configure script using autotools.
+run `bootstrap` to generate a configure script using `autotools`.
 
 Before compiling, you must run the `configure` script.  To run, type
 `./configure`.  Additional options may be provided if desired.  Run
 `./configure --help` for details.
 
 After successfully running `configure`, type `make` to build the
-`QUESO` library
+`QUESO` library.
 
 Then type `make install` to install it in the directory previously
 specified by the `--prefix` option of the `configure` script.
@@ -35,7 +38,13 @@ Documentation
 -------------
 
 `QUESO` documentation is available
-[here](http://libqueso.github.io/queso/docs/html/).
+[here](http://libqueso.github.io/queso/html/).
+
+Documentation for older versions:
+
+-  [v0.50.1](http://libqueso.github.io/queso/v0.50.1/html/)
+-  [v0.51.1](http://libqueso.github.io/queso/v0.51.1/html/)
+-  [v0.52.0](http://libqueso.github.io/queso/v0.52.0/html/)
 
 Dependencies
 ------------
@@ -63,7 +72,8 @@ capabilities of `QUESO`, then you also need the following dependencies:
 License
 -------
 
-See `LICENSE` file distributed with `QUESO` for more information.
+See [`LICENSE`](https://github.com/libqueso/queso/blob/dev/LICENSE) file
+distributed with `QUESO` for more information.
 
 Contributing
 ------------

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.65)
-AC_INIT([queso], [0.52.0], [queso-users@googlegroups.com])
+AC_INIT([queso], [0.53.0], [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"
@@ -17,6 +17,7 @@ AX_PREFIX_CONFIG_H(config_queso.h,QUESO,config_queso.h.tmp)
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CANONICAL_TARGET()
 AM_INIT_AUTOMAKE([color-tests subdir-objects])
+AM_SILENT_RULES(yes)  # use silent rules where available - automake 1.11
 
 # Release versioning
 
@@ -122,6 +123,7 @@ AC_CACHE_SAVE
 AC_LANG([C++])
 BOOST_REQUIRE([1.35])
 BOOST_PROGRAM_OPTIONS
+BOOST_FIND_HEADER([boost/scoped_ptr.hpp])
 AC_CACHE_SAVE
 
 # Check for GLPK (optional)
@@ -158,7 +160,7 @@ DX_CHI_FEATURE(OFF)
 DX_MAN_FEATURE(OFF)
 DX_RTF_FEATURE(OFF)
 DX_XML_FEATURE(OFF)
-DX_PDF_FEATURE(ON)
+DX_PDF_FEATURE(OFF)
 DX_PS_FEATURE(OFF)
 
 DX_INIT_DOXYGEN([queso],[doxygen/queso.dox],[docs])
@@ -194,7 +196,6 @@ AC_CONFIG_FILES([
   test/t04_bimodal/Makefile
   test/gsl_tests/Makefile
   test/gsl_tests/input
-  test/test_Environment/copy_env
   test/test_infinite/inf_options
   test/test_Regression/GaussianMean1DRegression_options
   test/test_Regression/gpmsa_cobra_input.txt
@@ -209,10 +210,14 @@ AC_CONFIG_FILES([
   test/test_Regression/test_jeffreys_samples.m
   test/test_Regression/adaptedcov_input.txt
   test/test_gaussian_likelihoods/queso_input.txt
+  test/test_InterpolationSurrogate/queso_input.txt
   doxygen/Makefile
   doxygen/queso.dox
   doxygen/txt_common/about_vpath.page
   test/test_gaussian_likelihoods/gaussian_consistency_input.txt
+  test/test_InputOptionsParser/test_options_good.txt
+  test/test_InputOptionsParser/test_options_bad.txt
+  test/test_InputOptionsParser/test_options_default.txt
 ])
 
 AC_CONFIG_FILES([test/test_Regression/test_cobra_samples_diff.sh

doxygen/queso.dox.in

@@ -570,10 +570,7 @@ INPUT  = @abs_top_srcdir@/doxygen/queso.page \
          @abs_top_srcdir@/doxygen/txt_common/acknowledgment.page \
          @abs_top_srcdir@/doxygen/txt_common/lgpl.page \
          @abs_top_srcdir@/doxygen/txt_common/noop.page \
-      	 @abs_top_srcdir@/src/core \
-      	 @abs_top_srcdir@/src/misc \
-      	 @abs_top_srcdir@/src/basic \
-      	 @abs_top_srcdir@/src/stats
+         @abs_top_srcdir@/src
 
 #      	 @abs_top_srcdir@/src/interface #C/Fortran interface that hasn't been touched since at least Revision 14611.
 #      	 @abs_top_srcdir@/examples/statisticalInverseProblem1/src \
@@ -1039,7 +1036,7 @@ PAPER_TYPE             = $(PAPER_SIZE)
 # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
 # packages that should be included in the LaTeX output.
 
-EXTRA_PACKAGES         = 
+EXTRA_PACKAGES         = amsmath amsfonts
 
 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
 # the generated latex document. The header should contain everything until 

examples/Makefile.am

@@ -212,11 +212,13 @@ dist_exTgaValidationCycle_gsl_DATA +=	${exTgaValidationCycle_gsl_SOURCES}
 ####################
 tga2_gsldir = $(prefix)/examples/validationCycle2
 
-tga2_gsl_DATA = $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/inputData/scenario_100_K_min.dat
-tga2_gsl_DATA += $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/inputData/scenario_25_K_min.dat
-tga2_gsl_DATA += $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/inputData/scenario_50_K_min.dat
-tga2_gsl_DATA += $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/inputData/scenario_5_K_min.dat
-tga2_gsl_DATA += $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/tgaCycle.inp
+tga2_gslinputdatadir = $(prefix)/examples/validationCycle2/inputData
+
+tga2_gslinputdata_DATA  = $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/inputData/scenario_100_K_min.dat
+tga2_gslinputdata_DATA += $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/inputData/scenario_25_K_min.dat
+tga2_gslinputdata_DATA += $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/inputData/scenario_50_K_min.dat
+tga2_gslinputdata_DATA += $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/inputData/scenario_5_K_min.dat
+tga2_gsl_DATA  = $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/tgaCycle.inp
 tga2_gsl_DATA += $(top_srcdir)/examples/validationCycle2/tests/test_2012_11_15/tga_cycle_plot.m
 
 tga2_gsl_PROGRAMS = tga2_gsl
@@ -367,6 +369,12 @@ gpmsa_scalar_SOURCES = gp/scalar/gpmsa_scalar.C
 gpmsa_scalar_LDADD = $(top_builddir)/src/libqueso.la
 gpmsa_scalar_CPPFLAGS = -I$(top_srcdir)/examples/gp/scalar $(QUESO_CPPFLAGS)
 
+dist_gpmsa_scalar_DATA =
+dist_gpmsa_scalar_DATA += ${gpmsa_scalar_SOURCES}
+dist_gpmsa_scalar_DATA += gp/scalar/dakota_pstudy.dat
+dist_gpmsa_scalar_DATA += gp/scalar/gpmsa_input.txt
+dist_gpmsa_scalar_DATA += gp/scalar/ctf_dat.txt
+
 #######################################
 # Canned Gaussian likelihood examples #
 #######################################
@@ -406,11 +414,32 @@ blockDiagonalCovarianceRandomCoefficients_SOURCES = gaussian_likelihoods/blockDi
 blockDiagonalCovarianceRandomCoefficients_LDADD = $(top_builddir)/src/libqueso.la
 blockDiagonalCovarianceRandomCoefficients_CPPFLAGS = -I$(top_srcdir)/examples/gaussian_likelihoods/blockDiagonalCovarianceRandomCoefficients $(QUESO_CPPFLAGS)
 
-dist_gpmsa_scalar_DATA =
-dist_gpmsa_scalar_DATA += ${gpmsa_scalar_SOURCES}
+####################################
+# Interpolation Surrogate examples #
+####################################
+interpsurrgdir = $(prefix)/examples/interpolation_surrogate
+
+interpsurrg_PROGRAMS = 4d_interp 4d_interp_read
+
+4d_interp_SOURCES = interpolation_surrogate/4d_interp.C
+4d_interp_LDADD = $(top_builddir)/src/libqueso.la
+4d_interp_CPPFLAGS = $(QUESO_CPPFLAGS)
+
+4d_interp_read_SOURCES = interpolation_surrogate/4d_interp_read.C
+4d_interp_read_LDADD = $(top_builddir)/src/libqueso.la
+4d_interp_read_CPPFLAGS = $(QUESO_CPPFLAGS)
+
+dist_interpsurrg_DATA =
+dist_interpsurrg_DATA += ${4d_interp_SOURCES}
+dist_interpsurrg_DATA += ${4d_interp_read_SOURCES}
+dist_interpsurrg_DATA += interpolation_surrogate/input.in
+dist_interpsurrg_DATA += interpolation_surrogate/4d_interp_data_coarse.dat
 
 if CODE_COVERAGE_ENABLED
   CLEANFILES = *.gcda *.gcno
 endif
 
+runalldir = $(prefix)/examples
+dist_runall_SCRIPTS = run_all.sh
+
 MAINTAINERCLEANFILES = Makefile.in

examples/gp/scalar/gpmsa_scalar.C

@@ -14,6 +14,11 @@ double readData(const std::vector<QUESO::GslVector *> & simulationScenarios,
     const std::vector<QUESO::GslVector *> & experimentScenarios,
     const std::vector<QUESO::GslVector *> & experimentOutputs) {
   FILE * fp_in = fopen("gp/scalar/dakota_pstudy.dat", "r");
+  if (!fp_in)
+    fp_in = fopen("dakota_pstudy.dat", "r");
+  if (!fp_in)
+    queso_error_msg("Cannot find dakota_pstudy.dat");
+
   unsigned int i, id, size = 512;
   double k_tmasl, k_tmoml, k_tnrgl, k_xkwlx, k_cd, pressure;
   char line[size];
@@ -59,6 +64,11 @@ double readData(const std::vector<QUESO::GslVector *> & simulationScenarios,
 
   // Read in experimental data
   fp_in = fopen("gp/scalar/ctf_dat.txt", "r");
+  if (!fp_in)
+    fp_in = fopen("ctf_dat.txt", "r");
+  if (!fp_in)
+    queso_error_msg("Cannot find ctf_dat.txt");
+
   i = 0;
   while (fscanf(fp_in, "%lf\n", &pressure) != EOF) {
     (*(experimentOutputs[i]))[0] = pressure;

examples/gravity/src/gravity_compute.C

@@ -88,8 +88,7 @@ void computeGravityAndTraveledDistance(const QUESO::FullEnvironment& env) {
   //------------------------------------------------------
   // SIP Step 1 of 6: Instantiate the parameter space
   //------------------------------------------------------
-  QUESO::VectorSpace<QUESO::GslVector,QUESO::GslMatrix> paramSpace(env,
-      "param_", 1, NULL);
+  QUESO::VectorSpace<> paramSpace(env, "param_", 1, NULL);
 
   //------------------------------------------------------
   // SIP Step 2 of 6: Instantiate the parameter domain
@@ -100,34 +99,28 @@ void computeGravityAndTraveledDistance(const QUESO::FullEnvironment& env) {
   paramMinValues[0] = 8.;
   paramMaxValues[0] = 11.;
 
-  QUESO::BoxSubset<QUESO::GslVector,QUESO::GslMatrix> paramDomain("param_",
-      paramSpace, paramMinValues, paramMaxValues);
+  QUESO::BoxSubset<> paramDomain("param_", paramSpace, paramMinValues,
+      paramMaxValues);
 
   //------------------------------------------------------
   // SIP Step 3 of 6: Instantiate the likelihood function
   // object to be used by QUESO.
   //------------------------------------------------------
-  Likelihood<QUESO::GslVector, QUESO::GslMatrix> lhood("like_", paramDomain);
+  Likelihood<> lhood("like_", paramDomain);
 
   //------------------------------------------------------
   // SIP Step 4 of 6: Define the prior RV
   //------------------------------------------------------
-  QUESO::UniformVectorRV<QUESO::GslVector,QUESO::GslMatrix> priorRv("prior_",
-      paramDomain);
+  QUESO::UniformVectorRV<> priorRv("prior_", paramDomain);
 
   //------------------------------------------------------
   // SIP Step 5 of 6: Instantiate the inverse problem
   //------------------------------------------------------
-  QUESO::GenericVectorRV<QUESO::GslVector,QUESO::GslMatrix>
-    postRv("post_",  // Extra prefix before the default "rv_" prefix
-           paramSpace);
+  // Extra prefix before the default "rv_" prefix
+  QUESO::GenericVectorRV<> postRv("post_", paramSpace);
 
-  QUESO::StatisticalInverseProblem<QUESO::GslVector,QUESO::GslMatrix>
-    ip("",          // No extra prefix before the default "ip_" prefix
-       NULL,
-       priorRv,
-       lhood,
-       postRv);
+  // No extra prefix before the default "ip_" prefix
+  QUESO::StatisticalInverseProblem<> ip("", NULL, priorRv, lhood, postRv);
 
   //------------------------------------------------------
   // SIP Step 6 of 6: Solve the inverse problem, that is,
@@ -157,8 +150,7 @@ void computeGravityAndTraveledDistance(const QUESO::FullEnvironment& env) {
   // SFP input RV = FIP posterior RV, so SFP parameter space
   // has been already defined.
   //------------------------------------------------------
-  QUESO::VectorSpace<QUESO::GslVector,QUESO::GslMatrix> qoiSpace(env, "qoi_",
-      1, NULL);
+  QUESO::VectorSpace<> qoiSpace(env, "qoi_", 1, NULL);
 
   //------------------------------------------------------
   // SFP Step 2 of 6: Instantiate the parameter domain
@@ -171,8 +163,7 @@ void computeGravityAndTraveledDistance(const QUESO::FullEnvironment& env) {
   // SFP Step 3 of 6: Instantiate the qoi object
   // to be used by QUESO.
   //------------------------------------------------------
-  Qoi<QUESO::GslVector, QUESO::GslMatrix, QUESO::GslVector, QUESO::GslMatrix>
-    qoi("qoi_", paramDomain, qoiSpace);
+  Qoi<> qoi("qoi_", paramDomain, qoiSpace);
 
   //------------------------------------------------------
   // SFP Step 4 of 6: Define the input RV
@@ -184,11 +175,9 @@ void computeGravityAndTraveledDistance(const QUESO::FullEnvironment& env) {
   //------------------------------------------------------
   // SFP Step 5 of 6: Instantiate the forward problem
   //------------------------------------------------------
-  QUESO::GenericVectorRV<QUESO::GslVector, QUESO::GslMatrix> qoiRv("qoi_",
-      qoiSpace);
+  QUESO::GenericVectorRV<> qoiRv("qoi_", qoiSpace);
 
-  QUESO::StatisticalForwardProblem<QUESO::GslVector, QUESO::GslMatrix,
-    QUESO::GslVector, QUESO::GslMatrix> fp("", NULL, postRv, qoi, qoiRv);
+  QUESO::StatisticalForwardProblem<> fp("", NULL, postRv, qoi, qoiRv);
 
   //------------------------------------------------------
   // SFP Step 6 of 6: Solve the forward problem

examples/gravity/src/gravity_likelihood.h

@@ -28,7 +28,7 @@
 #include <queso/ScalarFunction.h>
 #include <queso/GslMatrix.h>
 
-template<class V, class M>
+template<class V = QUESO::GslVector, class M = QUESO::GslMatrix>
 class Likelihood : public QUESO::BaseScalarFunction<V, M>
 {
 public: