Merge branch 'v0.54.0-release'

.gitignore

@@ -91,6 +91,7 @@ examples/fullCovarianceRandomCoefficient
 examples/blockDiagonalCovarianceRandomCoefficients
 examples/4d_interp
 examples/4d_interp_read
+examples/example_SharedPtr
 
 src/core/inc/queso.h
 src/libqueso.la
@@ -206,3 +207,10 @@ test/test_InterpolationSurrogateHelper
 test/test_build_InterpolationSurrogateBuilder
 test/test_write_InterpolationSurrogateBuilder_1.dat
 test/test_write_InterpolationSurrogateBuilder_2.dat
+test/output_test_optimizer_options
+test/test_optimizer/input_test_optimizer_options
+test/test_optimizer_options
+test/test_SharedPtr
+test/output_test_serialEnv
+test/test_Environment/input_test_serialEnv
+test/test_serialEnv

.travis.yml

@@ -7,5 +7,9 @@ before_script:
   - sudo apt-get install -q build-essential
   - sudo apt-get install -q libgsl0-dev
   - sudo apt-get install -q openmpi-bin openmpi-dev
-  - sudo apt-get install -q libboost-all-dev
-script: ./bootstrap && CC="mpicc" CXX="mpicxx" ./configure && make -j2 && make check
+  - sudo apt-get install -q libboost-dev libboost-math-dev libboost-program-options-dev
+script:
+  - ./bootstrap
+  - ./configure CC="mpicc" CXX="mpicxx"
+  - make -j4
+  - make check -j4

CHANGES

@@ -3,6 +3,16 @@ QUESO: Quantification of Uncertainty for Estimation,
 Simulation, and Optimization.
 -----------------------------------------------------
 
+Version 0.54.0
+  * Fix memory leak in test_GslVector
+  * Make MPI optional
+  * Optimise GSLMatrix::operator() and GslVector::operator[]
+  * Add 'txt' file output option
+  * Add SharedPtr
+  * Add input file options for optimisation and monitoring
+  * Fix some compiler warnings
+  * Fix HDF5 #include issues
+
 Version 0.53.0
   * Add linear interpolation surrogates
   * Refactor input options processing

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.65)
-AC_INIT([queso], [0.53.1], [queso-users@googlegroups.com])
+AC_INIT([queso], [0.54.0], [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"
@@ -75,17 +75,37 @@ else
    AC_MSG_RESULT(no)
 fi
 
+#############################################
+# Check if the user explicitly disabled mpi #
+#############################################
+AC_ARG_ENABLE(mpi,
+              AS_HELP_STRING([--disable-mpi],
+                             [build without message passing support]),
+              [enable_mpi=no],
+              [enable_mpi=yes])
+
 #-------------------
 # Compilers and MPI
 #-------------------
-
 AC_PROG_CC
 AC_PROG_CXX
 AC_PROG_FC
 AC_LANG([C])
-ACX_MPI([CC="$MPICC"], [AC_MSG_ERROR([Could not find MPI.])])
+
+HAVE_MPI=0
+if test "x$enable_mpi" = "xyes"; then
+    ACX_MPI(CC="$MPICC", [AC_MSG_ERROR([Could not find MPI.])])
+    HAVE_MPI=1
+fi
+
 AC_LANG([C++])
-ACX_MPI([CXX="$MPICXX"], [AC_MSG_ERROR([Could not find MPI.])])
+
+if test "x$enable_mpi" = "xyes"; then
+    ACX_MPI(CXX="$MPICXX", [AC_MSG_ERROR([Could not find MPI.])])
+    HAVE_MPI=1
+fi
+AC_SUBST(HAVE_MPI)
+AM_CONDITIONAL(MPI_ENABLED, test x$HAVE_MPI = x1)
 
 #-------------------------
 # External Library Checks
@@ -124,6 +144,7 @@ AC_LANG([C++])
 BOOST_REQUIRE([1.35])
 BOOST_PROGRAM_OPTIONS
 BOOST_FIND_HEADER([boost/scoped_ptr.hpp])
+BOOST_FIND_HEADER([boost/shared_ptr.hpp])
 AC_CACHE_SAVE
 
 # Check for GLPK (optional)
@@ -218,6 +239,8 @@ AC_CONFIG_FILES([
   test/test_InputOptionsParser/test_options_good.txt
   test/test_InputOptionsParser/test_options_bad.txt
   test/test_InputOptionsParser/test_options_default.txt
+  test/test_optimizer/input_test_optimizer_options
+  test/test_Environment/input_test_serialEnv
 ])
 
 AC_CONFIG_FILES([test/test_Regression/test_cobra_samples_diff.sh

examples/Makefile.am

@@ -436,6 +436,20 @@ dist_interpsurrg_DATA += ${4d_interp_read_SOURCES}
 dist_interpsurrg_DATA += interpolation_surrogate/input.in
 dist_interpsurrg_DATA += interpolation_surrogate/4d_interp_data_coarse.dat
 
+#####################
+# SharedPtr example #
+#####################
+pointersdir = $(prefix)/examples/pointers
+
+pointers_PROGRAMS = example_SharedPtr
+
+example_SharedPtr_SOURCES = pointers/example_SharedPtr.C
+example_SharedPtr_LDADD = $(top_builddir)/src/libqueso.la
+example_SharedPtr_CPPFLAGS = $(QUESO_CPPFLAGS)
+
+dist_pointers_DATA =
+dist_pointers_DATA += ${example_SharedPtr_SOURCES}
+
 if CODE_COVERAGE_ENABLED
   CLEANFILES = *.gcda *.gcno
 endif

examples/bimodal/src/bimodal_likelihood.C

@@ -76,7 +76,7 @@ double likelihoodRoutine(
 
   if (paramValues.env().exceptionalCircumstance()) {
     if ((paramValues.env().subDisplayFile()       ) &&
-        (paramValues.env().displayVerbosity() >= 0)) { // detailed output debug
+        (paramValues.env().displayVerbosity() > 0)) { // detailed output debug
       *paramValues.env().subDisplayFile() << "Leaving likelihood function"
                                           << ": paramValues = " << paramValues
                                           << ", returnValue = " << returnValue

examples/bimodal/src/bimodal_main.C

@@ -27,14 +27,20 @@
 int main(int argc, char* argv[])
 {
   // Initialize environment
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc,&argv);
   QUESO::FullEnvironment* env = new QUESO::FullEnvironment(MPI_COMM_WORLD,argv[1],"",NULL);
+#else
+  QUESO::FullEnvironment* env = new QUESO::FullEnvironment(argv[1],"",NULL);
+#endif
 
   // Compute
   compute(*env);
 
   // Finalize environment
   delete env;
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
   return 0;
 }

examples/gaussian_likelihoods/blockDiagonalCovariance.C

@@ -60,9 +60,12 @@ public:
 };
 
 int main(int argc, char ** argv) {
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc, &argv);
-
   QUESO::FullEnvironment env(MPI_COMM_WORLD, argv[1], "", NULL);
+#else
+  QUESO::FullEnvironment env(argv[1], "", NULL);
+#endif
 
   QUESO::VectorSpace<QUESO::GslVector, QUESO::GslMatrix> paramSpace(env,
       "param_", 1, NULL);
@@ -121,7 +124,9 @@ int main(int argc, char ** argv) {
 
   ip.solveWithBayesMetropolisHastings(NULL, paramInitials, &proposalCovMatrix);
 
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/gaussian_likelihoods/blockDiagonalCovarianceRandomCoefficients.C

@@ -60,9 +60,12 @@ public:
 };
 
 int main(int argc, char ** argv) {
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc, &argv);
-
   QUESO::FullEnvironment env(MPI_COMM_WORLD, argv[1], "", NULL);
+#else
+  QUESO::FullEnvironment env(argv[1], "", NULL);
+#endif
 
   // Need 3 dims because two are for the hyperparameters
   QUESO::VectorSpace<QUESO::GslVector, QUESO::GslMatrix> paramSpace(env,
@@ -127,7 +130,9 @@ int main(int argc, char ** argv) {
 
   ip.solveWithBayesMetropolisHastings(NULL, paramInitials, &proposalCovMatrix);
 
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/gaussian_likelihoods/diagonalCovariance.C

@@ -59,9 +59,12 @@ public:
 };
 
 int main(int argc, char ** argv) {
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc, &argv);
-
   QUESO::FullEnvironment env(MPI_COMM_WORLD, argv[1], "", NULL);
+#else
+  QUESO::FullEnvironment env(argv[1], "", NULL);
+#endif
 
   QUESO::VectorSpace<QUESO::GslVector, QUESO::GslMatrix> paramSpace(env,
       "param_", 1, NULL);
@@ -116,7 +119,9 @@ int main(int argc, char ** argv) {
 
   ip.solveWithBayesMetropolisHastings(NULL, paramInitials, &proposalCovMatrix);
 
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/gaussian_likelihoods/fullCovariance.C

@@ -59,9 +59,12 @@ public:
 };
 
 int main(int argc, char ** argv) {
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc, &argv);
-
   QUESO::FullEnvironment env(MPI_COMM_WORLD, argv[1], "", NULL);
+#else
+  QUESO::FullEnvironment env(argv[1], "", NULL);
+#endif
 
   QUESO::VectorSpace<QUESO::GslVector, QUESO::GslMatrix> paramSpace(env,
       "param_", 1, NULL);
@@ -118,7 +121,9 @@ int main(int argc, char ** argv) {
 
   ip.solveWithBayesMetropolisHastings(NULL, paramInitials, &proposalCovMatrix);
 
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/gaussian_likelihoods/fullCovarianceRandomCoefficient.C

@@ -65,16 +65,16 @@ public:
 };
 
 int main(int argc, char ** argv) {
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc, &argv);
-
   QUESO::FullEnvironment env(MPI_COMM_WORLD, argv[1], "", NULL);
+#else
+  QUESO::FullEnvironment env(argv[1], "", NULL);
+#endif
 
   QUESO::VectorSpace<QUESO::GslVector, QUESO::GslMatrix> paramSpace(env,
       "param_", 2, NULL);
 
-  double min_val = 0.0;
-  double max_val = 1.0;
-
   QUESO::GslVector paramMins(paramSpace.zeroVector());
   QUESO::GslVector paramMaxs(paramSpace.zeroVector());
 
@@ -131,7 +131,9 @@ int main(int argc, char ** argv) {
 
   ip.solveWithBayesMetropolisHastings(NULL, paramInitials, &proposalCovMatrix);
 
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/gaussian_likelihoods/scalarCovariance.C

@@ -59,9 +59,12 @@ public:
 };
 
 int main(int argc, char ** argv) {
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc, &argv);
-
   QUESO::FullEnvironment env(MPI_COMM_WORLD, argv[1], "", NULL);
+#else
+  QUESO::FullEnvironment env(argv[1], "", NULL);
+#endif
 
   QUESO::VectorSpace<QUESO::GslVector, QUESO::GslMatrix> paramSpace(env,
       "param_", 1, NULL);
@@ -111,7 +114,9 @@ int main(int argc, char ** argv) {
 
   ip.solveWithBayesMetropolisHastings(NULL, paramInitials, &proposalCovMatrix);
 
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/gp/scalar/gpmsa_scalar.C

@@ -98,10 +98,14 @@ int main(int argc, char ** argv) {
   unsigned int numEta = 1;  // Number of responses the model is returning
   unsigned int experimentSize = 1;  // Size of each experiment
 
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc, &argv);
 
   // Step 1: Set up QUESO environment
   QUESO::FullEnvironment env(MPI_COMM_WORLD, argv[1], "", NULL);
+#else
+  QUESO::FullEnvironment env(argv[1], "", NULL);
+#endif
 
   // Step 2: Set up prior for calibration parameters
   QUESO::VectorSpace<QUESO::GslVector, QUESO::GslMatrix> paramSpace(env,
@@ -283,7 +287,9 @@ int main(int argc, char ** argv) {
 
   ip.solveWithBayesMetropolisHastings(NULL, paramInitials, &proposalCovMatrix);
 
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/gravity/src/gravity_main.C

@@ -49,16 +49,23 @@
 int main(int argc, char* argv[])
 {
   // Initialize QUESO environment
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc,&argv);
   QUESO::FullEnvironment* env =
     new QUESO::FullEnvironment(MPI_COMM_WORLD,argv[1],"",NULL);
+#else
+  QUESO::FullEnvironment* env =
+    new QUESO::FullEnvironment(argv[1],"",NULL);
+#endif
 
   // Call application
   computeGravityAndTraveledDistance(*env);
 
   // Finalize QUESO environment
   delete env;
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/hysteretic/src/example_main.C

@@ -35,9 +35,14 @@
 int main(int argc, char* argv[])
 {
   // Initialize environment
+#ifdef QUESO_HAS_MPI
   MPI_Init(&argc,&argv);
   QUESO::FullEnvironment* env =
     new QUESO::FullEnvironment(MPI_COMM_WORLD,argv[1],"",NULL);
+#else
+  QUESO::FullEnvironment* env =
+    new QUESO::FullEnvironment(argv[1],"",NULL);
+#endif
 
   // Compute
 #if 1
@@ -48,7 +53,9 @@ int main(int argc, char* argv[])
 
   // Finalize environment
   delete env;
+#ifdef QUESO_HAS_MPI
   MPI_Finalize();
+#endif
 
   return 0;
 }

examples/infinite_dim/gaussian_fields/gaussian_random_field.C

@@ -4,6 +4,7 @@
 #include <libmesh/mesh.h>
 #include <libmesh/mesh_generation.h>
 #include <queso/Environment.h>
+#include <queso/EnvironmentOptions.h>
 #include <queso/FunctionOperatorBuilder.h>
 #include <queso/LibMeshFunction.h>
 #include <queso/LibMeshNegativeLaplacianOperator.h>