Merge remote-tracking branch 'borglab/develop' into develop

.travis.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # common tasks before either build or test
-function prepare ()
+function configure()
 {
   set -e   # Make sure any error makes the script to return an error code
   set -x   # echo
@@ -14,21 +14,23 @@ function prepare ()
   rm -fr $BUILD_DIR || true
   mkdir $BUILD_DIR && cd $BUILD_DIR
 
-  if [ -z "$CMAKE_BUILD_TYPE" ]; then
-    CMAKE_BUILD_TYPE=Debug
-  fi
-
-  if [ -z "$GTSAM_ALLOW_DEPRECATED_SINCE_V4" ]; then
-    GTSAM_ALLOW_DEPRECATED_SINCE_V4=OFF
-  fi
-
   if [ ! -z "$GCC_VERSION" ]; then
-    sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-$GCC_VERSION 60 \
+    export CC=gcc-$GCC_VERSION
-                         --slave /usr/bin/g++ g++ /usr/bin/g++-$GCC_VERSION
+    export CXX=g++-$GCC_VERSION
-    sudo update-alternatives --set gcc /usr/bin/gcc-$GCC_VERSION
   fi
+
+  # GTSAM_BUILD_WITH_MARCH_NATIVE=OFF: to avoid crashes in builder VMs
+  cmake $SOURCE_DIR \
+      -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE:-Debug} \
+      -DGTSAM_BUILD_TESTS=${GTSAM_BUILD_TESTS:-OFF} \
+      -DGTSAM_BUILD_UNSTABLE=${GTSAM_BUILD_UNSTABLE:-ON} \
+      -DGTSAM_BUILD_EXAMPLES_ALWAYS=${GTSAM_BUILD_EXAMPLES_ALWAYS:-ON} \
+      -DGTSAM_ALLOW_DEPRECATED_SINCE_V4=${GTSAM_ALLOW_DEPRECATED_SINCE_V4:-OFF} \
+      -DGTSAM_BUILD_WITH_MARCH_NATIVE=OFF \
+      -DCMAKE_VERBOSE_MAKEFILE=ON
 }
 
+
 # common tasks after either build or test
 function finish ()
 {
@@ -41,17 +43,12 @@ function finish ()
 # compile the code with the intent of populating the cache
 function build ()
 {
-  prepare
+  export GTSAM_BUILD_EXAMPLES_ALWAYS=ON
+  export GTSAM_BUILD_TESTS=OFF
 
-  cmake $SOURCE_DIR \
+  configure
-      -DCMAKE_BUILD_TYPE=$CMAKE_BUILD_TYPE \
-      -DGTSAM_BUILD_TESTS=OFF \
-      -DGTSAM_BUILD_UNSTABLE=$GTSAM_BUILD_UNSTABLE \
-      -DGTSAM_BUILD_EXAMPLES_ALWAYS=ON \
-      -DGTSAM_ALLOW_DEPRECATED_SINCE_V4=$GTSAM_ALLOW_DEPRECATED_SINCE_V4
 
-  # Actual build:
+  make -j2
-  VERBOSE=1 make -j2
 
   finish
 }
@@ -59,14 +56,10 @@ function build ()
 # run the tests
 function test ()
 {
-  prepare
+  export GTSAM_BUILD_EXAMPLES_ALWAYS=OFF
+  export GTSAM_BUILD_TESTS=ON
 
-  cmake $SOURCE_DIR \
+  configure
-      -DCMAKE_BUILD_TYPE=$CMAKE_BUILD_TYPE \
-      -DGTSAM_BUILD_TESTS=ON \
-      -DGTSAM_BUILD_UNSTABLE=$GTSAM_BUILD_UNSTABLE \
-      -DGTSAM_BUILD_EXAMPLES_ALWAYS=OFF \
-      -DGTSAM_ALLOW_DEPRECATED_SINCE_V4=OFF
 
   # Actual build:
   make -j2 check

.travis.yml

@@ -7,11 +7,12 @@ addons:
   apt:
     sources:
     - ubuntu-toolchain-r-test
+    - sourceline: 'deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-9 main'
+      key_url: 'https://apt.llvm.org/llvm-snapshot.gpg.key'
     packages:
-    - g++-8
+    - g++-9
-    - clang-3.8
+    - clang-9
-    - build-essential
+    - build-essential pkg-config
-    - pkg-config
     - cmake
     - libpython-dev python-numpy
     - libboost-all-dev
@@ -28,8 +29,14 @@ stages:
   - compile
   - test
 
+env:
+  global:
+    - MAKEFLAGS="-j2"
+    - CCACHE_SLOPPINESS=pch_defines,time_macros
+
 # Compile stage without building examples/tests to populate the caches.
 jobs:
+# -------- STAGE 1: COMPILE -----------
   include:
 # on Mac, GCC
   - stage: compile
@@ -68,46 +75,45 @@ jobs:
   - stage: compile
     os: linux
     compiler: clang
-    env: CMAKE_BUILD_TYPE=Debug GTSAM_BUILD_UNSTABLE=OFF
+    env: CC=clang-9 CXX=clang++-9 CMAKE_BUILD_TYPE=Debug GTSAM_BUILD_UNSTABLE=OFF
     script: bash .travis.sh -b
   - stage: compile
     os: linux
     compiler: clang
-    env: CMAKE_BUILD_TYPE=Release
+    env: CC=clang-9 CXX=clang++-9 CMAKE_BUILD_TYPE=Release
     script: bash .travis.sh -b
 # on Linux, with deprecated ON to make sure that path still compiles
   - stage: compile
     os: linux
     compiler: clang
-    env: CMAKE_BUILD_TYPE=Debug GTSAM_BUILD_UNSTABLE=OFF GTSAM_ALLOW_DEPRECATED_SINCE_V4=ON
+    env: CC=clang-9 CXX=clang++-9 CMAKE_BUILD_TYPE=Debug GTSAM_BUILD_UNSTABLE=OFF GTSAM_ALLOW_DEPRECATED_SINCE_V4=ON
     script: bash .travis.sh -b
-
+# -------- STAGE 2: TESTS -----------
-# Matrix configuration:
+# on Mac, GCC
-os:
+  - stage: test
-  - osx
+    os: osx
-  - linux
-compiler:
-  - gcc
-  - clang
-env:
-  global:
-    - MAKEFLAGS="-j2"
-    - CCACHE_SLOPPINESS=pch_defines,time_macros
-    - GTSAM_ALLOW_DEPRECATED_SINCE_V4=OFF
-    - GTSAM_BUILD_UNSTABLE=ON
-  matrix:
-    - CMAKE_BUILD_TYPE=Debug GTSAM_BUILD_UNSTABLE=OFF
-    - CMAKE_BUILD_TYPE=Release
-script:
-  - bash .travis.sh -t
-
-matrix:
-  exclude:
-    # Exclude g++ debug on Linux as it consistently times out
-    - os: linux
-      compiler: gcc
-      env : CMAKE_BUILD_TYPE=Debug GTSAM_BUILD_UNSTABLE=OFF
-    # Exclude clang on Linux/clang in release until issue #57 is solved
-    - os: linux
     compiler: clang
     env: CMAKE_BUILD_TYPE=Release
+    script: bash .travis.sh -t
+  - stage: test
+    os: osx
+    compiler: clang
+    env: CMAKE_BUILD_TYPE=Debug GTSAM_BUILD_UNSTABLE=OFF
+    script: bash .travis.sh -t
+  - stage: test
+    os: linux
+    compiler: gcc
+    env: CMAKE_BUILD_TYPE=Release
+    script: bash .travis.sh -t
+# Exclude g++ debug on Linux as it consistently times out
+#  - stage: test
+#    os: linux
+#    compiler: gcc
+#    env: CMAKE_BUILD_TYPE=Debug GTSAM_BUILD_UNSTABLE=OFF
+#    script: bash .travis.sh -t
+# Exclude clang on Linux/clang in release until issue #57 is solved
+#  - stage: test
+#    os: linux
+#    compiler: clang
+#    env: CC=clang-9 CXX=clang++-9 CMAKE_BUILD_TYPE=Release
+#    script: bash .travis.sh -t

CMakeLists.txt

@@ -434,7 +434,7 @@ add_subdirectory(timing)
 # Build gtsam_unstable
 if (GTSAM_BUILD_UNSTABLE)
     add_subdirectory(gtsam_unstable)
-endif(GTSAM_BUILD_UNSTABLE)
+endif()
 
 # Matlab toolbox
 if (GTSAM_INSTALL_MATLAB_TOOLBOX)

gtsam/base/ConcurrentMap.h

@@ -29,14 +29,22 @@
 #  undef max
 #  undef ERROR
 
+#include <functional> // std::hash()
+
 // Use TBB concurrent_unordered_map for ConcurrentMap
-#  define CONCURRENT_MAP_BASE tbb::concurrent_unordered_map<KEY, VALUE>
+template <typename KEY, typename VALUE>
+using ConcurrentMapBase = tbb::concurrent_unordered_map<
+  KEY,
+  VALUE,
+  std::hash<KEY>
+  >;
 
 #else
 
 // If we're not using TBB, use a FastMap for ConcurrentMap
 #include <gtsam/base/FastMap.h>
-#  define CONCURRENT_MAP_BASE gtsam::FastMap<KEY, VALUE>
+template <typename KEY, typename VALUE>
+using ConcurrentMapBase = gtsam::FastMap<KEY, VALUE>;
 
 #endif
 
@@ -57,11 +65,11 @@ namespace gtsam {
  * @addtogroup base
  */
 template<typename KEY, typename VALUE>
-class ConcurrentMap : public CONCURRENT_MAP_BASE {
+class ConcurrentMap : public ConcurrentMapBase<KEY,VALUE> {
 
 public:
 
-  typedef CONCURRENT_MAP_BASE Base;
+  typedef ConcurrentMapBase<KEY,VALUE> Base;
 
   /** Default constructor */
   ConcurrentMap() {}

gtsam/base/DSFMap.h

@@ -115,8 +115,8 @@ class DSFMap {
 /// Small utility class for representing a wrappable pairs of ints.
 class IndexPair : public std::pair<size_t,size_t> {
  public:
-  IndexPair(): std::pair<size_t,size_t>(0,0) {}
+  inline IndexPair(): std::pair<size_t,size_t>(0,0) {}
-  IndexPair(size_t i, size_t j) : std::pair<size_t,size_t>(i,j) {}
+  inline IndexPair(size_t i, size_t j) : std::pair<size_t,size_t>(i,j) {}
   inline size_t i() const { return first; };
   inline size_t j() const { return second; };
 };

gtsam/base/GenericValue.h

@@ -89,12 +89,9 @@ public:
 
     /**
      * Create a duplicate object returned as a pointer to the generic Value interface.
-     * For the sake of performance, this function use singleton pool allocator instead of the normal heap allocator.
-     * The result must be deleted with Value::deallocate_, not with the 'delete' operator.
      */
     virtual Value* clone_() const {
-      void *place = boost::singleton_pool<PoolTag, sizeof(GenericValue)>::malloc();
+      GenericValue* ptr = new GenericValue(*this); // calls copy constructor to fill in
-      GenericValue* ptr = new (place) GenericValue(*this); // calls copy constructor to fill in
       return ptr;
     }
 
@@ -102,8 +99,7 @@ public:
      * Destroy and deallocate this object, only if it was originally allocated using clone_().
      */
     virtual void deallocate_() const {
-      this->~GenericValue(); // Virtual destructor cleans up the derived object
+      delete this;
-      boost::singleton_pool<PoolTag, sizeof(GenericValue)>::free((void*) this); // Release memory from pool
     }
 
     /**
@@ -118,10 +114,7 @@ public:
       // Call retract on the derived class using the retract trait function
       const T retractResult = traits<T>::Retract(GenericValue<T>::value(), delta);
 
-      // Create a Value pointer copy of the result
+      Value* resultAsValue = new GenericValue(retractResult);
-      void* resultAsValuePlace =
-          boost::singleton_pool<PoolTag, sizeof(GenericValue)>::malloc();
-      Value* resultAsValue = new (resultAsValuePlace) GenericValue(retractResult);
 
       // Return the pointer to the Value base class
       return resultAsValue;
@@ -172,12 +165,6 @@ public:
       return *this;
     }
 
-  private:
-
-    /// Fake Tag struct for singleton pool allocator. In fact, it is never used!
-    struct PoolTag {
-    };
-
   private:
 
     /** Serialization function */

gtsam/base/ThreadsafeException.h

@@ -22,6 +22,7 @@
 #include <gtsam/config.h> // for GTSAM_USE_TBB
 
 #include <boost/optional/optional.hpp>
+#include <gtsam/dllexport.h>
 #include <string>
 #include <typeinfo>
 
@@ -117,7 +118,7 @@ public:
 };
 
 /// Thread-safe runtime error exception
-class RuntimeErrorThreadsafe: public ThreadsafeException<RuntimeErrorThreadsafe> {
+class GTSAM_EXPORT RuntimeErrorThreadsafe: public ThreadsafeException<RuntimeErrorThreadsafe> {
 public:
   /// Construct with a string describing the exception
   RuntimeErrorThreadsafe(const std::string& description) :

gtsam/base/timing.h

@@ -196,7 +196,7 @@ namespace gtsam {
     /**
      * Small class that calls internal::tic at construction, and internol::toc when destroyed
      */
-    class AutoTicToc {
+    class GTSAM_EXPORT AutoTicToc {
      private:
       size_t id_;
       const char* label_;

gtsam/nonlinear/NonlinearOptimizerParams.h

@@ -31,7 +31,7 @@ namespace gtsam {
 /** The common parameters for Nonlinear optimizers.  Most optimizers
  * deriving from NonlinearOptimizer also subclass the parameters.
  */
-class NonlinearOptimizerParams {
+class GTSAM_EXPORT NonlinearOptimizerParams {
 public:
   /** See NonlinearOptimizerParams::verbosity */
   enum Verbosity {
@@ -52,7 +52,7 @@ public:
 
   virtual ~NonlinearOptimizerParams() {
   }
-  GTSAM_EXPORT virtual void print(const std::string& str = "") const;
+  virtual void print(const std::string& str = "") const;
 
   size_t getMaxIterations() const { return maxIterations; }
   double getRelativeErrorTol() const { return relativeErrorTol; }
@@ -68,8 +68,8 @@ public:
     verbosity = verbosityTranslator(src);
   }
 
-  GTSAM_EXPORT static Verbosity verbosityTranslator(const std::string &s) ;
+  static Verbosity verbosityTranslator(const std::string &s) ;
-  GTSAM_EXPORT static std::string verbosityTranslator(Verbosity value) ;
+  static std::string verbosityTranslator(Verbosity value) ;
 
   /** See NonlinearOptimizerParams::linearSolverType */
   enum LinearSolverType {
@@ -144,10 +144,10 @@ public:
   }
 
 private:
-  GTSAM_EXPORT std::string linearSolverTranslator(LinearSolverType linearSolverType) const;
+  std::string linearSolverTranslator(LinearSolverType linearSolverType) const;
-  GTSAM_EXPORT LinearSolverType linearSolverTranslator(const std::string& linearSolverType) const;
+  LinearSolverType linearSolverTranslator(const std::string& linearSolverType) const;
-  GTSAM_EXPORT std::string orderingTypeTranslator(Ordering::OrderingType type) const;
+  std::string orderingTypeTranslator(Ordering::OrderingType type) const;
-  GTSAM_EXPORT Ordering::OrderingType orderingTypeTranslator(const std::string& type) const;
+  Ordering::OrderingType orderingTypeTranslator(const std::string& type) const;
 };
 
 // For backward compatibility:

gtsam/symbolic/SymbolicBayesTree.h

@@ -30,7 +30,7 @@ namespace gtsam {
 
   /* ************************************************************************* */
   /// A clique in a SymbolicBayesTree
-  class SymbolicBayesTreeClique :
+  class GTSAM_EXPORT SymbolicBayesTreeClique :
     public BayesTreeCliqueBase<SymbolicBayesTreeClique, SymbolicFactorGraph>
   {
   public:
@@ -45,7 +45,7 @@ namespace gtsam {
   /* ************************************************************************* */
   /// A Bayes tree that represents the connectivity between variables but is not associated with any
   /// probability functions.
-  class SymbolicBayesTree :
+  class GTSAM_EXPORT SymbolicBayesTree :
     public BayesTree<SymbolicBayesTreeClique>
   {
   private:
@@ -59,7 +59,7 @@ namespace gtsam {
     SymbolicBayesTree() {}
 
     /** check equality */
-    GTSAM_EXPORT bool equals(const This& other, double tol = 1e-9) const;
+    bool equals(const This& other, double tol = 1e-9) const;
 
   private:
     /** Serialization function */

gtsam_unstable/partition/GenericGraph.h

@@ -12,6 +12,7 @@
 #include <list>
 #include <vector>
 #include <stdexcept>
+#include <string>
 #include <boost/shared_ptr.hpp>
 
 #include "PartitionWorkSpace.h"