Building timing scripts using new timing script support in GtsamTesting.cmake. Fixed compile errors in timing scripts but disabled a couple.

CMakeLists.txt

@@ -303,6 +303,9 @@ add_subdirectory(tests)
 # Build examples
 add_subdirectory(examples)
 
+# Build timing
+add_subdirectory(timing)
+
 # Matlab toolbox
 if (GTSAM_INSTALL_MATLAB_TOOLBOX)
 	add_subdirectory(matlab)

gtsam/base/CMakeLists.txt

@@ -7,9 +7,3 @@ install(FILES ${base_headers_tree} DESTINATION include/gtsam/base/treeTraversal)
 
 # Build tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(base "gtsam" "gtsam" "${base_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)
-

gtsam/discrete/CMakeLists.txt

@@ -6,9 +6,3 @@ install(FILES ${discrete_headers} DESTINATION include/gtsam/discrete)
 
 # Add all tests
 add_subdirectory(tests)
-
-# Build timing scripts
-#if (GTSAM_BUILD_TIMING)
-#    gtsam_add_timing(discrete "${discrete_local_libs}")
-#endif(GTSAM_BUILD_TIMING)
-

gtsam/geometry/CMakeLists.txt

@@ -4,9 +4,3 @@ install(FILES ${geometry_headers} DESTINATION include/gtsam/geometry)
 
 # Build tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(geometry "gtsam" "gtsam" "${geometry_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)
-

gtsam/inference/CMakeLists.txt

@@ -4,9 +4,3 @@ install(FILES ${inference_headers} DESTINATION include/gtsam/inference)
 
 # Build tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(inference "gtsam" "gtsam" "${inference_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)
-

gtsam/linear/CMakeLists.txt

@@ -4,8 +4,3 @@ install(FILES ${linear_headers} DESTINATION include/gtsam/linear)
 
 # Build tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(linear "gtsam" "gtsam" "${linear_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)

gtsam/navigation/CMakeLists.txt

@@ -4,8 +4,3 @@ install(FILES ${navigation_headers} DESTINATION include/gtsam/navigation)
 
 # Add all tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(navigation "gtsam" "gtsam" "${navigation_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)

gtsam/nonlinear/CMakeLists.txt

@@ -4,9 +4,3 @@ install(FILES ${nonlinear_headers} DESTINATION include/gtsam/nonlinear)
 
 # Build tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(nonlinear "gtsam" "gtsam" "${nonlinear_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)
-

gtsam/slam/CMakeLists.txt

@@ -8,8 +8,3 @@ install(FILES ${slam_headers} DESTINATION include/gtsam/slam)
 
 # Build tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(slam "gtsam" "gtsam" "${slam_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)

gtsam/symbolic/CMakeLists.txt

@@ -4,9 +4,3 @@ install(FILES ${symbolic_headers} DESTINATION include/gtsam/symbolic)
 
 # Build tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(symbolic "gtsam" "gtsam" "${symbolic_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)
-

gtsam_unstable/CMakeLists.txt

@@ -118,6 +118,7 @@ endif(GTSAM_INSTALL_MATLAB_TOOLBOX)
 
 
 # Build examples
-if (GTSAM_BUILD_EXAMPLES)
+add_subdirectory(examples)
-    add_subdirectory(examples)
+
-endif(GTSAM_BUILD_EXAMPLES)
+# Build timing
+add_subdirectory(timing)

gtsam_unstable/base/CMakeLists.txt

@@ -4,8 +4,3 @@ install(FILES ${base_headers} DESTINATION include/gtsam_unstable/base)
 
 # Add all tests
 add_subdirectory(tests)
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    gtsam_add_subdir_timing(base_unstable "${base_full_libs}" "${base_full_libs}" "${base_excluded_files}") 
-endif(GTSAM_BUILD_TIMING)

gtsam_unstable/timing/CMakeLists.txt

@@ -0,0 +1 @@
+gtsamAddTimingGlob("*.cpp" "" "gtsam_unstable")

gtsam_unstable/timing/timeInertialNavFactor_GlobalVelocity.cpp

@@ -20,9 +20,9 @@
 #include <gtsam_unstable/slam/InertialNavFactor_GlobalVelocity.h>
 #include <gtsam/geometry/Pose3.h>
 #include <gtsam/nonlinear/Values.h>
-#include <gtsam/nonlinear/Key.h>
 #include <gtsam/base/numericalDerivative.h>
 #include <gtsam/base/LieVector.h>
+#include <gtsam/inference/Key.h>
 
 using namespace std;
 using namespace gtsam;
@@ -32,7 +32,7 @@ gtsam::Rot3 world_R_ECEF(
     0.85173,     -0.52399,            0,
     0.41733,      0.67835,     -0.60471);
 
-gtsam::Vector ECEF_omega_earth((Vec(3) << 0.0, 0.0, 7.292115e-5));
+gtsam::Vector ECEF_omega_earth((Vector(3) << 0.0, 0.0, 7.292115e-5));
 gtsam::Vector world_omega_earth(world_R_ECEF.matrix() * ECEF_omega_earth);
 
 /* ************************************************************************* */
@@ -54,16 +54,16 @@ int main() {
   gtsam::Key BiasKey1(31);
 
   double measurement_dt(0.1);
-  Vector world_g((Vec(3) << 0.0, 0.0, 9.81));
+  Vector world_g((Vector(3) << 0.0, 0.0, 9.81));
-  Vector world_rho((Vec(3) << 0.0, -1.5724e-05, 0.0)); // NED system
+  Vector world_rho((Vector(3) << 0.0, -1.5724e-05, 0.0)); // NED system
-  gtsam::Vector ECEF_omega_earth((Vec(3) << 0.0, 0.0, 7.292115e-5));
+  gtsam::Vector ECEF_omega_earth((Vector(3) << 0.0, 0.0, 7.292115e-5));
   gtsam::Vector world_omega_earth(world_R_ECEF.matrix() * ECEF_omega_earth);
 
   SharedGaussian model(noiseModel::Isotropic::Sigma(9, 0.1));
 
   // Second test: zero angular motion, some acceleration - generated in matlab
-  Vector measurement_acc((Vec(3) << 6.501390843381716,  -6.763926150509185,  -2.300389940090343));
+  Vector measurement_acc((Vector(3) << 6.501390843381716,  -6.763926150509185,  -2.300389940090343));
-  Vector measurement_gyro((Vec(3) << 0.1, 0.2, 0.3));
+  Vector measurement_gyro((Vector(3) << 0.1, 0.2, 0.3));
 
   InertialNavFactor_GlobalVelocity<Pose3, LieVector, imuBias::ConstantBias> f(PoseKey1, VelKey1, BiasKey1, PoseKey2, VelKey2, measurement_acc, measurement_gyro, measurement_dt, world_g, world_rho, world_omega_earth, model);
 
@@ -72,7 +72,7 @@ int main() {
       -0.652537293,  0.709880342,  0.265075427);
   Point3 t1(2.0,1.0,3.0);
   Pose3 Pose1(R1, t1);
-  LieVector Vel1(3,0.5,-0.5,0.4);
+  LieVector Vel1 = Vector((Vector(3) << 0.5,-0.5,0.4));
   Rot3 R2(0.473618898,   0.119523052,  0.872582019,
        0.609241153,   0.67099888, -0.422594037,
       -0.636011287,  0.731761397,  0.244979388);
@@ -99,7 +99,7 @@ int main() {
   GaussianFactorGraph graph;
   gttic_(LinearizeTiming);
   for(size_t i = 0; i < 100000; ++i) {
-    GaussianFactor::shared_ptr g = f.linearize(values, ordering);
+    GaussianFactor::shared_ptr g = f.linearize(values);
     graph.push_back(g);
   }
   gttoc_(LinearizeTiming);

tests/CMakeLists.txt

@@ -14,16 +14,3 @@ if(MSVC)
 	set_property(SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/testSerializationSLAM.cpp"
 		APPEND PROPERTY COMPILE_FLAGS "/bigobj")
 endif()
-
-# Build timing scripts
-if (GTSAM_BUILD_TIMING)
-    # Subdirectory target for timing - does not actually execute the scripts
-    add_custom_target(timing.tests)
-    set(is_test FALSE)
-
-    # Build grouped benchmarks
-    gtsam_add_grouped_scripts("tests"               # Use subdirectory as group label
-    "time*.cpp" timing "Timing Benchmark"         # Standard for all timing scripts
-    "${tests_full_libs}" "${tests_full_libs}" "${tests_exclude}"   # Pass in linking and exclusion lists
-    ${is_test})
-endif (GTSAM_BUILD_TIMING)

timing/CMakeLists.txt

@@ -0,0 +1,6 @@
+list(APPEND to_exclude
+    timeFactorOverhead.cpp
+    timeSLAMlike.cpp)
+gtsamAddTimingGlob("*.cpp" "${to_exclude}" "gtsam")
+
+target_link_libraries(timeGaussianFactorGraph CppUnitLite)

timing/timeCalibratedCamera.cpp

@@ -27,11 +27,11 @@ int main()
 {
   int n = 100000;
 
-  const Pose3 pose1((Matrix)(Mat(3,3) <<
+  const Pose3 pose1(Matrix3((Matrix(3,3) <<
       1., 0., 0.,
       0.,-1., 0.,
       0., 0.,-1.
-  ),
+  )),
   Point3(0,0,0.5));
 
   const CalibratedCamera camera(pose1);

timing/timeGaussianFactor.cpp

@@ -22,7 +22,7 @@
 using namespace std;
 
 #include <boost/tuple/tuple.hpp>
-#include <boost/assign/std/list.hpp> // for operator += in Ordering
+#include <boost/assign/list_of.hpp>
 
 #include <gtsam/base/Matrix.h>
 #include <gtsam/linear/JacobianFactor.h>
@@ -33,7 +33,7 @@ using namespace std;
 using namespace gtsam;
 using namespace boost::assign;
 
-static const Index _x1_=1, _x2_=2, _l1_=3;
+static const Key _x1_=1, _x2_=2, _l1_=3;
 
 /*
  * Alex's Machine
@@ -53,7 +53,7 @@ static const Index _x1_=1, _x2_=2, _l1_=3;
 int main()
 {
   // create a linear factor
-  Matrix Ax2 = (Mat(8, 2) <<
+  Matrix Ax2 = (Matrix(8, 2) <<
            // x2  
            -5., 0.,
            +0.,-5.,
@@ -65,7 +65,7 @@ int main()
            +0.,10.
            );
                      
-  Matrix Al1 = (Mat(8, 10) <<
+  Matrix Al1 = (Matrix(8, 10) <<
            // l1     
            5., 0.,1.,2.,3.,4.,5.,6.,7.,8.,
            0., 5.,1.,2.,3.,4.,5.,6.,7.,8.,
@@ -77,7 +77,7 @@ int main()
            0., 0.,1.,2.,3.,4.,5.,6.,7.,8.
            );
                      
-  Matrix Ax1 = (Mat(8, 2) <<
+  Matrix Ax1 = (Matrix(8, 2) <<
            // x1
            0.00,  0.,1.,2.,3.,4.,5.,6.,7.,8.,
            0.00,  0.,1.,2.,3.,4.,5.,6.,7.,8.,
@@ -108,7 +108,8 @@ int main()
   JacobianFactor::shared_ptr factor;
 
   for(int i = 0; i < n; i++)
-    conditional = JacobianFactor(combined).eliminateFirst();
+    boost::tie(conditional, factor) =
+        JacobianFactor(combined).eliminate(Ordering(boost::assign::list_of(_x2_)));
 
   long timeLog2 = clock();
   double seconds = (double)(timeLog2-timeLog)/CLOCKS_PER_SEC;

timing/timeGaussianFactorGraph.cpp

@@ -29,10 +29,10 @@ using namespace boost::assign;
 /* ************************************************************************* */
 // Create a Kalman smoother for t=1:T and optimize
 double timeKalmanSmoother(int T) {
-  pair<GaussianFactorGraph,Ordering> smoother_ordering = createSmoother(T);
+  GaussianFactorGraph smoother = createSmoother(T);
-  GaussianFactorGraph& smoother(smoother_ordering.first);
   clock_t start = clock();
-  GaussianSequentialSolver(smoother).optimize();
+  // Keys will come out sorted since keys() returns a set
+  smoother.optimize(Ordering(smoother.keys()));
   clock_t end = clock ();
   double dif = (double)(end - start) / CLOCKS_PER_SEC;
   return dif;
@@ -40,12 +40,10 @@ double timeKalmanSmoother(int T) {
 
 /* ************************************************************************* */
 // Create a planar factor graph and optimize
-// todo: use COLAMD ordering again (removed when linear baked-in ordering added)
 double timePlanarSmoother(int N, bool old = true) {
-  boost::tuple<GaussianFactorGraph, VectorValues> pg = planarGraph(N);
+  GaussianFactorGraph fg = planarGraph(N).get<0>();
-  GaussianFactorGraph& fg(pg.get<0>());
   clock_t start = clock();
-  GaussianSequentialSolver(fg).optimize();
+  fg.optimize();
   clock_t end = clock ();
   double dif = (double)(end - start) / CLOCKS_PER_SEC;
   return dif;
@@ -53,12 +51,10 @@ double timePlanarSmoother(int N, bool old = true) {
 
 /* ************************************************************************* */
 // Create a planar factor graph and eliminate
-// todo: use COLAMD ordering again (removed when linear baked-in ordering added)
 double timePlanarSmootherEliminate(int N, bool old = true) {
-  boost::tuple<GaussianFactorGraph, VectorValues> pg = planarGraph(N);
+  GaussianFactorGraph fg = planarGraph(N).get<0>();
-  GaussianFactorGraph& fg(pg.get<0>());
   clock_t start = clock();
-  GaussianSequentialSolver(fg).eliminate();
+  fg.eliminateMultifrontal();
   clock_t end = clock ();
   double dif = (double)(end - start) / CLOCKS_PER_SEC;
   return dif;

timing/timeMatrix.cpp

@@ -189,7 +189,7 @@ double timeColumn(size_t reps) {
  */
 double timeHouseholder(size_t reps) {
   // create a matrix
-  Matrix Abase = Mat(4, 7) <<
+  Matrix Abase = (Matrix(4, 7) <<
       -5,  0, 5, 0,  0,  0,  -1,
       00, -5, 0, 5,  0,  0, 1.5,
       10,  0, 0, 0,-10,  0,   2,

timing/timePinholeCamera.cpp

@@ -28,7 +28,7 @@ int main()
 {
   int n = 1000000;
 
-  const Pose3 pose1((Matrix)(Mat(3,3) <<
+  const Pose3 pose1((Matrix)(Matrix(3,3) <<
       1., 0., 0.,
       0.,-1., 0.,
       0., 0.,-1.

timing/timePose2.cpp

@@ -58,7 +58,7 @@ Pose2 Pose2betweenOptimized(const Pose2& r1, const Pose2& r2,
   if (H1) {
     double dt1 = -s2 * x + c2 * y;
     double dt2 = -c2 * x - s2 * y;
-    *H1 = (Mat(3,3) <<
+    *H1 = (Matrix(3,3) <<
       -c,  -s,  dt1,
       s,  -c,  dt2,
       0.0, 0.0,-1.0);

timing/timePose3.cpp

@@ -37,8 +37,8 @@ int main()
 
   double norm=sqrt(1.0+16.0+4.0);
   double x=1.0/norm, y=4.0/norm, z=2.0/norm;
-  Vector v = (Vec(6) << x, y, z, 0.1, 0.2, -0.1);
+  Vector v = (Vector(6) << x, y, z, 0.1, 0.2, -0.1);
-  Pose3 T = Pose3::Expmap((Vec(6) << 0.1, 0.1, 0.2, 0.1, 0.4, 0.2)), T2 = T.retract(v);
+  Pose3 T = Pose3::Expmap((Vector(6) << 0.1, 0.1, 0.2, 0.1, 0.4, 0.2)), T2 = T.retract(v);
   Matrix H1,H2;
 
   TEST(retract, T.retract(v))

timing/timeStereoCamera.cpp

@@ -27,7 +27,7 @@ int main()
 {
   int n = 100000;
 
-  const Pose3 pose1((Matrix)(Mat(3,3) <<
+  const Pose3 pose1((Matrix)(Matrix(3,3) <<
       1., 0., 0.,
       0.,-1., 0.,
       0., 0.,-1.