Some tests fail due to segmentation faults

[blooop]

I've installed gtsam from the devel branch with TBB but without mkl and without -march=native in release mode.

gtsam passes all tests except:

99% tests passed, 3 tests failed out of 237

Total Test time (real) =   1.30 sec

The following tests FAILED:
	 13 - testDSFVector (BAD_COMMAND)
	 80 - testSignature (BAD_COMMAND)
	 87 - testErrors (BAD_COMMAND)

when I run make check for gpmp2, 14 out of 36 tests fail because of a segmentation fault:

make check
[ 19%] Built target gpmp2
[ 21%] Built target testTimer
[ 23%] Built target testProductDynamicLieGroup
[ 25%] Built target testDynamicVector
[ 28%] Built target testPose2Vector
[ 30%] Built target testGaussianProcessInterpolatorPose3
[ 32%] Built target testGaussianProcessInterpolatorPose2
[ 34%] Built target testGaussianProcessPriorPose2Vector
[ 37%] Built target testGaussianProcessPriorPose3
[ 39%] Built target testGaussianProcessInterpolatorPose2Vector
[ 41%] Built target testGaussianProcessPriorLinear
[ 43%] Built target testGaussianProcessPriorPose2
[ 46%] Built target testGaussianProcessInterpolatorLinear
[ 48%] Built target testPose2MobileBase
[ 50%] Built target testPose2MobileArm
[ 52%] Built target testGaussianPriorWorkspacePose
[ 55%] Built target testArmModel
[ 57%] Built target testPose2MobileVetLinArm
[ 59%] Built target testGaussianPriorWorkspaceOrientation
[ 61%] Built target testMobileBaseUtils
[ 64%] Built target testPose2MobileVetLin2Arms
[ 66%] Built target testPointRobotModel
[ 68%] Built target testJointLimitFactorPose2Vector
[ 70%] Built target testGoalFactorArm
[ 73%] Built target testGaussianPriorWorkspacePosition
[ 75%] Built target testJointLimitFactorVector
[ 77%] Built target testPose2Mobile2Arms
[ 79%] Built target testArm
[ 82%] Built target testVehicleDynamics
[ 84%] Built target testObstaclePlanarSDFFactorArm
[ 86%] Built target testObstacleSDFFactorGPArm
[ 88%] Built target testObstacleSDFFactorArm
[ 91%] Built target testSignedDistanceField
[ 93%] Built target testObstaclePlanarSDFFactorGPArm
[ 95%] Built target testPlanarSDF
[ 97%] Built target testTrajUtils
[100%] Built target testISAM2TrajOptimizer
Test project /home/ags/projects/gpmp2/build
      Start  1: testProductDynamicLieGroup
 1/36 Test  #1: testProductDynamicLieGroup ...................   Passed    0.00 sec
      Start  2: testPose2Vector
 2/36 Test  #2: testPose2Vector ..............................   Passed    0.00 sec
      Start  3: testDynamicVector
 3/36 Test  #3: testDynamicVector ............................   Passed    0.00 sec
      Start  4: testGaussianProcessPriorPose2Vector
 4/36 Test  #4: testGaussianProcessPriorPose2Vector ..........   Passed    0.01 sec
      Start  5: testGaussianProcessInterpolatorPose2
 5/36 Test  #5: testGaussianProcessInterpolatorPose2 .........   Passed    0.00 sec
      Start  6: testGaussianProcessInterpolatorPose3
 6/36 Test  #6: testGaussianProcessInterpolatorPose3 .........   Passed    0.00 sec
      Start  7: testGaussianProcessPriorPose3
 7/36 Test  #7: testGaussianProcessPriorPose3 ................   Passed    0.01 sec
      Start  8: testGaussianProcessPriorLinear
 8/36 Test  #8: testGaussianProcessPriorLinear ...............   Passed    0.01 sec
      Start  9: testGaussianProcessPriorPose2
 9/36 Test  #9: testGaussianProcessPriorPose2 ................   Passed    0.01 sec
      Start 10: testGaussianProcessInterpolatorLinear
10/36 Test #10: testGaussianProcessInterpolatorLinear ........   Passed    0.00 sec
      Start 11: testGaussianProcessInterpolatorPose2Vector
11/36 Test #11: testGaussianProcessInterpolatorPose2Vector ...   Passed    0.00 sec
      Start 12: testArmModel
12/36 Test #12: testArmModel .................................***Exception: SegFault  0.00 sec

      Start 13: testGaussianPriorWorkspaceOrientation
13/36 Test #13: testGaussianPriorWorkspaceOrientation ........***Exception: SegFault  0.00 sec

      Start 14: testArm
14/36 Test #14: testArm ......................................***Exception: SegFault  0.00 sec

      Start 15: testMobileBaseUtils
15/36 Test #15: testMobileBaseUtils ..........................   Passed    0.00 sec
      Start 16: testPose2MobileArm
16/36 Test #16: testPose2MobileArm ...........................***Exception: SegFault  0.00 sec

      Start 17: testPose2MobileVetLin2Arms
17/36 Test #17: testPose2MobileVetLin2Arms ...................***Exception: SegFault  0.00 sec

      Start 18: testPose2MobileBase
18/36 Test #18: testPose2MobileBase ..........................   Passed    0.00 sec
      Start 19: testGaussianPriorWorkspacePose
19/36 Test #19: testGaussianPriorWorkspacePose ...............***Exception: SegFault  0.00 sec

      Start 20: testGaussianPriorWorkspacePosition
20/36 Test #20: testGaussianPriorWorkspacePosition ...........***Exception: SegFault  0.00 sec

      Start 21: testJointLimitFactorVector
21/36 Test #21: testJointLimitFactorVector ...................   Passed    0.01 sec
      Start 22: testPointRobotModel
22/36 Test #22: testPointRobotModel ..........................   Passed    0.00 sec
      Start 23: testPose2Mobile2Arms
23/36 Test #23: testPose2Mobile2Arms .........................***Exception: SegFault  0.00 sec

      Start 24: testPose2MobileVetLinArm
24/36 Test #24: testPose2MobileVetLinArm .....................***Exception: SegFault  0.00 sec

      Start 25: testJointLimitFactorPose2Vector
25/36 Test #25: testJointLimitFactorPose2Vector ..............   Passed    0.01 sec
      Start 26: testGoalFactorArm
26/36 Test #26: testGoalFactorArm ............................***Exception: SegFault  0.00 sec

      Start 27: testVehicleDynamics
27/36 Test #27: testVehicleDynamics ..........................   Passed    0.00 sec
      Start 28: testSignedDistanceField
28/36 Test #28: testSignedDistanceField ......................   Passed    0.00 sec
      Start 29: testObstacleSDFFactorGPArm
29/36 Test #29: testObstacleSDFFactorGPArm ...................***Exception: SegFault  0.00 sec

      Start 30: testObstaclePlanarSDFFactorArm
30/36 Test #30: testObstaclePlanarSDFFactorArm ...............***Exception: SegFault  0.00 sec

      Start 31: testPlanarSDF
31/36 Test #31: testPlanarSDF ................................   Passed    0.00 sec
      Start 32: testObstacleSDFFactorArm
32/36 Test #32: testObstacleSDFFactorArm .....................***Exception: SegFault  0.00 sec

      Start 33: testObstaclePlanarSDFFactorGPArm
33/36 Test #33: testObstaclePlanarSDFFactorGPArm .............***Exception: SegFault  0.00 sec

      Start 34: testISAM2TrajOptimizer
34/36 Test #34: testISAM2TrajOptimizer .......................   Passed    0.00 sec
      Start 35: testTrajUtils
35/36 Test #35: testTrajUtils ................................   Passed    0.00 sec
      Start 36: testTimer
36/36 Test #36: testTimer ....................................   Passed    0.01 sec

61% tests passed, 14 tests failed out of 36

Total Test time (real) =   0.18 sec

The following tests FAILED:
	 12 - testArmModel (SEGFAULT)
	 13 - testGaussianPriorWorkspaceOrientation (SEGFAULT)
	 14 - testArm (SEGFAULT)
	 16 - testPose2MobileArm (SEGFAULT)
	 17 - testPose2MobileVetLin2Arms (SEGFAULT)
	 19 - testGaussianPriorWorkspacePose (SEGFAULT)
	 20 - testGaussianPriorWorkspacePosition (SEGFAULT)
	 23 - testPose2Mobile2Arms (SEGFAULT)
	 24 - testPose2MobileVetLinArm (SEGFAULT)
	 26 - testGoalFactorArm (SEGFAULT)
	 29 - testObstacleSDFFactorGPArm (SEGFAULT)
	 30 - testObstaclePlanarSDFFactorArm (SEGFAULT)
	 32 - testObstacleSDFFactorArm (SEGFAULT)
	 33 - testObstaclePlanarSDFFactorGPArm (SEGFAULT)
Errors while running CTest
CMakeFiles/check.dir/build.make:57: recipe for target 'CMakeFiles/check' failed
make[3]: *** [CMakeFiles/check] Error 8
CMakeFiles/Makefile2:268: recipe for target 'CMakeFiles/check.dir/all' failed
make[2]: *** [CMakeFiles/check.dir/all] Error 2
CMakeFiles/Makefile2:275: recipe for target 'CMakeFiles/check.dir/rule' failed
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
Makefile:212: recipe for target 'check' failed
make: *** [check] Error 2

Is this ok?

Thanks

[mfinean]

The problems all arise due to Eigen alignment in Arm.cpp.

Wherever you see something like vector or vector, they should be replaced with
vector<Matrix4, Eigen::aligned_allocator>
or
vector<Matrix, Eigen::aligned_allocator>
respectively.

This needs to be done for defining H, Ho, dH, HoInv.

As well as cache dHoi_dqj which should become
vector<vector<Matrix4, Eigen::aligned_allocator>> dHo_dq(dof(), vector<Matrix4, Eigen::aligned_allocator>(dof()));

[ishaanmht]

Hey
My tests are still failing. I get this error:

type/value mismatch at argument 2 in template parameter list for ‘template<class _Tp, class _Alloc> class std::vector’
vector<Matrix4, Eigen::aligned_allocator> H(dof());

[jiaweimeng]

Hi guys,

I get the same issue after replacing vector with vector<Matrix, Eigen::aligned_allocator>. Have you already solved the issue?

Thanks.

[barbosafs]

Hello there,
after almost two days working on making GPMP2 run, I finally did it.

I was having the problems described in #42 which, after debugging, I could trace the problem to this issue here.
I tried following the suggestion by @mfinean, which is correct but not detailed enough.

To fix it I modified 5 lines in Arm.cpp:

vector<Matrix4, Eigen::aligned_allocator<Eigen::Matrix4f>> H(dof());
vector<Matrix4, Eigen::aligned_allocator<Eigen::Matrix4f>> Ho(dof()+1); // start from 1
vector<Matrix4, Eigen::aligned_allocator<Eigen::Matrix4f>> dH(dof());
vector<Matrix4, Eigen::aligned_allocator<Eigen::Matrix4f>> Hoinv(dof()+1); // start from 1
vector<vector<Matrix4, Eigen::aligned_allocator<Eigen::Matrix4f>> > dHo_dq(dof(), vector<Matrix4, Eigen::aligned_allocator<Eigen::Matrix4f>>(dof()));

Note that this is similar to previous suggestions but, instead of vector<Matrix, Eigen::aligned_allocator>, it needs to be vector<Matrix4, Eigen::aligned_allocator<Eigen::Matrix4f>>.

@mhmukadam @dongjing3309 I suggest doing a PR for this.

[hzyjerry]

@barbosafs this is heroic! Thanks for the fix

[mhmukadam]

Will close this since this is covered in #44.