单独编译库源文件时单元测试中的 Seg 错误

Question

I'm writing a small library and have until now added the library source file directly with the unit test in the add_executable command, similarly to below:

CMakeLists.txt (Resulting executable OK)

cmake_minimum_required(VERSION 3.0)
set(CMAKE_CXX_STANDARD 17) 
find_package(Eigen3 REQUIRED)
find_package(GTSAM 4.0.2 REQUIRED)

add_executable(my_test test/unit_test.cpp src/my_lib.cpp)
target_include_directories(my_test PUBLIC include ${EIGEN3_INCLUDE_DIR} ${GTSAM_INCLUDE_DIR})
target_link_libraries(my_test PUBLIC gtsam)

Everything worked fine until I created an actual library and linked the unit test, similarly to below:

CMakeLists.txt (Resulting executable not OK)

cmake_minimum_required(VERSION 3.0)
set(CMAKE_CXX_STANDARD 17) 

find_package(Eigen3 REQUIRED)
add_library(my_lib STATIC src/my_lib.cpp)
target_include_directories(my_lib PRIVATE include ${EIGEN3_INCLUDE_DIR})

find_package(GTSAM 4.0.2 REQUIRED)
add_executable(my_test test/unit_test.cpp)
target_include_directories(my_test PUBLIC include ${EIGEN3_INCLUDE_DIR} ${GTSAM_INCLUDE_DIR})
target_link_libraries(my_test PUBLIC gtsam my_lib)

Now, however, the test seg faults. valgrind reports the following:

==18501== Memcheck, a memory error detector
==18501== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==18501== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==18501== Command: ./my_test
==18501==
==18501== Invalid read of size 8
==18501==    at 0x509CFBB: gtsam::noiseModel::Diagonal::Sigmas(Eigen::Matrix<double, -1, 1, 0, -1, 1> const&, bool) (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4F3C713: _GLOBAL__sub_I_lago.cpp (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4010732: call_init (dl-init.c:72)
==18501==    by 0x4010732: _dl_init (dl-init.c:119)
==18501==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==18501==  Address 0x7241df8 is 8 bytes before a block of size 8 alloc'd
==18501==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==18501==    by 0x4ED9FD: Eigen::internal::aligned_malloc(unsigned long) (Memory.h:159)
==18501==    by 0x507875B: Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::resize(long, long) [clone .constprop.1340] (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x5085698: Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::PlainObjectBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1, 0, -1, 1> > >(Eigen::DenseBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1, 0, -1, 1> > > const&) (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x509CFA2: gtsam::noiseModel::Diagonal::Sigmas(Eigen::Matrix<double, -1, 1, 0, -1, 1> const&, bool) (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4F3C713: _GLOBAL__sub_I_lago.cpp (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4010732: call_init (dl-init.c:72)
==18501==    by 0x4010732: _dl_init (dl-init.c:119)
==18501==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==18501==
==18501== Invalid read of size 8
==18501==    at 0x4F3C71D: _GLOBAL__sub_I_lago.cpp (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4010732: call_init (dl-init.c:72)
==18501==    by 0x4010732: _dl_init (dl-init.c:119)
==18501==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==18501==  Address 0x7241da8 is 8 bytes before a block of size 8 alloc'd
==18501==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==18501==    by 0x4ED9FD: Eigen::internal::aligned_malloc(unsigned long) (Memory.h:159)
==18501==    by 0x51492E1: Eigen::Matrix<double, -1, 1, 0, -1, 1>::Matrix<int>(int const&) [clone .constprop.1305] (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4F3C6F4: _GLOBAL__sub_I_lago.cpp (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4010732: call_init (dl-init.c:72)
==18501==    by 0x4010732: _dl_init (dl-init.c:119)
==18501==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==18501==
==18501== Invalid read of size 8
==18501==    at 0x509CDD1: gtsam::noiseModel::Diagonal::Variances(Eigen::Matrix<double, -1, 1, 0, -1, 1> const&, bool) (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4F3C77A: _GLOBAL__sub_I_lago.cpp (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4010732: call_init (dl-init.c:72)
==18501==    by 0x4010732: _dl_init (dl-init.c:119)
==18501==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==18501==  Address 0x72420f8 is 8 bytes before a block of size 24 alloc'd
==18501==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==18501==    by 0x4ED9FD: Eigen::internal::aligned_malloc(unsigned long) (Memory.h:159)
==18501==    by 0x509A53B: Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::resize(long, long) [clone .constprop.1216] (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x50A4A0A: Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::PlainObjectBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_sqrt_op<double>, Eigen::Matrix<double, -1, 1, 0, -1, 1> const> >(Eigen::DenseBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_sqrt_op<double>, Eigen::Matrix<double, -1, 1, 0, -1, 1> const> > const&) (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x509CD63: gtsam::noiseModel::Diagonal::Variances(Eigen::Matrix<double, -1, 1, 0, -1, 1> const&, bool) (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4F3C77A: _GLOBAL__sub_I_lago.cpp (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4010732: call_init (dl-init.c:72)
==18501==    by 0x4010732: _dl_init (dl-init.c:119)
==18501==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==18501== Invalid read of size 8
==18501==    at 0x4F3C784: _GLOBAL__sub_I_lago.cpp (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4010732: call_init (dl-init.c:72)
==18501==    by 0x4010732: _dl_init (dl-init.c:119)
==18501==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==18501==  Address 0x7242098 is 8 bytes before a block of size 24 alloc'd
==18501==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==18501==    by 0x4ED9FD: Eigen::internal::aligned_malloc(unsigned long) (Memory.h:159)
==18501==    by 0x513A304: Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::PlainObjectBase<Eigen::Matrix<double, 3, 1, 0, 3, 1> >(Eigen::DenseBase<Eigen::Matrix<double, 3, 1, 0, 3, 1> > const&) (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4F3C766: _GLOBAL__sub_I_lago.cpp (in /usr/local/lib/libgtsam.so.4.0.2)
==18501==    by 0x4010732: call_init (dl-init.c:72)
==18501==    by 0x4010732: _dl_init (dl-init.c:119)
==18501==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==18501==
test_orient: /usr/local/include/eigen3/Eigen/src/Core/DenseStorage.h:128: Eigen::internal::plain_array<T, Size, MatrixOrArrayOptions, 32>::plain_array() [with T = double; int Size = 4; int MatrixOrArrayOptions = 0]: Assertion `(internal::UIntPtr(eigen_unaligned_array_assert_workaround_gcc47(array)) & (31)) == 0 && "this assertion is explained here: " "http://eigen.tuxfamily.org/dox-devel/group__TopicUnalignedArrayAssert.html" " **** READ THIS WEB PAGE !!! ****"' failed.
==18501==
==18501== Process terminating with default action of signal 6 (SIGABRT)
==18501==    at 0x5F95E97: raise (raise.c:51)
==18501==    by 0x5F97800: abort (abort.c:79)
==18501==    by 0x5F87399: __assert_fail_base (assert.c:92)
==18501==    by 0x5F87411: __assert_fail (assert.c:101)
==18501==    by 0x4D98AE: Eigen::internal::plain_array<double, 4, 0, 32>::plain_array() (DenseStorage.h:128)
==18501==    by 0x4D78AD: Eigen::DenseStorage<double, 4, 4, 1, 0>::DenseStorage() (DenseStorage.h:187)
==18501==    by 0x4D61C7: Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1, 0, 4, 1> >::PlainObjectBase() (PlainObjectBase.h:484)
==18501==    by 0x4D4DBB: Eigen::Matrix<double, 4, 1, 0, 4, 1>::Matrix() (Matrix.h:259)
==18501==    by 0x4ECF6A: orient::quaternionFromAngleAxis(Eigen::Matrix<double, 3, 1, 0, 3, 1> const&) (from_angle_axis.cpp:56)
==18501==    by 0x4D21C4: ____C_A_T_C_H____T_E_S_T____10() (from_angle_axis_test.cpp:95)
==18501==    by 0x3F5A43: Catch::TestInvokerAsFunction::invoke() const (catch2.hpp:14054)
==18501==    by 0x3F50A2: Catch::TestCase::invoke() const (catch2.hpp:13947)
==18501==
==18501== HEAP SUMMARY:
==18501==     in use at exit: 42,110 bytes in 347 blocks
==18501==   total heap usage: 4,871 allocs, 4,524 frees, 507,954 bytes allocated
==18501==
==18501== LEAK SUMMARY:
==18501==    definitely lost: 64 bytes in 4 blocks
==18501==    indirectly lost: 0 bytes in 0 blocks
==18501==      possibly lost: 0 bytes in 0 blocks
==18501==    still reachable: 42,046 bytes in 343 blocks
==18501==         suppressed: 0 bytes in 0 blocks
==18501== Rerun with --leak-check=full to see details of leaked memory
==18501==
==18501== For counts of detected and suppressed errors, rerun with: -v
==18501== ERROR SUMMARY: 4 errors from 4 contexts (suppressed: 0 from 0)

The link in the Eigen assert makes me none the wiser unfortunately.

My question is: Is the seg fault a result of incorrectly linking against either my own library or GTSAM? If so, how can I fix it? If not, should I assume that there is a bug in my library that manifests itself only in the second case?

EDIT:

Minimal working example to reproduce:

include/my_lib.hpp

#pragma once
void f();

src/my_lib.cpp

#include <my_lib.hpp>
#include <unsupported/Eigen/KroneckerProduct>

void f() 
{
  Eigen::Matrix3d A = Eigen::Matrix3d::Random();
  Eigen::Matrix<double, 9, 3> B = Eigen::Matrix<double, 9, 3>::Random();
  Eigen::Matrix3d I = Eigen::Matrix3d::Identity();
  Eigen::Matrix<double, 9, 3> tmp = Eigen::kroneckerProduct(I, A) * B;
}

test/unit_test.cpp

#include <my_lib.hpp>
#include <gtsam/base/numericalDerivative.h>

int main()
{
  f();
  return 0;
}

Answer 1

Your library uses Eigen3 library, which is also part of gtsam library used in the tests. You need to make sure that in both cases the same Eigen3 library is used, otherwise subtle bugs could happen (like the one you observe).

---

Technically, your library and gtsam-based test are separate objects files , so they are compiled independently and both of them are correct .

It is a linker who could perform unwanted optimizations like merging functions from these object files. Eg in case these functions have the same name. If you find a way to forbid such sort of optimizations for the linker, then resulted test could work correctly even in case of incompatible Eigen3 libraries used for your library in by gtsam.

However, disabling linker optimizations is a very subtle way from the view of stability of your project. Use this way only as the last resort.