PCL and GTSAM link error: double free or corruption (out)

[Rakshith Vishwanatha]

Hello, 

I have a snippet of code which creates a pcl::RangeImage and processes it. Later in the program, I need to add some nodes to a gtsam graph to denote identified landmarks based on the processing performed on the range image. While I was working on this I got the run time error "double free or corruption (out) Aborted (core dumped)". 

This error was thrown only when gtsam was linked to my code's executable. If gtsam was not linked to my code's executable everything runs fine. 

I have made a very simple test script to reproduce this error here: https://github.com/RakVish1342/gtsam-rangeimage-link-error

Code flow:

• This script calls a function func() from main(). 
• In func() a pointcloud with random points is created and a range_image is created from this pointcloud.
• range_image dimensions are printed and code exists func().
• Code exits main().

Observations and Issues Noticed:

• When CMakeLists.txt has "target_link_libraries(linkErr ${PCL_LIBRARIES})" the code works fine.
• When that line is replaced with "target_link_libraries(linkErr ${PCL_LIBRARIES} gtsam)" the code gets the runtime error.
• To help with debugging, additional observations are provided as a comment at the end of src/linkErr.cpp file.
  

For my use case, I can work around this issue by having two separate ros nodes (two separate executables). One that does range image processing and another which receives inputs from the first node and perform gtsam operations. However, it would be preferable to have both operations being performed in one single ros node (one single executable) to avoid any delays and packet buffers if there is speed mismatch between the range image processor ros node and the gtsam optimization ros node.

Any help here would be greatly appreciated!

Reagards, 

Rakshith Vishwanatha

[José Luis Blanco-Claraco]

If you are building GTSAM from sources, this *likely* is due to GTSAM
not using the same Eigen version and/or memory alignment than PCL.
Rebuild GTSAM with CMake variables:
- GTSAM_USE_SYSTEM_EIGEN=On
- GTSAM_BUILD_WITH_MARCH_NATIVE=Off
and check if the error goes away... Those are the most common usual suspects.

JL

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--

/**
* Jose Luis Blanco-Claraco
* Universidad de Almería - Departamento de Ingeniería
* [Homepage]( https://w3.ual.es/~jlblanco/ )
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[Rafael Spring]

If you're using clang or MSVC, you have a tool called Address Sanitizer. Just compile in debug with -fsanitize=address. That should give you more info where the problem is originating from.

https://clang.llvm.org/docs/AddressSanitizer.html

Rafael Spring

CTO, Co-Founder

DotProduct LLC / DotProduct GmbH

On Wed, Oct 27, 2021 at 12:59 AM Rakshith Vishwanatha <rvis...@asu.edu> wrote:

[Rakshith Vishwanatha]

Thank you for the suggestion. I will give this a try and update the thread depending on what happens.

[Rakshith Vishwanatha]

Thank you for the input. I will take a look into Address Sanitizer if recompilation based on Jose Luis Blanco-Claraco's suggestions does not solve the issue. 

I am currently using gcc and it looks like Address Sanitizer can be used with gcc as well: https://stackoverflow.com/questions/37970758/how-to-use-addresssanitizer-with-gcc

[Rakshith Vishwanatha]

Update on the issue: Re-building gtsam using "cmake -DGTSAM_BUILD_WITH_MARCH_NATIVE=Off .." resolved the issue. 

Side note: There was a version mismatch between the system's and gtsam's Eigen libraries. This did not seem to cause the problem however, and use of the GTSAM_USE_SYSTEM_EIGEN=On flag had no effect on runtime behavior my code. 

(The file "...Eigen/Eigen/src/Core/util/Macros.h" was used to check the version of Eigen)

Regards, 

Rakshith Vishwanatha