Open3d: Corruption in three::UniformTSDFVolume::UniformTSDFVolume

[cedrusx]

Hi, I'm running python3 make_fragments.py and always encounter the following corruption after several round of pose graph optimization.

Log
$ python3 make_fragments.py ~/datasets/SceneNN/016/
OpenCV is detected. Using ORB + 5pt algorithm
Fragment 000 / 013 :: RGBD matching between frame : 0 and 1
Fragment 000 / 013 :: RGBD matching between frame : 0 and 5
[ INFO:0] Initialize OpenCL runtime...
Fragment 000 / 013 :: RGBD matching between frame : 0 and 10
Fragment 000 / 013 :: RGBD matching between frame : 0 and 15
...
...
...
Fragment 003 / 013 :: RGBD matching between frame : 397 and 398
Fragment 003 / 013 :: RGBD matching between frame : 398 and 399
[GlobalOptimizationLM] Optimizing PoseGraph having 100 nodes and 239 edges.
Line process weight : 106.543373
[Initial ] residual : 1.885124e+03, lambda : 1.304716e+02
[Iteration 00] residual : 2.691353e+02, valid edges : 237, time : 0.002 sec.
[Iteration 01] residual : 2.388916e+02, valid edges : 237, time : 0.002 sec.
[Iteration 02] residual : 2.388890e+02, valid edges : 237, time : 0.002 sec.
Delta.norm() < 1.000000e-06 * (x.norm() + 1.000000e-06)
[GlobalOptimizationLM] total time : 0.008 sec.
[GlobalOptimizationLM] Optimizing PoseGraph having 100 nodes and 237 edges.
Line process weight : 107.125251
[Initial ] residual : 7.086356e+01, lambda : 1.384627e+02
[Iteration 00] residual : 7.067094e+01, valid edges : 237, time : 0.002 sec.
[Iteration 01] residual : 7.066952e+01, valid edges : 237, time : 0.002 sec.
Delta.norm() < 1.000000e-06 * (x.norm() + 1.000000e-06)
[GlobalOptimizationLM] total time : 0.006 sec.
CompensateReferencePoseGraphNode : reference : 0
Fragment 003 / 013 :: integrate rgbd frame 300 (1 of 100).
* Error in `python3': double free or corruption (out): 0x00007f4a93ffcc40 *
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f4b8914c7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f4b8915537a]
/lib/x86_64-linux-gnu/libc.so.6(+0x816d8)[0x7f4b891566d8]
/lib/x86_64-linux-gnu/libc.so.6(+0x82743)[0x7f4b89157743]
/lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x54)[0x7f4b89159184]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_Znwm+0x18)[0x7f4b5bda6e78]
/home/xuesongs/.local/lib/python3.5/site-packages/open3d.cpython-35m-x86_64-linux-gnu.so(_ZN5three17UniformTSDFVolumeC2EdidNS_19TSDFVolumeColorTypeERKN5Eigen6MatrixIdLi3ELi1ELi0ELi3ELi1EEE+0x11e)[0x7f4b5d058c8e]
/home/xuesongs/.local/lib/python3.5/site-packages/open3d.cpython-35m-x86_64-linux-gnu.so(_ZN5three18ScalableTSDFVolume14OpenVolumeUnitERKN5Eigen6MatrixIiLi3ELi1ELi0ELi3ELi1EEE+0x1f3)[0x7f4b5d05d873]
/home/xuesongs/.local/lib/python3.5/site-packages/open3d.cpython-35m-x86_64-linux-gnu.so(_ZN5three18ScalableTSDFVolume9IntegrateERKNS_9RGBDImageERKNS_22PinholeCameraIntrinsicERKN5Eigen6MatrixIdLi4ELi4ELi0ELi4ELi4EEE+0x788)[0x7f4b5d05e0f8]
/home/xuesongs/.local/lib/python3.5/site-packages/open3d.cpython-35m-x86_64-linux-gnu.so(+0xfad75)[0x7f4b5cf5dd75]
/home/xuesongs/.local/lib/python3.5/site-packages/open3d.cpython-35m-x86_64-linux-gnu.so(+0x133058)[0x7f4b5cf96058]
python3(PyCFunction_Call+0x77)[0x4e9ba7]
python3(PyEval_EvalFrameEx+0x59f5)[0x53c6d5]
python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4]
python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4]
python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4]
python3[0x540199]
python3(PyEval_EvalCode+0x1f)[0x540e4f]
python3[0x60c272]
python3(PyRun_FileExFlags+0x9a)[0x60e71a]
python3(PyRun_SimpleFileExFlags+0x1bc)[0x60ef0c]
python3(Py_Main+0x456)[0x63fb26]
python3(main+0xe1)[0x4cfeb1]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f4b890f5830]
python3(_start+0x29)[0x5d6049]
======= Memory map: ========
00400000-007a9000 r-xp 00000000 08:02 8920098 /usr/bin/python3.5
009a9000-009ab000 r--p 003a9000 08:02 8920098 /usr/bin/python3.5
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200000000-200200000 rw-s 00000000 00:06 483 /dev/nvidiactl
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7f4b10200000-7f4b10400000 rw-s 00000000 00:06 483 /dev/nvidiactl
7f4b10400000-7f4b10600000 rw-s 00000000 00:05 2002526 /dev/zero (deleted)
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7f4b49ffd000-7f4b4a7fd000 rw-p 00000000 00:00 0
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7f4b4a7fe000-7f4b4affe000 rw-p 00000000 00:00 0
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7f4b4afff000-7f4b4b7ff000 rw-p 00000000 00:00 0
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7f4b4b800000-7f4b4c000000 rw-p 00000000 00:00 0
7f4b4c000000-7f4b4c386000 rw-p 00000000 00:00 0
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7f4b50513000-7f4b50d13000 rw-p 00000000 00:00 0
7f4b50d13000-7f4b50de3000 r-xp 00000000 08:02 20056714 /home/xuesongs/.local/lib/python3.5/site-packages/matplotlib/ft2font.cpython-35m-x86_64-linux-gnu.so
7f4b50de3000-7f4b50fe3000 ---p 000d0000 08:02 20056714 /home/xuesongs/.local/lib/python3.5/site-packages/matplotlib/ft2font.cpython-35m-x86_64-linux-gnu.so
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7f4b56535000-7f4b56d09000 rw-p 00000000 00:00 0
7f4b56d09000-7f4b56d19000 rw-p 00c29000 08:02 22416622 /home/xuesongs/.local/lib/python3.5/site-packages/cv2/.libs/libavcodec-b858321f.so.58.19.100
7f4b56d19000-7f4b56d2d000 r-xp 00000000 08:02 22416621 /home/xuesongs/.local/lib/python3.5/site-packages/cv2/.libs/libz-a147dcb0.so.1.2.3
7f4b56d2d000-7f4b56f2c000 ---p 00014000 08:02 22416621 /home/xuesongs/.local/lib/python3.5/site-packages/cv2/.libs/libz-a147dcb0.so.1.2.3
7f4b56f2c000-7f4b56f2d000 rw-p 00013000 08:02 22416621 /home/xuesongs/.local/lib/python3.5/site-packages/cv2/.libs/libz-a147dcb0.so.1.2.3Aborted (core dumped)

[syncle]

Oh, this is the issue I have never seen before. Could you share information of your environment too?

Here are my quick comments:

• Are you using virtual environment that has limited memory space?
• In the last line of the log, I can only find error message like /home/xuesongs/.local/lib/python3.5/site-packages/cv2/.libs/libz-a147dcb0.so.1.2.3Aborted (core dumped). This might be arisen from the opencv issue. You can run reconstruction system without opencv. For example, open ReconstructionSystem/make_fragments.py and change with_opencv = initialize_opencv() to be with_opencv = False.

[cedrusx]

Jaesik, thanks for the prompt feedback. I cannot access my Ubuntu machine right now so I'm only giving a little information and will update more tomorrow. Would you specify any questions about the environment that might be relevent? Thanks.

I was not using any virtual env. I was running it on a pretty powerful desktop PC with i7. The last line of the log is part of the memory map rather than the call stack, so might be irrevelent to the error. The call stack indicates that the corruption was in the constructor of UniformTSDFVolume. I did some debugging and found that it was in the construction of UniformTSDFVolume::color_ (with size 4096), but I could not figure out the root cause. By setting export MALLOC_CHECK_=2, the issue seemed to be avoided, but I need more experiments to verify. Will update tomorrow.

Quick questions: is the program multi-threaded in this part? Will it allocate lots of memory for this task? Sorry I just started to try with Open3D today and am not familiar with the code at all. Thanks for your patience.

[cedrusx]

Hi Jaesik, this problem has not been reproduced after several system crashes and reboots. Shall we consider it as a temporary system environment problem and close the issue?

[syncle]

Sure. Let me close the issue. You can reopen or close this if necessary.

[cedrusx]

Update: the issue was caused by some hardware issue of my desktop. Fixed by updating BIOS...