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robotology / idyntree

Multibody Dynamics Library designed for Free Floating Robots
BSD 3-Clause "New" or "Revised" License
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iDynTree inverse kinematics crashes in MATLAB on Ubuntu 18.04 LTS #686

Closed gabrielenava closed 4 years ago

gabrielenava commented 4 years ago

With @claudia-lat we tried to run the iDynTree inverse kinematics in MATLAB using the MATLAB bindings on Ubuntu. MATLAB crashes right after IPOPT is opened:

******************************************************************************

This program contains Ipopt, a library for large-scale nonlinear optimization.

 Ipopt is released as open source code under the Eclipse Public License (EPL).

         For more information visit http://projects.coin-or.org/Ipopt

******************************************************************************

--------------------------------------------------------------------------------

       Segmentation violation detected at mer apr 29 12:23:44 2020 +0200

--------------------------------------------------------------------------------

Configuration:

  Crash Decoding           : Disabled - No sandbox or build area path

  Crash Mode               : continue (default)

  Default Encoding         : UTF-8

  Deployed                 : false

  GNU C Library            : 2.27 stable

  Graphics Driver          : Unknown software 

  Graphics card 1          : 0x10de ( 0x10de ) 0x1b06 Version 435.21.0.0 (0-0-0)

  Java Version             : Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

  MATLAB Architecture      : glnxa64

  MATLAB Entitlement ID    : 6829974

  MATLAB Root              : /usr/local/MATLAB/R2019b

  MATLAB Version           : 9.7.0.1296695 (R2019b) Update 4

  OpenGL                   : software

  Operating System         : Ubuntu 18.04.3 LTS

  Process ID               : 21823

  Processor ID             : x86 Family 6 Model 85 Stepping 4, GenuineIntel

  Session Key              : 657523bf-e38c-4e7d-b020-bc18a66b64c1

  Static TLS mitigation    : Disabled: Unnecessary

  Window System            : No active display

Fault Count: 12

Abnormal termination:

Segmentation violation

Register State (from fault):

  RAX = 5555d62a4a7d8870  RBX = 578286ffeaaaaab1

  RCX = 4852bfe2f5284d00  RDX = 046677ff55555548

  RSP = 00007fe4eddb4cc0  RBP = 00007fe4eddb4db0

  RSI = 3b1f57e2f5284d28  RDI = df4877e2f5284d08

   R8 = a4299fe2f5284d20   R9 = 5555d6324a7d8878

  R10 = 0000000000000008  R11 = d2150fe2f5284d30

  R12 = 0000000800000008  R13 = 690ac7e2f5284d38

  R14 = 0000000000000000  R15 = 5555d6024a7d8848

  RIP = 00007fe4efe5613e  EFL = 0000000000010202

  CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):

[  0] 0x00007fe4efe5613e        /usr/local/MATLAB/R2019b/bin/glnxa64/mkl.so+20001086 mkl_blas_avx512_xdcopy+00000398

[  1] 0x00007fe4ef167e45        /usr/local/MATLAB/R2019b/bin/glnxa64/mkl.so+06442565 mkl_blas_dcopy+00000949

[  2] 0x00007fe63047e7d3 /usr/local/MATLAB/R2019b/bin/glnxa64/../../sys/os/glnxa64/libiomp5.so+00931795 __kmp_invoke_microtask+00000147

[  3] 0x00007fe63044554a /usr/local/MATLAB/R2019b/bin/glnxa64/../../sys/os/glnxa64/libiomp5.so+00697674

[  4] 0x00007fe630444c0b /usr/local/MATLAB/R2019b/bin/glnxa64/../../sys/os/glnxa64/libiomp5.so+00695307

[  5] 0x00007fe63047ec30 /usr/local/MATLAB/R2019b/bin/glnxa64/../../sys/os/glnxa64/libiomp5.so+00932912

[  6] 0x00007fe64ac266db              /lib/x86_64-linux-gnu/libpthread.so.0+00030427

[  7] 0x00007fe64a3b788f                    /lib/x86_64-linux-gnu/libc.so.6+01185935 clone+00000063

[  8] 0x0000000000000000                                   <unknown-module>+00000000

** This crash report has been saved to disk as /home/icub/matlab_crash_dump.21823-2 **

MATLAB is exiting because of fatal error

Killed

The error is reproducible on UBUNTU 18.04 LTS with iDynTree in the latest devel branch. Looking at the logger, it seems there is a problem with the mkl.so library. In particular I've found this comment online. I think it is related to the issue we are experiencing, but I don't know how to properly fix the problem.

cc @lrapetti @bemilio

bemilio commented 4 years ago

related https://github.com/robotology/idyntree/issues/684

CC @traversaro @S-Dafarra

gabrielenava commented 4 years ago

Side note: we tested the code on the DIC shared computer monster. I also tested on my personal laptop and I had the same issue, but curiously I can use standalone IPOPT bindings without errors. I've created the standalone bindings following the instructions here: https://github.com/ebertolazzi/mexIPOPT.

traversaro commented 4 years ago

As suggested by @bemilio, I think it is worth trying the workaround mentioned in https://github.com/robotology/idyntree/issues/684 . mexIPOPT probably works because it uses its own static version of the used blas library, see https://github.com/ebertolazzi/mexIPOPT/blob/master/README_linux_how_to_compile_ipopt.md .

traversaro commented 4 years ago

By the way, I suggest to continue to post in https://github.com/robotology/idyntree/issues/684 (as the problem is the same) and mark this issue as duplicated.

gabrielenava commented 4 years ago

Closing the issue as duplicated of #684.