MATLAB on Linux crashes when importing Python module

Any time I try to import a Python module, whether it's from the standard library, installed, or custom, MATLAB crashed when I call py.importlib.import_module(). Here's the crash log I get:

--------------------------------------------------------------------------------
               abort() detected at Thu Jun 27 16:12:00 2019 -0400
--------------------------------------------------------------------------------

Configuration:
  Crash Decoding           : Disabled - No sandbox or build area path
  Crash Mode               : continue (default)
  Default Encoding         : UTF-8
  Deployed                 : false
  Desktop Environment      : ubuntu:GNOME
  GNU C Library            : 2.27 stable
  Graphics Driver          : Unknown hardware 
  Java Version             : Java 1.8.0_144-b01 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
  MATLAB Architecture      : glnxa64
  MATLAB Entitlement ID    : 5340214
  MATLAB Root              : /usr/local/MATLAB/R2018a
  MATLAB Version           : 9.4.0.813654 (R2018a)
  OpenGL                   : hardware
  Operating System         : Ubuntu 18.04.2 LTS
  Process ID               : 72835
  Processor ID             : x86 Family 143 Model 1 Stepping 1, AuthenticAMD
  Session Key              : 0f3fa0ad-c4e3-4220-bbe7-b8df6cca1d4a
  Static TLS mitigation    : Disabled: Cannot load X11
  Window System            : The X.Org Foundation (12001000), display :0

Fault Count: 1


Abnormal termination

Register State (from fault):
  RAX = 0000000000000000  RBX = 00007f805bff5860
  RCX = 00007f80804a1e97  RDX = 0000000000000000
  RSP = 00007f805bff55f0  RBP = 00007f805bff5960
  RSI = 00007f805bff55f0  RDI = 0000000000000002

   R8 = 0000000000000000   R9 = 00007f805bff55f0
  R10 = 0000000000000008  R11 = 0000000000000246
  R12 = 00007f805bff5860  R13 = 0000000000001000
  R14 = 0000000000000000  R15 = 0000000000000030

  RIP = 00007f80804a1e97  EFL = 0000000000000246

   CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x00007f80804a1e97                    /lib/x86_64-linux-gnu/libc.so.6+00257687 gsignal+00000199
[  1] 0x00007f80804a3801                    /lib/x86_64-linux-gnu/libc.so.6+00264193 abort+00000321
[  2] 0x00007f80804ec897                    /lib/x86_64-linux-gnu/libc.so.6+00563351
[  3] 0x00007f80804f390a                    /lib/x86_64-linux-gnu/libc.so.6+00592138
[  4] 0x00007f80804fae1c                    /lib/x86_64-linux-gnu/libc.so.6+00622108 cfree+00001228
[  5] 0x00007f7e75d8456d /home/mlh6/anaconda3/lib/python3.7/lib-dynload/../../libcrypto.so.1.1+01406317 EVP_MD_CTX_reset+00000205
[  6] 0x00007f7e75d8459a /home/mlh6/anaconda3/lib/python3.7/lib-dynload/../../libcrypto.so.1.1+01406362 EVP_MD_CTX_free+00000010
[  7] 0x00007f7f0c002e87 /home/mlh6/anaconda3/lib/python3.7/lib-dynload/_hashlib.cpython-37m-x86_64-linux-gnu.so+00011911
[  8] 0x00007f7e772140cc          /home/mlh6/anaconda3/lib/libpython3.7m.so+00426188 _PyEval_EvalFrameDefault+00008396
[  9] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 10] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 11] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[ 12] 0x00007f7e773d4284          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261636 _PyEval_EvalCodeWithName+00002756
[ 13] 0x00007f7e773d436f          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261871 PyEval_EvalCodeEx+00000063
[ 14] 0x00007f7e772a3abc          /home/mlh6/anaconda3/lib/libpython3.7m.so+01014460 PyEval_EvalCode+00000028
[ 15] 0x00007f7e772a790e          /home/mlh6/anaconda3/lib/libpython3.7m.so+01030414
[ 16] 0x00007f7e772c9561          /home/mlh6/anaconda3/lib/libpython3.7m.so+01168737 _PyMethodDef_RawFastCallDict+00000769
[ 17] 0x00007f7e772c9be6          /home/mlh6/anaconda3/lib/libpython3.7m.so+01170406 _PyCFunction_FastCallDict+00000038
[ 18] 0x00007f7e77218d61          /home/mlh6/anaconda3/lib/libpython3.7m.so+00445793 _PyEval_EvalFrameDefault+00028001
[ 19] 0x00007f7e773d4284          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261636 _PyEval_EvalCodeWithName+00002756
[ 20] 0x00007f7e772c9680          /home/mlh6/anaconda3/lib/libpython3.7m.so+01169024 _PyFunction_FastCallKeywords+00000144
[ 21] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 22] 0x00007f7e7721910a          /home/mlh6/anaconda3/lib/libpython3.7m.so+00446730 _PyEval_EvalFrameDefault+00028938
[ 23] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 24] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 25] 0x00007f7e77214cb9          /home/mlh6/anaconda3/lib/libpython3.7m.so+00429241 _PyEval_EvalFrameDefault+00011449
[ 26] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 27] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 28] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[ 29] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 30] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 31] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[ 32] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 33] 0x00007f7e772c9a2f          /home/mlh6/anaconda3/lib/libpython3.7m.so+01169967 _PyFunction_FastCallDict+00000703
[ 34] 0x00007f7e772ca4c3          /home/mlh6/anaconda3/lib/libpython3.7m.so+01172675
[ 35] 0x00007f7e772ca76a          /home/mlh6/anaconda3/lib/libpython3.7m.so+01173354 _PyObject_CallMethodIdObjArgs+00000186
[ 36] 0x00007f7e772fdea0          /home/mlh6/anaconda3/lib/libpython3.7m.so+01384096 PyImport_ImportModuleLevelObject+00001328
[ 37] 0x00007f7e77218f7a          /home/mlh6/anaconda3/lib/libpython3.7m.so+00446330 _PyEval_EvalFrameDefault+00028538
[ 38] 0x00007f7e773d4284          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261636 _PyEval_EvalCodeWithName+00002756
[ 39] 0x00007f7e773d436f          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261871 PyEval_EvalCodeEx+00000063
[ 40] 0x00007f7e772a3abc          /home/mlh6/anaconda3/lib/libpython3.7m.so+01014460 PyEval_EvalCode+00000028
[ 41] 0x00007f7e772a790e          /home/mlh6/anaconda3/lib/libpython3.7m.so+01030414
[ 42] 0x00007f7e772c9561          /home/mlh6/anaconda3/lib/libpython3.7m.so+01168737 _PyMethodDef_RawFastCallDict+00000769
[ 43] 0x00007f7e772c9be6          /home/mlh6/anaconda3/lib/libpython3.7m.so+01170406 _PyCFunction_FastCallDict+00000038
[ 44] 0x00007f7e77218d61          /home/mlh6/anaconda3/lib/libpython3.7m.so+00445793 _PyEval_EvalFrameDefault+00028001
[ 45] 0x00007f7e773d4284          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261636 _PyEval_EvalCodeWithName+00002756
[ 46] 0x00007f7e772c9680          /home/mlh6/anaconda3/lib/libpython3.7m.so+01169024 _PyFunction_FastCallKeywords+00000144
[ 47] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 48] 0x00007f7e7721910a          /home/mlh6/anaconda3/lib/libpython3.7m.so+00446730 _PyEval_EvalFrameDefault+00028938
[ 49] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 50] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 51] 0x00007f7e77214cb9          /home/mlh6/anaconda3/lib/libpython3.7m.so+00429241 _PyEval_EvalFrameDefault+00011449
[ 52] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 53] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 54] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[ 55] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 56] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 57] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[ 58] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 59] 0x00007f7e772c9a2f          /home/mlh6/anaconda3/lib/libpython3.7m.so+01169967 _PyFunction_FastCallDict+00000703
[ 60] 0x00007f7e772ca4c3          /home/mlh6/anaconda3/lib/libpython3.7m.so+01172675
[ 61] 0x00007f7e772ca76a          /home/mlh6/anaconda3/lib/libpython3.7m.so+01173354 _PyObject_CallMethodIdObjArgs+00000186
[ 62] 0x00007f7e772fdea0          /home/mlh6/anaconda3/lib/libpython3.7m.so+01384096 PyImport_ImportModuleLevelObject+00001328
[ 63] 0x00007f7e77218f7a          /home/mlh6/anaconda3/lib/libpython3.7m.so+00446330 _PyEval_EvalFrameDefault+00028538
[ 64] 0x00007f7e773d4284          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261636 _PyEval_EvalCodeWithName+00002756
[ 65] 0x00007f7e773d436f          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261871 PyEval_EvalCodeEx+00000063
[ 66] 0x00007f7e772a3abc          /home/mlh6/anaconda3/lib/libpython3.7m.so+01014460 PyEval_EvalCode+00000028
[ 67] 0x00007f7e772a790e          /home/mlh6/anaconda3/lib/libpython3.7m.so+01030414
[ 68] 0x00007f7e772c9561          /home/mlh6/anaconda3/lib/libpython3.7m.so+01168737 _PyMethodDef_RawFastCallDict+00000769
[ 69] 0x00007f7e772c9be6          /home/mlh6/anaconda3/lib/libpython3.7m.so+01170406 _PyCFunction_FastCallDict+00000038
[ 70] 0x00007f7e77218d61          /home/mlh6/anaconda3/lib/libpython3.7m.so+00445793 _PyEval_EvalFrameDefault+00028001
[ 71] 0x00007f7e773d4284          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261636 _PyEval_EvalCodeWithName+00002756
[ 72] 0x00007f7e772c9680          /home/mlh6/anaconda3/lib/libpython3.7m.so+01169024 _PyFunction_FastCallKeywords+00000144
[ 73] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 74] 0x00007f7e7721910a          /home/mlh6/anaconda3/lib/libpython3.7m.so+00446730 _PyEval_EvalFrameDefault+00028938
[ 75] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 76] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 77] 0x00007f7e77214cb9          /home/mlh6/anaconda3/lib/libpython3.7m.so+00429241 _PyEval_EvalFrameDefault+00011449
[ 78] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 79] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 80] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[ 81] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 82] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[ 83] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[ 84] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[ 85] 0x00007f7e772c9a2f          /home/mlh6/anaconda3/lib/libpython3.7m.so+01169967 _PyFunction_FastCallDict+00000703
[ 86] 0x00007f7e772ca4c3          /home/mlh6/anaconda3/lib/libpython3.7m.so+01172675
[ 87] 0x00007f7e772ca76a          /home/mlh6/anaconda3/lib/libpython3.7m.so+01173354 _PyObject_CallMethodIdObjArgs+00000186
[ 88] 0x00007f7e772fdea0          /home/mlh6/anaconda3/lib/libpython3.7m.so+01384096 PyImport_ImportModuleLevelObject+00001328
[ 89] 0x00007f7e77218f7a          /home/mlh6/anaconda3/lib/libpython3.7m.so+00446330 _PyEval_EvalFrameDefault+00028538
[ 90] 0x00007f7e773d4284          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261636 _PyEval_EvalCodeWithName+00002756
[ 91] 0x00007f7e773d436f          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261871 PyEval_EvalCodeEx+00000063
[ 92] 0x00007f7e772a3abc          /home/mlh6/anaconda3/lib/libpython3.7m.so+01014460 PyEval_EvalCode+00000028
[ 93] 0x00007f7e772a790e          /home/mlh6/anaconda3/lib/libpython3.7m.so+01030414
[ 94] 0x00007f7e772c9561          /home/mlh6/anaconda3/lib/libpython3.7m.so+01168737 _PyMethodDef_RawFastCallDict+00000769
[ 95] 0x00007f7e772c9be6          /home/mlh6/anaconda3/lib/libpython3.7m.so+01170406 _PyCFunction_FastCallDict+00000038
[ 96] 0x00007f7e77218d61          /home/mlh6/anaconda3/lib/libpython3.7m.so+00445793 _PyEval_EvalFrameDefault+00028001
[ 97] 0x00007f7e773d4284          /home/mlh6/anaconda3/lib/libpython3.7m.so+02261636 _PyEval_EvalCodeWithName+00002756
[ 98] 0x00007f7e772c9680          /home/mlh6/anaconda3/lib/libpython3.7m.so+01169024 _PyFunction_FastCallKeywords+00000144
[ 99] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[100] 0x00007f7e7721910a          /home/mlh6/anaconda3/lib/libpython3.7m.so+00446730 _PyEval_EvalFrameDefault+00028938
[101] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[102] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[103] 0x00007f7e77214cb9          /home/mlh6/anaconda3/lib/libpython3.7m.so+00429241 _PyEval_EvalFrameDefault+00011449
[104] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[105] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[106] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[107] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3.7m.so+00450096
[108] 0x00007f7e7721b0f6          /home/mlh6/anaconda3/lib/libpython3.7m.so+00454902
[109] 0x00007f7e77216808          /home/mlh6/anaconda3/lib/libpython3.7m.so+00436232 _PyEval_EvalFrameDefault+00018440
[110] 0x00007f7e77219e30          /home/mlh6/anaconda3/lib/libpython3

[Stephen Lam]

I'm having this same issue. Was there ever any resolution?

Answer 1

[Satwik]

Hi Michael,

Here is an existing MATLAB answer post which talks about a similar issue and has workarounds to resolve it:

https://www.mathworks.com/matlabcentral/answers/265247-importing-custom-python-module-fails

The suggested workaround is to set the 'dlopen' flag to RTLD_NOW | RTLD_DEEPBIND. This can be done by using Python's 'sys.setdlpenflags' as shown below:

>> RTLD_NOW = 2;
>> RTLD_DEEPBIND = 8;
>> flag = bitor(RTLD_NOW, RTLD_DEEPBIND); % RTLD_NOW | RTLD_DEEPBIND
>> py.sys.setdlopenflags(int32(flag));
>> py.importlib.import_module('fabio');

You may refer to the links given below for more information:

• http://linux.die.net/man/3/dlopen - search for 'RTLD_DEEPBIND'.
• https://docs.python.org/2/library/sys.html#sys.setdlopenflags

I hope this helps!