Issue installing standalone SPM (Ubuntu 20.04)

I am trying to install the standalone version of SPM, however during installation the process fails (segmenation violation). I am following the installation of SPM found here (https://en.wikibooks.org/wiki/SPM/Standalone). The command I run is ./run_spm12.sh /usr/local/MATLAB/MATLAB_Runtime/v97

I have also tried to install it using v910 and v911, and all return the same error:

--------------------------------------------------------------------------------
       Segmentation violation detected at Tue Apr 12 13:23:54 2022 +1000
--------------------------------------------------------------------------------

Configuration:
  Crash Decoding           : Disabled - No sandbox or build area path
  Crash Mode               : continue (default)
  Default Encoding         : UTF-8
  Desktop Environment      : ubuntu:GNOME
  GNU C Library            : 2.31 stable
  MATLAB Architecture      : glnxa64
  MATLAB Root              : /usr/local/MATLAB/MATLAB_Runtime/v97
  MATLAB Version           : 9.7.0.1247435 (R2019b) Update 2
  Operating System         : Ubuntu 20.04.4 LTS
  Process ID               : 2973636
  Processor ID             : x86 Family 6 Model 140 Stepping 1, GenuineIntel
  Static TLS mitigation    : Enabled: Full

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 0000000000000000  RBX = 00007ffe766e01c0
  RCX = 0000000000000000  RDX = 00000000006030a0
  RSP = 00007ffe766dff10  RBP = 00007ffe766e0120
  RSI = 0000000000000001  RDI = 00007ffe766e01c0

   R8 = 0000000000000000   R9 = 0000000000400a95
  R10 = 000000000040063a  R11 = 00007fe2144695a0
  R12 = 00007ffe766e01c0  R13 = 0000000000000001
  R14 = 0000000000000000  R15 = 00000000011126e0

  RIP = 00007fe201299c83  EFL = 0000000000010202

   CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x00007fe201299c83 /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwmclmcr.so+02686083
[  1] 0x00007fe2012909fd /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwmclmcr.so+02648573 mclInitializeComponentInstanceNonEmbeddedStandalone+00000061
[  2] 0x00007fe2144695e2 /usr/local/MATLAB/MATLAB_Runtime/v97/runtime/glnxa64/libmwmclmcrrt.so+00103906 mclInitializeComponentInstanceNonEmbeddedStandalone_proxy+00000066
[  3] 0x0000000000400b46 /home/unimelb.edu.au/acapon/Desktop/spm12/spm12_glnxa64+00002886
[  4] 0x0000000000400b64 /home/unimelb.edu.au/acapon/Desktop/spm12/spm12_glnxa64+00002916
[  5] 0x0000000000400bb2 /home/unimelb.edu.au/acapon/Desktop/spm12/spm12_glnxa64+00002994
[  6] 0x00007fe20e8bd220 /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwmclbase.so+00352800
[  7] 0x00007fe200880587 /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwMVMLocal.so+00570759 _ZN7mwboost6detail8function21function_obj_invoker0INS_3_bi6bind_tINS3_11unspecifiedENS_9function1IiRKSt6vectorINSt7__cxx1112basic_stringIDsSt11char_traitsIDsESaIDsEEESaISD_EEEENS3_5list1INS3_5valueISF_EEEEEEiE6invokeERNS1_15function_bufferE+00000039
[  8] 0x00007fe20e7a9487 /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwmcr.so+00865415
[  9] 0x00007fe20e7a99c8 /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwmcr.so+00866760
[ 10] 0x00007fe20e7a9c74 /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwmcr.so+00867444 _Z12mcr_run_mainRKN7mwboost9function0IiEEbb+00000196
[ 11] 0x00007fe2008752e4 /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwMVMLocal.so+00525028
[ 12] 0x00007fe20e5f91d7 /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwmvm.so+02986455 _ZN3mvm6detail11SessionImpl7runMainERKN7mwboost9function1IiRKSt6vectorINSt7__cxx1112basic_stringIDsSt11char_traitsIDsESaIDsEEESaISA_EEEESE_+00000087
[ 13] 0x00007fe20e8bd71a /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libmwmclbase.so+00354074 mclRunMain+00001194
[ 14] 0x0000000000400c59 /home/unimelb.edu.au/acapon/Desktop/spm12/spm12_glnxa64+00003161
[ 15] 0x00007fe2140fa0b3                    /lib/x86_64-linux-gnu/libc.so.6+00147635 __libc_start_main+00000243
[ 16] 0x00000000004009ba /home/unimelb.edu.au/acapon/Desktop/spm12/spm12_glnxa64+00002490
[ 17] 0x0000000000000000                                   <unknown-module>+00000000

Additional info:

To get this far I had to alter the file /sys/os/glnxa64/libstdc++.so -> /sys/os/glnxa64/libstdc++.soold.

This removed this error:

libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: swrast 

I am running Ubuntu 20.04.04 LTS on a Dell Latitude 5320.

Any help with this problem would be greatly appreciated!

Cheers,

Aaron

Answer 1

[Infinite_king]

Hi dubs,

It appears that the issue is related to a compatibility problem between SPM and the MATLAB Runtime. Here are some troubleshooting steps,

• Ensure that you are using the correct MATLAB Runtime version that is compatible with SPM. You mentioned trying v910, v911, and v97. Make sure you are using the exact version recommended by SPM.
• Refer the following resource to check the compatible versions of MCR, https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone/#:~:text=The%20default%20SPM%20standalone%20requires%20the%20MATLAB%20Compiler%20Runtime%20(MCR)%207.13%20of%20MATLAB%20R2010a%20available%20from%20the%20MCR%20folder%20from%20the%20link%20you%20will%20have%20been%20given.%20Otherwise%20more%20recent%20MATLAB%20Runtimes%20are%20downloadable%20from%20here
• Ensure that you have the correct version of libstdc++ for your MATLAB Runtime. The MATLAB Runtime comes with its own libraries, and modifying them might lead to compatibility issues.
• Check if all the required libraries are installed. You can install them using the following command,

sudo apt-get install libxt6 libxmu6 libxpm4

• Check if the user running the script has the necessary permissions to access MATLAB Runtime and the SPM installation directory.
• Refer the following resource for installation steps and FAQ's, https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone/

Hope this is helpful.