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Issue installing standalone SPM (Ubuntu 20.04)

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dubs
dubs on 12 Apr 2022
Answered: Infinite_king on 12 Jan 2024
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

Answers (1)

Infinite_king
Infinite_king on 12 Jan 2024
Hi dubs,
It appears that the issue is related to a compatibility problem between SPM and the MATLAB Runtime. Here are some troubleshooting steps,
sudo apt-get install libxt6 libxmu6 libxpm4
Hope this is helpful.

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