spm cannot find matlab runtime

[shania3322]

I used install_matlab_runtime -v R2025b -p SOME_OTHER_DIRECTORY. After that I ran python -c "import spm;print(spm.spm('Version'))". It automatically tried to download matlab runtime again but failed because the default directory (/usr/local/ ) is not available in my environment. Can someone help?

My system: Linux and connects to HPC clusters

I ran the following commands:
conda create -n spm25 python=3.13 scipy

conda activate spm25

pip install spm-python[R2025b]

install_matlab_runtime -v R2025b -p /export/home/usrname/MATLAB/MATLAB_RUNTIME -y

python -c "import spm; print(spm.spm('Version'))"

Results:

Initializing Matlab Runtime...

Downloading installer from https://...

[johmedr]

Hi Shania,

Thank you for using SPM Python and for bringing this issue up! The program in charge of installing the runtime is matlab-runtime, spm-python then calls that package to guess your installation prefix. Because you are using a custom installation prefix, you would need to tell it where to find the runtime.

You can do that by setting the environment variable MATLAB_RUNTIME_PATH. You have a few choices for that:

1) Set it temporarily before calling Python

MATLAB_RUNTIME_PATH='/export/home/usrname/MATLAB/MATLAB_RUNTIME' python -c "import spm; print(spm.spm('Version'))"

2) Set it for your current session

export MATLAB_RUNTIME_PATH='/export/home/usrname/MATLAB/MATLAB_RUNTIME' 

You can automate that by adding it to your ~/.bashrc.

3) Set it in your Python program

# Set the environment variable 
import os 
os.environ['MATLAB_RUNTIME_PATH'] = '/export/home/usrname/MATLAB/MATLAB_RUNTIME' 

# Then run an spm-python command
import spm
print(spm.spm('Version'))

I hope it helps, please let me know if that fixes your issue

[shania3322]

Hi Johmedr,

I tried what you have suggested. Another issue came up. Matlab runtime R2025b requires gcc version higher than the one shipped with linux system. Do you have any suggestions the safest way to solve the issue?

Thank you!

The linux system is Rocky 8.10 and is shipped with gcc 8.5.0.

Initializing Matlab Runtime...
Traceback (most recent call last):
      ...
        File
      "/export/home/usrname/miniconda3/envs/spm25/lib/python3.13/site-packages/mpython/runtime.py",
      line 45, in call
          res = cls.instance().mpython_endpoint(fn, *args, **kwargs)
        File
      "/export/home/usrname/miniconda3/envs/spm25/lib/python3.13/site-packages/spm_runtime/_endpoint.py",
      line 20, in __call__
          self._init_endpoint()
          ~~~~~~~~~~~~~~~~~~~^^
        File
      "/export/home/usrname/miniconda3/envs/spm25/lib/python3.13/site-packages/spm_runtime/_endpoint.py",
      line 15, in _init_endpoint
          matlab_runtime.init(__matlab_release__, install_if_missing=True)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File
      "/export/home/usrname/miniconda3/envs/spm25/lib/python3.13/site-packages/matlab_runtime/impl.py",
      line 344, in init
          importlib.import_module(_CPP)
          ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
        File
      "/export/home/usrname/miniconda3/envs/spm25/lib/python3.13/importlib/__init__.py",
      line 88, in import_module
          return _bootstrap._gcd_import(name[level:], package, level)
                 ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "<frozen importlib._bootstrap>", line 1395, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1331, in
      _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 921, in _load_unlocked
        File "<frozen importlib._bootstrap>", line 813, in module_from_spec
        File "<frozen importlib._bootstrap_external>", line 1317, in
      create_module
        File "<frozen importlib._bootstrap>", line 488, in
      _call_with_frames_removed
      ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found
      (required by
       /export/home/usrname/MATLAB/MATLAB_RUNTIME/R2025b/bin/glnxa64/matlabruntimeforpython_abi3.so)

Then I fell back to python3.8 + matlab runtime R2023a. The error message said

No module named 'matlabruntimeforpython_abi3'

Indeed, there is no such module under /export/home/usrname/MATLAB/MATLAB_RUNTIME/R2025b/bin/glnxa64/

[johmedr]

Hi Shania,

Let me look into this issue. In the meantime, I see that you are working on an HPC cluster. In that situation, it might be easier to load the Matlab module in your environment (assuming the cluster you are using provides it) than to install the runtime manually, as the runtime is necessary only if Matlab is not installed.
You can run

module load matlab

and then, your code should work

conda activate spm25
python -c "import spm; spm.spm('Version')"

Hope this help
Johan