Problem Installing SCT


#1

I’ve been trying to install SCT but I’m encountering the following problem,

    ~/dev/spinalcordtoolbox(master*) » ./install_sct -d -b -p -v                                                                                                       gmartinez@Guillermos-MacBook-Pro

    Welcome to the SCT installer!
     data directory will not be (re)-installed
     SCT binaries will not be (re)-installed 
     Multiprocessing using MPI activated
     Full verbose!
    .
    .
    .

    Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: + read add_to_path
    y
    + [[ ! y =~ ^([Yy](es)?|[Nn]o?)$ ]]
    + echo ''

    + [[ y =~ ^[Yy] ]]
    + edit_bashrc
    + [[ -z '' ]]
    + echo

    + echo ''
    ++ date '+%Y-%m-%d %H:%M:%S'
    + echo '# SPINALCORDTOOLBOX (installed on 2019-07-21 08:14:01)'
    + echo export 'PATH="/Users/gmartinez/dev/spinalcordtoolbox/bin:${PATH}"'
    + echo 'export SCT_DIR=/Users/gmartinez/dev/spinalcordtoolbox'
    + echo 'export MPLBACKEND=Agg'
    + echo ''
    + echo -e 'Validate installation...'
    Validate installation...
    + sct_check_dependencies
    Traceback (most recent call last):
      File "/Users/gmartinez/dev/spinalcordtoolbox/bin/sct_check_dependencies", line 11, in <module>
        load_entry_point('spinalcordtoolbox', 'console_scripts', 'sct_check_dependencies')()
      File "/Users/gmartinez/dev/spinalcordtoolbox/spinalcordtoolbox/compat/launcher.py", line 34, in main
        os.execvpe(cmd[0], cmd[0:], env)
      File "/Users/gmartinez/dev/spinalcordtoolbox/python/envs/venv_sct/lib/python3.6/os.py", line 568, in execvpe
        _execvpe(file, args, env)
      File "/Users/gmartinez/dev/spinalcordtoolbox/python/envs/venv_sct/lib/python3.6/os.py", line 604, in _execvpe
        raise last_exc.with_traceback(tb)
      File "/Users/gmartinez/dev/spinalcordtoolbox/python/envs/venv_sct/lib/python3.6/os.py", line 594, in _execvpe
        exec_func(fullname, *argrest)
    FileNotFoundError: [Errno 2] No such file or directory: b'/Applications/VMware/mpiexec'
    + echo -e 'Installation validation Failed!'
    Installation validation Failed!
    + echo -e 'Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):'
    Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):
    + echo -e 'http://forum.spinalcordmri.org/c/sct\n'
    http://forum.spinalcordmri.org/c/sct

    + exit 1
    + finish
    + value=1
    + cd /Users/gmartinez/dev/spinalcordtoolbox
    + '[' 1 -eq 0 ']'
    + '[' 1 -eq 99 ']'
    + echo -e 'Installation failed\n'
    Installation failed

    + rm -r /var/folders/_t/pxl23c8j27jbnnrmsmhl6qwc0001b8/T/tmp.ir7scPQ6

Am I missing something? (I couldn’t paste the whole console output since the input box is limited to 32000 chars.)

Regards.


#2

Hi @gmotzespina,

Thank you for reporting this bug. We haven’t used MPI for a while and after we did major refactoring, we didn’t check that MPI installation was still working. Apparently it is not!

We are planning to drop support for MPI. Issue opened here

For now, you can just install SCT with default option (i.e. don’t use -p),

Cheers,
Julien