On import ClearMap.Environment getting 'command 'gcc' failed with exit status 1', macOS about clearmap2

[ChristophKirst]

The erorr shows:
unsupported option -fopenmp

which points to a missing multiprocessing library OpenMP / MPI

Installing that library might fix the problem ? I fit is installed making its path available could help too.

We don't run ClearMap under Mac at this point, so I cannot be of much more help how to do that (possibly homebrew
or similar tools?) A software company is working on making the software available on Mac and Windows
(though this might take several months).

Hope that helps ?

[cudmore]

Thanks for the info and solid lead about OpenMP. Looks like the stock clang on macOS (Sierra) does not support the multiprocessing library (OpenMP) out of the box. See Enable OpenMP support in clang in Mac OS X... for some tips.

Caveat: If your on macOS, no guarantee this will work. This was done on an older version (Sierra) and might not work on other versions. Also, I got ClearMap to compile but now can't really test if this compilation actually works as the pipeline for the full brain example data on osf.io/q6atb is way too big for my machine, see my post here. Would be great if we had a toy example with maybe 4 stacks rather than 100's? Goal would be for non-super-humans/computer to run the code :)

I got ClearMap to compile in two main steps:

1. Install llvm and libomp

brew update # took >1 hour
brew install llvm libomp 

The important llvm file is now in /usr/local/opt/llvm/include

2. Modify Python source code in conda environment

Need to modify the file envs/ClearMap/lib/python3.7/distutils/unixccompiler.py as follows ...

Basically, each time -fopenmp is passed to both compile and link steps, it needs to be preceded with the path to llvm, /usr/local/opt/llvm/include. Like this -I/usr/local/opt/llvm/include -fopenmp.

In def _compile()

       # start added by bob
       if extra_postargs:
        	if extra_postargs[-1] == '-fopenmp':
        		extra_postargs[-1] = '-I/usr/local/opt/llvm/include -fopenmp'        
       # end added by bob
       try:
            self.spawn(compiler_so + cc_args + [src, '-o', obj] +
                       extra_postargs)
        except DistutilsExecError as msg:
            raise CompileError(msg)

In def link()

                # start added by bob
                if ld_args:
        	        if ld_args[-1] == '-fopenmp':
        	        	ld_args[-1] = '-I/usr/local/opt/llvm/include -fopenmp'
                # end added by bob
                self.spawn(linker + ld_args) # original code

Then at an ipython prompt, the following works

import ClearMap.Compile 

Hope this helps some people on macOS?

[ChristophKirst]

Thanks for figuring this out !
We will include this in our updates!

[ChristophKirst]

This seems fixed, I am closing this issue. Feel free to reopen.

[Yannan-Chen]

Faced same problem but on Ubuntu 20.04.3. Solved by running:

sudo apt-get install g++