Symbol not found: _GOMP_parallel

[lmurrow]

Hello, I am relatively new to python. Sorry if I am missing any information.

Velocyto installation completed, but when running velocyto --help to test installation I receive the following error:

$ velocyto --help
Traceback (most recent call last):
  File "/anaconda3/bin/velocyto", line 7, in <module>
    from velocyto.commands.velocyto import cli
  File "/anaconda3/lib/python3.6/site-packages/velocyto/__init__.py", line 13, in <module>
    from .estimation import fit_slope, _fit1_slope, clusters_stats
  File "/anaconda3/lib/python3.6/site-packages/velocyto/estimation.py", line 7, in <module>
    from .speedboosted import _colDeltaCor, _colDeltaCorLog10, _colDeltaCorSqrt
ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/velocyto/speedboosted.cpython-36m-darwin.so, 2): Symbol not found: _GOMP_parallel
  Referenced from: /anaconda3/lib/python3.6/site-packages/velocyto/speedboosted.cpython-36m-darwin.so
  Expected in: flat namespace
 in /anaconda3/lib/python3.6/site-packages/velocyto/speedboosted.cpython-36m-darwin.so

I think this likely has something to do with my gcc version, but I'm not sure how to fix the problem.

$ python -V
Python 3.6.3 :: Anaconda custom (64-bit)
$ which gcc
/anaconda3/bin/gcc
$ gcc --version
gcc (GCC) 4.8.5
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[gioelelm]

Please install according to the instructions (using conda). Currently the problem is that the compilation step was performed with a compiler not supporting openmp. But this should not happen using the gcc version provided by conda.

[lmurrow]

Thanks for responding so quickly. Sorry but I am confused. I did use conda to install all dependencies (as in the instructions), but used pip to install velocyto. I don't see any version of the velocyto package that is available to install using conda.

[gioelelm]

Is this solved?
If not, try conda install llvm, conda install gcc or conda install libgcc.
If this also does not work, try adding -c conda-forge I am pretty sure the version of the compiler provided by conda forge supports openmp.

[gioelelm]

Finally, if this does not work as well I had prepared a hacky solution for this occurrence.

• Unistall the current version.
• Get the source code cloning the repo.
• Change the setup.py script setting C_COMPILE = False
• Run pip install -e .

This will install the estensions that I precompiled on my machine.

[lmurrow]

Thank you, the first option worked! Will close this out.

[Julie-UM]

Is this solved? If not, try conda install llvm, conda install gcc or conda install libgcc. If this also does not work, try adding -c conda-forge I am pretty sure the version of the compiler provided by conda forge supports openmp.

Hi, when I use conda to RUN velocyto in terminal of macbook pro, it retruns such problem. Do you have any ideas to resolve it? Many thanks! I had tried The methods you mentioned above, but is not suitable for my problem.