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popgenmethods / momi2

Infer demographic history with the Moran model
GNU General Public License v3.0
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ImportError: /miniconda3/lib/python3.6/site-packages/../../libgsl.so.23: undefined symbol: cblas_dasum #25

Closed kevinmneal closed 5 years ago

kevinmneal commented 5 years ago

Hi,

I keep encountering this issue when I try to run the program. Googling the issue hasn't yielded much help, so I wonder if anyone here might have any insights into the problem. If it helps, I did NOT install in a separate environment like the tutorial does, and I installed using miniconda3.

python -m momi.read_vcf Traceback (most recent call last): File "/home/kevin/miniconda3/lib/python3.6/runpy.py", line 183, in _run_module_as_main mod_name, mod_spec, code = _get_module_details(mod_name, _Error) File "/home/kevin/miniconda3/lib/python3.6/runpy.py", line 109, in _get_module_details __import__(pkg_name) File "/home/kevin/miniconda3/lib/python3.6/site-packages/momi/__init__.py", line 8, in <module> from .likelihood import SfsLikelihoodSurface File "/home/kevin/miniconda3/lib/python3.6/site-packages/momi/likelihood.py", line 11, in <module> from .demography import Demography File "/home/kevin/miniconda3/lib/python3.6/site-packages/momi/demography.py", line 8, in <module> import msprime File "/home/kevin/miniconda3/lib/python3.6/site-packages/msprime/__init__.py", line 26, in <module> from _msprime import FORWARD # NOQA ImportError: /home/kevin/miniconda3/lib/python3.6/site-packages/../../libgsl.so.23: undefined symbol: cblas_dasum

kevinmneal commented 5 years ago

After some digging, the issue was with msprime. When I followed the commands to install momi2, it seems only msprime 0.6.1 was installed. Issue seems fixed when ensuring it's updated to 0.6.2 via conda install -c conda-forge msprime

More info here: https://github.com/conda-forge/msprime-feedstock/issues/20

didier-aurelle commented 5 years ago

Hi I apparently have the same error when trying to run momi2: ImportError: /home/aurelle/anaconda3/envs/momi_py36/lib/python3.6/site-packages/../../libgsl.so.23: undefined symbol: cblas_dasum I installed msprime again but it still doesn't work thanks

terhorst commented 5 years ago

From the discussions linked above, it's due to having mismatching / multiple BLAS libraries installed. It's not something we can address in momi2.

jackkamm commented 5 years ago

Maybe bumping the msprime version requirement to 0.6.2 or 0.7.0 would help?

@didier-aurelle can you show your msprime version with 

conda list | grep msprime
didier-aurelle commented 5 years ago

Hi, here is what I get: msprime 0.7.0 py36h1f597ea_1 conda-forge apparently I have the right version but as an update, I can now import momi from Python in my bash shell, but I can't do it (same error as above) from my jupyter notebook... Didier

terhorst commented 5 years ago

Can you paste the output of which jupyter?

didier-aurelle commented 5 years ago

here it is: /home/aurelle/anaconda3/bin/jupyter but apparently I found a solution: new installation from jupyter and it works thanks