Comments (8)
It looks like there is a missing mkl symbol -- perhaps an older than expected version of MKL on the system? No real way to debug or productively speculate from here as this gets into Anaconda + MKL territory with which I'm entirely unfamiliar. I can tell you that we have successfully tested with Ananconda on Ubuntu.
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ok, no worries, as far as I know I have the latest anaconda dist, do you know whether you have tested it against the latest version?:
$ conda list | grep -E "mkl|numpy"
mkl 2017.0.1 0
mkl-rt 11.1 p0
mkl-service 1.1.2 py36_3
numpy 1.11.3 py36_0
numpydoc 0.6.0 py36_0
The missing symbol is defined in libmkl_core.so:
$ nm -A /home/joe/anaconda3/lib/libmkl* | grep mkl_pds_lp64_pardiso_getenv_f
/home/joe/anaconda3/lib/libmkl_core.so:0000000000e67d80 T mkl_pds_lp64_pardiso_getenv_f
/home/joe/anaconda3/lib/libmkl_intel_lp64.so: U mkl_pds_lp64_pardiso_getenv_f
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Here's what I get:
$ conda list | grep -E "mkl|numpy"
mkl 2017.0.1 0
numpy 1.11.3 py35_0
$ conda --version
conda 4.2.13
$ ~/anaconda3/bin/python --version
Python 3.5.2 :: Anaconda 4.2.0 (64-bit)
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After updating I now get output that looks more like yours:
conda list | grep -E "mkl|numpy"
mkl 2017.0.1 0
mkl-service 1.1.2 py35_3
numpy 1.11.3 py35_0
numpydoc 0.6.0 py35_0
And things still work.
from reticulate.
For completeness:
$ conda --version
conda 4.3.11
python --version
Python 3.6.0 :: Anaconda custom (64-bit)
Not sure what the 'custom' version is all about.. Looks like the main difference is python 3.5 vs 3.6, which I guess means that this is likely a problem local to my machine? Thanks a lot for following this all up, and doesn't seem like there is an obvious fix so I'll just use the stock python for now.
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I blew away my existing install and re-installed the latest version of Anaconda. Things still work. Here's my Python version info:
$ python --version
Python 3.6.0 :: Anaconda 4.3.0 (64-bit)
So it's something in the "custom" that's doing you in!
I'm going to close this issue. Feel free to re-open if you discover what's going on and think there is something we can do to address this in the package.
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I think I've narrowed down the problem - microsoft r open and anaconda don't play nice together, everything works if I use a different R. Sorry, I should have mentioned I was using R open earlier. I'm happy using a non-anaconda python so please don't re-open this issue on my behalf. Cheers.
from reticulate.
Makes sense since both want to load their own versions of MKL! Glad you figured this out.
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