undefined symbol: mkl_pds_lp64_pardiso_getenv_f when using anaconda python about reticulate HOT 8 CLOSED

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.

from reticulate.

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

from reticulate.

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)

from reticulate.

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.

from reticulate.

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.

from reticulate.

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.

from reticulate.