Error while importing

[blankjul]

I have two machines I am working on. On my mac everything works fine. On the hpcc of my university I am not able to run the same script. The following error message while importing GPy is shown:

ImportError: miniconda3/lib/python3.6/site-packages/GPy/util/linalg_cython.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _Py_ZeroStruct

uname -a
Linux dev-intel16-k80 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

To reproduce the error I used a clean version of miniconda3 and executed pip install GPy to see if any side effects cause the problem. But I still run into the same error.

Traceback (most recent call last):
  File "test.py", line 1, in <module>
    import GPy
  File "miniconda3-clean/lib/python3.6/site-packages/GPy/__init__.py", line 6, in <module>
    from . import core
  File "miniconda3-clean/lib/python3.6/site-packages/GPy/core/__init__.py", line 8, in <module>
    from .gp import GP
  File "miniconda3-clean/lib/python3.6/site-packages/GPy/core/gp.py", line 8, in <module>
    from .. import likelihoods
  File "miniconda3-clean/lib/python3.6/site-packages/GPy/likelihoods/__init__.py", line 1, in <module>
    from .bernoulli import Bernoulli
  File "miniconda3-clean/lib/python3.6/site-packages/GPy/likelihoods/bernoulli.py", line 5, in <module>
    from ..util.univariate_Gaussian import std_norm_pdf, std_norm_cdf, derivLogCdfNormal, logCdfNormal
  File "miniconda3-clean/lib/python3.6/site-packages/GPy/util/__init__.py", line 5, in <module>
    from . import linalg
  File "miniconda3-clean/lib/python3.6/site-packages/GPy/util/linalg.py", line 15, in <module>
    from . import linalg_cython
ImportError: miniconda3-clean/lib/python3.6/site-packages/GPy/util/linalg_cython.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _Py_ZeroStruct

asn1crypto                0.22.0           py36h265ca7c_1
ca-certificates           2017.08.26           h1d4fec5_0
certifi                   2017.7.27.1      py36h8b7b77e_0
cffi                      1.10.0           py36had8d393_1
chardet                   3.0.4            py36h0f667ec_1
conda                     4.3.27           py36h2866c0b_0
conda-env                 2.6.0                h36134e3_1
cryptography              2.0.3            py36ha225213_1
decorator                 4.1.2                     <pip>
GPy                       1.8.4                     <pip>
idna                      2.6              py36h82fb2a8_1
libedit                   3.1                  heed3624_0
libffi                    3.2.1                h4deb6c0_3
libgcc-ng                 7.2.0                hcbc56d2_1
libstdcxx-ng              7.2.0                h24385c6_1
ncurses                   6.0                  h06874d7_1
numpy                     1.13.3                    <pip>
openssl                   1.0.2l               h9d1a558_3
paramz                    0.8.5                     <pip>
pip                       9.0.1            py36h30f8307_2
pycosat                   0.6.2            py36h1a0ea17_1
pycparser                 2.18             py36hf9f622e_1
pyopenssl                 17.2.0           py36h5cc804b_0
pysocks                   1.6.7            py36hd97a5b1_1
python                    3.6.2               hdfe5801_15
readline                  7.0                  hac23ff0_3
requests                  2.18.4           py36he2e5f8d_1
ruamel_yaml               0.11.14          py36ha2fb22d_2
scipy                     0.19.1                    <pip>
setuptools                36.5.0           py36he42e2e1_0
six                       1.10.0           py36hcac75e4_1
sqlite                    3.20.1               h6d8b0f3_1
tk                        8.6.7                h5979e9b_1
urllib3                   1.22             py36hbe7ace6_0
wheel                     0.29.0           py36he7f4e38_1
xz                        5.2.3                h2bcbf08_1
yaml                      0.1.7                h96e3832_1
zlib                      1.2.11               hfbfcf68_1

Any idea what might cause this error?

Thanks in advance, Julian

[zhenwendai]

With some searching on Internet, it seems that it might because the Python environment used to compile GPy is different from the Python environment used to run.

[mzwiessele]

Has this been resolved with the newest version of GPy?