Comments (5)
On a fresh DSVM, I pip-installed CNTK and then did the following:
> py_config()
Error in py_run_string_impl(paste0("import sys; sys.path.append('", system.file("python", :
ImportError:
Importing the multiarray numpy extension module failed. Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control). Otherwise reinstall numpy.
Detailed traceback:
File "/home/alizaidi/.conda/envs/cntk-py35/lib/python3.5/site-packages/numpy/__init__.py", line 146, in <module>
from . import add_newdocs
File "/home/alizaidi/.conda/envs/cntk-py35/lib/python3.5/site-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/home/alizaidi/.conda/envs/cntk-py35/lib/python3.5/site-packages/numpy/lib/__init__.py", line 8, in <module>
from .type_check import *
File "/home/alizaidi/.conda/envs/cntk-py35/lib/python3.5/site-packages/numpy/lib/type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "/home/alizaidi/.conda/envs/cntk-py35/lib/python3.5/site-packages/numpy/core/__init__.p
> q()
(cntk-py35) alizaidi@azcntkr:~$ pip install -U numpy
Collecting numpy
Downloading numpy-1.13.1-cp35-cp35m-manylinux1_x86_64.whl (16.9MB)
100% |████████████████████████████████| 16.9MB 87kB/s
Installing collected packages: numpy
Found existing installation: numpy 1.12.1
Uninstalling numpy-1.12.1:
Successfully uninstalled numpy-1.12.1
Successfully installed numpy-1.13.1
(cntk-py35) alizaidi@azcntkr:~$ R
R version 3.3.3 (2017-03-06) -- "Another Canoe"
> library(reticulate)
> use_condaenv("cntk-py35")
> py_config()
python: /home/alizaidi/.conda/envs/cntk-py35/bin/python
libpython: /home/alizaidi/.conda/envs/cntk-py35/lib/libpython3.5m.so
pythonhome: /home/alizaidi/.conda/envs/cntk-py35:/home/alizaidi/.conda/envs/cntk-py35
version: 3.5.3 |Anaconda 4.4.0 (64-bit)| (default, Mar 6 2017, 11:58:13) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
numpy: /home/alizaidi/.conda/envs/cntk-py35/lib/python3.5/site-packages/numpy
numpy_version: 1.13.1
python versions found:
/home/alizaidi/.conda/envs/cntk-py35/bin/python
/usr/bin/python
/usr/bin/python3
> reticulate::py_module_available("cntk")
[1] TRUE
One difference now appears to be anaconda3
vs 2.7, but I don't think that's the issue. I'll keep looking.
from cntk-r.
Additional information:
adevries@adv-ug-dsvm-1708:~$ source activate cntk-py35
(cntk-py35) adevries@adv-ug-dsvm-1708:~$ python
Python 3.5.4 |Continuum Analytics, Inc.| (default, Aug 14 2017, 13:26:58)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cntk
>>> print(cntk.__version__)
2.1
>>> exit()
(cntk-py35) adevries@adv-ug-dsvm-1708:~$ pip install -U numpy
Requirement already up-to-date: numpy in ./anaconda3/envs/cntk-py35/lib/python3.5/site-packages
(cntk-py35) adevries@adv-ug-dsvm-1708:~$ pip freeze
cntk==2.1
h5py==2.7.0
numpy==1.13.1
scipy==0.19.1
six==1.10.0
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reticulate_1.1.0.9002 RevoUtilsMath_10.0.0 RevoUtils_10.0.3 RevoMods_11.0.0
[5] MicrosoftML_1.3.0 RevoScaleR_9.1.0 lattice_0.20-34 rpart_4.1-10
loaded via a namespace (and not attached):
[1] Rcpp_0.12.12 codetools_0.2-15 CompatibilityAPI_1.1.0 foreach_1.4.3
[5] grid_3.3.3 R6_2.2.0 jsonlite_1.3 iterators_1.0.8
[9] tools_3.3.3 mrupdate_1.0.1
from cntk-r.
I don't understand this. I created a new DSVM, followed these instructions, and I get:
> use_condaenv("cntk-py35")
Error: Unable to find conda binary. Is Anaconda installed?
If I also specify the conda environment, then I don't get an error, but R points to python 2.7
> use_condaenv("cntk-py35", conda = "/home/adevries/.conda/envs/cntk-py35/bin/conda", required = TRUE)
> py_config()
python: /usr/bin/python
libpython: /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so
pythonhome: /usr:/usr
version: 2.7.12 (default, Nov 19 2016, 06:48:10) [GCC 5.4.0 20160609]
numpy: [NOT FOUND]
python versions found:
/usr/bin/python
/usr/bin/python3
I also don't understand how conda decides where to put the envs:
(cntk-py35) adevries@adv-ug-dsvm-1709:~$ conda env list
# conda environments:
#
cntk-py35 * /home/adevries/.conda/envs/cntk-py35
py35 /anaconda/envs/py35
root /anaconda
from cntk-r.
I tried again, this time forcing a reinstall of numpy
, and now it seems to work:
pip install --upgrade --force-reinstall numpy
from cntk-r.
Hi @andrie, is it OK to close this issue?
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