I have installed ecCodes library with
pip install eccodes
When I check it with 'pip list' it seems like it is installed as 0.9.7 ver but command:
python -m eccodes selfcheck
Returns error
RuntimeError: Could not load the ecCodes library!
The same error occurs when I try to import eccodes. I am using Windows 10 and Python 3.7.6
Any thougths what is wrong?
Full error:
import eccodes
Traceback (most recent call last):
File "<ipython-input-1-cfa7540a6bb2>", line 1, in <module>
import eccodes
File "C:\Users\admin1\anaconda3\lib\site-packages\eccodes\__init__.py", line 15, in <module>
from .eccodes import *
File "C:\Users\admin1\anaconda3\lib\site-packages\eccodes\eccodes.py", line 12, in <module>
from gribapi import __version__
File "C:\Users\admin1\anaconda3\lib\site-packages\gribapi\__init__.py", line 13, in <module>
from .gribapi import * # noqa
File "C:\Users\admin1\anaconda3\lib\site-packages\gribapi\gribapi.py", line 2217, in <module>
__version__ = grib_get_api_version()
File "C:\Users\admin1\anaconda3\lib\site-packages\gribapi\gribapi.py", line 2207, in grib_get_api_version
raise RuntimeError("Could not load the ecCodes library!")
RuntimeError: Could not load the ecCodes library!
The python package eccodes is only a binding to the C library eccodes made by ECMWF.
https://confluence.ecmwf.int/display/ECC/ecCodes+installation
As you can read on this website, they do not support Windows.
Advise from me: you won't get happy reading grib files (and working with meteorological data in general) on Windows. You could consider using Ubuntu or another Linux distro, maybe also just on a VM.
There is a conda package eccodes for the C library:
conda install -c conda-forge eccodes
Alternately, you can install those outside of your conda environment, for example, by compiling from source.
Then there is a pypi package eccodes that contains only the Python bindings:
pip install eccodes
You need both! From your error message, it seems that you have the Python bindings, but not the underlying C library.
For more (slightly dated) information, see the ECMWF Confluence wiki:
https://confluence.ecmwf.int/display/UDOC/How+to+install+ecCodes+with+Python+bindings+in+conda+-+ecCodes+FAQ
Related
So I was able to install sklearn for python2 but for some reason I having issues with doing the same for python3. I am getting this error:
Traceback (most recent call last):
File "/home/ajshack_pg/sklearn/__check_build/__init__.py", line 44, in <module>
from ._check_build import check_build # noqa
ImportError: /home/ajshack_pg/sklearn/__check_build/_check_build.so: undefined symbol: PyUnicodeUCS4_DecodeUTF8
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/ajshack_pg/sklearn/__init__.py", line 133, in <module>
from . import __check_build
File "/home/ajshack_pg/sklearn/__check_build/__init__.py", line 46, in <module>
raise_build_error(e)
File "/home/ajshack_pg/sklearn/__check_build/__init__.py", line 41, in raise_build_error
%s""" % (e, local_dir, ''.join(dir_content).strip(), msg))
ImportError: /home/ajshack_pg/sklearn/__check_build/_check_build.so: undefined symbol: PyUnicodeUCS4_DecodeUTF8
___________________________________________________________________________
Contents of /home/ajshack_pg/sklearn/__check_build:
setup.py setup.pyc __init__.pyc
_check_build.so __init__.py
___________________________________________________________________________
It seems that scikit-learn has not been built correctly.
If you have installed scikit-learn from source, please do not forget
to build the package before using it: run `python setup.py install` or
`make` in the source directory.
If you have used an installer, please check that it is suited for your
Python version, your operating system and your platform.
I tried to go into the source directory and type in what they say to no avail. Any insight here?
Thanks!
If you installed sklearn from source for Python 2.x, some of its binaries may have persisted if you didn't fully remove all sklearn files. Python 2.x and 3.x are quite incompatible with each other, so this might be a reason why it's failing to build.
A few steps to take:
Consider using a virtualenv for your sklearn projects, especially if you have a lot of different packages or Python versions floating around. It's great for keeping different development environments with different Python packages and libraries isolated. Follow this guide if you don't have it already. When creating your virtualenv, make sure to install it with Python 3.x by using this command when creating your virtualenv:
virtualenv -p python3 envname
If building from source: Redownload the sklearn source for your Python 3 version and place it in your virtualenv. Closely follow all build instructions. That should hopefully give you a clean install of sklearn.
If installing with pip: Activate your virtualenv, then:
pip install -U scikit-learn after installing numpy and scipy.
I am trying to install ruamel.yaml python library in a Centos 7 machine where I don't have internet connection. I tried this:
installed libyaml-devel, python-devel, python-pip using a local repository
downloaded ruamel.yaml-0.13.14.tar & ruamel.ordereddict-0.4.6.tar(dependency) from pypi.
now I am able to install ruamel.ordereddict using pip install .,
but when I tried to install ruamel.yaml in the same way, I got the following exception:
[root#limulus ruamel.yaml-0.13.14]# pip install .
Processing /tmp/python/ruamel.yaml-0.13.14
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib/python2.7/site-packages/setuptools/__init__.py", line 2, in <module>
from setuptools.extension import Extension, Library
File "/usr/lib/python2.7/site-packages/setuptools/extension.py", line 5, in <module>
from setuptools.dist import _get_unpatched
File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 7, in <module>
from setuptools.command.install import install
File "/usr/lib/python2.7/site-packages/setuptools/command/__init__.py", line 8, in <module>
from setuptools.command import install_scripts
File "/usr/lib/python2.7/site-packages/setuptools/command/install_scripts.py", line 3, in <module>
from pkg_resources import Distribution, PathMetadata, ensure_directory
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 74, in <module>
import parser
File "parser.py", line 77, in <module>
from ruamel.yaml.error import MarkedYAMLError # type: ignore
File "/usr/lib64/python2.7/site-packages/ruamel/__init__.py", line 5, in <module>
__import__('pkg_resources').declare_namespace(__name__)
AttributeError: 'module' object has no attribute 'declare_namespace'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-oOWX1x-build/
What is the correct way of installing a python library in offline mode?
It looks like you have been expanding the tar files, which is not necessary, but I am not sure if that is the reason why you get this error, you probably are also missing the typing dependency.
What you shouldn't do is use the system installed pip, it is almost out of date and on some systems actually causes problems because of unfixed bugs in those old versions.
What you also should not do is install packages using pip outside of a Python virtualenv, as this might break your system when it updates/overwrites things in the systems site-packages/dist-packages directory. The solution provided below only installs pip/wheels/virtualenv in the system directory, that is AFAIK safe, but there are ways around that as well if it would necessary.
You should also consider using the provided wheels to install packages. That way C extension don't need compilation.
On a machine that is online do:
mkdir /tmp/offline
cd /tmp/offline
# your python-pip installed pip might not support wheels
wget https://pypi.python.org/packages/11/b6/abcb525026a4be042b486df43905d6893fb04f05aac21c32c638e939e447/pip-9.0.1.tar.gz
wget https://pypi.python.org/packages/a7/37/947b4329c4a3c72093b6c8e9b4be8c7f10c32dbb78848d3a234ce01c059d/wheel-0.30.0a0.tar.gz
wget https://pypi.python.org/packages/6f/86/3dc328ee7b1a6419ebfac7896d882fba83c48e3561d22ddddf38294d3e83/virtualenv-15.1.0-py2.py3-none-any.whl
Now download the required wheels (.tar.gz if not available):
wget https://pypi.python.org/packages/96/4b/5251bf469f37e49e0c92f841b5b3ef01a1c9d652cc018df470e5ae235eb8/ruamel.ordereddict-0.4.9-cp27-cp27mu-manylinux1_x86_64.whl
wget https://pypi.python.org/packages/63/40/c38b857ec6a083e534ee9a9f655741120d4bfd9139232681f976cf44272b/ruamel.yaml-0.13.14-cp27-cp27mu-manylinux1_x86_64.whl
wget https://pypi.python.org/packages/b6/0c/53c42edca789378b8c05a5496e689f44e5dd82bc6861d1ae5a926ee51b84/typing-3.5.3.0.tar.gz
Copy the six files to a new directory your offline system, and there do
sudo pip install pip*.tar.gz wheel*.tar.gz
sudo pip install virtualenv*
virtualenv ~/ruamel
source ~/ruamel/bin/activate
pip install typing* ruamel*
That gives you a virtualenv with ruamel.yaml installed, just add your application in there as well.
The downloads used here are current as of 2017-01-07, you can get more up-to-date ones using your browser (on the on-line system) if necessary.
I am using Anaconda. I first switched to Python2 (Version 2.7.11).
python -V
Python 2.7.11 :: Continuum Analytics, Inc.
I used the following command to install xgboost in anaconda.
conda install -c https://conda.anaconda.org/akode xgboost
I then checked that xgboost is installed.
conda list
xgboost 0.3 py27_0 akode
I run python in terminal, import xgboost and got the following errors.
import xgboost as xgb
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "//anaconda/envs/wen2/lib/python2.7/site-packages/xgboost.py", line 82, in <module>
xglib = load_xglib()
File "//anaconda/envs/wen2/lib/python2.7/site-packages/xgboost.py", line 59, in load_xglib
lib = ctypes.cdll.LoadLibrary(lib_path[0])
File "//anaconda/envs/wen2/lib/python2.7/ctypes/__init__.py", line 443, in LoadLibrary
return self._dlltype(name)
File "//anaconda/envs/wen2/lib/python2.7/ctypes/__init__.py", line 365, in __init__
self._handle = _dlopen(self._name, mode)
OSError: dlopen(//anaconda/envs/wen2/lib/python2.7/site-packages/libxgboostwrapper.so, 6): Library not loaded: #rpath/./libgomp.1.dylib
Referenced from: //anaconda/envs/wen2/lib/python2.7/site-packages/libxgboostwrapper.so
Reason: image not found
I have no idea what to do next.
The package image you download is corrupt.
What you should do :
First remove your xgboost package with (in the terminal) :
conda remove xgboost
Then reinstall with an other package at https://anaconda.org/aterrel/xgboost
So just write :
conda install py-xgboost
Then you can check the installation in the python console :
import xgboost
It should be ok.
I had the same error. I completely uninstalled xgboost by pip unistall. then installed it back by:
conda install -c bioconda xgboost=0.6a2
This seems to solve the problem
You first need to build the library through "make", then you can install using anaconda prompt.
First follow the official guide with the following procedure (in Git Bash on Windows):
git clone --recursive https://github.com/dmlc/xgboost
git submodule init
git submodule update
install TDM-GCC here
alias make='mingw32-make'
cp make/mingw64.mk config.mk; make -j4
Last, do the following using anaconda prompt:
cd xgboost\python-package
python setup.py install
Also refer to these great resources:
Official Guide
Installing Xgboost on Windows
Installing XGBoost For Anaconda on Windows
Did you try using pip?
source activate yourenvironment
pip install xgboost
Library not loaded: #rpath/./libgomp.1.dylib
This is the key.
In my case, it is " Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgomp.1.dylib"
I check my path "/usr/local/opt/gcc/lib/gcc"
and there is only a folder named 7 there , no 6.
So i use "sudo find / -name libgomp.1.dylib" to locate all the gcc version i have installed, with I found that there is a version 6 in another location.
Then I create a folder named 6 under '/usr/local/opt/gcc/lib/gcc' and copy those gcc 6 files in there .
Finally , "import xgboost" works with no error .
I had a similar problem
>>> import xgboost
/usr/local/anaconda2/lib/python2.7/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
"This module will be removed in 0.20.", DeprecationWarning)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/anaconda2/lib/python2.7/site-packages/xgboost/__init__.py", line 11, in <module>
from .core import DMatrix, Booster
File "/usr/local/anaconda2/lib/python2.7/site-packages/xgboost/core.py", line 112, in <module>
_LIB = _load_lib()
File "/usr/local/anaconda2/lib/python2.7/site-packages/xgboost/core.py", line 106, in _load_lib
lib = ctypes.cdll.LoadLibrary(lib_path[0])
File "/usr/local/anaconda2/lib/python2.7/ctypes/__init__.py", line 440, in LoadLibrary
return self._dlltype(name)
File "/usr/local/anaconda2/lib/python2.7/ctypes/__init__.py", line 362, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /usr/local/anaconda2/bin/../lib/libgomp.so.1: version `GOMP_4.0' not found (required by /usr/local/anaconda2/lib/python2.7/site-packages/xgboost/./lib/libxgboost.so)
In my case the problem is that i installed xgboost with a regular user. So i did
sudo su
pip uninstall xgboost
pip install xgboost
python
>>> import xgboost
/usr/local/anaconda2/lib/python2.7/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
"This module will be removed in 0.20.", DeprecationWarning)
>>> ~
Hope this can help!
in the my ubuntu 14.04,
first: install anaconda
second: git clone the xgboost, and make and install, complie the python package
third: setup the xgboost with anaconda. for example:
1) cd yourpath/xgboost/python-package
2) find you anaconda python python path:
anaconda/bin/python setup.py install
I am trying to install the base map for use with matplotlib python v2.7 running on Mac OSX Mavericks. I have all the latest versions of all modules (matplotlib, etc) running using anaconda, but keep getting the following error:
Traceback (most recent call last):
File "simpletest.py", line 1, in <module>
from mpl_toolkits.basemap import Basemap
File "/Users/felishalawrence/anaconda/lib/python2.7/site-packages/mpl_toolkits/basemap/__init__.py", line 37, in <module>
import _geoslib.so
ImportError: dlopen(/Users/felishalawrence/anaconda/lib/python2.7/site-packages/_geoslib.so, 2): Library not loaded: libgeos_c.1.dylib
Referenced from: /Users/felishalawrence/anaconda/lib/python2.7/site-packages/_geoslib.so
Reason: no suitable image found. Did find:
/usr/local/bin/gcc-4.9/libgeos_c.1.dylib: stat() failed with errno=20
Can someone please give me an idea of what is wrong? Thanks!
Try installing the following packages with Homebrew:
brew install numpy
brew install proj
brew install geos
export GEOS_DIR="/usr/local/Cellar/geos/3.10.3/"
I'm trying to call a function from the cluster module, like so:
import sklearn
db = sklearn.cluster.DBSCAN()
and I get the following error:
AttributeError: 'module' object has no attribute 'cluster'
Tab-completing in IPython, I seem to have access to the base, clone, externals, re, setup_module, sys, and warning modules. Nothing else, though others (including cluster) are in the sklearn directory.
Following pbu's advice below and using
from sklearn import cluster
I get:
Traceback (most recent call last):
File "test.py", line 2, in <module>
from sklearn import cluster
File "C:\Python34\lib\site-packages\sklearn\cluster\__init__.py", line 6, in <module>
from .spectral import spectral_clustering, SpectralClustering
File "C:\Python34\lib\site-packages\sklearn\cluster\spectral.py", line 13, in <module>
from ..utils import check_random_state, as_float_array
File "C:\Python34\lib\site-packages\sklearn\utils\__init__.py", line 16, in <module>
from .class_weight import compute_class_weight, compute_sample_weight
File "C:\Python34\lib\site-packages\sklearn\utils\class_weight.py", line 7, in <module>
from ..utils.fixes import in1d
File "C:\Python34\lib\site-packages\sklearn\utils\fixes.py", line 318, in <module>
from scipy.sparse.linalg import lsqr as sparse_lsqr
File "C:\Python34\lib\site-packages\scipy\sparse\linalg\__init__.py", line 109, in <module>
from .isolve import *
File "C:\Python34\lib\site-packages\scipy\sparse\linalg\isolve\__init__.py", line 6, in <module>
from .iterative import *
File "C:\Python34\lib\site-packages\scipy\sparse\linalg\isolve\iterative.py", line 7, in <module>
from . import _iterative
ImportError: DLL load failed: The specified module could not be found.
I'm using Python 3.4 on Windows, scikit-learn 0.16.1.
You probably don't use Numpy+MKL, but only Numpy.
I had the same problem and reinstalling Numpy with MKL
pip install --upgrade --force-reinstall "numpy‑1.16.3+mkl‑cp37‑cp37m‑win32.whl"
fixed it.
Note: update the file to the latest version, possibly 64bit - see the list of available Windows binaries
Problem was with scipy/numpy install. I'd been using the (normally excellent!) unofficial installers from http://www.lfd.uci.edu/~gohlke/pythonlibs/. Uninstall/re-install from there made no difference, but installing with the official installers (linked from http://www.scipy.org/install.html) did the trick.
I am using anaconda got the same error as the OP, when loading Orange, or PlotNine.
I can't recall when this start to happen.
Tracing the dependency of Anaconda3\Lib\site-packages\scipy\special\_ufuncs.cp36-win32.pyd, libifcoremd.dll and libmmd.dll are missing in DependencyWalk. Searching them in anaconda root directry, they are located in both ICC_RT and one version of MKL package.
Adding Anaconda3\pkgs\mkl-2017.0.3-0\Library\bin to PATH, seems to fix SciPy and NumPy related DLL load failure, the above package starts to work again.
I still don't know how to fix this properly. Apparently the downside is that the MKL package could be updated and versions may change so does the path. In this aspect Its equally inconvenient as adding a non-managed package.
Reinstalling ICC_RT fixed the issue for me, libmmd.dll and the related dlls are automatically copied into anaconda3/library/bin afterwards, which is automatically added into PATH by activate command. All previous numpy/scipy related cant load DLL errors are gone now.
From the error log, it shows that scipy module is the most recent module fails to import
File "C:\Python34\lib\site-packages\sklearn\utils\fixes.py", line 318, in <module>
from scipy.sparse.linalg import lsqr as sparse_lsqr
File "C:\Python34\lib\site-packages\scipy\sparse\linalg\__init__.py", line 109, in <module>
from .isolve import *
File "C:\Python34\lib\site-packages\scipy\sparse\linalg\isolve\__init__.py", line 6, in <module>
from .iterative import *
File "C:\Python34\lib\site-packages\scipy\sparse\linalg\isolve\iterative.py", line 7, in <module>
from . import _iterative
ImportError: DLL load failed: The specified module could not be found.
I have the same error that show the same log, the problem'd gone when I uninstall/install scipy:
pip uninstall scipy
pip install scipy
Place this line on top of the python file
from sklearn import cluster
That should do it :))
For me what fixed it were these commands:
pip uninstall sklearn
pip uninstall scikit-learn
pip uninstall scipy
pip install scipy
pip install scikit-learnhere
I had the same issue and solved it by installing/updating the mkl package:
conda install mkl
or
pip install mkl
Just for full information, this also downgraded the following packages:
The following packages will be UPDATED:
mkl: 2017.0.4-h6d528fc_0 defaults --> 2018.0.3-1 defaults
The following packages will be DOWNGRADED:
numpy: 1.11.3-py34_0 defaults --> 1.10.1-py34_0 defaults
pandas: 0.19.2-np111py34_1 defaults --> 0.18.1-np110py34_0 defaults
scikit-learn: 0.18.1-np111py34_1 defaults --> 0.17-np110py34_1 defaults
scipy: 0.19.1-np111py34_0 defaults --> 0.16.0-np110py34_0 defaults
I struggled trying to figure this one out; tried to download and install the (unofficial) Numpy+MKL library from the website (risky/tedious?).
Ultimately found success by:
Login to command prompt using admin rights; how to here: https://superuser.com/questions/968214/open-cmd-as-admin-with-windowsr-shortcut
Uninstall existing/tangled version of Scipy & Numpy
pip uninstall scipy
pip uninstall numpy
Fresh install Scipy & Numpy
pip install scipy
pip install numpy
Run Jupyter notebook; it worked for me.
The message ImportError: DLL load failed: The specified module could not be found
informs that there is failure to identify and source the required DLL(s) to use the scikit-learn library; a fresh install of scipy/numpy probably enables a better routing of DLL connections called from Jupyter notebook code(s).
download microsoft visual c++ distribution
link : https://www.microsoft.com/en-in/download/details.aspx?id=53840
vc_redist.x64.exe
install and run this .exe file in your computer.. the DLL import module error will not appear after this
now it will work fine enjoy :)