Iris for Anaconda, fails to read .grib

Question

I've just downloaded Iris and am trying to view the contents of a .grib file. I have tried a very simple bit of code below but get a selection of errors. Can anyone see what might be causing the problems?

Thanks

import iris

fn='C:\Users\mmso2\Desktop\grib files ECMWF\2006\_mars-atls17-95e2cf679cd58ee9b4db4dd119a05a8d-GOnSTm.grib'
cubes = iris.load(fn)

errors:

C:\Anaconda2\python.exe "C:/Users/mmso2/Google Drive/MABL Wind/_Semester 2 2016/_PGR Training/CENTA/MATLAB/In class ex/SAR_data/grib_files_check.py"
Traceback (most recent call last):
  File "C:/Users/mmso2/Google Drive/MABL Wind/_Semester 2 2016/_PGR Training/CENTA/MATLAB/In class ex/SAR_data/grib_files_check.py", line 2, in <module>
    import iris
  File "C:\Anaconda2\lib\site-packages\iris\__init__.py", line 110, in <module>
    import iris.cube
  File "C:\Anaconda2\lib\site-packages\iris\cube.py", line 39, in <module>
    import iris.analysis
  File "C:\Anaconda2\lib\site-packages\iris\analysis\__init__.py", line 61, in <module>
    from iris.analysis._area_weighted import AreaWeightedRegridder
  File "C:\Anaconda2\lib\site-packages\iris\analysis\_area_weighted.py", line 23, in <module>
    from iris.analysis._interpolation import get_xy_dim_coords, snapshot_grid
  File "C:\Anaconda2\lib\site-packages\iris\analysis\_interpolation.py", line 31, in <module>
    from iris.analysis.cartography import wrap_lons as wrap_circular_points
  File "C:\Anaconda2\lib\site-packages\iris\analysis\cartography.py", line 29, in <module>
    import cf_units
  File "C:\Anaconda2\lib\site-packages\cf_units\__init__.py", line 394, in <module>
    _status_msg, _error_msg))
OSError: [UT_OPEN_ARG] Failed to open UDUNITS-2 XML unit database : "No such file or directory"

Process finished with exit code 1

Update: Conda environment

# packages in environment at C:\Anaconda2:
#
Using Anaconda Cloud api site https://api.anaconda.org
alabaster                 0.7.7                    py27_0    defaults
anaconda                  4.0.0               np110py27_0    defaults
anaconda-client           1.4.0                    py27_0    defaults
anaconda-navigator        1.1.0                    py27_0    defaults
basemap                   1.0.7               np110py27_0    anaconda
argcomplete               1.0.0                    py27_1    defaults
astropy                   1.1.2               np110py27_0    defaults
babel                     2.2.0                    py27_0    defaults
backports_abc             0.4                      py27_0    defaults
beautifulsoup4            4.4.1                    py27_0    defaults
bitarray                  0.8.1                    py27_1    defaults
blaze                     0.9.1                    py27_0    defaults
bokeh                     0.11.1                   py27_0    defaults
boto                      2.39.0                   py27_0    defaults
bottleneck                1.0.0               np110py27_0    defaults
bzip2                     1.0.6                     vc9_2  [vc9]  defaults
cdecimal                  2.3                      py27_1    defaults
cffi                      1.5.2                    py27_0    defaults
chest                     0.2.3                    py27_0    defaults
cloudpickle               0.1.1                    py27_0    defaults
clyent                    1.2.1                    py27_0    defaults
colorama                  0.3.7                    py27_0    defaults
comtypes                  1.1.2                    py27_0    defaults
conda                     4.1.11                   py27_0    defaults
conda-build               1.20.0                   py27_0    defaults
conda-env                 2.5.2                    py27_0    defaults
conda-manager             0.3.1                    py27_0    defaults
configobj                 5.0.6                    py27_0    defaults
console_shortcut          0.1.1                    py27_1    defaults
cryptography              1.3                      py27_0    defaults
curl                      7.45.0                    vc9_1  [vc9]  defaults
cycler                    0.10.0                   py27_0    defaults
cython                    0.23.4                   py27_0    defaults
cytoolz                   0.7.5                    py27_0    defaults
dask                      0.8.1                    py27_0    defaults
datashape                 0.5.1                    py27_0    defaults
decorator                 4.0.9                    py27_0    defaults
dill                      0.2.4                    py27_0    defaults
docutils                  0.12                     py27_1    defaults
ecmwf-api-client          1.4.1                     <pip>
enum34                    1.1.2                    py27_0    defaults
et_xmlfile                1.0.1                    py27_0    defaults
fastcache                 1.0.2                    py27_0    defaults
flask                     0.10.1                   py27_1    defaults
flask-cors                2.1.2                    py27_0    defaults
freetype                  2.5.5                     vc9_0  [vc9]  defaults
funcsigs                  0.4                      py27_0    defaults
futures                   3.0.3                    py27_0    defaults
geos                      3.5.0                     vc9_0  [vc9]  defaults
gevent                    1.1.0                    py27_0    defaults
greenlet                  0.4.9                    py27_0    defaults
grin                      1.2.1                    py27_2    defaults
h5py                      2.5.0               np110py27_4    defaults
hdf5                      1.8.15.1                  vc9_4  [vc9]  defaults
heapdict                  1.0.0                    py27_0    defaults
idna                      2.0                      py27_0    defaults
ipaddress                 1.0.14                   py27_0    defaults
ipykernel                 4.3.1                    py27_0    defaults
ipython                   4.1.2                    py27_1    defaults
ipython_genutils          0.1.0                    py27_0    defaults
ipywidgets                4.1.1                    py27_0    defaults
itsdangerous              0.24                     py27_0    defaults
jdcal                     1.2                      py27_0    defaults
jedi                      0.9.0                    py27_0    defaults
jinja2                    2.8                      py27_0    defaults
jpeg                      8d                        vc9_0  [vc9]  defaults
jsonschema                2.4.0                    py27_0    defaults
jupyter                   1.0.0                    py27_2    defaults
jupyter_client            4.2.2                    py27_0    defaults
jupyter_console           4.1.1                    py27_0    defaults
jupyter_core              4.1.0                    py27_0    defaults
libpng                    1.6.17                    vc9_1  [vc9]  defaults
libsodium                 1.0.3                         0    defaults
libtiff                   4.0.6                     vc9_1  [vc9]  defaults
llvmlite                  0.9.0                    py27_0    defaults
locket                    0.2.0                    py27_0    defaults
lxml                      3.6.0                    py27_0    defaults
markupsafe                0.23                     py27_1    defaults
matplotlib                1.5.1               np110py27_0    defaults
menuinst                  1.3.2                    py27_0    defaults
mistune                   0.7.2                    py27_0    defaults
mkl                       11.3.1                        0    defaults
mkl-service               1.1.2                    py27_0    defaults
mock                      1.3.0                    py27_0    defaults
mpmath                    0.19                     py27_0    defaults
multipledispatch          0.4.8                    py27_0    defaults
nbconvert                 4.1.0                    py27_0    defaults
nbformat                  4.0.1                    py27_0    defaults
netcdf4                   1.2.2               np110py27_0    defaults
netCDF4                   1.2.4                     <pip>
networkx                  1.11                     py27_0    defaults
nltk                      3.2                      py27_0    defaults
nose                      1.3.7                    py27_0    defaults
notebook                  4.1.0                    py27_2    defaults
numba                     0.24.0              np110py27_0    defaults
numexpr                   2.5                 np110py27_0    defaults
numpy                     1.10.4                   py27_0    defaults
odo                       0.4.2                    py27_0    defaults
openpyxl                  2.3.2                    py27_0    defaults
openssl                   1.0.2g                    vc9_0  [vc9]  defaults
pandas                    0.18.0              np110py27_0    defaults
partd                     0.3.2                    py27_1    defaults
path.py                   8.1.2                    py27_1    defaults
patsy                     0.4.0               np110py27_0    defaults
pbr                       1.3.0                    py27_0    defaults
pep8                      1.7.0                    py27_0    defaults
pickleshare               0.5                      py27_0    defaults
pillow                    3.1.1                    py27_0    defaults
pip                       8.1.2                    py27_0    defaults
ply                       3.8                      py27_0    defaults
psutil                    4.1.0                    py27_0    defaults
py                        1.4.31                   py27_0    defaults
pyasn1                    0.1.9                    py27_0    defaults
pycosat                   0.6.1                    py27_0    defaults
pycparser                 2.14                     py27_0    defaults
pycrypto                  2.6.1                    py27_3    defaults
pyflakes                  1.1.0                    py27_0    defaults
pygments                  2.1.1                    py27_0    defaults
pyopenssl                 0.15.1                   py27_2    defaults
pyparsing                 2.0.3                    py27_0    defaults
pyproj                    1.9.5.1                  py27_0    defaults
pyqt                      4.11.4                   py27_5    defaults
pyreadline                2.1                      py27_0    defaults
pytables                  3.2.2               np110py27_2    defaults
pytest                    2.8.5                    py27_0    defaults
python                    2.7.12                        0    defaults
python-dateutil           2.5.1                    py27_0    defaults
python-hdf4               0.9                       <pip>
pytz                      2016.2                   py27_0    defaults
pywin32                   220                      py27_1    defaults
pyyaml                    3.11                     py27_3    defaults
pyzmq                     15.2.0                   py27_0    defaults
qt                        4.8.7                     vc9_7  [vc9]  defaults
qtawesome                 0.3.2                    py27_0    defaults
qtconsole                 4.2.0                    py27_1    defaults
qtpy                      1.0                      py27_0    defaults
requests                  2.9.1                    py27_0    defaults
rope                      0.9.4                    py27_1    defaults
ruamel_yaml               0.11.7                   py27_0    defaults
scikit-image              0.12.3              np110py27_0    defaults
scikit-learn              0.17.1              np110py27_0    defaults
scipy                     0.17.0              np110py27_0    defaults
biggus                    0.14.0                   py27_0    scitools
cartopy                   0.14.2              np110py27_0    scitools
cf_units                  1.1                      py27_0    scitools
expat                     2.1.0                         6    scitools
iris                      1.9.2               np110py27_0    scitools
owslib                    0.10.3                   py27_0    scitools
proj.4                    4.9.1                    py27_1    scitools
pyepsg                    0.2.0                    py27_0    scitools
pyke                      1.1.1                    py27_1    scitools
pyshp                     1.2.3                    py27_0    scitools
shapely                   1.5.13              np110py27_1    scitools
udunits2                  2.2.20                        0    scitools
setuptools                20.3                     py27_0    defaults
simplegeneric             0.8.1                    py27_0    defaults
singledispatch            3.4.0.3                  py27_0    defaults
sip                       4.16.9                   py27_2    defaults
six                       1.10.0                   py27_0    defaults
snowballstemmer           1.2.1                    py27_0    defaults
sockjs-tornado            1.0.1                    py27_0    defaults
sphinx                    1.3.5                    py27_0    defaults
sphinx_rtd_theme          0.1.9                    py27_0    defaults
spyder                    2.3.8                    py27_1    defaults
sqlalchemy                1.0.12                   py27_0    defaults
ssl_match_hostname        3.4.0.2                  py27_0    defaults
statsmodels               0.6.1               np110py27_0    defaults
sympy                     1.0                      py27_0    defaults
tk                        8.5.18                    vc9_0  [vc9]  defaults
toolz                     0.7.4                    py27_0    defaults
tornado                   4.3                      py27_0    defaults
traitlets                 4.2.1                    py27_0    defaults
unicodecsv                0.14.1                   py27_0    defaults
vs2008_runtime            9.00.30729.1                  0    defaults
vs2010_runtime            10.00.40219.1                 0    defaults
werkzeug                  0.11.4                   py27_0    defaults
wheel                     0.29.0                   py27_0    defaults
xlrd                      0.9.4                    py27_0    defaults
xlsxwriter                0.8.4                    py27_0    defaults
xlwings                   0.7.0                    py27_0    defaults
xlwt                      1.0.0                    py27_0    defaults
zlib                      1.2.8                     vc9_2  [vc9]  defaults

Would you mind sharing your conda environment? ``conda list --show-channel-urls`` — pelson, Aug 16 '16 at 16:35

score 3 · Answer 1 · answered Aug 17 '16 at 09:55

Unfortunately this is currently a known issue (on Windows) with cf_units on Anaconda cloud: see this conda-recipes-scitools GitHub issue. The bottom comment in this issue contains a workaround for this: notice the extra 'Library' string in the path for _alt_xml_path. This is actually the entirety of the problem: the UDUNITS2 XML file is installed in a subtly different location on Windows than it is on Linux or OSX. You can apply the same workaround by modifying your file C:\Anaconda2\lib\site-packages\cf_units\__init__.py in the same way, assuming you have write permissions to this file.

Please note that even then you unfortunately cannot currently load GRIB files using Iris on Windows. This is because the ECMWF grib_api, which underlies Iris' GRIB capabilities, cannot itself currently be installed on Windows.

Incidentally, none of these are issues on a Unix-like system, so if you have access to a Linux or OSX system may I suggest that you try viewing your GRIB file on one of them instead? Should it be helpful, VirtualBox is a good and fairly simple way of getting Linux running in a Virtual Machine under Windows.

By the way, cf_units v1.1.1 (which includes the XML path fix) is available now on [PyPI](https://pypi.python.org/pypi/cf_units/1.1.1). You can install this into your conda environment by typing the following on the Windows command-line: `pip install cf_units --upgrade` Here the `--upgrade` flag notifies conda that you intend to upgrade the existing cf_units you installed. This should solve your cf_units XML issue at least! — DPeterK, Aug 17 '16 at 10:46

Iris for Anaconda, fails to read .grib

1 Answers1