Open roxyboy opened 8 years ago
Hi,
Could you please run the command "conda list" with your PyNIO environment activated and post the output? I'm curious to see which versions of the dependency packages are installed.
Thanks, Kevin
I have the same issue...
My error is:
ImportError: dlopen(/Users/ajoros/anaconda/envs/py2711/lib/python2.7/site-packages/PyNIO/nio.so, 2): Library not loaded: @rpath/libnetcdf.11.dylib
Referenced from: /Users/ajoros/anaconda/envs/py2711/lib/python2.7/site-packages/PyNIO/nio.so
Reason: Incompatible library version: nio.so requires version 12.0.0 or later, but libnetcdf.11.dylib provides version 11.0.0
@khallock here is my conda list output:
ajoros @ ~/Dropbox/AIC/NWP/MOSarchive/GFSMOS/rawGFSdata * master
[4] → conda list
# packages in environment at /Users/ajoros/anaconda/envs/py2711:
#
appnope 0.1.0 py27_0 defaults
backports-abc 0.4 <pip>
backports.shutil-get-terminal-size 1.0.0 <pip>
backports.shutil_get_terminal_size 1.0.0 py27_0 conda-forge
backports.ssl-match-hostname 3.5.0.1 <pip>
backports_abc 0.4 py27_0 defaults
blas 1.1 openblas conda-forge
bokeh 0.12.0 py27_0 defaults
boto3 1.3.1 py27_0 defaults
botocore 1.4.37 py27_0 defaults
bottleneck 1.1.0 np111py27_0 defaults
click 6.6 py27_0 conda-forge
cloudpickle 0.2.1 py27_2 conda-forge
curl 7.49.1 0 conda-forge
cyordereddict 1.0.0 py27_0 conda-forge
dask 0.10.1 py27_1 conda-forge
decorator 4.0.10 py27_0 conda-forge
distributed 1.11.2 py27_0 conda-forge
docutils 0.12 py27_2 defaults
expat 2.1.0 1 conda-forge
freexl 1.0.2 1 conda-forge
futures 3.0.5 py27_0 defaults
g2clib 1.5.0 4 conda-forge
gdal 1.11.4 np111py27_10 conda-forge
geos 3.4.2 2 conda-forge
giflib 5.1.2 1 conda-forge
h5netcdf 0.2.2 py27_0 conda-forge
h5py 2.6.0 np111py27_4 conda-forge
hdf4 4.2.11 4 conda-forge
hdf5 1.8.17 2 conda-forge
hdfeos2 2.19.1 4 conda-forge
hdfeos5 5.1.15 5 conda-forge
icu 56.1 4 conda-forge
ipython 4.2.0 py27_0 conda-forge
ipython-genutils 0.1.0 <pip>
ipython_genutils 0.1.0 py27_0 defaults
jasper 1.900.1 2 conda-forge
jinja2 2.8 py27_1 defaults
jmespath 0.9.0 py27_0 conda-forge
jpeg 9b 0 conda-forge
json-c 0.12 0 conda-forge
krb5 1.14.2 0 conda-forge
libgcc 4.8.5 1 defaults
libgdal 1.11.2 1 defaults
libgfortran 3.0.0 0 conda-forge
libiconv 1.14 2 conda-forge
libnetcdf 4.4.0 1 conda-forge
libpng 1.6.23 0 conda-forge
libspatialite 4.3.0a 8 conda-forge
libtiff 4.0.6 6 conda-forge
libxml2 2.9.3 9 conda-forge
locket 0.2.0 py27_1 defaults
markupsafe 0.23 py27_2 defaults
msgpack-python 0.4.6 py27_0 defaults
netcdf4 1.2.4 np111py27_2 conda-forge
numpy 1.11.1 py27_blas_openblas_200 [blas_openblas] conda-forge
openblas 0.2.18 3 conda-forge
openjpeg 2.1.0 5 conda-forge
openssl 1.0.2h 1 defaults
pandas 0.18.1 np111py27_0 conda-forge
partd 0.3.4 py27_0 conda-forge
pathlib2 2.1.0 py27_0 conda-forge
pexpect 4.1.0 py27_0 conda-forge
pickleshare 0.7.3 py27_0 conda-forge
pip 8.1.2 py27_0 conda-forge
postgresql 9.5.3 py27_0 conda-forge
proj.4 4.9.2 0 conda-forge
proj4 4.9.2 0 defaults
prompt-toolkit 1.0.3 <pip>
prompt_toolkit 1.0.3 py27_0 conda-forge
psutil 4.3.0 py27_0 conda-forge
ptyprocess 0.5.1 py27_0 conda-forge
pygments 2.1.3 py27_0 defaults
pynio 1.5.0_beta20160623 np111py27_0 dbrown
python 2.7.12 1 defaults
python-dateutil 2.5.3 py27_0 defaults
python.app 1.2 py27_4 <unknown>
pytz 2016.6.1 py27_0 defaults
pyyaml 3.11 py27_4 defaults
readline 6.2 2 <unknown>
requests 2.10.0 py27_0 conda-forge
s3fs 0.0.6 py27_0 conda-forge
scipy 0.17.1 np111py27_blas_openblas_202 [blas_openblas] conda-forge
setuptools 23.0.0 py27_0 conda-forge
simplegeneric 0.8.1 py27_1 defaults
singledispatch 3.4.0.3 py27_0 defaults
six 1.10.0 py27_0 defaults
sqlite 3.13.0 1 conda-forge
ssl_match_hostname 3.5.0.1 py27_0 conda-forge
tblib 1.3.0 py27_0 defaults
tk 8.5.18 0 <unknown>
toolz 0.8.0 py27_0 conda-forge
tornado 4.3 py27_1 defaults
tqdm 4.7.6 py27_0 conda-forge
traitlets 4.2.2 py27_0 conda-forge
wcwidth 0.1.7 py27_0 conda-forge
wheel 0.29.0 py27_0 defaults
xarray 0.7.2 py27_0 conda-forge
xerces-c 3.1.4 2 conda-forge
xz 5.2.2 0 conda-forge
yaml 0.1.6 0 <unknown>
zlib 1.2.8 3 defaults
(py2711)
Hi @ajoros,
Thanks for the "conda list" output. I see that you are using some conda-forge packages in your py2711 conda environment. We have definitely noticed that installing packages from multiple conda channels (dbrown and conda-forge in this case) into the same environment can cause bizarre dependency issues. Specifically, I suspect that the particular "libnetcdf" package (conda-forge) that is installed may have been built with different options than the "pynio" package (dbrown) expects from "libnetcdf" (I believe @david-ian-brown has historically built PyNIO against the "libnetcdf" package from the defaults channel).
We strive to make PyNIO as compatible as possible with other conda packages, but sometimes resolving the dependencies for PyNIO and other complex packages simultaneously can result situations like this.
There is a version of PyNIO that has been included in the conda-forge channel, although we are not the maintainers of that package. This build appears to be based on commit 0f6c689, so it is 4 commits (3 months) out of date. Regardless, I believe that build may work better for you at the moment since you are already using other software from the conda-forge channel.
The following commands should overwrite the currently installed version of the "pynio" package with the conda-forge version (you may need to remove the existing "pynio" package first):
conda remove -n py2711 pynio #may not be necessary
conda install -n py2711 -c conda-forge pynio
I hope this helps!
Kevin
OK, thanks @khallock I think that fixed that issue... But now I get this error (Is it because im missing a library?):
ImportError: dlopen(/Users/ajoros/anaconda/envs/py2711/lib/python2.7/site-packages/PyNIO/nio.so, 2): Library not loaded: @loader_path/./libnetcdf.7.dylib
Referenced from: /Users/ajoros/anaconda/envs/py2711/lib/libgdal.1.dylib
Reason: image not found
My most recent CONDA LIST:
# packages in environment at /Users/ajoros/anaconda/envs/py2711:
#
appnope 0.1.0 py27_0 defaults
backports-abc 0.4 <pip>
backports.shutil-get-terminal-size 1.0.0 <pip>
backports.shutil_get_terminal_size 1.0.0 py27_0 conda-forge
backports.ssl-match-hostname 3.5.0.1 <pip>
backports_abc 0.4 py27_0 defaults
blas 1.1 openblas conda-forge
bokeh 0.12.0 py27_0 defaults
boto3 1.3.1 py27_0 defaults
botocore 1.4.37 py27_0 defaults
bottleneck 1.1.0 np111py27_0 defaults
click 6.6 py27_0 conda-forge
cloudpickle 0.2.1 py27_2 conda-forge
curl 7.49.1 0 conda-forge
cyordereddict 1.0.0 py27_0 conda-forge
dask 0.10.1 py27_1 conda-forge
decorator 4.0.10 py27_0 conda-forge
distributed 1.11.2 py27_0 conda-forge
docutils 0.12 py27_2 defaults
expat 2.1.0 1 conda-forge
freexl 1.0.2 1 conda-forge
futures 3.0.5 py27_0 defaults
g2clib 1.5.0 4 conda-forge
gdal 1.11.4 np111py27_10 conda-forge
geos 3.4.2 2 conda-forge
giflib 5.1.2 1 conda-forge
h5netcdf 0.2.2 py27_0 conda-forge
h5py 2.6.0 np111py27_4 conda-forge
hdf4 4.2.11 4 conda-forge
hdf5 1.8.17 2 conda-forge
hdfeos2 2.19.1 4 conda-forge
hdfeos5 5.1.15 5 conda-forge
icu 56.1 4 conda-forge
ipython 4.2.0 py27_0 conda-forge
ipython-genutils 0.1.0 <pip>
ipython_genutils 0.1.0 py27_0 defaults
jasper 1.900.1 2 conda-forge
jinja2 2.8 py27_1 defaults
jmespath 0.9.0 py27_0 conda-forge
jpeg 9b 0 conda-forge
json-c 0.12 0 conda-forge
krb5 1.14.2 0 conda-forge
libgcc 4.8.5 1 defaults
libgdal 1.11.2 1 defaults
libgfortran 3.0.0 0 conda-forge
libiconv 1.14 2 conda-forge
libnetcdf 4.4.0 1 conda-forge
libpng 1.6.23 0 conda-forge
libspatialite 4.3.0a 8 conda-forge
libtiff 4.0.6 6 conda-forge
libxml2 2.9.3 9 conda-forge
locket 0.2.0 py27_1 defaults
markupsafe 0.23 py27_2 defaults
msgpack-python 0.4.6 py27_0 defaults
netcdf4 1.2.4 np111py27_2 conda-forge
numpy 1.11.1 py27_blas_openblas_200 [blas_openblas] conda-forge
openblas 0.2.18 3 conda-forge
openjpeg 2.1.0 5 conda-forge
openssl 1.0.2h 1 defaults
pandas 0.18.1 np111py27_0 conda-forge
partd 0.3.4 py27_0 conda-forge
pathlib2 2.1.0 py27_0 conda-forge
pexpect 4.1.0 py27_0 conda-forge
pickleshare 0.7.3 py27_0 conda-forge
pip 8.1.2 py27_0 conda-forge
postgresql 9.5.3 py27_0 conda-forge
proj.4 4.9.2 0 conda-forge
proj4 4.9.2 0 defaults
prompt-toolkit 1.0.3 <pip>
prompt_toolkit 1.0.3 py27_0 conda-forge
psutil 4.3.0 py27_0 conda-forge
ptyprocess 0.5.1 py27_0 conda-forge
pygments 2.1.3 py27_0 defaults
pynio 1.5.0beta np111py27_6 conda-forge
python 2.7.12 1 defaults
python-dateutil 2.5.3 py27_0 defaults
python.app 1.2 py27_4 <unknown>
pytz 2016.6.1 py27_0 defaults
pyyaml 3.11 py27_4 defaults
readline 6.2 2 <unknown>
requests 2.10.0 py27_0 conda-forge
s3fs 0.0.6 py27_0 conda-forge
scipy 0.17.1 np111py27_blas_openblas_202 [blas_openblas] conda-forge
setuptools 23.0.0 py27_0 conda-forge
simplegeneric 0.8.1 py27_1 defaults
singledispatch 3.4.0.3 py27_0 defaults
six 1.10.0 py27_0 defaults
sqlite 3.13.0 1 conda-forge
ssl_match_hostname 3.5.0.1 py27_0 conda-forge
tblib 1.3.0 py27_0 defaults
tk 8.5.18 0 <unknown>
toolz 0.8.0 py27_0 conda-forge
tornado 4.3 py27_1 defaults
tqdm 4.7.6 py27_0 conda-forge
traitlets 4.2.2 py27_0 conda-forge
wcwidth 0.1.7 py27_0 conda-forge
wheel 0.29.0 py27_0 defaults
xarray 0.7.2 py27_0 conda-forge
xerces-c 3.1.4 2 conda-forge
xz 5.2.2 0 conda-forge
yaml 0.1.6 0 <unknown>
zlib 1.2.8 3 defaults
(py2711)
Additionally I did a clean install of an xarray environment [And still get the same error] using python 2.7 and xarray using:
conda create -n py2711xr python=2.7.11 xarray
and the conda list results in:
# packages in environment at /Users/ajoros/anaconda/envs/py2711xr:
#
appnope 0.1.0 py27_0 defaults
backports-abc 0.4 <pip>
backports.shutil-get-terminal-size 1.0.0 <pip>
backports.shutil_get_terminal_size 1.0.0 py27_0 conda-forge
backports.ssl-match-hostname 3.5.0.1 <pip>
backports_abc 0.4 py27_0 defaults
bokeh 0.12.0 py27_0 defaults
boto3 1.3.1 py27_0 defaults
botocore 1.4.37 py27_0 defaults
bottleneck 1.0.0 np110py27_1 defaults
click 6.6 py27_0 conda-forge
cloudpickle 0.2.1 py27_2 conda-forge
curl 7.49.1 0 conda-forge
cyordereddict 1.0.0 py27_0 conda-forge
dask 0.10.1 py27_1 conda-forge
decorator 4.0.10 py27_0 conda-forge
distributed 1.11.2 py27_0 conda-forge
docutils 0.12 py27_2 defaults
expat 2.1.0 1 conda-forge
freexl 1.0.2 1 conda-forge
futures 3.0.5 py27_0 defaults
g2clib 1.5.0 4 conda-forge
gdal 2.1.0 np110py27_7 conda-forge
geos 3.4.2 2 conda-forge
giflib 5.1.2 1 conda-forge
h5netcdf 0.2.2 py27_0 conda-forge
h5py 2.6.0 np110py27_4 conda-forge
hdf4 4.2.11 4 conda-forge
hdf5 1.8.17 2 conda-forge
hdfeos2 2.19.1 4 conda-forge
hdfeos5 5.1.15 5 conda-forge
icu 56.1 4 conda-forge
ipython 5.0.0 py27_0 conda-forge
ipython-genutils 0.1.0 <pip>
ipython_genutils 0.1.0 py27_0 defaults
jasper 1.900.1 2 conda-forge
jinja2 2.8 py27_1 defaults
jmespath 0.9.0 py27_0 conda-forge
jpeg 9b 0 conda-forge
json-c 0.12 0 conda-forge
kealib 1.4.6 2 conda-forge
krb5 1.14.2 0 conda-forge
libgcc 4.8.5 1 defaults
libiconv 1.14 2 conda-forge
libnetcdf 4.4.1 0 defaults
libpng 1.6.23 0 conda-forge
libspatialite 4.3.0a 8 conda-forge
libtiff 4.0.6 6 conda-forge
libxml2 2.9.3 9 conda-forge
locket 0.2.0 py27_1 defaults
markupsafe 0.23 py27_2 defaults
mkl 11.3.3 0 defaults
msgpack-python 0.4.6 py27_0 defaults
netcdf4 1.2.4 np110py27_2 conda-forge
numpy 1.10.4 py27_2 defaults
openjpeg 2.1.0 5 conda-forge
openssl 1.0.2h 1 defaults
pandas 0.18.1 np110py27_0 conda-forge
partd 0.3.4 py27_0 conda-forge
pathlib2 2.1.0 py27_0 conda-forge
pexpect 4.1.0 py27_0 conda-forge
pickleshare 0.7.3 py27_0 conda-forge
pip 8.1.2 py27_0 conda-forge
postgresql 9.5.3 py27_0 conda-forge
proj.4 4.9.2 0 conda-forge
prompt-toolkit 1.0.3 <pip>
prompt_toolkit 1.0.3 py27_0 conda-forge
psutil 4.3.0 py27_0 conda-forge
ptyprocess 0.5.1 py27_0 conda-forge
pygments 2.1.3 py27_0 defaults
pynio 1.5.0beta np110py27_0 conda-forge
python 2.7.12 1 defaults
python-dateutil 2.5.3 py27_0 defaults
python.app 1.2 py27_4 <unknown>
pytz 2016.6.1 py27_0 defaults
pyyaml 3.11 py27_4 defaults
readline 6.2 2 <unknown>
requests 2.10.0 py27_0 conda-forge
s3fs 0.0.6 py27_0 conda-forge
scipy 0.17.1 np110py27_1 defaults
setuptools 23.0.0 py27_0 conda-forge
simplegeneric 0.8.1 py27_1 defaults
singledispatch 3.4.0.3 py27_0 defaults
six 1.10.0 py27_0 defaults
sqlite 3.13.0 1 conda-forge
ssl_match_hostname 3.5.0.1 py27_0 conda-forge
tblib 1.3.0 py27_0 defaults
tk 8.5.18 0 <unknown>
toolz 0.8.0 py27_0 conda-forge
tornado 4.3 py27_1 defaults
traitlets 4.2.2 py27_0 conda-forge
wcwidth 0.1.7 py27_0 conda-forge
wheel 0.29.0 py27_0 defaults
xarray 0.7.2 py27_0 conda-forge
xerces-c 3.1.4 2 conda-forge
xz 5.2.2 0 conda-forge
yaml 0.1.6 0 <unknown>
zlib 1.2.8 3 defaults
(py2711xr)
I may have solved it. This was my order of installation, even after adding the conda-forge channel:
conda create -n py2711xr python=2.7
conda config --add channels conda-forge
source activate py2711xr
conda install xarray dask netCDF4 bottleneck
I also installed ipython to test out the grb loading process and executed this line:
test=xr.open_dataset('gfs.t12z.pgrb2.0p25.f060.grb', engine='pynio')
The variable "test" now outputs the following:
Out[5]:
<xarray.Dataset>
Dimensions: (lat_0: 721, lon_0: 1440, lv_AMSL1: 3, lv_DBLL12: 4, lv_HTGL2: 3, lv_HTGL4: 2, lv_HTGL7: 3, lv_ISBL0: 31, lv_ISBL10: 17, lv_ISBL11: 19, lv_ISBL6: 21, lv_ISBL8: 26, lv_PVL3: 2, lv_SIGL5: 4, lv_SPDL9: 2)
Coordinates:
* lv_ISBL11 (lv_ISBL11) float32 10000.0 15000.0 20000.0 ...
* lv_ISBL10 (lv_ISBL10) float32 100.0 200.0 300.0 500.0 ...
* lv_ISBL8 (lv_ISBL8) float32 1000.0 2000.0 3000.0 5000.0 ...
* lv_HTGL4 (lv_HTGL4) float32 2.0 80.0
* lv_ISBL0 (lv_ISBL0) float32 100.0 200.0 300.0 500.0 ...
* lv_HTGL7 (lv_HTGL7) float32 10.0 80.0 100.0
* lv_HTGL2 (lv_HTGL2) float32 2.0 80.0 100.0
* lv_ISBL6 (lv_ISBL6) float32 10000.0 15000.0 20000.0 ...
* lat_0 (lat_0) float32 90.0 89.75 89.5 89.25 89.0 ...
* lon_0 (lon_0) float32 0.0 0.25 0.5 0.75 1.0 1.25 1.5 ...
* lv_PVL3 (lv_PVL3) float32 -2e-06 2e-06
* lv_AMSL1 (lv_AMSL1) float32 1829.0 2743.0 3658.0
* lv_DBLL12 (lv_DBLL12) int64 0 1 2 3
* lv_SIGL5 (lv_SIGL5) int64 0 1 2 3
* lv_SPDL9 (lv_SPDL9) int64 0 1
Data variables:
APCP_P8_L1_GLL0_acc6h (lat_0, lon_0) float64 0.0 0.0 0.0 0.0 0.0 0.0 ...
TOZNE_P0_L200_GLL0 (lat_0, lon_0) float64 301.8 301.8 301.8 301.8 ...
PRES_P0_L242_GLL0 (lat_0, lon_0) float64 nan nan nan nan nan nan ...
VFLX_P8_L1_GLL0_avg6h (lat_0, lon_0) float64 -0.001 -0.001 -0.001 ...
HGT_P0_L100_GLL0 (lv_ISBL0, lat_0, lon_0) float64 4.971e+04 ...
VVEL_P0_L100_GLL0 (lv_ISBL6, lat_0, lon_0) float64 0.0 0.0 0.0 ...
ULWRF_P8_L1_GLL0_avg6h (lat_0, lon_0) float64 313.0 313.0 313.0 313.0 ...
UGRD_P0_L6_GLL0 (lat_0, lon_0) float64 -3.6 -3.7 -3.7 -3.7 ...
HGT_P0_L7_GLL0 (lat_0, lon_0) float64 1.003e+04 1.003e+04 ...
To whom it may concern,
I have tried installing pynio on my Mac osX system by running
conda install -c dbrown pynio
. The results give:so it seems to be installed. However, when I try to import Nio, an error shows up as:
I looked for the libnetcdf.11.dylib library by running
otool -L /(package_path)/PyNIO/nio.so
, which shows that it is downloaded:Could you please tell me how to resolve this issue? Thank you very much for your attention and support.