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ImportError: libmfhdf.so.0: cannot open shared object file (when updating to netcdf4 1.2.4-np111py27_0) #574
Description
Hi all,
I get the error ImportError:libmfhdf.so.0: cannot open shared object file: No such file or directory when my group upgraded netCDF4:
[root@gridlogin-0-0:/share/apps/gnu/Miniconda-3.7.0]# conda update netcdf4
Fetching package metadata .........
Solving package specifications: ..........
Package plan for installation in environment /share/apps/gnu/Miniconda-3.7.0:
The following packages will be downloaded:
package | build
---------------------------|-----------------
curl-7.49.0 | 1 543 KB
The following packages will be UPDATED:
curl: 7.45.0-0 --> 7.49.0-1
hdf5: 1.8.15.1-2 --> 1.8.17-0
libnetcdf: 4.3.3.1-3 --> 4.4.1-0
netcdf4: 1.2.2-np111py27_0 --> 1.2.4-np111py27_0
Here is the error when I attempt to execute from netCDF4 import Dataset:
Python 2.7.12 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:42:40)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> from netCDF4 import Dataset
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Input/WRF_AIC/src/miniconda/lib/python2.7/site-packages/netCDF4/__init__.py", line 3, in <module>
from ._netCDF4 import *
ImportError: libmfhdf.so.0: cannot open shared object file: No such file or directory
Any help would be appreciated.
Our group has reverted to netcdf4 1.2.2 instead as seen below (although we'd like to use the most up to date version):
# packages in environment at /share/apps/gnu/Miniconda-3.7.0:
#
hdf5 1.8.15.1 2
netcdf4 1.2.2 np111py27_0
Thanks
Activity
[-]ImportError: libmfhdf.so.0: cannot open shared object file when updating to netcdf4 1.2.4-np111py27_0[/-][+]ImportError: libmfhdf.so.0: cannot open shared object file (when updating to netcdf4 1.2.4-np111py27_0)[/+]dopplershift commentedon Jul 26, 2016
You might try installing hdf4:
conda install hdf4since that's the package that should be providing that library--I'm not sure why things broke suddenly for you.
Otherwise, I'd send a message to the Anaconda mailing list: https://groups.google.com/a/continuum.io/forum/?fromgroups#!forum/anaconda
We don't maintain the netcdf4 package in anaconda/miniconda, so there's not much else we can do.
rsignell-usgs commentedon Jul 27, 2016
@ajoros , did the problematic package come from the defaults channel, or from conda-forge or another channel?
You can type:
and then you will be able to see what channels your packages came from.
Add hdf4 to requirements file