Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure

[Pablo C. <pc...@cn...>]

Hi Wolfgang.

This error also happens (actually yesterday)  when there is something in 
PYTHONPATH variable pointing to old scipion2 paths. Could this be your case?

Could you send the output of:

echo $LD_LIBRARY_PATH

echo $PYTHONPATH


NOTE: If you look inside "scipion3" launcher it it a small python script 
setting up the environment and is "conserving" the content of both 
variables. To be honest, I do not see a strong reason for this or the 
opposite, but if this is the case, not conserving the values would work:

You should have this:

os.environ["LD_LIBRARY_PATH"] = 
":".join([os.environ.get("LD_LIBRARY_PATH", ""), join(scipionHome, 
"software", "lib")])
os.environ["PYTHONPATH"] = ":".join([os.environ.get("PYTHONPATH", ""), 
join(scipionHome, "software", "bindings")])

Suggested change:

os.environ["LD_LIBRARY_PATH"] =  join(scipionHome, "software", "lib")
os.environ["PYTHONPATH"] = join(scipionHome, "software", "bindings")

But not sure if this is your case.


On 2/10/20 10:49, Lugmayr, Wolfgang wrote:
> Hi,
>
> I have a problem with xmipp_cuda_movie_alignment_correlation dying with Signal 6 and before posting I tried to update xmipp yesterday.
>
> I updated xmipp via the plugin manager (together with the scipion-em-tomo package).
> Now i get the error message below.
>
> Starting "scipion3 last" prints the following:_
>
> $ scipion3
> Scipion v3.0.3 () devel
>
>   >>> WARNING: Image library not found!
>    > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
>
>
>   > error when importing from xmipp3.protocols: cannot import name 'isMdEmpty' from 'xmipp3.base' (/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/base.py)
>     File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
>     Check the plugin manager (Configuration->Plugins in Scipion manager window)
>     or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
>     it could be a versions compatibility issue.
>
> Here are the xmipp infos:
> scipion-em-tomo                3.0.6      [X]
> scipion-em-xmipp               20.7rc1    [X]
> scipion-em-xmipp2              3.0.0      [X]
>
> I think the hint should be now:
> scipion3 installp --help --checkUpdates
>
> Cheers,
> Wolfgang
>
>
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*