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

[David M. <dma...@cn...>]

Hi Wolfgang,

After updating the scipion-em-xmipp plugin, it is necessary to install also
the xmippSrc-3.20.07rc1 bundle using the plugin manager or via

*scipion3 installb xmippSrc -j 8*


Also, you can check

scipion3 config -p xmipp3


it prints the XMIPP_HOME detected (usually ...scipion3/software/em/xmipp) ,
then check that path via

ls -l <XMIPP_HOME>    # replace <XMIPP_HOME> for your value


it should be a link pointing to xmipp-3.20.07rc1/build


Thanks for reporting,

Cheers.

<http://ucm.es/>

*_____Dr. David Maluenda Niubó*
dma...@cn... - (+34) 619 029 310
CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

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On Fri, Oct 2, 2020 at 11:30 AM Pablo Conesa <pc...@cn...> wrote:

> 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*
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