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Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure
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From: Pablo C. <pc...@cn...> - 2020-10-02 11:35:02
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Thanks Wolfgang!
There is something on our side that I think is not smooth when updating
xmipp. I think we need to review this case.
On 2/10/20 12:43, Lugmayr, Wolfgang wrote:
> Hi,
>
> I fixed it. I deleted the extracted xmipp b1 version and put some path
> to the scipion module.
> Now the error disappeared.
>
> $ m show scipion
> -------------------------------------------------------------------
> /beegfs/cssb/software/modulefiles/em/scipion/3.0-dev:
>
> module-whatis development version, default build
> module load deps/gcc8-openmpi4-cuda10
> prepend-path PATH /beegfs/cssb/software/em/scipion/3.0/devel
> setenv SCIPION_HOME /beegfs/cssb/software/em/scipion/3.0/devel
> prepend-path PYTHONPATH
> /beegfs/cssb/software/em/scipion/3.0/devel/software/em/xmipp/pylib
> prepend-path PYTHONPATH
> /beegfs/cssb/software/em/scipion/3.0/devel/software/em/xmipp/bindings/python
>
>
> Cheers,
> Wolfgang
>
>
> ------------------------------------------------------------------------
> *From: *"Lugmayr, Wolfgang" <w.l...@uk...>
> *To: *"Mailing list for Scipion users"
> <sci...@li...>
> *Sent: *Friday, 2 October, 2020 12:28:34
> *Subject: *Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure
>
> Hi,
>
> in software/em xmipp pointed to
> xmipp -> xmippSrc-v3.20.07b1/build/
> I fixed it by hand to
> xmipp -> xmippSrc-v3.20.07rc/build/
> but the message still comes.
>
> $ m show scipion
> -------------------------------------------------------------------
> /beegfs/cssb/software/modulefiles/em/scipion/3.0-dev:
>
> module-whatis development version, default build
> module load deps/gcc8-openmpi4-cuda10
> prepend-path PATH /beegfs/cssb/software/em/scipion/3.0/devel
> setenv SCIPION_HOME /beegfs/cssb/software/em/scipion/3.0/devel
> -------------------------------------------------------------------
>
> $ m load scipion
> CUDA 10.1 loaded
>
> $ echo $LD_LIBRARY_PATH
> /beegfs/cssb/software/devel/gcc/8.4.0/lib64:/beegfs/cssb/software/devel/mpc/1.0.3/lib:/beegfs/cssb/software/devel/mpfr/3.1.4/lib:/beegfs/cssb/software/devel/hwloc/2.1.0/lib:/beegfs/cssb/software/devel/ucx/1.8.0/lib:/beegfs/cssb/software/devel/openmpi/4.0.3/lib:/usr/local/cuda-10.1/lib64
>
> $ echo $PATHONPATH
>
> $ 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.
>
> Cheers,
> Wolfgang
>
>
> ------------------------------------------------------------------------
> *From: *"Pablo Conesa" <pc...@cn...>
> *To: *"Mailing list for Scipion users"
> <sci...@li...>
> *Sent: *Friday, 2 October, 2020 11:30:00
> *Subject: *Re: [scipion-users] scipion-em-xmipp 20.7rc1 update failure
>
> 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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--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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