Re: [scipion-users] Antw: RE: deep consensus pickling error

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

Thanks Christian.

In theory, xmipp defines dependencies strictly 
(https://github.com/I2PC/xmipp/blob/devel/src/xmipp/bindings/python/xmipp_conda_envs.py)

I do not know how it ended up with higher versions, but something to 
keep an eye on.

On 20/4/21 7:00, Christian Tüting wrote:
> Hi all,
>
> first the conda path looks actually very strange, and I fixed this
> direclty. We had some other issues, which were tensorflow-related, but
> this is fixed.
>
>
> Just to comment on that, there were first an issue with the tensorflow
> module. Installing the latest release (2.x) gives an error on "module
> 'tensorflow' has no attribute 'Session'". After fixing that by
> downgrading, keras was giving an error, that the module does not have no
> attribute "tf", which was also fixed by downgrading.
>
>
>
> TL;DR Eventually, downgrading tensorflow to 1.15.0 and downgrading keras
> to 2.2.4 (from 2.2.5) solved the issue
>
>
> Best
> Christian
>
>
>>>> "Dmitry A. Semchonok" <sem...@gm...> 19.04.21 16.24 Uhr >>>
> Dear Carlos Oscar, Pablo, David, Ruben,
>
>
> Thank you very much for your fast response.
>
>
> Currently, deep learning is running.
> A colleague of mine, Christian, kindly looked at the problem.
>
>
> Let me, please post the errors we had and where we are now.
> May be Christian can comment more on this issue.
>
>
> Please see the errors here.
> https://yadi.sk/d/KlTeKv1O9UCTQg
>
>
> Sincerely,
> Dmitry
>
>
>
>
>
>
>
>   
> Sent from Mail for Windows 10
>   
> From: Carlos Oscar Sorzano
> Sent: Monday, April 19, 2021 12:57 PM
> To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David
> Maluenda
> Subject: Re: [scipion-users] deep consensus pickling error
>
>   
> Dear Dmitry,
> let us see if David or Rubén knows where this environment is coming
> from.
> Kind regards, Carlos Oscar
> El 19/04/2021 a las 9:37, Pablo Conesa escribió:
>
> Hi Dmitry... you have no environment for xmipp_DLTK_v0.3.
> You have a "weird" xmipp_DLTK_v0.3_BACKUP2
> /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2
>
> On 17/4/21 8:56, Dmitry A. Semchonok wrote:
>
> Dear colleagues,
>   
> During deep consensus pickling I received the following error
>   
> Any ideas?
>   
> Thank you
>   
> Sincerely,
> Dmitry
>   
>   
>   
> [Parallel(n_jobs=12)]: Done 176 tasks      | elapsed:  1.8min
> [Parallel(n_jobs=12)]: Done 426 tasks      | elapsed:  4.3min
> [Parallel(n_jobs=12)]: Done 776 tasks      | elapsed:  7.5min
> [Parallel(n_jobs=12)]: Done 1226 tasks      | elapsed: 11.5min
> [Parallel(n_jobs=12)]: Done 1776 tasks      | elapsed: 16.7min
> [Parallel(n_jobs=12)]: Done 2426 tasks      | elapsed: 23.7min
> [Parallel(n_jobs=12)]: Done 3176 tasks      | elapsed: 32.1min
> [Parallel(n_jobs=12)]: Done 4026 tasks      | elapsed: 41.4min
> [Parallel(n_jobs=12)]: Done 4976 tasks      | elapsed: 51.8min
> [Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished
> [35mFINISHED[0m: extractParticles, step 12, time 2021-04-17
> 04:05:07.093613
> [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17
> 04:05:07.574152
> [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17
> 04:26:59.879548
> [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444
> None None None None
>   
> $ /usr/local/EMAN_2.21/bin/conda info --env
> # conda environments:
> #
> 3DFSC                    /home/panos/.conda/envs/3DFSC
> cryoassess-0.1.0         /home/panos/.conda/envs/cryoassess-0.1.0
> cryolo                   /home/panos/.conda/envs/cryolo
> xmipp_DLTK_v0.3_BACKUP2
> /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2
> cryolo                   /usr/local/EMAN_2.21/envs/cryolo
> cryolo-1.5.4             /usr/local/EMAN_2.21/envs/cryolo-1.5.4
> fsc                      /usr/local/EMAN_2.21/envs/fsc
> topaz                    /usr/local/EMAN_2.21/envs/topaz
> root                  *  /usr/local/EMAN_2.21
>   
>   
>>>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)
> Traceback (most recent call last):
>    File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 189, in run
>      self._run()
>    File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 240, in _run
>      resultFiles = self._runFunc()
>    File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 236, in _runFunc
>      return self._func(*self._args)
>    File
> "/opt/Scipion    env=self.getCondaEnv())
>    File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py",
> line 204, in getCondaEnv
>      return CondaEnvManager.getCondaEnv(env, envName)
>    File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in
> getCondaEnv
>      envBin = os.path.join(environDir, "bin")
>    File "/usr/lib64/python3.6/posixpath.py", line 80, in join
>      a = os.fspath(a)
> TypeError: expected str, bytes or os.PathLike object, not NoneType
> [31mProtocol failed: expected str, bytes or os.PathLike object, not
> NoneType[0m
> [35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417
> *** Last status is failed
> Sent from Mail for Windows 10
>   
>
>
>
>
> _______________________________________________scipion-users mailing
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>
> Pablo Conesa - Madrid Scipion team
>
>
>
>
>
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>   
>
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*