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

[Christian T. <chr...@bi...>]

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
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