Menu
▾
▴
Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error
|
From: Pablo C. <pc...@cn...> - 2021-04-22 12:58:44
|
Removing (rm -rf SCIPION_HOME) would be enough in case of virtualenv installations for a full fresh start. For "conda" like ones, you may want to remove the conda enviroment too for scipion3. Try not to use eman as conda manager. I guess, that not having eman initialized in the shell will do. On 22/4/21 13:02, Christian Tüting wrote: > Hi all, > > thank you for your valuable input. > > > I think, the best would be to wait till all running jobs are done and do > a clean reinstallation of Scipion3 with a clean conda environment. The > current situation was generated over iterative dirty and/or (not-so) > temporary fixes. > > So is there anything, we should be aware of? Or just deleting the > current installation and start with a clean conda/miniconda enviroment > and follow the installation guide? > > Thanks in advance > Christian > > >>>> Pablo Conesa <pc...@cn...> 04/21/21 7:06 PM >>> > You have eman2 acting as a conda manager, that is a problem. > > At least the environment is not listed there. > > Does the other plugins work? e.g. cryolo? > > Can you send the output of: > > scipion3 printenv > > and > > scipion3 run printenv > > ? > > On 21/4/21 17:06, Dmitry Semchonok wrote: >> Dear colleagues, >> Just to add our current error from the xmipp deep learning > installation. >> Interestingly we almost fun to an end of this step but conda issue >> appeared. >> >> Any suggestions? >> >> >> >> currentDir: /data1/ScipionUserData/projects/Image_processing_cn_10688 >> 00890: workingDir: Runs/007643_XmippProtScreenDeepLearning >> 00891: runMode: Continue >> 00892: MPI: 1 >> 00893: threads: 4 >> 00894: Starting at step: 3 >> 00895: Running steps >> 00896: STARTED: predict, step 3, time 2021-04-20 11:08:26.633086 >> 00897: >> 00898: $ /usr/local/EMAN_2.21/bin/conda info --env >> 00899: # conda environments: >> 00900: # >> 00901: 3DFSC /home/panos/.conda/envs/3DFSC >> 00902: cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 >> 00903: cryolo /home/panos/.conda/envs/cryolo >> 00904: cryolo /usr/local/EMAN_2.21/envs/cryolo >> 00905: cryolo-1.5.4 > /usr/local/EMAN_2.21/envs/cryolo-1.5.4 >> 00906: fsc /usr/local/EMAN_2.21/envs/fsc >> 00907: topaz /usr/local/EMAN_2.21/envs/topaz >> 00908: root * /usr/local/EMAN_2.21 >> 00909: >> 00910: >> 00911: >>> 'xmipp_DLTK_v0.3' conda environment not found... (check >> list above) >> 00912: Traceback (most recent call last): >> 00913: File >> > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > >> line 189, in run >> 00914: self._run() >> 00915: File >> > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > >> line 240, in _run >> 00916: resultFiles = self._runFunc() >> 00917: File >> > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > >> line 236, in _runFunc >> 00918: return self._func(*self._args) >> 00919: File >> > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deeplearning.py", > >> line 319, in predict >> 00920: env=self.getCondaEnv()) >> 00921: File >> > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", > >> line 204, in getCondaEnv >> 00922: return CondaEnvManager.getCondaEnv(env, envName) >> 00923: File "/opt/Scipion3/software/bindings/xmipp_base.py", line >> 245, in getCondaEnv >> 00924: envBin = os.path.join(environDir, "bin") >> 00925: File "/usr/lib64/python3.6/posixpath.py", line 80, in join >> 00926: a = os.fspath(a) >> 00927: TypeError: expected str, bytes or os.PathLike object, not >> NoneType >> 00928: Protocol failed: expected str, bytes or os.PathLike object, >> not NoneType >> 00929: FAILED: predict, step 3, time 2021-04-20 11:08:27.020467 >> 00930: *** Last status is failed >> 00931: ------------------- PROTOCOL FAILED (DONE 3/4) >> >> >> Thank you! >> >> >> Sincerely, >> Dmitry >> >> >> >>> On 20. Apr 2021, at 11:25, Christian Tüting >>> <chr...@bi... >>> <mailto:chr...@bi...>> wrote: >>> >>> Hi, >>> >>> thank you for your response. I tried this twice. The first time, the >>> "_BACKUP2" folder was popping up again under .conda/envs, so I > followed >>> your steps again, deleting t>> running a job gives this error: ">>> 'xmipp_DLTK_v0.3' conda > environment >>> not found... (check list above)". >>> >>> Another long-term job is currently running, after this is done, we > will >>> restart everything to have a clean system. But do you have any >>> additional tips? >>> >>> Thanks in advance >>> Christian >>> >>> >>> >>>>>> David Maluenda <dma...@ub... <mailto:dma...@ub...>> >>>>>> 20.04.21 10.02 Uhr >>> >>> Hi Christian, >>> >>> If it already works, I would leave it as it is. >>> >>> To make a clear installation, you don't need to reinstall the whole >>> xmipp. You can just reinstall the deepLearningToolkit by >>> >>> rm -rf /opt/Scipion3/software/em/deepLearningToolkit >>> conda env remove --name xmipp_DLTK_v0.3_BACKUP2 >>> scipion3 installb deepLearningToolkit >>> >>> >>> Cheers, >>> >>> <http://ucm.es/ <http://ucm.es/>> >>> _____ >>> Dr. David Maluenda Niubó >>> dma...@ub... <mailto:dma...@ub...><mailto:dma...@ub... >>> <mailto:dma...@ub...>> - (+34) 619 029 310 >>> Wavefront Engineering >>> > Group<https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA >>> <https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA>> >>> Applied Physics - UB<https://www.ub.edu/portal/web/dp-fisica-aplicada >>> <https://www.ub.edu/portal/web/dp-fisica-aplicada>> >>> >>> This email message and any documents attached to it may contain >>> confidential or legally protected material and are intended solely > for >>> the use of the individual or organization to whom they are addressed. > We >>> remind you that if you are not the intended recipient of this email >>> message or the person responsible for processing it, then you are not >>> authorized to read, save, modify, send, copy or disclose any of its >>> contents. If you have received this email message by mistake, we > kindly >>> ask you to inform the sender of this and to eliminate both the > message >>> and any attachments it carries from your account. Thank you for your >>> collaboration. >>> >>> >>> >>> On Tue, Apr 20, 2021 at 9:53 AM Christian Tüting >>> <chr...@bi... >>> > <mailto:chr...@bi...><mailto:chr...@bi... > >>> <mailto:chr...@bi...>>> >>> wrote: >>> Hi Pablo, >>> >>> I will take an eye on this. I have a question regarding dependencies: >>> tensorflow 1.15 requires keras-application>=1.0.8 and >>> keras-preprocessing>=1.0.5, but keras 2.2 requieres older versions >>> (1.0.2 and 1.0.1, respectivly). >>> >>> Should we try to uninstall and a clean reinstall of xmipp, to resolve >>> all dependency issues? >>> >>> Thank you for your support. >>> >>> Best >>> Christian >>> >>> >>>>>> Pablo Conesa <pc...@cn... >>>>>> <mailto:pc...@cn...><mailto:pc...@cn... >>>>>> <mailto:pc...@cn...>>> >>> 20.04.21 9.16 Uhr >>> >>> Thanks Christian. >>> >>> In theory, xmipp defines dependencies strictly >>> > (https://github.com/I2PC/xmipp/blob/devel/src/xmipp/bindings/python/xmipp_conda_envs.py > > <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>> <mailto: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 <https://yadi.sk/d/KlTeKv1O9UCTQg> >>>> >>>> >>>> Since> 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> 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(>>> [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 >>>> >>> lis...@li...https >>> > <mailto:lis...@li...https>://lists.sourceforge.net/lists/listinfo/scipion-users--<http://lists.sourceforge.net/lists/listinfo/scipion-users--> >>>> Pablo Conesa - Madrid Scipion team >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________scipion-users mailing >>>> >>> lis...@li...https >>> <mailto:lis...@li...https>:/> >>>> >>>> >>> -- >>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es >>> <http://scipion.i2pc.es>> team* >>> >>> >>> >>> Aquest missatge, i els fitxers adjunts que hi pugui haver, pot > contenir >>> informació confidencial o protegida legalment i s’adreça > exclusivament a >>> la persona o entitat destinatària. Si no consteu com a destinatari > final >>> o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, >>> retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el >>> contingut. Si l’heu rebut per error, informeu-ne el remitent i > elimineu >>> del sistema tant el missatge com els fitxers adjunts que hi pugui > haver. >>> Este mensaje, y los ficheros adjuntos que pueda incluir, puede > contener >>> información confidencial o legalmente protegida y está exclusivamente >>> dirigido a la persona o entidad destinataria. Si usted no consta como >>> destinatario final ni es la persona encargada de recibirlo, no está >>> autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, > ni >>> a revelar su contenido. Si lo ha recibido por error, informe de ello > al >>> remitente y elimine del sistema tanto el mensaje como los ficheros >>> adjuntos que pueda contener. >>> >>> This email message and any attachments it carries may contain >>> confidential or legally protected material and are intended solely > for >>> the individual or organization to whom they are addressed. If you are >>> not the intended recipient of this message or the person responsible > for >>> processing it, then you are not authorized to read, save, modify, > send, >>> copy or disclose any part of it. If you have received the message by >>> mistake, please inform the sender of this and eliminate the message > and >>> any attachments it carries from your account. >>> >>> >>> Aquest missatge, i els fitxers adjunts que hi pugui haver, pot > contenir >>> informació confidencial o protegida legalment i s’adreça > exclusivament a >>> la persona o entitat destinatària. Si no consteu com a destinatari > final >>> o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, >>> retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el >>> contingut. Si l’heu rebut per error, informeu-ne el remitent i > elimineu >>> del sistema tant el missatge com els fitxers adjunts que hi pugui > haver. >>> Este mensaje, y los ficheros adjuntos que pueda incluir, puede > contener >>> información confidencial o legalmente protegida y está exclusivamente >>> dirigido a la persona o entidad destinataria. Si usted no consta como >>> destinatario final ni es la persona encargada de recibirlo, no está >>> autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, > ni >>> a revelar su contenido. Si lo ha recibido por error, informe de ello > al >>> remitente y elimine del sistema tanto el mensaje como los ficheros >>> adjuntos que pueda contener. >>> >>> This email message and any attachments it carries may contain >>> confidential or legally protected material and are intended solely > for >>> the individual or organization to whom they are addressed. If you are >>> not the intended recipient of this message or the person responsible > for >>> processing it, then you are not authorized to read, save, modify, > send, >>> copy or disclose any part of it. If you have>> mistake, please inform the sender of this and eliminate the message > and >>> any attachments it carries from your account. >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
