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From: Dmitry S. <Sem...@gm...> - 2021-04-28 09:32:09
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Dear Pablo, I am not sure how to get the stack, containing my particles out from (standing alone) - Relion - Cryosparc So I am 1 step behind import. Or do you mean I can in SCIPION select — import averages and then as an input specify the 2D classification file from relion // or cryosparc? Thank you! Sincerely, Dmitry > On 28. Apr 2021, at 10:22, Pablo Conesa <pc...@cn...> wrote: > > Hi Dmitry, have you tried "Import averages" to import the 2d classes stack? > > And then from there you should be able to run any initial model method , except CS one that uses particles instead. > > On 28/4/21 9:59, Dmitry Semchonok wrote: >> Hello Jorge, >> >> Yes, or into SCIPION. >> >> Example: — we started a project in relion. >> We have some nice 2D class averages. >> But the initial modelling for some reason does not work. >> >> So I would like somehow to: >> >> a) extract those particles (mrc // stk), >> b) import them to SCIPION. >> c) run initial modelling in SCIPION. >> d) Export this initial model to relion and proceed. >> >> >> >> >> >> Thank you >> >> >> Sincerely, >> Dmitry >> >> >> >> >>> On 28. Apr 2021, at 09:39, Jorge Jimenez <su...@bc... <mailto:su...@bc...>> wrote: >>> >>> Hi Dmitry, >>> Do you mean moving from Relion or Cryosparc from outside of Scipion to process their results inside Scipion? >>> Best, >>> Scipion Team >>> >>> Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/921 <https://bcucnb.freshdesk.com/helpdesk/tickets/921> >>> >>> Activo Lun, 26 Abr a 9:39 AM , Mailing list for Scipion users <sci...@li... <mailto:sci...@li...>> Escrito: >>> Dear colleagues, >>> >>> Small question – >>> >>> Do you know how to extract particles from relion & cryosparc to run them in SCIPION? >>> >>> Thank you! >>> >>> Sincerely, >>> Dmitry >>> Biocomputing unit - National Center for Biotechnology powered by Freshdesk <https://freshdesk.com/freshdesk-demo?utm_source=emailfooter&referrer=bcucnb.freshdesk.com> 921:553135 >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > -- > Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es/> team > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2021-04-28 08:22:27
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Hi Dmitry, have you tried "Import averages" to import the 2d classes stack? And then from there you should be able to run any initial model method , except CS one that uses particles instead. On 28/4/21 9:59, Dmitry Semchonok wrote: > Hello Jorge, > > Yes, or into SCIPION. > > Example: — we started a project in relion. > We have some nice 2D class averages. > But the initial modelling for some reason does not work. > > So I would like somehow to: > > a) extract those particles (mrc // stk), > b) import them to SCIPION. > c) run initial modelling in SCIPION. > d) Export this initial model to relion and proceed. > > > > > > Thank you > > > Sincerely, > Dmitry > > > > >> On 28. Apr 2021, at 09:39, Jorge Jimenez >> <su...@bc... <mailto:su...@bc...>> >> wrote: >> >> Hi Dmitry, >> Do you mean moving from Relion or Cryosparc from outside of Scipion >> to process their results inside Scipion? >> Best, >> Scipion Team >> >> Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/921 >> <https://bcucnb.freshdesk.com/helpdesk/tickets/921> >> >> Activo Lun, 26 Abr a 9:39 AM , Mailing list for Scipion users >> <sci...@li... >> <mailto:sci...@li...>> Escrito: >> Dear colleagues, >> Small question – >> Do you know how to extract particles from relion & cryosparc to >> run them in SCIPION? >> Thank you! >> Sincerely, >> Dmitry >> >> Biocomputing unit - National Center for Biotechnology powered by >> Freshdesk >> <https://freshdesk.com/freshdesk-demo?utm_source=emailfooter&referrer=bcucnb.freshdesk.com> >> 921:553135 >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry S. <Sem...@gm...> - 2021-04-28 08:00:27
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Hello Jorge, Yes, or into SCIPION. Example: — we started a project in relion. We have some nice 2D class averages. But the initial modelling for some reason does not work. So I would like somehow to: a) extract those particles (mrc // stk), b) import them to SCIPION. c) run initial modelling in SCIPION. d) Export this initial model to relion and proceed. Thank you Sincerely, Dmitry > On 28. Apr 2021, at 09:39, Jorge Jimenez <su...@bc...> wrote: > > Hi Dmitry, > Do you mean moving from Relion or Cryosparc from outside of Scipion to process their results inside Scipion? > Best, > Scipion Team > > Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/921 <https://bcucnb.freshdesk.com/helpdesk/tickets/921> > > Activo Lun, 26 Abr a 9:39 AM , Mailing list for Scipion users <sci...@li...> Escrito: > Dear colleagues, > > Small question – > > Do you know how to extract particles from relion & cryosparc to run them in SCIPION? > > Thank you! > > Sincerely, > Dmitry > Biocomputing unit - National Center for Biotechnology powered by Freshdesk <https://freshdesk.com/freshdesk-demo?utm_source=emailfooter&referrer=bcucnb.freshdesk.com> 921:553135 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Jorge J. <su...@bc...> - 2021-04-28 07:55:05
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Hi Dmitry, Do you mean moving from Relion or Cryosparc from outside of Scipion to process their results inside Scipion? Best, Scipion Team Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/921 Activo Lun, 26 Abr a 9:39 AM , Mailing list for Scipion users <sci...@li...> Escrito: Dear colleagues, Small question – Do you know how to extract particles from relion & cryosparc to run them in SCIPION? Thank you! Sincerely, Dmitry |
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From: Dmitry S. <Sem...@gm...> - 2021-04-26 07:39:41
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Dear colleagues, Small question – Do you know how to extract particles from relion & cryosparc to run them in SCIPION? Thank you! Sincerely, Dmitry |
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From: Anne M D. <do...@uw...> - 2021-04-25 16:29:27
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Hello, I am a graduate student in Neil King's group at the University of Washington. We have been trying to get scipion installed on our server recently but have been running into several python/other package dependency errors. Specifically, I am trying to get the local rec plugin working properly. So far, we have scipion installed and running some things in it works (relion jobs work fine), but the define subparticles module within local rec does not work and is really what I need to use. I get the following error in my terminal about Xmipp when I try to run it: >>> 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' (/home/doseya/.local/lib/python3.8/site-packages/xmipp3/base.py) And then there's a "'NoneType' object as no attribute 'AddObject'" error in the output.log. I also think I have xmipp installed as a plugin (black box is there next to scipion-em-xmipp) but then there's a sub-plugin for xmipp under that that won't install for some reason (see screenshot), so not sure how to properly install xmipp, which may fix this issue? Thanks for any help on this issue! Annie Dosey |
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From: Jose L. V. P. <jos...@ce...> - 2021-04-25 09:25:23
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Pablo, I will put a warning window if a parameter is needed to avoid these kind of behaviour. We regret the inconvenience, Simone Best Jose Luis ________________________________ De: Pablo Conesa <pc...@cn...> Enviado: viernes, 23 de abril de 2021 8:05 Para: sci...@li... <sci...@li...> Asunto: Re: [scipion-users] Problem with local MonoRes What is your parameter for "Low" resolution? In theory, it allows empty values, but seems it does not like it. Maybe a "fatal combination" of params? On 22/4/21 22:10, Simone Pellegrino wrote: Dear Scipion community, I have installed the latest version (v3.0.7) of Scipion. I am trying to run "local MonoRes" but the job is ending with the following error: STARTED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 20:39:35.846906 00022: Traceback (most recent call last): 00023: File "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 189, in run 00024: self._run() 00025: File "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run 00026: resultFiles = self._runFunc() 00027: File "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc 00028: return self._func(*self._args) 00029: File "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_monogenic_signal.py", line 266, in resolutionMonogenicSignalStep 00030: params += ' --maxRes %f' % self.maxRes.get() 00031: TypeError: must be real number, not NoneType 00032: Protocol failed: must be real number, not NoneType 00033: FAILED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 20:39:35.849098 00034: *** Last status is failed 00035: ------------------- PROTOCOL FAILED (DONE 2/4) Could you please advise? Many thanks in advance Best Simone _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team [https://www.uchceu.es/img/logos/wur.jpg] Este mensaje y sus archivos adjuntos, enviados desde FUNDACI?N UNIVERSITARIA SAN PABLO-CEU, pueden contener informaci?n confidencial y est? destinado a ser le?do s?lo por la persona a la que va dirigido, por lo que queda prohibida la difusi?n, copia o utilizaci?n de dicha informaci?n por terceros. Si usted lo recibiera por error, por favor, notif?quelo al remitente y destruya el mensaje y cualquier documento adjunto que pudiera contener. Cualquier informaci?n, opini?n, conclusi?n, recomendaci?n, etc. contenida en el presente mensaje no relacionada con la actividad de FUNDACI?N UNIVERSITARIA SAN PABLO-CEU, y/o emitida por persona no autorizada para ello, deber? considerarse como no proporcionada ni aprobada por FUNDACI?N UNIVERSITARIA SAN PABLO-CEU, que pone los medios a su alcance para garantizar la seguridad y ausencia de errores en la correspondencia electr?nica, pero no puede asegurar la inexistencia de virus o la no alteraci?n de los documentos transmitidos electr?nicamente, por lo que declina cualquier responsabilidad a este respecto. This message and its attachments, sent from FUNDACI?N UNIVERSITARIA SAN PABLO-CEU, may contain confidential information and is intended to be read only by the person it is directed. Therefore any disclosure, copying or use by third parties of this information is prohibited. If you receive this in error, please notify the sender and destroy the message and any attachments may contain. Any information, opinion, conclusion, recommendation,... contained in this message and which is unrelated to the business activity of FUNDACI?N UNIVERSITARIA SAN PABLO-CEU and/or issued by unauthorized personnel, shall be considered unapproved by FUNDACI?N UNIVERSITARIA SAN PABLO-CEU. FUNDACI?N UNIVERSITARIA SAN PABLO-CEU implements control measures to ensure, as far as possible, the security and reliability of all its electronic correspondence. However, FUNDACI?N UNIVERSITARIA SAN PABLO-CEU does not guarantee that emails are virus-free or that documents have not be altered, and does not take responsibility in this respect. |
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From: Jose M. de la R. T. <del...@gm...> - 2021-04-25 08:59:57
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Hi, Maybe the protocol should have a validation to prevent users to input an incorrect set of parameters. Best, Jose Miguel On Sun, Apr 25, 2021 at 10:43 AM Simone Pellegrino <sp...@ca...> wrote: > Dear Carlos Oscar, > > thank you for your email. It is true, I left as default. Now I have put > both values (Low and High for Resolution Range) and it worked. > > Thank you for your hint. > > Best regards > > Simone > > > > On 23/04/2021 05:51, Carlos Oscar Sorzano wrote: > > Dear Simone, > > > > it would seem as if the field maxRes (maximum resolution to explore > > during the analysis) is not filled in the form, can that be? > > > > Kind regards, Carlos Oscar > > > > El 22/04/2021 a las 22:10, Simone Pellegrino escribió: > >> Dear Scipion community, > >> > >> I have installed the latest version (v3.0.7) of Scipion. > >> > >> I am trying to run "local MonoRes" but the job is ending with the > >> following error: > >> > >> > >> STARTED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 > >> 20:39:35.846906 > >> 00022: Traceback (most recent call last): > >> 00023: File > >> > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > > >> line 189, in run > >> 00024: self._run() > >> 00025: File > >> > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > > >> line 240, in _run > >> 00026: resultFiles = self._runFunc() > >> 00027: File > >> > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > > >> line 236, in _runFunc > >> 00028: return self._func(*self._args) > >> 00029: File > >> > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_monogenic_signal.py", > > >> line 266, in resolutionMonogenicSignalStep > >> 00030: params += ' --maxRes %f' % self.maxRes.get() > >> 00031: TypeError: must be real number, not NoneType > >> 00032: Protocol failed: must be real number, not NoneType > >> 00033: FAILED: resolutionMonogenicSignalStep, step 2, time > >> 2021-04-22 20:39:35.849098 > >> 00034: *** Last status is failed > >> 00035: ------------------- PROTOCOL FAILED (DONE 2/4) > >> > >> > >> Could you please advise? > >> > >> Many thanks in advance > >> > >> Best > >> > >> Simone > >> > >> > >> > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Simone P. <sp...@ca...> - 2021-04-25 08:43:25
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Dear Carlos Oscar, thank you for your email. It is true, I left as default. Now I have put both values (Low and High for Resolution Range) and it worked. Thank you for your hint. Best regards Simone On 23/04/2021 05:51, Carlos Oscar Sorzano wrote: > Dear Simone, > > it would seem as if the field maxRes (maximum resolution to explore > during the analysis) is not filled in the form, can that be? > > Kind regards, Carlos Oscar > > El 22/04/2021 a las 22:10, Simone Pellegrino escribió: >> Dear Scipion community, >> >> I have installed the latest version (v3.0.7) of Scipion. >> >> I am trying to run "local MonoRes" but the job is ending with the >> following error: >> >> >> STARTED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 >> 20:39:35.846906 >> 00022: Traceback (most recent call last): >> 00023: File >> "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 189, in run >> 00024: self._run() >> 00025: File >> "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 240, in _run >> 00026: resultFiles = self._runFunc() >> 00027: File >> "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 236, in _runFunc >> 00028: return self._func(*self._args) >> 00029: File >> "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_monogenic_signal.py", >> line 266, in resolutionMonogenicSignalStep >> 00030: params += ' --maxRes %f' % self.maxRes.get() >> 00031: TypeError: must be real number, not NoneType >> 00032: Protocol failed: must be real number, not NoneType >> 00033: FAILED: resolutionMonogenicSignalStep, step 2, time >> 2021-04-22 20:39:35.849098 >> 00034: *** Last status is failed >> 00035: ------------------- PROTOCOL FAILED (DONE 2/4) >> >> >> Could you please advise? >> >> Many thanks in advance >> >> Best >> >> Simone >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos O. S. <co...@cn...> - 2021-04-25 08:40:03
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Dear Simone, it would seem as if the field maxRes (maximum resolution to explore during the analysis) is not filled in the form, can that be? Kind regards, Carlos Oscar El 22/04/2021 a las 22:10, Simone Pellegrino escribió: > Dear Scipion community, > > I have installed the latest version (v3.0.7) of Scipion. > > I am trying to run "local MonoRes" but the job is ending with the > following error: > > > STARTED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 > 20:39:35.846906 > 00022: Traceback (most recent call last): > 00023: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 189, in run > 00024: self._run() > 00025: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 240, in _run > 00026: resultFiles = self._runFunc() > 00027: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 236, in _runFunc > 00028: return self._func(*self._args) > 00029: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_monogenic_signal.py", > line 266, in resolutionMonogenicSignalStep > 00030: params += ' --maxRes %f' % self.maxRes.get() > 00031: TypeError: must be real number, not NoneType > 00032: Protocol failed: must be real number, not NoneType > 00033: FAILED: resolutionMonogenicSignalStep, step 2, time > 2021-04-22 20:39:35.849098 > 00034: *** Last status is failed > 00035: ------------------- PROTOCOL FAILED (DONE 2/4) > > > Could you please advise? > > Many thanks in advance > > Best > > Simone > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2021-04-25 08:40:00
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What is your parameter for "Low" resolution? In theory, it allows empty values, but seems it does not like it. Maybe a "fatal combination" of params? On 22/4/21 22:10, Simone Pellegrino wrote: > Dear Scipion community, > > I have installed the latest version (v3.0.7) of Scipion. > > I am trying to run "local MonoRes" but the job is ending with the > following error: > > > STARTED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 > 20:39:35.846906 > 00022: Traceback (most recent call last): > 00023: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 189, in run > 00024: self._run() > 00025: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 240, in _run > 00026: resultFiles = self._runFunc() > 00027: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 236, in _runFunc > 00028: return self._func(*self._args) > 00029: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_monogenic_signal.py", > line 266, in resolutionMonogenicSignalStep > 00030: params += ' --maxRes %f' % self.maxRes.get() > 00031: TypeError: must be real number, not NoneType > 00032: Protocol failed: must be real number, not NoneType > 00033: FAILED: resolutionMonogenicSignalStep, step 2, time > 2021-04-22 20:39:35.849098 > 00034: *** Last status is failed > 00035: ------------------- PROTOCOL FAILED (DONE 2/4) > > > Could you please advise? > > Many thanks in advance > > Best > > Simone > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Jose L. V. <jlv...@gm...> - 2021-04-25 08:32:52
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Dear simone, A limit value for the low resolution is required. I think the low resolution box in the form is empty, is this the case? Best wishes Jose Luis Vilas On Fri, Apr 23, 2021, 8:00 AM Simone Pellegrino <sp...@ca...> wrote: > Dear Scipion community, > > I have installed the latest version (v3.0.7) of Scipion. > > I am trying to run "local MonoRes" but the job is ending with the > following error: > > > STARTED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 > 20:39:35.846906 > 00022: Traceback (most recent call last): > 00023: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > > line 189, in run > 00024: self._run() > 00025: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > > line 240, in _run > 00026: resultFiles = self._runFunc() > 00027: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > > line 236, in _runFunc > 00028: return self._func(*self._args) > 00029: File > "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_monogenic_signal.py", > > line 266, in resolutionMonogenicSignalStep > 00030: params += ' --maxRes %f' % self.maxRes.get() > 00031: TypeError: must be real number, not NoneType > 00032: Protocol failed: must be real number, not NoneType > 00033: FAILED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 > 20:39:35.849098 > 00034: *** Last status is failed > 00035: ------------------- PROTOCOL FAILED (DONE 2/4) > > > Could you please advise? > > Many thanks in advance > > Best > > Simone > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Simone P. <sp...@ca...> - 2021-04-22 20:11:03
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Dear Scipion community, I have installed the latest version (v3.0.7) of Scipion. I am trying to run "local MonoRes" but the job is ending with the following error: STARTED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 20:39:35.846906 00022: Traceback (most recent call last): 00023: File "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 189, in run 00024: self._run() 00025: File "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run 00026: resultFiles = self._runFunc() 00027: File "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc 00028: return self._func(*self._args) 00029: File "/home/miniconda3/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_monogenic_signal.py", line 266, in resolutionMonogenicSignalStep 00030: params += ' --maxRes %f' % self.maxRes.get() 00031: TypeError: must be real number, not NoneType 00032: Protocol failed: must be real number, not NoneType 00033: FAILED: resolutionMonogenicSignalStep, step 2, time 2021-04-22 20:39:35.849098 00034: *** Last status is failed 00035: ------------------- PROTOCOL FAILED (DONE 2/4) Could you please advise? Many thanks in advance Best Simone |
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From: Pablo C. <pc...@cn...> - 2021-04-22 12:58:44
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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* |
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From: David M. <dma...@gm...> - 2021-04-22 11:52:27
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Hi, I agree with Grigory. Please, be sure that no old environs are left in your conda environs before re-installing. I would suggest to add a line with CONDA_ACTIVATION_CMD = . /path/to/miniconda3/etc/profile.d/conda.sh in the SCIPION_HOME/config/scipion.conf file (you can create that file if it doesn't exist). Cheers, *_____Dr. David Maluenda Niubó* dma...@gm... (+34) 619 029 310 LinkedIn <https://www.linkedin.com/in/davidmaluenda/> - GoogleScholar <https://scholar.google.es/citations?user=r6uOuj0AAAAJ&hl=es> 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 Thu, Apr 22, 2021 at 1:07 PM Grigory Sharov <sha...@gm...> wrote: > Hi, > > imho, using eman2's conda as default for all envs will mess up both eman > and scipion etc. I'd suggest having a separately installed miniconda3. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Thu, Apr 22, 2021 at 12:03 PM Christian Tüting < > chr...@bi...> 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* >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > 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. > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Grigory S. <sha...@gm...> - 2021-04-22 11:07:21
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Hi, imho, using eman2's conda as default for all envs will mess up both eman and scipion etc. I'd suggest having a separately installed miniconda3. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Apr 22, 2021 at 12:03 PM Christian Tüting < chr...@bi...> 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* > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Christian T. <chr...@bi...> - 2021-04-22 11:03:09
|
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* |
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From: Pablo C. <pc...@cn...> - 2021-04-22 07:47:35
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Dear Dmitry, there is a inconsistency there. deepLearningToolkit is reported as installed, but in the list of the enviroments it is not. Could you please, remove the "files that flags deepearningtoolkit as installed": scipion3 run rm -rf '$SCIPION_HOME/software/em/deepLearningToolkit*' And try to install deeplearning toolkit again? scipionprod installb deepLearningToolkit On 21/4/21 22:47, Dmitry A. Semchonok wrote: > > Dear Pablo, > > Thank you! > > Please see the result of > > *Scipion3 installb* > > ere** > > Sincerely, > > Dmitry > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > *From: *pc...@cn... <mailto:pc...@cn...> > *Sent: *Wednesday, April 21, 2021 10:19 PM > *To: *Mailing list for Scipion users > <mailto:sci...@li...> > *Subject: *Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus > pickling error > > Providing Eman Fonda can handle environments the same way a standard > conda installation does, then, I'd say the deepLearningToolkit > environment is not present. > > What is the output of > > Scipion3 instalb? > > El 21 abr. 2021 20:28, "Dmitry A. Semchonok" <sem...@gm...> > escribió: > > Dear Pablo, > > Thank you ! please have a look below. > > Sincerely, > > Dmitry > > *scipion3 printenv * > > [panos@cryoem01 ~]$ scipion3 printenv > > Scipion v3.0.7 - Eugenius > > export ASCP="~/.aspera/connect/bin/ascp" > > export ASPERA_SCP_PASS="" > > export ATSAS_HOME="/opt/Scipion3/software/em/atsas-3.0.1" > > export BSOFT_HOME="/opt/Scipion3/software/em/bsoft-2.0.7" > > export CCP4_HOME="/opt/Scipion3/software/em/ccp4-7.0.056" > > export CHIMERA_HOME="/opt/Scipion3/software/em/chimerax-1.1" > > export CISTEM_HOME="/opt/Scipion3/software/em/cistem-1.0.0-beta" > > export CONDA_ACTIVATION_CMD="eval > "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash > hook)"" > > export CONTINUOUSFLEX_HOME="/opt/Scipion3/software/em/xmipp" > > export CRYOASSESS_ENV_ACTIVATION="conda activate cryoassess-0.1.0" > > export > CRYOASSESS_MODEL_2D="/opt/Scipion3/software/em/cryoassess-models/2dassess_062119.h5" > > export > CRYOASSESS_MODEL_MIC="/opt/Scipion3/software/em/cryoassess-models/micassess_051419.h5" > > export CRYOLO_CUDA_LIB="/usr/local/cuda/lib64" > > export CRYOLO_ENV_ACTIVATION="conda activate cryolo-1.7.6" > > export CRYOLO_ENV_ACTIVATION_CPU="conda activate cryoloCPU-1.7.6" > > export > CRYOLO_GENERIC_DENOISED_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5" > > export > CRYOLO_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5" > > export > CRYOLO_NS_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5" > > export CRYOSPARC_HOME="/home/panos/software/cryosparc" > > export CRYOSPARC_USER="ctueting" > > export > CRYO_PROJECTS_DIR="/data1/ScipionUserData/projects/cryosparc_plugin" > > export CTFFIND4_HOME="/opt/Scipion3/software/em/ctffind4-4.1.14" > > export DOGPICKER_HOME="/opt/Scipion3/software/em/dogpicker-0.2.1.1" > > export DYNAMO_HOME="/opt/Scipion3/software/em/dynamo-1.146" > > export EMAN2SCRATCHDIR="/tmp" > > export EMAN2_HOME="/opt/Scipion3/software/em/eman-2.31" > > export EMFACILITIES_HOME="/opt/Scipion3/software/em/" > > export EMPIAR_TOKEN="" > > export EMXLIB_HOME="/opt/Scipion3/software/em/emx_export-1.0.0" > > export EM_ROOT="software/em" > > export ETHAN_HOME="/opt/Scipion3/software/em/ethan-1.2" > > export FSC3D_ACTIVATION_CMD="conda activate 3DFSC" > > export FSC3D_HOME="/opt/Scipion3/software/em/fsc3D-3.0" > > export GAUTOMATCH="Gautomatch_v0.56_sm30-75_cu10.1" > > export GAUTOMATCH_CUDA_LIB="/usr/local/cuda/lib64" > > export GAUTOMATCH_HOME="/opt/Scipion3/software/em/gautomatch-0.56" > > export GCTF="Gctf-v1.06_sm_30_cu8.0_x86_64" > > export GCTF_CUDA_LIB="/usr/local/cuda-8.0/lib64" > > export GCTF_HOME="/opt/Scipion3/software/em/Gctf_v1.06" > > export IMAGIC_HOME="/opt/Scipion3/software/em/imagic-190830" > > export IMOD_HOME="/opt/Scipion3/software/em/imod-4.10.42/IMOD" > > export > JANNI_GENERIC_MODEL="/opt/Scipion3/software/em/janni_model-20190703/gmodel_janni_20190703.h5" > > export JAVA_MAX_MEMORY="12" > > export LOCSCALE_HOME="/opt/Scipion3/software/em/locscale-0.1" > > export MAXIT_HOME="/opt/Scipion3/software/em/maxit-10.1" > > export MOTIONCOR2_BIN="MotionCor2_1.3.2-Cuda100" > > export MOTIONCOR2_CUDA_LIB="/usr/local/cuda/lib64" > > export MOTIONCOR2_HOME="/opt/Scipion3/software/em/motioncor2-1.3.2" > > export NMA_HOME="/opt/Scipion3/software/em/nma" > > export NOVACTF_HOME="/opt/Scipion3/software/em/novactf-master" > > export PHENIX_HOME="/opt/Scipion3/software/em/phenix-" > > export RELION_CUDA_BIN="/usr/local/cuda/bin" > > export RELION_CUDA_LIB="/usr/local/cuda/lib64" > > export RELION_HOME="/opt/Scipion3/software/em/relion-3.1.0" > > export RESMAP="ResMap-1.95-cuda-Centos7x64" > > export RESMAP_GPU_LIB="ResMap_krnl-cuda-V8.0.61-sm60_gpu.so" > > export RESMAP_HOME="/opt/Scipion3/software/em/resmap-1.95" > > export SCIPION_CONFIG="/opt/Scipion3/config/scipion.conf" > > export SCIPION_CWD="/home/panos" > > export SCIPION_DOMAIN="pwem" > > export SCIPION_FONT_NAME="Helvetica" > > export SCIPION_HOME="/opt/Scipion3" > > export SCIPION_HOSTS="/opt/Scipion3/config/hosts.conf" > > export SCIPION_LOCAL_CONFIG="/home/panos/.config/scipion/scipion.conf" > > export SCIPION_LOG="/home/panos/ScipionUserData/logs/scipion.log" > > export SCIPION_LOGO="scipion_logo.gif" > > export SCIPION_LOGS="/home/panos/ScipionUserData/logs" > > export SCIPION_NOTES_FILE="notes.txt" > > export SCIPION_NOTIFY="True" > > export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/" > > export SCIPION_PROTOCOLS="/opt/Scipion3/config/protocols.conf" > > export SCIPION_SOFTWARE="/opt/Scipion3/software" > > export SCIPION_SUPPORT_EMAIL="sc...@cn..." > > export SCIPION_TESTS="/opt/Scipion3/data/tests" > > export SCIPION_TESTS_CMD="scipion3 tests" > > export SCIPION_TESTS_OUTPUT="/home/panos/ScipionUserData/Tests" > > export SCIPION_TMP="/home/panos/ScipionUserData/tmp" > > export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion" > > export > SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software" > > export > SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests" > > export SCIPION_USER_DATA="/data1/ScipionUserData" > > export SCIPION_VERSION="v3.0.7 - Eugenius" > > export SIDESPLITTER_HOME="/opt/Scipion3/software/em/sidesplitter-1.2" > > export SPIDER="spider_linux_mp_intel64" > > export SPIDER_HOME="/opt/Scipion3/software/em/spider-26.06" > > export SPIDER_MPI="spider_linux_mpi_opt64" > > export TOPAZ_ENV_ACTIVATION="conda activate topaz-0.2.3" > > export VMD_HOME="/usr/local/lib/vmd" > > export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]" > > export XMIPP2_HOME="/opt/Scipion3/software/em/Xmipp-2.4-src" > > export XMIPP_HOME="/opt/Scipion3/software/em/xmipp" > > [panos@cryoem01 ~]$ > > *scipion3 run printenv* > > [panos@cryoem01 ~]$ scipion3 run printenv > > Scipion v3.0.7 - Eugenius > > ** Running command: printenv > > SCIPION_VERSION=v3.0.7 - Eugenius > > SCIPION_LOGO=scipion_logo.gif > > GAUTOMATCH_CUDA_LIB=/usr/local/cuda/lib64 > > MAXIT_HOME=software/em/maxit-10.1 > > XDG_SESSION_ID=c3 > > SSH_AGENT_PID=2160 > > IMOD_DIR=/usr/local/IMOD > > HOSTNAME=cryoem01 > > SCIPION_FONT_NAME=Helvetica > > RELION_CUDA_BIN=/usr/local/cuda/bin > > IMSETTINGS_INTEGRATE_DESKTOP=yes > > XRDP_SOCKET_PATH=/run/xrdp > > CRYOLO_GENERIC_DENOISED_MODEL=software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > > SCIPION_TESTS_CMD=scipion3 tests > > VTE_VERSION=5204 > > XDG_MENU_PREFIX=gnome- > > SHELL=/bin/bash > > TERM=xterm-256color > > SIDESPLITTER_HOME=software/em/sidesplitter-1.2 > > HISTSIZE=1000 > > IMOD_QTLIBDIR=/usr/local/IMOD/qtlib > > SCIPION_NOTIFY=True > > SCIPION_URL=http://scipion.cnb.csic.es/downloads/scipion > > CISTEM_HOME=software/em/cistem-1.0.0-beta > > SPIDER_HOME=software/em/spider-26.06 > > SCIPION_DOMAIN=pwem > > SCIPION_USER_DATA=/data1/ScipionUserData > > CRYOLO_GENERIC_MODEL=software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > > SCIPION_TESTS_OUTPUT=/home/panos/ScipionUserData/Tests > > GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/409e3dd0_2aca_48db_a92c_2905ab5689a1 > > GJS_DEBUG_OUTPUT=stderr > > DOGPICKER_HOME=software/em/dogpicker-0.2.1.1 > > SCIPION_PROTOCOLS=/opt/Scipion3/config/protocols.conf > > CCP4_HOME=software/em/ccp4-7.0.056 > > CRYOASSESS_ENV_ACTIVATION=conda activate cryoassess-0.1.0 > > DYNAMO_HOME=software/em/dynamo-1.146 > > PHENIX_HOME=software/em/phenix- > > GJS_DEBUG_TOPICS=JS ERROR;JS LOG > > SCIPION_HOSTS=/opt/Scipion3/config/hosts.conf > > GAUTOMATCH_HOME=software/em/gautomatch-0.56 > > SCIPION_PLUGIN_REPO_URL=http://scipion.i2pc.es/getplugins/ > > CRYOLO_NS_GENERIC_MODEL=software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > > GCTF_HOME=software/em/Gctf_v1.06 > > LC_ALL=en_US.UTF-8 > > CRYOASSESS_MODEL_MIC=software/em/cryoassess-models/micassess_051419.h5 > > IMSETTINGS_MODULE=none > > CUDA_HOME=/usr/local/cuda > > USER=panos > > 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> > LD_LIBRARY_PATH=/usr/local/cuda-10.0/lib64:/opt/Scipion3/software/lib > > SCIPION_URL_TESTDATA=http://scipion.cnb.csic.es/downloads/scipion/data/tests > > MOTIONCOR2_BIN=MotionCor2_1.3.2-Cuda100 > > GNOME_TERMINAL_SERVICE=:1.103 > > SCIPION_SUPPORT_EMAIL=sc...@cn... > > GCTF=Gctf-v1.06_sm_30_cu8.0_x86_64 > > XMIPP_HOME=software/em/xmipp > > FSC3D_HOME=software/em/fsc3D-3.0 > > SSH_AUTH_SOCK=/tmp/ssh-ZJq5X9BOWO6G/agent.1847 > > SPIDER_MPI=spider_linux_mpi_opt64 > > SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/1847,unix/unix:/tmp/.ICE-unix/1847 > > CRYOLO_ENV_ACTIVATION_CPU=conda activate cryoloCPU-1.7.6 > > EMPIAR_TOKEN= > > VIRTUAL_ENV=/opt/Scipion3/.scipion3env > > XRDP_PULSE_SINK_SOCKET=xrdp_chansrv_audio_out_socket_10 > > SCIPION_CWD=/home/panos > > PULSE_SCRIPT=/etc/xrdp/pulse/default.pa > > SCIPION_TESTS=/opt/Scipion3/data/tests > > SPIDER=spider_linux_mp_intel64 > > GNOME_SHELL_SESSION_MODE=classic > > CRYOSPARC_USER=ctueting > > MAIL=/var/spool/mail/panos > > PATH=/opt/Scipion3/.scipion3env/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/sbin:/bin:/usr/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin > > SCIPION_LOGS=/home/panos/ScipionUserData/logs > > SCIPION_CONFIG=/opt/Scipion3/config/scipion.conf > > IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug > > QT_IM_MODULE=ibus > > _=/bin/printenv > > CRYOLO_ENV_ACTIVATION=conda activate cryolo-1.7.6 > > WIZARD_MASK_COLOR=[0.125, 0.909, 0.972] > > ATSAS_HOME=software/em/atsas-3.0.1 > > JANNI_GENERIC_MODEL=software/em/janni_model-20190703/gmodel_janni_20190703.h5 > > PWD=/home/panos > > XMODIFIERS=@im=ibus > > CRYOLO_CUDA_LIB=/usr/local/cuda/lib64 > > ETHAN_HOME=software/em/ethan-1.2 > > GCTF_CUDA_LIB=/usr/local/cuda-8.0/lib64 > > MOTIONCOR2_HOME=software/em/motioncor2-1.3.2 > > XMIPP2_HOME=software/em/Xmipp-2.4-src > > pkgdir=/usr/local/I-TASSER5.1 > > XRDP_SESSION=1 > > IMOD_JAVADIR=/usr/local/java > > SCIPION_SOFTWARE=/opt/Scipion3/software > > LANG=en_US.UTF-8 > > XRDP_PULSE_SOURCE_SOCKET=xrdp_chansrv_audio_in_socket_10 > > SCIPION_NOTES_FILE=notes.txt > > CRYOASSESS_MODEL_2D=software/em/cryoassess-models/2dassess_062119.h5 > > CRYOSPARC_HOME=/home/panos/software/cryosparc > > MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles > > SCIPION_URL_SOFTWARE=http://scipion.cnb.csic.es/downloads/scipion/software > > GAUTOMATCH=Gautomatch_v0.56_sm30-75_cu10.1 > > RELION_CUDA_LIB=/usr/local/cuda/lib64 > > LOADEDMODULES= > > LOCSCALE_HOME=software/em/locscale-0.1 > > FOR_DISABLE_STACK_TRACE=1 > > EMFACILITIES_HOME=software/em/ > > ASCP=~/.aspera/connect/bin/ascp > > RESMAP_HOME=software/em/resmap-1.95 > > SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass > > HISTCONTROL=ignoredups > > ASPERA_SCP_PASS= > > SHLVL=5 > > HOME=/home/panos > > CONDA_ACTIVATION_CMD=eval > "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash > hook)" > > CTFFIND4_HOME=software/em/ctffind4-4.1.14 > > MOTIONCOR2_CUDA_LIB=/usr/local/cuda/lib64 > > SCIPION_TMP=/home/panos/ScipionUserData/tmp > > EMAN2_HOME=software/em/eman-2.31 > > GNOME_DESKTOP_SESSION_ID=this-is-deprecated > > CRYO_PROJECTS_DIR=/data1/ScipionUserData/projects/cryosparc_plugin > > IMAGIC_HOME=software/em/imagic-190830 > > SCIPION_LOCAL_CONFIG=/home/panos/.config/scipion/scipion.conf > > PYTHONPATH=:/opt/Scipion3/software/bindings > > LOGNAME=panos > > NOVACTF_HOME=software/em/novactf-master > > BSOFT_HOME=software/em/bsoft-2.0.7 > > DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-FKQakXHYCC,guid=649474707764c616b7441e9f60802f4a > > XDG_DATA_DIRS=/home/panos/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share > > MODULESHOME=/usr/share/Modules > > MPI_HOME=/usr/local/mpich-3.2.1 > > UID=1000 > > CONTINUOUSFLEX_HOME=software/em/xmipp > > LESSOPEN=||/usr/bin/lesspipe.sh %s > > IMOD_CALIB_DIR=/usr/local/ImodCalib > > JAVA_MAX_MEMORY=12 > > RESMAP=ResMap-1.95-cuda-Centos7x64 > > EMAN2SCRATCHDIR=/tmp > > SCIPION_HOME=/opt/Scipion3 > > FSC3D_ACTIVATION_CMD=conda activate 3DFSC > > RELION_HOME=software/em/relion-3.1.0 > > VMD_HOME=/usr/local/lib/vmd > > VIEWERS={"Volume":["pwem.viewers.DataViewer"], > "VolumeMask":["pwem.viewers.DataViewer"]} > > DISPLAY=:10.0 > > XDG_RUNTIME_DIR=/run/user/1000 > > SCIPION_LOG=/home/panos/ScipionUserData/logs/scipion.log > > XDG_CURRENT_DESKTOP=GNOME > > EM_ROOT=software/em > > NMA_HOME=software/em/nma > > COLORTERM=truecolor > > CHIMERA_HOME=software/em/chimerax-1.1 > > EMXLIB_HOME=software/em/emx_export-1.0.0 > > IMOD_HOME=software/em/imod-4.10.42/IMOD > > RESMAP_GPU_LIB=ResMap_krnl-cuda-V8.0.61-sm60_gpu.so > > TOPAZ_ENV_ACTIVATION=conda activate topaz-0.2.3 > > BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` > > } > > [panos@cryoem01 ~]$ > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> > for Windows 10 > > *From: *Pablo Conesa <mailto:pc...@cn...> > *Sent: *Wednesday, April 21, 2021 7:06 PM > *To: *sci...@li... > <mailto:sci...@li...> > *Subject: *Re: [scipion-users] Antw: Re: Re: Antw: RE: deep > consensus pickling error > > 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 the folder under software and > removed the > conda enviroment, and now, no enviroment is generated at > all. Logically, > 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 A. Semchonok" > > <sem...@gm... > <mailto:sem...@gm...><mailto:sem...@gm... > <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(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 > > lis...@li...https > <mailto:lis...@li...https>://lists.sourceforge.net/lists/listinfo/scipion-users--<http://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 received the > message by > 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... <mailto:sci...@li...> > > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry A. S. <sem...@gm...> - 2021-04-21 20:48:03
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<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} </style><![endif]--><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} pre {mso-style-priority:99; mso-style-link:"HTML Preformatted Char"; margin:0in; font-size:10.0pt; font-family:"Courier New";} span.HTMLPreformattedChar {mso-style-name:"HTML Preformatted Char"; mso-style-priority:99; mso-style-link:"HTML Preformatted"; font-family:"Courier New";} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-GB>Dear Pablo,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thank you!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Please see the result of <o:p></o:p></span></p><p class=MsoNormal><b><span lang=EN-GB>Scipion3 installb<o:p></o:p></span></b></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><img width=458 height=460 style='width:4.7708in;height:4.7864in' id="Picture_x0020_3" src="cid:image003.png@01D73700.5498B2A0"><b><span lang=EN-GB><o:p></o:p></span></b></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</p><p class=MsoNormal>Dmitry</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:pc...@cn...">pc...@cn...</a><br><b>Sent: </b>Wednesday, April 21, 2021 10:19 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Providing Eman Fonda can handle environments the same way a standard conda installation does, then, I'd say the deepLearningToolkit environment is not present. </p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>What is the output of</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Scipion3 instalb?</p></div></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>El 21 abr. 2021 20:28, "Dmitry A. Semchonok" <sem...@gm...> escribió:</p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><p>Dear Pablo,</p><p>Thank you ! please have a look below.</p><p> </p><p>Sincerely,</p><p>Dmitry</p><p> </p><p><b><span style='color:black;background:yellow'>scipion3 printenv</span> </b></p><p><span style='color:red'>[panos@cryoem01 ~]$ scipion3 printenv</span></p><p><span style='color:red'>Scipion v3.0.7 - Eugenius</span></p><p><span style='color:red'>export ASCP="~/.aspera/connect/bin/ascp"</span></p><p><span style='color:red'>export ASPERA_SCP_PASS=""</span></p><p><span style='color:red'>export ATSAS_HOME="/opt/Scipion3/software/em/atsas-3.0.1"</span></p><p><span style='color:red'>export BSOFT_HOME="/opt/Scipion3/software/em/bsoft-2.0.7"</span></p><p><span style='color:red'>export CCP4_HOME="/opt/Scipion3/software/em/ccp4-7.0.056"</span></p><p><span style='color:red'>export CHIMERA_HOME="/opt/Scipion3/software/em/chimerax-1.1"</span></p><p><span style='color:red'>export CISTEM_HOME="/opt/Scipion3/software/em/cistem-1.0.0-beta"</span></p><p><span style='color:red'>export CONDA_ACTIVATION_CMD="eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)""</span></p><p><span style='color:red'>export CONTINUOUSFLEX_HOME="/opt/Scipion3/software/em/xmipp"</span></p><p><span style='color:red'>export CRYOASSESS_ENV_ACTIVATION="conda activate cryoassess-0.1.0"</span></p><p><span style='color:red'>export CRYOASSESS_MODEL_2D="/opt/Scipion3/software/em/cryoassess-models/2dassess_062119.h5"</span></p><p><span style='color:red'>export CRYOASSESS_MODEL_MIC="/opt/Scipion3/software/em/cryoassess-models/micassess_051419.h5"</span></p><p><span style='color:red'>export CRYOLO_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style='color:red'>export CRYOLO_ENV_ACTIVATION="conda activate cryolo-1.7.6"</span></p><p><span style='color:red'>export CRYOLO_ENV_ACTIVATION_CPU="conda activate cryoloCPU-1.7.6"</span></p><p><span style='color:red'>export CRYOLO_GENERIC_DENOISED_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5"</span></p><p><span style='color:red'>export CRYOLO_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5"</span></p><p><span style='color:red'>export CRYOLO_NS_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5"</span></p><p><span style='color:red'>export CRYOSPARC_HOME="/home/panos/software/cryosparc"</span></p><p><span style='color:red'>export CRYOSPARC_USER="ctueting"</span></p><p><span style='color:red'>export CRYO_PROJECTS_DIR="/data1/ScipionUserData/projects/cryosparc_plugin"</span></p><p><span style='color:red'>export CTFFIND4_HOME="/opt/Scipion3/software/em/ctffind4-4.1.14"</span></p><p><span style='color:red'>export DOGPICKER_HOME="/opt/Scipion3/software/em/dogpicker-0.2.1.1"</span></p><p><span style='color:red'>export DYNAMO_HOME="/opt/Scipion3/software/em/dynamo-1.146"</span></p><p><span style='color:red'>export EMAN2SCRATCHDIR="/tmp"</span></p><p><span style='color:red'>export EMAN2_HOME="/opt/Scipion3/software/em/eman-2.31"</span></p><p><span style='color:red'>export EMFACILITIES_HOME="/opt/Scipion3/software/em/"</span></p><p><span style='color:red'>export EMPIAR_TOKEN=""</span></p><p><span style='color:red'>export EMXLIB_HOME="/opt/Scipion3/software/em/emx_export-1.0.0"</span></p><p><span style='color:red'>export EM_ROOT="software/em"</span></p><p><span style='color:red'>export ETHAN_HOME="/opt/Scipion3/software/em/ethan-1.2"</span></p><p><span style='color:red'>export FSC3D_ACTIVATION_CMD="conda activate 3DFSC"</span></p><p><span style='color:red'>export FSC3D_HOME="/opt/Scipion3/software/em/fsc3D-3.0"</span></p><p><span style='color:red'>export GAUTOMATCH="Gautomatch_v0.56_sm30-75_cu10.1"</span></p><p><span style='color:red'>export GAUTOMATCH_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style='color:red'>export GAUTOMATCH_HOME="/opt/Scipion3/software/em/gautomatch-0.56"</span></p><p><span style='color:red'>export GCTF="Gctf-v1.06_sm_30_cu8.0_x86_64"</span></p><p><span style='color:red'>export GCTF_CUDA_LIB="/usr/local/cuda-8.0/lib64"</span></p><p><span style='color:red'>export GCTF_HOME="/opt/Scipion3/software/em/Gctf_v1.06"</span></p><p><span style='color:red'>export IMAGIC_HOME="/opt/Scipion3/software/em/imagic-190830"</span></p><p><span style='color:red'>export IMOD_HOME="/opt/Scipion3/software/em/imod-4.10.42/IMOD"</span></p><p><span style='color:red'>export JANNI_GENERIC_MODEL="/opt/Scipion3/software/em/janni_model-20190703/gmodel_janni_20190703.h5"</span></p><p><span style='color:red'>export JAVA_MAX_MEMORY="12"</span></p><p><span style='color:red'>export LOCSCALE_HOME="/opt/Scipion3/software/em/locscale-0.1"</span></p><p><span style='color:red'>export MAXIT_HOME="/opt/Scipion3/software/em/maxit-10.1"</span></p><p><span style='color:red'>export MOTIONCOR2_BIN="MotionCor2_1.3.2-Cuda100"</span></p><p><span style='color:red'>export MOTIONCOR2_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style='color:red'>export MOTIONCOR2_HOME="/opt/Scipion3/software/em/motioncor2-1.3.2"</span></p><p><span style='color:red'>export NMA_HOME="/opt/Scipion3/software/em/nma"</span></p><p><span style='color:red'>export NOVACTF_HOME="/opt/Scipion3/software/em/novactf-master"</span></p><p><span style='color:red'>export PHENIX_HOME="/opt/Scipion3/software/em/phenix-"</span></p><p><span style='color:red'>export RELION_CUDA_BIN="/usr/local/cuda/bin"</span></p><p><span style='color:red'>export RELION_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style='color:red'>export RELION_HOME="/opt/Scipion3/software/em/relion-3.1.0"</span></p><p><span style='color:red'>export RESMAP="ResMap-1.95-cuda-Centos7x64"</span></p><p><span style='color:red'>export RESMAP_GPU_LIB="ResMap_krnl-cuda-V8.0.61-sm60_gpu.so"</span></p><p><span style='color:red'>export RESMAP_HOME="/opt/Scipion3/software/em/resmap-1.95"</span></p><p><span style='color:red'>export SCIPION_CONFIG="/opt/Scipion3/config/scipion.conf"</span></p><p><span style='color:red'>export SCIPION_CWD="/home/panos"</span></p><p><span style='color:red'>export SCIPION_DOMAIN="pwem"</span></p><p><span style='color:red'>export SCIPION_FONT_NAME="Helvetica"</span></p><p><span style='color:red'>export SCIPION_HOME="/opt/Scipion3"</span></p><p><span style='color:red'>export SCIPION_HOSTS="/opt/Scipion3/config/hosts.conf"</span></p><p><span style='color:red'>export SCIPION_LOCAL_CONFIG="/home/panos/.config/scipion/scipion.conf"</span></p><p><span style='color:red'>export SCIPION_LOG="/home/panos/ScipionUserData/logs/scipion.log"</span></p><p><span style='color:red'>export SCIPION_LOGO="scipion_logo.gif"</span></p><p><span style='color:red'>export SCIPION_LOGS="/home/panos/ScipionUserData/logs"</span></p><p><span style='color:red'>export SCIPION_NOTES_FILE="notes.txt"</span></p><p><span style='color:red'>export SCIPION_NOTIFY="True"</span></p><p><span style='color:red'>export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/"</span></p><p><span style='color:red'>export SCIPION_PROTOCOLS="/opt/Scipion3/config/protocols.conf"</span></p><p><span style='color:red'>export SCIPION_SOFTWARE="/opt/Scipion3/software"</span></p><p><span style='color:red'>export SCIPION_SUPPORT_EMAIL="sc...@cn..."</span></p><p><span style='color:red'>export SCIPION_TESTS="/opt/Scipion3/data/tests"</span></p><p><span style='color:red'>export SCIPION_TESTS_CMD="scipion3 tests"</span></p><p><span style='color:red'>export SCIPION_TESTS_OUTPUT="/home/panos/ScipionUserData/Tests"</span></p><p><span style='color:red'>export SCIPION_TMP="/home/panos/ScipionUserData/tmp"</span></p><p><span style='color:red'>export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion"</span></p><p><span style='color:red'>export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software"</span></p><p><span style='color:red'>export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests"</span></p><p><span style='color:red'>export SCIPION_USER_DATA="/data1/ScipionUserData"</span></p><p><span style='color:red'>export SCIPION_VERSION="v3.0.7 - Eugenius"</span></p><p><span style='color:red'>export SIDESPLITTER_HOME="/opt/Scipion3/software/em/sidesplitter-1.2"</span></p><p><span style='color:red'>export SPIDER="spider_linux_mp_intel64"</span></p><p><span style='color:red'>export SPIDER_HOME="/opt/Scipion3/software/em/spider-26.06"</span></p><p><span style='color:red'>export SPIDER_MPI="spider_linux_mpi_opt64"</span></p><p><span style='color:red'>export TOPAZ_ENV_ACTIVATION="conda activate topaz-0.2.3"</span></p><p><span style='color:red'>export VMD_HOME="/usr/local/lib/vmd"</span></p><p><span style='color:red'>export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]"</span></p><p><span style='color:red'>export XMIPP2_HOME="/opt/Scipion3/software/em/Xmipp-2.4-src"</span></p><p><span style='color:red'>export XMIPP_HOME="/opt/Scipion3/software/em/xmipp"</span></p><p><span style='color:red'>[panos@cryoem01 ~]$</span></p><p><b><span style='color:black;background:yellow'>scipion3 run printenv</span></b></p><p> </p><p><span style='color:red'>[panos@cryoem01 ~]$ scipion3 run printenv</span></p><p><span style='color:red'>Scipion v3.0.7 - Eugenius</span></p><p><span style='color:red'>** Running command: printenv </span></p><p><span style='color:red'>SCIPION_VERSION=v3.0.7 - Eugenius</span></p><p><span style='color:red'>SCIPION_LOGO=scipion_logo.gif</span></p><p><span style='color:red'>GAUTOMATCH_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style='color:red'>MAXIT_HOME=software/em/maxit-10.1</span></p><p><span style='color:red'>XDG_SESSION_ID=c3</span></p><p><span style='color:red'>SSH_AGENT_PID=2160</span></p><p><span style='color:red'>IMOD_DIR=/usr/local/IMOD</span></p><p><span style='color:red'>HOSTNAME=cryoem01</span></p><p><span style='color:red'>SCIPION_FONT_NAME=Helvetica</span></p><p><span style='color:red'>RELION_CUDA_BIN=/usr/local/cuda/bin</span></p><p><span style='color:red'>IMSETTINGS_INTEGRATE_DESKTOP=yes</span></p><p><span style='color:red'>XRDP_SOCKET_PATH=/run/xrdp</span></p><p><span style='color:red'>CRYOLO_GENERIC_DENOISED_MODEL=software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5</span></p><p><span style='color:red'>SCIPION_TESTS_CMD=scipion3 tests</span></p><p><span style='color:red'>VTE_VERSION=5204</span></p><p><span style='color:red'>XDG_MENU_PREFIX=gnome-</span></p><p><span style='color:red'>SHELL=/bin/bash</span></p><p><span style='color:red'>TERM=xterm-256color</span></p><p><span style='color:red'>SIDESPLITTER_HOME=software/em/sidesplitter-1.2</span></p><p><span style='color:red'>HISTSIZE=1000</span></p><p><span style='color:red'>IMOD_QTLIBDIR=/usr/local/IMOD/qtlib</span></p><p><span style='color:red'>SCIPION_NOTIFY=True</span></p><p><span style='color:red'>SCIPION_URL=http://scipion.cnb.csic.es/downloads/scipion</span></p><p><span style='color:red'>CISTEM_HOME=software/em/cistem-1.0.0-beta</span></p><p><span style='color:red'>SPIDER_HOME=software/em/spider-26.06</span></p><p><span style='color:red'>SCIPION_DOMAIN=pwem</span></p><p><span style='color:red'>SCIPION_USER_DATA=/data1/ScipionUserData</span></p><p><span style='color:red'>CRYOLO_GENERIC_MODEL=software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5</span></p><p><span style='color:red'>SCIPION_TESTS_OUTPUT=/home/panos/ScipionUserData/Tests</span></p><p><span style='color:red'>GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/409e3dd0_2aca_48db_a92c_2905ab5689a1</span></p><p><span style='color:red'>GJS_DEBUG_OUTPUT=stderr</span></p><p><span style='color:red'>DOGPICKER_HOME=software/em/dogpicker-0.2.1.1</span></p><p><span style='color:red'>SCIPION_PROTOCOLS=/opt/Scipion3/config/protocols.conf</span></p><p><span style='color:red'>CCP4_HOME=software/em/ccp4-7.0.056</span></p><p><span style='color:red'>CRYOASSESS_ENV_ACTIVATION=conda activate cryoassess-0.1.0</span></p><p><span style='color:red'>DYNAMO_HOME=software/em/dynamo-1.146</span></p><p><span style='color:red'>PHENIX_HOME=software/em/phenix-</span></p><p><span style='color:red'>GJS_DEBUG_TOPICS=JS ERROR;JS LOG</span></p><p><span style='color:red'>SCIPION_HOSTS=/opt/Scipion3/config/hosts.conf</span></p><p><span style='color:red'>GAUTOMATCH_HOME=software/em/gautomatch-0.56</span></p><p><span style='color:red'>SCIPION_PLUGIN_REPO_URL=http://scipion.i2pc.es/getplugins/</span></p><p><span style='color:red'>CRYOLO_NS_GENERIC_MODEL=software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5</span></p><p><span style='color:red'>GCTF_HOME=software/em/Gctf_v1.06</span></p><p><span style='color:red'>LC_ALL=en_US.UTF-8</span></p><p><span style='color:red'>CRYOASSESS_MODEL_MIC=software/em/cryoassess-models/micassess_051419.h5</span></p><p><span style='color:red'>IMSETTINGS_MODULE=none</span></p><p><span style='color:red'>CUDA_HOME=/usr/local/cuda</span></p><p><span style='color:red'>USER=panos</span></p><p><span style='color:red'>LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:</span></p><p><span style='color:red'>LD_LIBRARY_PATH=/usr/local/cuda-10.0/lib64:/opt/Scipion3/software/lib</span></p><p><span style='color:red'>SCIPION_URL_TESTDATA=http://scipion.cnb.csic.es/downloads/scipion/data/tests</span></p><p><span style='color:red'>MOTIONCOR2_BIN=MotionCor2_1.3.2-Cuda100</span></p><p><span style='color:red'>GNOME_TERMINAL_SERVICE=:1.103</span></p><p><span style='color:red'>SCIPION_SUPPORT_EMAIL=sc...@cn...</span></p><p><span style='color:red'>GCTF=Gctf-v1.06_sm_30_cu8.0_x86_64</span></p><p><span style='color:red'>XMIPP_HOME=software/em/xmipp</span></p><p><span style='color:red'>FSC3D_HOME=software/em/fsc3D-3.0</span></p><p><span style='color:red'>SSH_AUTH_SOCK=/tmp/ssh-ZJq5X9BOWO6G/agent.1847</span></p><p><span style='color:red'>SPIDER_MPI=spider_linux_mpi_opt64</span></p><p><span style='color:red'>SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/1847,unix/unix:/tmp/.ICE-unix/1847</span></p><p><span style='color:red'>CRYOLO_ENV_ACTIVATION_CPU=conda activate cryoloCPU-1.7.6</span></p><p><span style='color:red'>EMPIAR_TOKEN=</span></p><p><span style='color:red'>VIRTUAL_ENV=/opt/Scipion3/.scipion3env</span></p><p><span style='color:red'>XRDP_PULSE_SINK_SOCKET=xrdp_chansrv_audio_out_socket_10</span></p><p><span style='color:red'>SCIPION_CWD=/home/panos</span></p><p><span style='color:red'>PULSE_SCRIPT=/etc/xrdp/pulse/default.pa</span></p><p><span style='color:red'>SCIPION_TESTS=/opt/Scipion3/data/tests</span></p><p><span style='color:red'>SPIDER=spider_linux_mp_intel64</span></p><p><span style='color:red'>GNOME_SHELL_SESSION_MODE=classic</span></p><p><span style='color:red'>CRYOSPARC_USER=ctueting</span></p><p><span style='color:red'>MAIL=/var/spool/mail/panos</span></p><p><span style='color:red'>PATH=/opt/Scipion3/.scipion3env/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/sbin:/bin:/usr/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin</span></p><p><span style='color:red'>SCIPION_LOGS=/home/panos/ScipionUserData/logs</span></p><p><span style='color:red'>SCIPION_CONFIG=/opt/Scipion3/config/scipion.conf</span></p><p><span style='color:red'>IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug</span></p><p><span style='color:red'>QT_IM_MODULE=ibus</span></p><p><span style='color:red'>_=/bin/printenv</span></p><p><span style='color:red'>CRYOLO_ENV_ACTIVATION=conda activate cryolo-1.7.6</span></p><p><span style='color:red'>WIZARD_MASK_COLOR=[0.125, 0.909, 0.972]</span></p><p><span style='color:red'>ATSAS_HOME=software/em/atsas-3.0.1</span></p><p><span style='color:red'>JANNI_GENERIC_MODEL=software/em/janni_model-20190703/gmodel_janni_20190703.h5</span></p><p><span style='color:red'>PWD=/home/panos</span></p><p><span style='color:red'>XMODIFIERS=@im=ibus</span></p><p><span style='color:red'>CRYOLO_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style='color:red'>ETHAN_HOME=software/em/ethan-1.2</span></p><p><span style='color:red'>GCTF_CUDA_LIB=/usr/local/cuda-8.0/lib64</span></p><p><span style='color:red'>MOTIONCOR2_HOME=software/em/motioncor2-1.3.2</span></p><p><span style='color:red'>XMIPP2_HOME=software/em/Xmipp-2.4-src</span></p><p><span style='color:red'>pkgdir=/usr/local/I-TASSER5.1</span></p><p><span style='color:red'>XRDP_SESSION=1</span></p><p><span style='color:red'>IMOD_JAVADIR=/usr/local/java</span></p><p><span style='color:red'>SCIPION_SOFTWARE=/opt/Scipion3/software</span></p><p><span style='color:red'>LANG=en_US.UTF-8</span></p><p><span style='color:red'>XRDP_PULSE_SOURCE_SOCKET=xrdp_chansrv_audio_in_socket_10</span></p><p><span style='color:red'>SCIPION_NOTES_FILE=notes.txt</span></p><p><span style='color:red'>CRYOASSESS_MODEL_2D=software/em/cryoassess-models/2dassess_062119.h5</span></p><p><span style='color:red'>CRYOSPARC_HOME=/home/panos/software/cryosparc</span></p><p><span style='color:red'>MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles</span></p><p><span style='color:red'>SCIPION_URL_SOFTWARE=http://scipion.cnb.csic.es/downloads/scipion/software</span></p><p><span style='color:red'>GAUTOMATCH=Gautomatch_v0.56_sm30-75_cu10.1</span></p><p><span style='color:red'>RELION_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style='color:red'>LOADEDMODULES=</span></p><p><span style='color:red'>LOCSCALE_HOME=software/em/locscale-0.1</span></p><p><span style='color:red'>FOR_DISABLE_STACK_TRACE=1</span></p><p><span style='color:red'>EMFACILITIES_HOME=software/em/</span></p><p><span style='color:red'>ASCP=~/.aspera/connect/bin/ascp</span></p><p><span style='color:red'>RESMAP_HOME=software/em/resmap-1.95</span></p><p><span style='color:red'>SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass</span></p><p><span style='color:red'>HISTCONTROL=ignoredups</span></p><p><span style='color:red'>ASPERA_SCP_PASS=</span></p><p><span style='color:red'>SHLVL=5</span></p><p><span style='color:red'>HOME=/home/panos</span></p><p><span style='color:red'>CONDA_ACTIVATION_CMD=eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)"</span></p><p><span style='color:red'>CTFFIND4_HOME=software/em/ctffind4-4.1.14</span></p><p><span style='color:red'>MOTIONCOR2_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style='color:red'>SCIPION_TMP=/home/panos/ScipionUserData/tmp</span></p><p><span style='color:red'>EMAN2_HOME=software/em/eman-2.31</span></p><p><span style='color:red'>GNOME_DESKTOP_SESSION_ID=this-is-deprecated</span></p><p><span style='color:red'>CRYO_PROJECTS_DIR=/data1/ScipionUserData/projects/cryosparc_plugin</span></p><p><span style='color:red'>IMAGIC_HOME=software/em/imagic-190830</span></p><p><span style='color:red'>SCIPION_LOCAL_CONFIG=/home/panos/.config/scipion/scipion.conf</span></p><p><span style='color:red'>PYTHONPATH=:/opt/Scipion3/software/bindings</span></p><p><span style='color:red'>LOGNAME=panos</span></p><p><span style='color:red'>NOVACTF_HOME=software/em/novactf-master</span></p><p><span style='color:red'>BSOFT_HOME=software/em/bsoft-2.0.7</span></p><p><span style='color:red'>DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-FKQakXHYCC,guid=649474707764c616b7441e9f60802f4a</span></p><p><span style='color:red'>XDG_DATA_DIRS=/home/panos/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share</span></p><p><span style='color:red'>MODULESHOME=/usr/share/Modules</span></p><p><span style='color:red'>MPI_HOME=/usr/local/mpich-3.2.1</span></p><p><span style='color:red'>UID=1000</span></p><p><span style='color:red'>CONTINUOUSFLEX_HOME=software/em/xmipp</span></p><p><span style='color:red'>LESSOPEN=||/usr/bin/lesspipe.sh %s</span></p><p><span style='color:red'>IMOD_CALIB_DIR=/usr/local/ImodCalib</span></p><p><span style='color:red'>JAVA_MAX_MEMORY=12</span></p><p><span style='color:red'>RESMAP=ResMap-1.95-cuda-Centos7x64</span></p><p><span style='color:red'>EMAN2SCRATCHDIR=/tmp</span></p><p><span style='color:red'>SCIPION_HOME=/opt/Scipion3</span></p><p><span style='color:red'>FSC3D_ACTIVATION_CMD=conda activate 3DFSC</span></p><p><span style='color:red'>RELION_HOME=software/em/relion-3.1.0</span></p><p><span style='color:red'>VMD_HOME=/usr/local/lib/vmd</span></p><p><span style='color:red'>VIEWERS={"Volume":["pwem.viewers.DataViewer"], "VolumeMask":["pwem.viewers.DataViewer"]}</span></p><p><span style='color:red'>DISPLAY=:10.0</span></p><p><span style='color:red'>XDG_RUNTIME_DIR=/run/user/1000</span></p><p><span style='color:red'>SCIPION_LOG=/home/panos/ScipionUserData/logs/scipion.log</span></p><p><span style='color:red'>XDG_CURRENT_DESKTOP=GNOME</span></p><p><span style='color:red'>EM_ROOT=software/em</span></p><p><span style='color:red'>NMA_HOME=software/em/nma</span></p><p><span style='color:red'>COLORTERM=truecolor</span></p><p><span style='color:red'>CHIMERA_HOME=software/em/chimerax-1.1</span></p><p><span style='color:red'>EMXLIB_HOME=software/em/emx_export-1.0.0</span></p><p><span style='color:red'>IMOD_HOME=software/em/imod-4.10.42/IMOD</span></p><p><span style='color:red'>RESMAP_GPU_LIB=ResMap_krnl-cuda-V8.0.61-sm60_gpu.so</span></p><p><span style='color:red'>TOPAZ_ENV_ACTIVATION=conda activate topaz-0.2.3</span></p><p><span style='color:red'>BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`</span></p><p><span style='color:red'>}</span></p><p><span style='color:red'>[panos@cryoem01 ~]$</span></p><p><span style='color:red'> </span></p><p> </p><p>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p> </p><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p><b>From: </b><a href="mailto:pc...@cn...">Pablo Conesa</a><br><b>Sent: </b>Wednesday, April 21, 2021 7:06 PM<br><b>To: </b><a href="mailto:sci...@li...">sci...@li...</a><br><b>Subject: </b>Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error</p></div><p> </p><p>You have eman2 acting as a conda manager, that is a problem.</p><p>At least the environment is not listed there. </p><p>Does the other plugins work? e.g. cryolo?</p><p>Can you send the output of:</p><p>scipion3 printenv </p><p>and </p><p>scipion3 run printenv</p><p>?</p><div><p>On 21/4/21 17:06, Dmitry Semchonok wrote:</p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Dear colleagues, </p><div><p>Just to add our current error from the xmipp deep learning installation.</p></div><div><p> </p></div><div><p>Interestingly we almost fun to an end of this step but conda issue appeared.</p></div><div><p> </p></div><div><p>Any suggestions?</p></div><div><p> </p></div><div><p> </p></div><div><p> </p></div><div><p><span style='color:#0433FF'>currentDir: /data1/ScipionUserData/projects/Image_processing_cn_10688</span></p></div><div><p><span style='color:#0433FF'>00890: workingDir: Runs/007643_XmippProtScreenDeepLearning</span></p></div><div><p><span style='color:#0433FF'>00891: runMode: Continue</span></p></div><div><p><span style='color:#0433FF'>00892: MPI: 1</span></p></div><div><p><span style='color:#0433FF'>00893: threads: 4</span></p></div><div><p><span style='color:#0433FF'>00894: Starting at step: 3</span></p></div><div><p><span style='color:#0433FF'>00895: Running steps</span></p></div><div><p><span style='color:#0433FF'>00896: STARTED: predict, step 3, time 2021-04-20 11:08:26.633086</span></p></div><div><p><span style='color:#0433FF'>00897: </span></p></div><div><p><span style='color:#0433FF'>00898: $ /usr/local/EMAN_2.21/bin/conda info --env</span></p></div><div><p><span style='color:#0433FF'>00899: # conda environments:</span></p></div><div><p><span style='color:#0433FF'>00900: #</span></p></div><div><p><span style='color:#0433FF'>00901: 3DFSC /home/panos/.conda/envs/3DFSC</span></p></div><div><p><span style='color:#0433FF'>00902: cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0</span></p></div><div><p><span style='color:#0433FF'>00903: cryolo /home/panos/.conda/envs/cryolo</span></p></div><div><p><span style='color:#0433FF'>00904: cryolo /usr/local/EMAN_2.21/envs/cryolo</span></p></div><div><p><span style='color:#0433FF'>00905: cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4</span></p></div><div><p><span style='color:#0433FF'>00906: fsc /usr/local/EMAN_2.21/envs/fsc</span></p></div><div><p><span style='color:#0433FF'>00907: topaz /usr/local/EMAN_2.21/envs/topaz</span></p></div><div><p><span style='color:#0433FF'>00908: root * /usr/local/EMAN_2.21</span></p></div><div><p><span style='color:#0433FF'>00909: </span></p></div><div><p><span style='color:#0433FF'>00910: </span></p></div><div><p><span style='color:#0433FF'>00911: >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)</span></p></div><div><p><span style='color:#0433FF'>00912: Traceback (most recent call last):</span></p></div><div><p><span style='color:#0433FF'>00913: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run</span></p></div><div><p><span style='color:#0433FF'>00914: self._run()</span></p></div><div><p><span style='color:#0433FF'>00915: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run</span></p></div><div><p><span style='color:#0433FF'>00916: resultFiles = self._runFunc()</span></p></div><div><p><span style='color:#0433FF'>00917: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc</span></p></div><div><p><span style='color:#0433FF'>00918: return self._func(*self._args)</span></p></div><div><p><span style='color:#0433FF'>00919: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deeplearning.py", line 319, in predict</span></p></div><div><p><span style='color:#0433FF'>00920: env=self.getCondaEnv())</span></p></div><div><p><span style='color:#0433FF'>00921: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv</span></p></div><div><p><span style='color:#0433FF'>00922: return CondaEnvManager.getCondaEnv(env, envName)</span></p></div><div><p><span style='color:#0433FF'>00923: File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv</span></p></div><div><p><span style='color:#0433FF'>00924: envBin = os.path.join(environDir, "bin")</span></p></div><div><p><span style='color:#0433FF'>00925: File "/usr/lib64/python3.6/posixpath.py", line 80, in join</span></p></div><div><p><span style='color:#0433FF'>00926: a = os.fspath(a)</span></p></div><div><p><span style='color:#0433FF'>00927: TypeError: expected str, bytes or os.PathLike object, not NoneType</span></p></div><div><p><span style='color:#0433FF'>00928: Protocol failed: expected str, bytes or os.PathLike object, not NoneType</span></p></div><div><p><span style='color:#0433FF'>00929: FAILED: predict, step 3, time 2021-04-20 11:08:27.020467</span></p></div><div><p><span style='color:#0433FF'>00930: *** Last status is failed </span></p></div><div><p><span style='color:#0433FF'>00931: ------------------- PROTOCOL FAILED (DONE 3/4)</span></p></div><div><p> </p></div><div><p> </p></div><div><p>Thank you!</p></div><div><p> </p></div><div><p> </p></div><div><p>Sincerely,</p></div><div><p>Dmitry</p></div><div><p> </p></div><div><p> </p><div><p style='margin-bottom:12.0pt'><o:p> </o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p>On 20. Apr 2021, at 11:25, Christian Tüting <<a href="mailto:chr...@bi...">chr...@bi...</a>> wrote:</p></div><p> </p><div><div><p style='margin-bottom:12.0pt'>Hi,<br><br>thank you for your response. I tried this twice. The first time, the<br>"_BACKUP2" folder was popping up again under .conda/envs, so I followed<br>your steps again, deleting the folder under software and removed the<br>conda enviroment, and now, no enviroment is generated at all. Logically,<br>running a job gives this error: ">>> 'xmipp_DLTK_v0.3' conda environment<br>not found... (check list above)". <br><br>Another long-term job is currently running, after this is done, we will<br>restart everything to have a clean system. But do you have any<br>additional tips?<br><br>Thanks in advance<br>Christian<br><br><br><br></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>David Maluenda <<a href="mailto:dma...@ub...">dma...@ub...</a>> 20.04.21 10.02 Uhr >>></p></blockquote></blockquote></blockquote><p style='margin-bottom:12.0pt'>Hi Christian,<br><br>If it already works, I would leave it as it is.<br><br>To make a clear installation, you don't need to reinstall the whole<br>xmipp. You can just reinstall the deepLearningToolkit by<br><br>rm -rf /opt/Scipion3/software/em/deepLearningToolkit<br>conda env remove --name xmipp_DLTK_v0.3_BACKUP2<br>scipion3 installb deepLearningToolkit<br><br><br>Cheers,<br><br><<a href="http://ucm.es/">http://ucm.es/</a>><br>_____<br>Dr. David Maluenda Niubó<br><a href="mailto:dma...@ub...">dma...@ub...</a><<a href="mailto:dma...@ub...">mailto:dma...@ub...</a>> - (+34) 619 029 310<br>Wavefront Engineering<br>Group<<a href="https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA">https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA</a>><br>Applied Physics - UB<<a href="https://www.ub.edu/portal/web/dp-fisica-aplicada">https://www.ub.edu/portal/web/dp-fisica-aplicada</a>><br><br>This email message and any documents attached to it may contain<br>confidential or legally protected material and are intended solely for<br>the use of the individual or organization to whom they are addressed. We<br>remind you that if you are not the intended recipient of this email<br>message or the person responsible for processing it, then you are not<br>authorized to read, save, modify, send, copy or disclose any of its<br>contents. If you have received this email message by mistake, we kindly<br>ask you to inform the sender of this and to eliminate both the message<br>and any attachments it carries from your account. Thank you for your<br>collaboration.<br><br><br><br>On Tue, Apr 20, 2021 at 9:53 AM Christian Tüting<br><<a href="mailto:chr...@bi...">chr...@bi...</a><<a href="mailto:chr...@bi...">mailto:chr...@bi...</a>>><br>wrote:<br>Hi Pablo,<br><br>I will take an eye on this. I have a question regarding dependencies:<br>tensorflow 1.15 requires keras-application>=1.0.8 and<br>keras-preprocessing>=1.0.5, but keras 2.2 requieres older versions<br>(1.0.2 and 1.0.1, respectivly).<br><br>Should we try to uninstall and a clean reinstall of xmipp, to resolve<br>all dependency issues?<br><br>Thank you for your support.<br><br>Best<br>Christian<br><br><br></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Pablo Conesa <<a href="mailto:pc...@cn...">pc...@cn...</a><<a href="mailto:pc...@cn...">mailto:pc...@cn...</a>>></p></blockquote></blockquote></blockquote><p style='margin-bottom:12.0pt'>20.04.21 9.16 Uhr >>><br>Thanks Christian.<br><br>In theory, xmipp defines dependencies strictly<br>(<a href="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</a>)<br><br>I do not know how it ended up with higher versions, but something to<br>keep an eye on.<br><br>On 20/4/21 7:00, Christian Tüting wrote:</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Hi all,<br><br>first the conda path looks actually very strange, and I fixed this<br>direclty. We had some other issues, which were tensorflow-related, but<br>this is fixed.<br><br><br>Just to comment on that, there were first an issue with the tensorflow<br>module. Installing the latest release (2.x) gives an error on "module<br>'tensorflow' has no attribute 'Session'". After fixing that by<br>downgrading, keras was giving an error, that the module does not have</p></blockquote><p style='margin-bottom:12.0pt'>no</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>attribute "tf", which was also fixed by downgrading.<br><br><br><br>TL;DR Eventually, downgrading tensorflow to 1.15.0 and downgrading</p></blockquote><p style='margin-bottom:12.0pt'>keras</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>to 2.2.4 (from 2.2.5) solved the issue<br><br><br>Best<br>Christian<br><br><br></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>"Dmitry A. Semchonok"</p></blockquote></blockquote></blockquote></blockquote><p style='margin-bottom:12.0pt'><<a href="mailto:sem...@gm...">sem...@gm...</a><<a href="mailto:sem...@gm...">mailto:sem...@gm...</a>>> 19.04.21 16.24 Uhr >>></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Dear Carlos Oscar, Pablo, David, Ruben,<br><br><br>Thank you very much for your fast response.<br><br><br>Currently, deep learning is running.<br>A colleague of mine, Christian, kindly looked at the problem.<br><br><br>Let me, please post the errors we had and where we are now.<br>May be Christian can comment more on this issue.<br><br><br>Please see the errors here.<br><a href="https://yadi.sk/d/KlTeKv1O9UCTQg">https://yadi.sk/d/KlTeKv1O9UCTQg</a><br><br><br>Since> Sent: Monday, April 19, 2021 12:57 PM<br>To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David<br>Maluenda<br>Subject: Re: [scipion-users] deep consensus pickling error<br><br><br>Dear Dmitry,<br>let us see if David or Rubén knows where this environment is coming<br>from.<br>Kind regards, Carlos Oscar<br>El 19/04/2021 a las 9:37, Pablo Conesa escribió:<br><br>Hi Dmitry... you have no environment for xmipp_DLTK_v0.3.<br>You have a "weird" xmipp_DLTK_v0.3_BACKUP2<br>/home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2<br><br>On 17/4/21 8:56, Dmitry A. Semchonok wrote:<br><br>Dear colleagues,<br><br>During deep consensus pickling I received the following error<br><br>Any ideas?<br><br>Thank you<br><br>Sincerely,<br>Dmitry<br><br><br><br>[Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min<br>[Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min<br>[Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min<br>[Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min<br>[Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min<br>[Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min<br>[Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min<br>[Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min<br>[Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min<br>[Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min</p></blockquote><p style='margin-bottom:12.0pt'>finished</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>[35mFINISHED[0m: extractParticles, step 12, time 2021-04-17<br>04:05:07.093613<br>[35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17<br>04:05:07.574152<br>[35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17<br>04:26:59.879548<br>[35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444<br>None None None None<br><br>$ /usr/local/EMAN_2.21/bin/conda info --env<br># conda environments:<br>#<br>3DFSC /home/panos/.conda/envs/3DFSC<br>cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0<br>cryolo /home/panos/.conda/envs/cryolo> cryolo </p></blockquote><p style='margin-bottom:12.0pt'> /usr/local/EMAN_2.21/envs/cryolo</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4<br>fsc /usr/local/EMAN_2.21/envs/fsc<br>topaz /usr/local/EMAN_2.21/envs/topaz<br>root * /usr/local/EMAN_2.21<br><br><br></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>'xmipp_DLTK_v0.3' conda environment not found... (check list above)</p></blockquote></blockquote></blockquote><p style='margin-bottom:12.0pt'>Traceback (most recent call last):<br> File</p></blockquote><p style='margin-bottom:12.0pt'>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>line 189, in run<br> self._run()<br> File</p></blockquote><p style='margin-bottom:12.0pt'>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>line 240, in _run<br> resultFiles = self._runFunc()<br> File</p></blockquote><p style='margin-bottom:12.0pt'>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>line 236, in _runFunc<br> return self._func(*self._args)<br> File<br>"/opt/Scipion env=self.getCondaEnv())<br> File</p></blockquote><p style='margin-bottom:12.0pt'>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py",</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>line 204, in getCondaEnv<br> return CondaEnvManager.getCondaEnv(env, envName)<br> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in<br>getCondaEnv<br> envBin = os.path.join(environDir, "bin")<br> File "/usr/lib64/python3.6/posixpath.py", line 80, in join<br> a = os.fspath(a)<br>TypeError: expected str, bytes or os.PathLike object, not NoneType<br>[31mProtocol failed: expected str, bytes or os.PathLike object, not<br>NoneType[0m<br>[35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417<br>*** Last status is failed<br>Sent from Mail for Windows 10<br><br><br><br><br><br>_______________________________________________scipion-users mailing</p></blockquote><p style='margin-bottom:12.0pt'><a href="mailto:lis...@li...https">lis...@li...https</a>://lists.sourceforge.net/lists/listinfo/scipion-users--<a href="http://lists.sourceforge.net/lists/listinfo/scipion-users--"><http://lists.sourceforge.net/lists/listinfo/scipion-users--></a></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'><br>Pablo Conesa - Madrid Scipion team<br><br><br><br><br><br>_______________________________________________scipion-users mailing</p></blockquote><p style='margin-bottom:12.0pt'><a href="mailto:lis...@li...https">lis...@li...https</a>:/></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'><o:p> </o:p></p></blockquote><p style='margin-bottom:12.0pt'>--<br>Pablo Conesa - *Madrid Scipion <<a href="http://scipion.i2pc.es">http://scipion.i2pc.es</a>> team*<br><br><br><br>Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir<br>informació confidencial o protegida legalment i s’adreça exclusivament a<br>la persona o entitat destinatària. Si no consteu com a destinatari final<br>o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo,<br>retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el<br>contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu<br>del sistema tant el missatge com els fitxers adjunts que hi pugui haver.<br><br>Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener<br>información confidencial o legalmente protegida y está exclusivamente<br>dirigido a la persona o entidad destinataria. Si usted no consta como<br>destinatario final ni es la persona encargada de recibirlo, no está<br>autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni<br>a revelar su contenido. Si lo ha recibido por error, informe de ello al<br>remitente y elimine del sistema tanto el mensaje como los ficheros<br>adjuntos que pueda contener.<br><br>This email message and any attachments it carries may contain<br>confidential or legally protected material and are intended solely for<br>the individual or organization to whom they are addressed. If you are<br>not the intended recipient of this message or the person responsible for<br>processing it, then you are not authorized to read, save, modify, send,<br>copy or disclose any part of it. If you have received the message by<br>mistake, please inform the sender of this and eliminate the message and<br>any attachments it carries from your account.<br><br><br>Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir<br>informació confidencial o protegida legalment i s’adreça exclusivament a<br>la persona o entitat destinatària. Si no consteu com a destinatari final<br>o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo,<br>retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el<br>contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu<br>del sistema tant el missatge com els fitxers adjunts que hi pugui haver.<br><br>Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener<br>información confidencial o legalmente protegida y está exclusivamente<br>dirigido a la persona o entidad destinataria. Si usted no consta como<br>destinatario final ni es la persona encargada de recibirlo, no está<br>autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni<br>a revelar su contenido. Si lo ha recibido por error, informe de ello al<br>remitente y elimine del sistema tanto el mensaje como los ficheros<br>adjuntos que pueda contener.<br><br>This email message and any attachments it carries may contain<br>confidential or legally protected material and are intended solely for<br>the individual or organization to whom they are addressed. If you are<br>not the intended recipient of this message or the person responsible for<br>processing it, then you are not authorized to read, save, modify, send,<br>copy or disclose any part of it. If you have received the message by<br>mistake, please inform the sender of this and eliminate the message and<br>any attachments it carries from your account.</p></div></div></blockquote></div><p> </p></div><p style='margin-bottom:12.0pt'><br><br></p><pre>_______________________________________________</pre><pre>scipion-users mailing list</pre><pre><a href="mailto:sci...@li...">sci...@li...</a></pre><pre><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre></blockquote><p>-- <br>Pablo Conesa - <strong><span style='font-family:"Calibri",sans-serif'>Madrid <a href="http://scipion.i2pc.es">Scipion</a> team</span></strong></p><p> </p></div></div></blockquote></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: <pc...@cn...> - 2021-04-21 20:19:29
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<div dir='auto'>Providing Eman Fonda can handle environments the same way a standard conda installation does, then, I'd say the deepLearningToolkit environment is not present. <div dir="auto"><br></div><div dir="auto">What is the output of</div><div dir="auto"><br></div><div dir="auto">Scipion3 instalb?</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 21 abr. 2021 20:28, "Dmitry A. Semchonok" <sem...@gm...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><p>Dear Pablo,</p><p>Thank you ! please have a look below.</p><p> </p><p>Sincerely,</p><p>Dmitry</p><p> </p><p><b><span style="background:yellow">scipion3 printenv</span> </b></p><p><span style="color:red">[panos@cryoem01 ~]$ scipion3 printenv</span></p><p><span style="color:red">Scipion v3.0.7 - Eugenius</span></p><p><span style="color:red">export ASCP="~/.aspera/connect/bin/ascp"</span></p><p><span style="color:red">export ASPERA_SCP_PASS=""</span></p><p><span style="color:red">export ATSAS_HOME="/opt/Scipion3/software/em/atsas-3.0.1"</span></p><p><span style="color:red">export BSOFT_HOME="/opt/Scipion3/software/em/bsoft-2.0.7"</span></p><p><span style="color:red">export CCP4_HOME="/opt/Scipion3/software/em/ccp4-7.0.056"</span></p><p><span style="color:red">export CHIMERA_HOME="/opt/Scipion3/software/em/chimerax-1.1"</span></p><p><span style="color:red">export CISTEM_HOME="/opt/Scipion3/software/em/cistem-1.0.0-beta"</span></p><p><span style="color:red">export CONDA_ACTIVATION_CMD="eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)""</span></p><p><span style="color:red">export CONTINUOUSFLEX_HOME="/opt/Scipion3/software/em/xmipp"</span></p><p><span style="color:red">export CRYOASSESS_ENV_ACTIVATION="conda activate cryoassess-0.1.0"</span></p><p><span style="color:red">export CRYOASSESS_MODEL_2D="/opt/Scipion3/software/em/cryoassess-models/2dassess_062119.h5"</span></p><p><span style="color:red">export CRYOASSESS_MODEL_MIC="/opt/Scipion3/software/em/cryoassess-models/micassess_051419.h5"</span></p><p><span style="color:red">export CRYOLO_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style="color:red">export CRYOLO_ENV_ACTIVATION="conda activate cryolo-1.7.6"</span></p><p><span style="color:red">export CRYOLO_ENV_ACTIVATION_CPU="conda activate cryoloCPU-1.7.6"</span></p><p><span style="color:red">export CRYOLO_GENERIC_DENOISED_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5"</span></p><p><span style="color:red">export CRYOLO_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5"</span></p><p><span style="color:red">export CRYOLO_NS_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5"</span></p><p><span style="color:red">export CRYOSPARC_HOME="/home/panos/software/cryosparc"</span></p><p><span style="color:red">export CRYOSPARC_USER="ctueting"</span></p><p><span style="color:red">export CRYO_PROJECTS_DIR="/data1/ScipionUserData/projects/cryosparc_plugin"</span></p><p><span style="color:red">export CTFFIND4_HOME="/opt/Scipion3/software/em/ctffind4-4.1.14"</span></p><p><span style="color:red">export DOGPICKER_HOME="/opt/Scipion3/software/em/dogpicker-0.2.1.1"</span></p><p><span style="color:red">export DYNAMO_HOME="/opt/Scipion3/software/em/dynamo-1.146"</span></p><p><span style="color:red">export EMAN2SCRATCHDIR="/tmp"</span></p><p><span style="color:red">export EMAN2_HOME="/opt/Scipion3/software/em/eman-2.31"</span></p><p><span style="color:red">export EMFACILITIES_HOME="/opt/Scipion3/software/em/"</span></p><p><span style="color:red">export EMPIAR_TOKEN=""</span></p><p><span style="color:red">export EMXLIB_HOME="/opt/Scipion3/software/em/emx_export-1.0.0"</span></p><p><span style="color:red">export EM_ROOT="software/em"</span></p><p><span style="color:red">export ETHAN_HOME="/opt/Scipion3/software/em/ethan-1.2"</span></p><p><span style="color:red">export FSC3D_ACTIVATION_CMD="conda activate 3DFSC"</span></p><p><span style="color:red">export FSC3D_HOME="/opt/Scipion3/software/em/fsc3D-3.0"</span></p><p><span style="color:red">export GAUTOMATCH="Gautomatch_v0.56_sm30-75_cu10.1"</span></p><p><span style="color:red">export GAUTOMATCH_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style="color:red">export GAUTOMATCH_HOME="/opt/Scipion3/software/em/gautomatch-0.56"</span></p><p><span style="color:red">export GCTF="Gctf-v1.06_sm_30_cu8.0_x86_64"</span></p><p><span style="color:red">export GCTF_CUDA_LIB="/usr/local/cuda-8.0/lib64"</span></p><p><span style="color:red">export GCTF_HOME="/opt/Scipion3/software/em/Gctf_v1.06"</span></p><p><span style="color:red">export IMAGIC_HOME="/opt/Scipion3/software/em/imagic-190830"</span></p><p><span style="color:red">export IMOD_HOME="/opt/Scipion3/software/em/imod-4.10.42/IMOD"</span></p><p><span style="color:red">export JANNI_GENERIC_MODEL="/opt/Scipion3/software/em/janni_model-20190703/gmodel_janni_20190703.h5"</span></p><p><span style="color:red">export JAVA_MAX_MEMORY="12"</span></p><p><span style="color:red">export LOCSCALE_HOME="/opt/Scipion3/software/em/locscale-0.1"</span></p><p><span style="color:red">export MAXIT_HOME="/opt/Scipion3/software/em/maxit-10.1"</span></p><p><span style="color:red">export MOTIONCOR2_BIN="MotionCor2_1.3.2-Cuda100"</span></p><p><span style="color:red">export MOTIONCOR2_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style="color:red">export MOTIONCOR2_HOME="/opt/Scipion3/software/em/motioncor2-1.3.2"</span></p><p><span style="color:red">export NMA_HOME="/opt/Scipion3/software/em/nma"</span></p><p><span style="color:red">export NOVACTF_HOME="/opt/Scipion3/software/em/novactf-master"</span></p><p><span style="color:red">export PHENIX_HOME="/opt/Scipion3/software/em/phenix-"</span></p><p><span style="color:red">export RELION_CUDA_BIN="/usr/local/cuda/bin"</span></p><p><span style="color:red">export RELION_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style="color:red">export RELION_HOME="/opt/Scipion3/software/em/relion-3.1.0"</span></p><p><span style="color:red">export RESMAP="ResMap-1.95-cuda-Centos7x64"</span></p><p><span style="color:red">export RESMAP_GPU_LIB="ResMap_krnl-cuda-V8.0.61-sm60_gpu.so"</span></p><p><span style="color:red">export RESMAP_HOME="/opt/Scipion3/software/em/resmap-1.95"</span></p><p><span style="color:red">export SCIPION_CONFIG="/opt/Scipion3/config/scipion.conf"</span></p><p><span style="color:red">export SCIPION_CWD="/home/panos"</span></p><p><span style="color:red">export SCIPION_DOMAIN="pwem"</span></p><p><span style="color:red">export SCIPION_FONT_NAME="Helvetica"</span></p><p><span style="color:red">export SCIPION_HOME="/opt/Scipion3"</span></p><p><span style="color:red">export SCIPION_HOSTS="/opt/Scipion3/config/hosts.conf"</span></p><p><span style="color:red">export SCIPION_LOCAL_CONFIG="/home/panos/.config/scipion/scipion.conf"</span></p><p><span style="color:red">export SCIPION_LOG="/home/panos/ScipionUserData/logs/scipion.log"</span></p><p><span style="color:red">export SCIPION_LOGO="scipion_logo.gif"</span></p><p><span style="color:red">export SCIPION_LOGS="/home/panos/ScipionUserData/logs"</span></p><p><span style="color:red">export SCIPION_NOTES_FILE="notes.txt"</span></p><p><span style="color:red">export SCIPION_NOTIFY="True"</span></p><p><span style="color:red">export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/"</span></p><p><span style="color:red">export SCIPION_PROTOCOLS="/opt/Scipion3/config/protocols.conf"</span></p><p><span style="color:red">export SCIPION_SOFTWARE="/opt/Scipion3/software"</span></p><p><span style="color:red">export SCIPION_SUPPORT_EMAIL="scipion@cnb.csic.es"</span></p><p><span style="color:red">export SCIPION_TESTS="/opt/Scipion3/data/tests"</span></p><p><span style="color:red">export SCIPION_TESTS_CMD="scipion3 tests"</span></p><p><span style="color:red">export SCIPION_TESTS_OUTPUT="/home/panos/ScipionUserData/Tests"</span></p><p><span style="color:red">export SCIPION_TMP="/home/panos/ScipionUserData/tmp"</span></p><p><span style="color:red">export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion"</span></p><p><span style="color:red">export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software"</span></p><p><span style="color:red">export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests"</span></p><p><span style="color:red">export SCIPION_USER_DATA="/data1/ScipionUserData"</span></p><p><span style="color:red">export SCIPION_VERSION="v3.0.7 - Eugenius"</span></p><p><span style="color:red">export SIDESPLITTER_HOME="/opt/Scipion3/software/em/sidesplitter-1.2"</span></p><p><span style="color:red">export SPIDER="spider_linux_mp_intel64"</span></p><p><span style="color:red">export SPIDER_HOME="/opt/Scipion3/software/em/spider-26.06"</span></p><p><span style="color:red">export SPIDER_MPI="spider_linux_mpi_opt64"</span></p><p><span style="color:red">export TOPAZ_ENV_ACTIVATION="conda activate topaz-0.2.3"</span></p><p><span style="color:red">export VMD_HOME="/usr/local/lib/vmd"</span></p><p><span style="color:red">export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]"</span></p><p><span style="color:red">export XMIPP2_HOME="/opt/Scipion3/software/em/Xmipp-2.4-src"</span></p><p><span style="color:red">export XMIPP_HOME="/opt/Scipion3/software/em/xmipp"</span></p><p><span style="color:red">[panos@cryoem01 ~]$</span></p><p><b><span style="background:yellow">scipion3 run printenv</span></b></p><p> </p><p><span style="color:red">[panos@cryoem01 ~]$ scipion3 run printenv</span></p><p><span style="color:red">Scipion v3.0.7 - Eugenius</span></p><p><span style="color:red">** Running command: printenv </span></p><p><span style="color:red">SCIPION_VERSION=v3.0.7 - Eugenius</span></p><p><span style="color:red">SCIPION_LOGO=scipion_logo.gif</span></p><p><span style="color:red">GAUTOMATCH_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style="color:red">MAXIT_HOME=software/em/maxit-10.1</span></p><p><span style="color:red">XDG_SESSION_ID=c3</span></p><p><span style="color:red">SSH_AGENT_PID=2160</span></p><p><span style="color:red">IMOD_DIR=/usr/local/IMOD</span></p><p><span style="color:red">HOSTNAME=cryoem01</span></p><p><span style="color:red">SCIPION_FONT_NAME=Helvetica</span></p><p><span style="color:red">RELION_CUDA_BIN=/usr/local/cuda/bin</span></p><p><span style="color:red">IMSETTINGS_INTEGRATE_DESKTOP=yes</span></p><p><span style="color:red">XRDP_SOCKET_PATH=/run/xrdp</span></p><p><span style="color:red">CRYOLO_GENERIC_DENOISED_MODEL=software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5</span></p><p><span style="color:red">SCIPION_TESTS_CMD=scipion3 tests</span></p><p><span style="color:red">VTE_VERSION=5204</span></p><p><span style="color:red">XDG_MENU_PREFIX=gnome-</span></p><p><span style="color:red">SHELL=/bin/bash</span></p><p><span style="color:red">TERM=xterm-256color</span></p><p><span style="color:red">SIDESPLITTER_HOME=software/em/sidesplitter-1.2</span></p><p><span style="color:red">HISTSIZE=1000</span></p><p><span style="color:red">IMOD_QTLIBDIR=/usr/local/IMOD/qtlib</span></p><p><span style="color:red">SCIPION_NOTIFY=True</span></p><p><span style="color:red">SCIPION_URL=http://scipion.cnb.csic.es/downloads/scipion</span></p><p><span style="color:red">CISTEM_HOME=software/em/cistem-1.0.0-beta</span></p><p><span style="color:red">SPIDER_HOME=software/em/spider-26.06</span></p><p><span style="color:red">SCIPION_DOMAIN=pwem</span></p><p><span style="color:red">SCIPION_USER_DATA=/data1/ScipionUserData</span></p><p><span style="color:red">CRYOLO_GENERIC_MODEL=software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5</span></p><p><span style="color:red">SCIPION_TESTS_OUTPUT=/home/panos/ScipionUserData/Tests</span></p><p><span style="color:red">GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/409e3dd0_2aca_48db_a92c_2905ab5689a1</span></p><p><span style="color:red">GJS_DEBUG_OUTPUT=stderr</span></p><p><span style="color:red">DOGPICKER_HOME=software/em/dogpicker-0.2.1.1</span></p><p><span style="color:red">SCIPION_PROTOCOLS=/opt/Scipion3/config/protocols.conf</span></p><p><span style="color:red">CCP4_HOME=software/em/ccp4-7.0.056</span></p><p><span style="color:red">CRYOASSESS_ENV_ACTIVATION=conda activate cryoassess-0.1.0</span></p><p><span style="color:red">DYNAMO_HOME=software/em/dynamo-1.146</span></p><p><span style="color:red">PHENIX_HOME=software/em/phenix-</span></p><p><span style="color:red">GJS_DEBUG_TOPICS=JS ERROR;JS LOG</span></p><p><span style="color:red">SCIPION_HOSTS=/opt/Scipion3/config/hosts.conf</span></p><p><span style="color:red">GAUTOMATCH_HOME=software/em/gautomatch-0.56</span></p><p><span style="color:red">SCIPION_PLUGIN_REPO_URL=http://scipion.i2pc.es/getplugins/</span></p><p><span style="color:red">CRYOLO_NS_GENERIC_MODEL=software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5</span></p><p><span style="color:red">GCTF_HOME=software/em/Gctf_v1.06</span></p><p><span style="color:red">LC_ALL=en_US.UTF-8</span></p><p><span style="color:red">CRYOASSESS_MODEL_MIC=software/em/cryoassess-models/micassess_051419.h5</span></p><p><span style="color:red">IMSETTINGS_MODULE=none</span></p><p><span style="color:red">CUDA_HOME=/usr/local/cuda</span></p><p><span style="color:red">USER=panos</span></p><p><span style="color:red">LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:</span></p><p><span style="color:red">LD_LIBRARY_PATH=/usr/local/cuda-10.0/lib64:/opt/Scipion3/software/lib</span></p><p><span style="color:red">SCIPION_URL_TESTDATA=http://scipion.cnb.csic.es/downloads/scipion/data/tests</span></p><p><span style="color:red">MOTIONCOR2_BIN=MotionCor2_1.3.2-Cuda100</span></p><p><span style="color:red">GNOME_TERMINAL_SERVICE=:1.103</span></p><p><span style="color:red">SCIPION_SUPPORT_EMAIL=scipion@cnb.csic.es</span></p><p><span style="color:red">GCTF=Gctf-v1.06_sm_30_cu8.0_x86_64</span></p><p><span style="color:red">XMIPP_HOME=software/em/xmipp</span></p><p><span style="color:red">FSC3D_HOME=software/em/fsc3D-3.0</span></p><p><span style="color:red">SSH_AUTH_SOCK=/tmp/ssh-ZJq5X9BOWO6G/agent.1847</span></p><p><span style="color:red">SPIDER_MPI=spider_linux_mpi_opt64</span></p><p><span style="color:red">SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/1847,unix/unix:/tmp/.ICE-unix/1847</span></p><p><span style="color:red">CRYOLO_ENV_ACTIVATION_CPU=conda activate cryoloCPU-1.7.6</span></p><p><span style="color:red">EMPIAR_TOKEN=</span></p><p><span style="color:red">VIRTUAL_ENV=/opt/Scipion3/.scipion3env</span></p><p><span style="color:red">XRDP_PULSE_SINK_SOCKET=xrdp_chansrv_audio_out_socket_10</span></p><p><span style="color:red">SCIPION_CWD=/home/panos</span></p><p><span style="color:red">PULSE_SCRIPT=/etc/xrdp/pulse/default.pa</span></p><p><span style="color:red">SCIPION_TESTS=/opt/Scipion3/data/tests</span></p><p><span style="color:red">SPIDER=spider_linux_mp_intel64</span></p><p><span style="color:red">GNOME_SHELL_SESSION_MODE=classic</span></p><p><span style="color:red">CRYOSPARC_USER=ctueting</span></p><p><span style="color:red">MAIL=/var/spool/mail/panos</span></p><p><span style="color:red">PATH=/opt/Scipion3/.scipion3env/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/sbin:/bin:/usr/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin</span></p><p><span style="color:red">SCIPION_LOGS=/home/panos/ScipionUserData/logs</span></p><p><span style="color:red">SCIPION_CONFIG=/opt/Scipion3/config/scipion.conf</span></p><p><span style="color:red">IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug</span></p><p><span style="color:red">QT_IM_MODULE=ibus</span></p><p><span style="color:red">_=/bin/printenv</span></p><p><span style="color:red">CRYOLO_ENV_ACTIVATION=conda activate cryolo-1.7.6</span></p><p><span style="color:red">WIZARD_MASK_COLOR=[0.125, 0.909, 0.972]</span></p><p><span style="color:red">ATSAS_HOME=software/em/atsas-3.0.1</span></p><p><span style="color:red">JANNI_GENERIC_MODEL=software/em/janni_model-20190703/gmodel_janni_20190703.h5</span></p><p><span style="color:red">PWD=/home/panos</span></p><p><span style="color:red">XMODIFIERS=@im=ibus</span></p><p><span style="color:red">CRYOLO_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style="color:red">ETHAN_HOME=software/em/ethan-1.2</span></p><p><span style="color:red">GCTF_CUDA_LIB=/usr/local/cuda-8.0/lib64</span></p><p><span style="color:red">MOTIONCOR2_HOME=software/em/motioncor2-1.3.2</span></p><p><span style="color:red">XMIPP2_HOME=software/em/Xmipp-2.4-src</span></p><p><span style="color:red">pkgdir=/usr/local/I-TASSER5.1</span></p><p><span style="color:red">XRDP_SESSION=1</span></p><p><span style="color:red">IMOD_JAVADIR=/usr/local/java</span></p><p><span style="color:red">SCIPION_SOFTWARE=/opt/Scipion3/software</span></p><p><span style="color:red">LANG=en_US.UTF-8</span></p><p><span style="color:red">XRDP_PULSE_SOURCE_SOCKET=xrdp_chansrv_audio_in_socket_10</span></p><p><span style="color:red">SCIPION_NOTES_FILE=notes.txt</span></p><p><span style="color:red">CRYOASSESS_MODEL_2D=software/em/cryoassess-models/2dassess_062119.h5</span></p><p><span style="color:red">CRYOSPARC_HOME=/home/panos/software/cryosparc</span></p><p><span style="color:red">MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles</span></p><p><span style="color:red">SCIPION_URL_SOFTWARE=http://scipion.cnb.csic.es/downloads/scipion/software</span></p><p><span style="color:red">GAUTOMATCH=Gautomatch_v0.56_sm30-75_cu10.1</span></p><p><span style="color:red">RELION_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style="color:red">LOADEDMODULES=</span></p><p><span style="color:red">LOCSCALE_HOME=software/em/locscale-0.1</span></p><p><span style="color:red">FOR_DISABLE_STACK_TRACE=1</span></p><p><span style="color:red">EMFACILITIES_HOME=software/em/</span></p><p><span style="color:red">ASCP=~/.aspera/connect/bin/ascp</span></p><p><span style="color:red">RESMAP_HOME=software/em/resmap-1.95</span></p><p><span style="color:red">SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass</span></p><p><span style="color:red">HISTCONTROL=ignoredups</span></p><p><span style="color:red">ASPERA_SCP_PASS=</span></p><p><span style="color:red">SHLVL=5</span></p><p><span style="color:red">HOME=/home/panos</span></p><p><span style="color:red">CONDA_ACTIVATION_CMD=eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)"</span></p><p><span style="color:red">CTFFIND4_HOME=software/em/ctffind4-4.1.14</span></p><p><span style="color:red">MOTIONCOR2_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style="color:red">SCIPION_TMP=/home/panos/ScipionUserData/tmp</span></p><p><span style="color:red">EMAN2_HOME=software/em/eman-2.31</span></p><p><span style="color:red">GNOME_DESKTOP_SESSION_ID=this-is-deprecated</span></p><p><span style="color:red">CRYO_PROJECTS_DIR=/data1/ScipionUserData/projects/cryosparc_plugin</span></p><p><span style="color:red">IMAGIC_HOME=software/em/imagic-190830</span></p><p><span style="color:red">SCIPION_LOCAL_CONFIG=/home/panos/.config/scipion/scipion.conf</span></p><p><span style="color:red">PYTHONPATH=:/opt/Scipion3/software/bindings</span></p><p><span style="color:red">LOGNAME=panos</span></p><p><span style="color:red">NOVACTF_HOME=software/em/novactf-master</span></p><p><span style="color:red">BSOFT_HOME=software/em/bsoft-2.0.7</span></p><p><span style="color:red">DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-FKQakXHYCC,guid=649474707764c616b7441e9f60802f4a</span></p><p><span style="color:red">XDG_DATA_DIRS=/home/panos/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share</span></p><p><span style="color:red">MODULESHOME=/usr/share/Modules</span></p><p><span style="color:red">MPI_HOME=/usr/local/mpich-3.2.1</span></p><p><span style="color:red">UID=1000</span></p><p><span style="color:red">CONTINUOUSFLEX_HOME=software/em/xmipp</span></p><p><span style="color:red">LESSOPEN=||/usr/bin/lesspipe.sh %s</span></p><p><span style="color:red">IMOD_CALIB_DIR=/usr/local/ImodCalib</span></p><p><span style="color:red">JAVA_MAX_MEMORY=12</span></p><p><span style="color:red">RESMAP=ResMap-1.95-cuda-Centos7x64</span></p><p><span style="color:red">EMAN2SCRATCHDIR=/tmp</span></p><p><span style="color:red">SCIPION_HOME=/opt/Scipion3</span></p><p><span style="color:red">FSC3D_ACTIVATION_CMD=conda activate 3DFSC</span></p><p><span style="color:red">RELION_HOME=software/em/relion-3.1.0</span></p><p><span style="color:red">VMD_HOME=/usr/local/lib/vmd</span></p><p><span style="color:red">VIEWERS={"Volume":["pwem.viewers.DataViewer"], "VolumeMask":["pwem.viewers.DataViewer"]}</span></p><p><span style="color:red">DISPLAY=:10.0</span></p><p><span style="color:red">XDG_RUNTIME_DIR=/run/user/1000</span></p><p><span style="color:red">SCIPION_LOG=/home/panos/ScipionUserData/logs/scipion.log</span></p><p><span style="color:red">XDG_CURRENT_DESKTOP=GNOME</span></p><p><span style="color:red">EM_ROOT=software/em</span></p><p><span style="color:red">NMA_HOME=software/em/nma</span></p><p><span style="color:red">COLORTERM=truecolor</span></p><p><span style="color:red">CHIMERA_HOME=software/em/chimerax-1.1</span></p><p><span style="color:red">EMXLIB_HOME=software/em/emx_export-1.0.0</span></p><p><span style="color:red">IMOD_HOME=software/em/imod-4.10.42/IMOD</span></p><p><span style="color:red">RESMAP_GPU_LIB=ResMap_krnl-cuda-V8.0.61-sm60_gpu.so</span></p><p><span style="color:red">TOPAZ_ENV_ACTIVATION=conda activate topaz-0.2.3</span></p><p><span style="color:red">BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`</span></p><p><span style="color:red">}</span></p><p><span style="color:red">[panos@cryoem01 ~]$</span></p><p><span style="color:red"> </span></p><p> </p><p>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p> </p><div style="border:none;border-top:solid #e1e1e1 1pt;padding:3pt 0in 0in 0in"><p style="border:none;padding:0in"><b>From: </b><a href="mailto:pconesa@cnb.csic.es">Pablo Conesa</a><br /><b>Sent: </b>Wednesday, April 21, 2021 7:06 PM<br /><b>To: </b><a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a><br /><b>Subject: </b>Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error</p></div><p> </p><p>You have eman2 acting as a conda manager, that is a problem.</p><p>At least the environment is not listed there. </p><p>Does the other plugins work? e.g. cryolo?</p><p>Can you send the output of:</p><p>scipion3 printenv </p><p>and </p><p>scipion3 run printenv</p><p>?</p><div><p>On 21/4/21 17:06, Dmitry Semchonok wrote:</p></div><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>Dear colleagues, </p><div><p>Just to add our current error from the xmipp deep learning installation.</p></div><div><p> </p></div><div><p>Interestingly we almost fun to an end of this step but conda issue appeared.</p></div><div><p> </p></div><div><p>Any suggestions?</p></div><div><p> </p></div><div><p> </p></div><div><p> </p></div><div><p><span style="color:#0433ff">currentDir: /data1/ScipionUserData/projects/Image_processing_cn_10688</span></p></div><div><p><span style="color:#0433ff">00890: workingDir: Runs/007643_XmippProtScreenDeepLearning</span></p></div><div><p><span style="color:#0433ff">00891: runMode: Continue</span></p></div><div><p><span style="color:#0433ff">00892: MPI: 1</span></p></div><div><p><span style="color:#0433ff">00893: threads: 4</span></p></div><div><p><span style="color:#0433ff">00894: Starting at step: 3</span></p></div><div><p><span style="color:#0433ff">00895: Running steps</span></p></div><div><p><span style="color:#0433ff">00896: STARTED: predict, step 3, time 2021-04-20 11:08:26.633086</span></p></div><div><p><span style="color:#0433ff">00897: </span></p></div><div><p><span style="color:#0433ff">00898: $ /usr/local/EMAN_2.21/bin/conda info --env</span></p></div><div><p><span style="color:#0433ff">00899: # conda environments:</span></p></div><div><p><span style="color:#0433ff">00900: #</span></p></div><div><p><span style="color:#0433ff">00901: 3DFSC /home/panos/.conda/envs/3DFSC</span></p></div><div><p><span style="color:#0433ff">00902: cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0</span></p></div><div><p><span style="color:#0433ff">00903: cryolo /home/panos/.conda/envs/cryolo</span></p></div><div><p><span style="color:#0433ff">00904: cryolo /usr/local/EMAN_2.21/envs/cryolo</span></p></div><div><p><span style="color:#0433ff">00905: cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4</span></p></div><div><p><span style="color:#0433ff">00906: fsc /usr/local/EMAN_2.21/envs/fsc</span></p></div><div><p><span style="color:#0433ff">00907: topaz /usr/local/EMAN_2.21/envs/topaz</span></p></div><div><p><span style="color:#0433ff">00908: root * /usr/local/EMAN_2.21</span></p></div><div><p><span style="color:#0433ff">00909: </span></p></div><div><p><span style="color:#0433ff">00910: </span></p></div><div><p><span style="color:#0433ff">00911: >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)</span></p></div><div><p><span style="color:#0433ff">00912: Traceback (most recent call last):</span></p></div><div><p><span style="color:#0433ff">00913: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run</span></p></div><div><p><span style="color:#0433ff">00914: self._run()</span></p></div><div><p><span style="color:#0433ff">00915: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run</span></p></div><div><p><span style="color:#0433ff">00916: resultFiles = self._runFunc()</span></p></div><div><p><span style="color:#0433ff">00917: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc</span></p></div><div><p><span style="color:#0433ff">00918: return self._func(*self._args)</span></p></div><div><p><span style="color:#0433ff">00919: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deeplearning.py", line 319, in predict</span></p></div><div><p><span style="color:#0433ff">00920: env=self.getCondaEnv())</span></p></div><div><p><span style="color:#0433ff">00921: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv</span></p></div><div><p><span style="color:#0433ff">00922: return CondaEnvManager.getCondaEnv(env, envName)</span></p></div><div><p><span style="color:#0433ff">00923: File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv</span></p></div><div><p><span style="color:#0433ff">00924: envBin = os.path.join(environDir, "bin")</span></p></div><div><p><span style="color:#0433ff">00925: File "/usr/lib64/python3.6/posixpath.py", line 80, in join</span></p></div><div><p><span style="color:#0433ff">00926: a = os.fspath(a)</span></p></div><div><p><span style="color:#0433ff">00927: TypeError: expected str, bytes or os.PathLike object, not NoneType</span></p></div><div><p><span style="color:#0433ff">00928: Protocol failed: expected str, bytes or os.PathLike object, not NoneType</span></p></div><div><p><span style="color:#0433ff">00929: FAILED: predict, step 3, time 2021-04-20 11:08:27.020467</span></p></div><div><p><span style="color:#0433ff">00930: *** Last status is failed </span></p></div><div><p><span style="color:#0433ff">00931: ------------------- PROTOCOL FAILED (DONE 3/4)</span></p></div><div><p> </p></div><div><p> </p></div><div><p>Thank you!</p></div><div><p> </p></div><div><p> </p></div><div><p>Sincerely,</p></div><div><p>Dmitry</p></div><div><p> </p></div><div><p> </p><div><p><br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><div><p>On 20. Apr 2021, at 11:25, Christian Tüting <<a href="mailto:christian.tueting@biochemtech.uni-halle.de">christian.tueting@biochemtech.uni-halle.de</a>> wrote:</p></div><p> </p><div><div><p>Hi,<br /><br />thank you for your response. I tried this twice. The first time, the<br />"_BACKUP2" folder was popping up again under .conda/envs, so I followed<br />your steps again, deleting the folder under software and removed the<br />conda enviroment, and now, no enviroment is generated at all. Logically,<br />running a job gives this error: ">>> 'xmipp_DLTK_v0.3' conda environment<br />not found... (check list above)". <br /><br />Another long-term job is currently running, after this is done, we will<br />restart everything to have a clean system. But do you have any<br />additional tips?<br /><br />Thanks in advance<br />Christian<br /><br /><br /><br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><blockquote style="margin-top:5pt;margin-bottom:5pt"><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>David Maluenda <<a href="mailto:dmaluenda@ub.edu">dmaluenda@ub.edu</a>> 20.04.21 10.02 Uhr >>></p></blockquote></blockquote></blockquote><p>Hi Christian,<br /><br />If it already works, I would leave it as it is.<br /><br />To make a clear installation, you don't need to reinstall the whole<br />xmipp. You can just reinstall the deepLearningToolkit by<br /><br />rm -rf /opt/Scipion3/software/em/deepLearningToolkit<br />conda env remove --name xmipp_DLTK_v0.3_BACKUP2<br />scipion3 installb deepLearningToolkit<br /><br /><br />Cheers,<br /><br /><<a href="http://ucm.es/">http://ucm.es/</a>><br />_____<br />Dr. David Maluenda Niubó<br /><a href="mailto:dmaluenda@ub.edu">dmaluenda@ub.edu</a><<a href="mailto:dmaluenda@ub.edu">mailto:dmaluenda@ub.edu</a>> - (+34) 619 029 310<br />Wavefront Engineering<br />Group<<a href="https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA">https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA</a>><br />Applied Physics - UB<<a href="https://www.ub.edu/portal/web/dp-fisica-aplicada">https://www.ub.edu/portal/web/dp-fisica-aplicada</a>><br /><br />This email message and any documents attached to it may contain<br />confidential or legally protected material and are intended solely for<br />the use of the individual or organization to whom they are addressed. We<br />remind you that if you are not the intended recipient of this email<br />message or the person responsible for processing it, then you are not<br />authorized to read, save, modify, send, copy or disclose any of its<br />contents. If you have received this email message by mistake, we kindly<br />ask you to inform the sender of this and to eliminate both the message<br />and any attachments it carries from your account. Thank you for your<br />collaboration.<br /><br /><br /><br />On Tue, Apr 20, 2021 at 9:53 AM Christian Tüting<br /><<a href="mailto:christian.tueting@biochemtech.uni-halle.de">christian.tueting@biochemtech.uni-halle.de</a><<a href="mailto:christian.tueting@biochemtech.uni-halle.de">mailto:christian.tueting@biochemtech.uni-halle.de</a>>><br />wrote:<br />Hi Pablo,<br /><br />I will take an eye on this. I have a question regarding dependencies:<br />tensorflow 1.15 requires keras-application>=1.0.8 and<br />keras-preprocessing>=1.0.5, but keras 2.2 requieres older versions<br />(1.0.2 and 1.0.1, respectivly).<br /><br />Should we try to uninstall and a clean reinstall of xmipp, to resolve<br />all dependency issues?<br /><br />Thank you for your support.<br /><br />Best<br />Christian<br /><br /><br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><blockquote style="margin-top:5pt;margin-bottom:5pt"><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>Pablo Conesa <<a href="mailto:pconesa@cnb.csic.es">pconesa@cnb.csic.es</a><<a href="mailto:pconesa@cnb.csic.es">mailto:pconesa@cnb.csic.es</a>>></p></blockquote></blockquote></blockquote><p>20.04.21 9.16 Uhr >>><br />Thanks Christian.<br /><br />In theory, xmipp defines dependencies strictly<br />(<a href="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</a>)<br /><br />I do not know how it ended up with higher versions, but something to<br />keep an eye on.<br /><br />On 20/4/21 7:00, Christian Tüting wrote:<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>Hi all,<br /><br />first the conda path looks actually very strange, and I fixed this<br />direclty. We had some other issues, which were tensorflow-related, but<br />this is fixed.<br /><br /><br />Just to comment on that, there were first an issue with the tensorflow<br />module. Installing the latest release (2.x) gives an error on "module<br />'tensorflow' has no attribute 'Session'". After fixing that by<br />downgrading, keras was giving an error, that the module does not have</p></blockquote><p>no<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>attribute "tf", which was also fixed by downgrading.<br /><br /><br /><br />TL;DR Eventually, downgrading tensorflow to 1.15.0 and downgrading</p></blockquote><p>keras<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>to 2.2.4 (from 2.2.5) solved the issue<br /><br /><br />Best<br />Christian<br /><br /><br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><blockquote style="margin-top:5pt;margin-bottom:5pt"><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>"Dmitry A. Semchonok"</p></blockquote></blockquote></blockquote></blockquote><p><<a href="mailto:semchonok@gmail.com">semchonok@gmail.com</a><<a href="mailto:semchonok@gmail.com">mailto:semchonok@gmail.com</a>>> 19.04.21 16.24 Uhr >>><br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>Dear Carlos Oscar, Pablo, David, Ruben,<br /><br /><br />Thank you very much for your fast response.<br /><br /><br />Currently, deep learning is running.<br />A colleague of mine, Christian, kindly looked at the problem.<br /><br /><br />Let me, please post the errors we had and where we are now.<br />May be Christian can comment more on this issue.<br /><br /><br />Please see the errors here.<br /><a href="https://yadi.sk/d/KlTeKv1O9UCTQg">https://yadi.sk/d/KlTeKv1O9UCTQg</a><br /><br /><br />Since> Sent: Monday, April 19, 2021 12:57 PM<br />To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David<br />Maluenda<br />Subject: Re: [scipion-users] deep consensus pickling error<br /><br /><br />Dear Dmitry,<br />let us see if David or Rubén knows where this environment is coming<br />from.<br />Kind regards, Carlos Oscar<br />El 19/04/2021 a las 9:37, Pablo Conesa escribió:<br /><br />Hi Dmitry... you have no environment for xmipp_DLTK_v0.3.<br />You have a "weird" xmipp_DLTK_v0.3_BACKUP2<br />/home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2<br /><br />On 17/4/21 8:56, Dmitry A. Semchonok wrote:<br /><br />Dear colleagues,<br /><br />During deep consensus pickling I received the following error<br /><br />Any ideas?<br /><br />Thank you<br /><br />Sincerely,<br />Dmitry<br /><br /><br /><br />[Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min<br />[Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min<br />[Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min<br />[Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min<br />[Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min<br />[Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min<br />[Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min<br />[Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min<br />[Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min<br />[Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min</p></blockquote><p>finished<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>[35mFINISHED[0m: extractParticles, step 12, time 2021-04-17<br />04:05:07.093613<br />[35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17<br />04:05:07.574152<br />[35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17<br />04:26:59.879548<br />[35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444<br />None None None None<br /><br />$ /usr/local/EMAN_2.21/bin/conda info --env<br /># conda environments:<br />#<br />3DFSC /home/panos/.conda/envs/3DFSC<br />cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0<br />cryolo /home/panos/.conda/envs/cryolo> cryolo </p></blockquote><p> /usr/local/EMAN_2.21/envs/cryolo<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4<br />fsc /usr/local/EMAN_2.21/envs/fsc<br />topaz /usr/local/EMAN_2.21/envs/topaz<br />root * /usr/local/EMAN_2.21<br /><br /><br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><blockquote style="margin-top:5pt;margin-bottom:5pt"><blockquote style="margin-top:5pt;margin-bottom:5pt"><p>'xmipp_DLTK_v0.3' conda environment not found... (check list above)</p></blockquote></blockquote></blockquote><p style="margin-bottom:12pt">Traceback (most recent call last):<br /> File</p></blockquote><p>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p style="margin-bottom:12pt">line 189, in run<br /> self._run()<br /> File</p></blockquote><p>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p style="margin-bottom:12pt">line 240, in _run<br /> resultFiles = self._runFunc()<br /> File</p></blockquote><p>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p style="margin-bottom:12pt">line 236, in _runFunc<br /> return self._func(*self._args)<br /> File<br />"/opt/Scipion env=self.getCondaEnv())<br /> File</p></blockquote><p>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py",<br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p style="margin-bottom:12pt">line 204, in getCondaEnv<br /> return CondaEnvManager.getCondaEnv(env, envName)<br /> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in<br />getCondaEnv<br /> envBin = os.path.join(environDir, "bin")<br /> File "/usr/lib64/python3.6/posixpath.py", line 80, in join<br /> a = os.fspath(a)<br />TypeError: expected str, bytes or os.PathLike object, not NoneType<br />[31mProtocol failed: expected str, bytes or os.PathLike object, not<br />NoneType[0m<br />[35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417<br />*** Last status is failed<br />Sent from Mail for Windows 10<br /><br /><br /><br /><br /><br />_______________________________________________scipion-users mailing</p></blockquote><p><a href="mailto:listscipion-users@lists.sourceforge.nethttps">listscipion-users@lists.sourceforge.nethttps</a>://lists.sourceforge.net/lists/listinfo/scipion-users--<a href="http://lists.sourceforge.net/lists/listinfo/scipion-users--"><http://lists.sourceforge.net/lists/listinfo/scipion-users--></a><br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p style="margin-bottom:12pt"><br />Pablo Conesa - Madrid Scipion team<br /><br /><br /><br /><br /><br />_______________________________________________scipion-users mailing</p></blockquote><p><a href="mailto:listscipion-users@lists.sourceforge.nethttps">listscipion-users@lists.sourceforge.nethttps</a>:/><br /><br /></p><blockquote style="margin-top:5pt;margin-bottom:5pt"><p style="margin-bottom:12pt"><br /><br /></p></blockquote><p style="margin-bottom:12pt">--<br />Pablo Conesa - *Madrid Scipion <<a href="http://scipion.i2pc.es">http://scipion.i2pc.es</a>> team*<br /><br /><br /><br />Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir<br />informació confidencial o protegida legalment i s’adreça exclusivament a<br />la persona o entitat destinatària. Si no consteu com a destinatari final<br />o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo,<br />retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el<br />contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu<br />del sistema tant el missatge com els fitxers adjunts que hi pugui haver.<br /><br />Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener<br />información confidencial o legalmente protegida y está exclusivamente<br />dirigido a la persona o entidad destinataria. Si usted no consta como<br />destinatario final ni es la persona encargada de recibirlo, no está<br />autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni<br />a revelar su contenido. Si lo ha recibido por error, informe de ello al<br />remitente y elimine del sistema tanto el mensaje como los ficheros<br />adjuntos que pueda contener.<br /><br />This email message and any attachments it carries may contain<br />confidential or legally protected material and are intended solely for<br />the individual or organization to whom they are addressed. If you are<br />not the intended recipient of this message or the person responsible for<br />processing it, then you are not authorized to read, save, modify, send,<br />copy or disclose any part of it. If you have received the message by<br />mistake, please inform the sender of this and eliminate the message and<br />any attachments it carries from your account.<br /><br /><br />Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir<br />informació confidencial o protegida legalment i s’adreça exclusivament a<br />la persona o entitat destinatària. Si no consteu com a destinatari final<br />o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo,<br />retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el<br />contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu<br />del sistema tant el missatge com els fitxers adjunts que hi pugui haver.<br /><br />Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener<br />información confidencial o legalmente protegida y está exclusivamente<br />dirigido a la persona o entidad destinataria. Si usted no consta como<br />destinatario final ni es la persona encargada de recibirlo, no está<br />autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni<br />a revelar su contenido. Si lo ha recibido por error, informe de ello al<br />remitente y elimine del sistema tanto el mensaje como los ficheros<br />adjuntos que pueda contener.<br /><br />This email message and any attachments it carries may contain<br />confidential or legally protected material and are intended solely for<br />the individual or organization to whom they are addressed. If you are<br />not the intended recipient of this message or the person responsible for<br />processing it, then you are not authorized to read, save, modify, send,<br />copy or disclose any part of it. If you have received the message by<br />mistake, please inform the sender of this and eliminate the message and<br />any attachments it carries from your account.</p></div></div></blockquote></div><p> </p></div><p><br /><br /><br /></p><pre>_______________________________________________</pre><pre>scipion-users mailing list</pre><pre><a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a></pre><pre><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre></blockquote><p>-- <br />Pablo Conesa - <strong><span style="font-family:'calibri' , sans-serif">Madrid <a href="http://scipion.i2pc.es">Scipion</a> team</span></strong></p><p> </p></div></div> </blockquote></div><br></div> |
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From: Dmitry A. S. <sem...@gm...> - 2021-04-21 18:28:38
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} pre {mso-style-priority:99; mso-style-link:"HTML Preformatted Char"; margin:0in; font-size:10.0pt; font-family:"Courier New";} span.HTMLPreformattedChar {mso-style-name:"HTML Preformatted Char"; mso-style-priority:99; mso-style-link:"HTML Preformatted"; font-family:"Courier New";} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p>Dear Pablo,</p><p>Thank you ! please have a look below.</p><p><o:p> </o:p></p><p>Sincerely,</p><p>Dmitry</p><p><o:p> </o:p></p><p><b><span style='background:yellow;mso-highlight:yellow'>scipion3 printenv</span> <o:p></o:p></b></p><p><span style='color:red'>[panos@cryoem01 ~]$ scipion3 printenv<o:p></o:p></span></p><p><span style='color:red'>Scipion v3.0.7 - Eugenius<o:p></o:p></span></p><p><span style='color:red'>export ASCP="~/.aspera/connect/bin/ascp"<o:p></o:p></span></p><p><span style='color:red'>export ASPERA_SCP_PASS=""<o:p></o:p></span></p><p><span style='color:red'>export ATSAS_HOME="/opt/Scipion3/software/em/atsas-3.0.1"<o:p></o:p></span></p><p><span style='color:red'>export BSOFT_HOME="/opt/Scipion3/software/em/bsoft-2.0.7"<o:p></o:p></span></p><p><span style='color:red'>export CCP4_HOME="/opt/Scipion3/software/em/ccp4-7.0.056"<o:p></o:p></span></p><p><span style='color:red'>export CHIMERA_HOME="/opt/Scipion3/software/em/chimerax-1.1"<o:p></o:p></span></p><p><span style='color:red'>export CISTEM_HOME="/opt/Scipion3/software/em/cistem-1.0.0-beta"<o:p></o:p></span></p><p><span style='color:red'>export CONDA_ACTIVATION_CMD="eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)""<o:p></o:p></span></p><p><span style='color:red'>export CONTINUOUSFLEX_HOME="/opt/Scipion3/software/em/xmipp"<o:p></o:p></span></p><p><span style='color:red'>export CRYOASSESS_ENV_ACTIVATION="conda activate cryoassess-0.1.0"<o:p></o:p></span></p><p><span style='color:red'>export CRYOASSESS_MODEL_2D="/opt/Scipion3/software/em/cryoassess-models/2dassess_062119.h5"<o:p></o:p></span></p><p><span style='color:red'>export CRYOASSESS_MODEL_MIC="/opt/Scipion3/software/em/cryoassess-models/micassess_051419.h5"<o:p></o:p></span></p><p><span style='color:red'>export CRYOLO_CUDA_LIB="/usr/local/cuda/lib64"<o:p></o:p></span></p><p><span style='color:red'>export CRYOLO_ENV_ACTIVATION="conda activate cryolo-1.7.6"<o:p></o:p></span></p><p><span style='color:red'>export CRYOLO_ENV_ACTIVATION_CPU="conda activate cryoloCPU-1.7.6"<o:p></o:p></span></p><p><span style='color:red'>export CRYOLO_GENERIC_DENOISED_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5"<o:p></o:p></span></p><p><span style='color:red'>export CRYOLO_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5"<o:p></o:p></span></p><p><span style='color:red'>export CRYOLO_NS_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5"<o:p></o:p></span></p><p><span style='color:red'>export CRYOSPARC_HOME="/home/panos/software/cryosparc"<o:p></o:p></span></p><p><span style='color:red'>export CRYOSPARC_USER="ctueting"<o:p></o:p></span></p><p><span style='color:red'>export CRYO_PROJECTS_DIR="/data1/ScipionUserData/projects/cryosparc_plugin"<o:p></o:p></span></p><p><span style='color:red'>export CTFFIND4_HOME="/opt/Scipion3/software/em/ctffind4-4.1.14"<o:p></o:p></span></p><p><span style='color:red'>export DOGPICKER_HOME="/opt/Scipion3/software/em/dogpicker-0.2.1.1"<o:p></o:p></span></p><p><span style='color:red'>export DYNAMO_HOME="/opt/Scipion3/software/em/dynamo-1.146"<o:p></o:p></span></p><p><span style='color:red'>export EMAN2SCRATCHDIR="/tmp"<o:p></o:p></span></p><p><span style='color:red'>export EMAN2_HOME="/opt/Scipion3/software/em/eman-2.31"<o:p></o:p></span></p><p><span style='color:red'>export EMFACILITIES_HOME="/opt/Scipion3/software/em/"<o:p></o:p></span></p><p><span style='color:red'>export EMPIAR_TOKEN=""<o:p></o:p></span></p><p><span style='color:red'>export EMXLIB_HOME="/opt/Scipion3/software/em/emx_export-1.0.0"<o:p></o:p></span></p><p><span style='color:red'>export EM_ROOT="software/em"<o:p></o:p></span></p><p><span style='color:red'>export ETHAN_HOME="/opt/Scipion3/software/em/ethan-1.2"<o:p></o:p></span></p><p><span style='color:red'>export FSC3D_ACTIVATION_CMD="conda activate 3DFSC"<o:p></o:p></span></p><p><span style='color:red'>export FSC3D_HOME="/opt/Scipion3/software/em/fsc3D-3.0"<o:p></o:p></span></p><p><span style='color:red'>export GAUTOMATCH="Gautomatch_v0.56_sm30-75_cu10.1"<o:p></o:p></span></p><p><span style='color:red'>export GAUTOMATCH_CUDA_LIB="/usr/local/cuda/lib64"<o:p></o:p></span></p><p><span style='color:red'>export GAUTOMATCH_HOME="/opt/Scipion3/software/em/gautomatch-0.56"<o:p></o:p></span></p><p><span style='color:red'>export GCTF="Gctf-v1.06_sm_30_cu8.0_x86_64"<o:p></o:p></span></p><p><span style='color:red'>export GCTF_CUDA_LIB="/usr/local/cuda-8.0/lib64"<o:p></o:p></span></p><p><span style='color:red'>export GCTF_HOME="/opt/Scipion3/software/em/Gctf_v1.06"<o:p></o:p></span></p><p><span style='color:red'>export IMAGIC_HOME="/opt/Scipion3/software/em/imagic-190830"<o:p></o:p></span></p><p><span style='color:red'>export IMOD_HOME="/opt/Scipion3/software/em/imod-4.10.42/IMOD"<o:p></o:p></span></p><p><span style='color:red'>export JANNI_GENERIC_MODEL="/opt/Scipion3/software/em/janni_model-20190703/gmodel_janni_20190703.h5"<o:p></o:p></span></p><p><span style='color:red'>export JAVA_MAX_MEMORY="12"<o:p></o:p></span></p><p><span style='color:red'>export LOCSCALE_HOME="/opt/Scipion3/software/em/locscale-0.1"<o:p></o:p></span></p><p><span style='color:red'>export MAXIT_HOME="/opt/Scipion3/software/em/maxit-10.1"<o:p></o:p></span></p><p><span style='color:red'>export MOTIONCOR2_BIN="MotionCor2_1.3.2-Cuda100"<o:p></o:p></span></p><p><span style='color:red'>export MOTIONCOR2_CUDA_LIB="/usr/local/cuda/lib64"<o:p></o:p></span></p><p><span style='color:red'>export MOTIONCOR2_HOME="/opt/Scipion3/software/em/motioncor2-1.3.2"<o:p></o:p></span></p><p><span style='color:red'>export NMA_HOME="/opt/Scipion3/software/em/nma"<o:p></o:p></span></p><p><span style='color:red'>export NOVACTF_HOME="/opt/Scipion3/software/em/novactf-master"<o:p></o:p></span></p><p><span style='color:red'>export PHENIX_HOME="/opt/Scipion3/software/em/phenix-"<o:p></o:p></span></p><p><span style='color:red'>export RELION_CUDA_BIN="/usr/local/cuda/bin"<o:p></o:p></span></p><p><span style='color:red'>export RELION_CUDA_LIB="/usr/local/cuda/lib64"<o:p></o:p></span></p><p><span style='color:red'>export RELION_HOME="/opt/Scipion3/software/em/relion-3.1.0"<o:p></o:p></span></p><p><span style='color:red'>export RESMAP="ResMap-1.95-cuda-Centos7x64"<o:p></o:p></span></p><p><span style='color:red'>export RESMAP_GPU_LIB="ResMap_krnl-cuda-V8.0.61-sm60_gpu.so"<o:p></o:p></span></p><p><span style='color:red'>export RESMAP_HOME="/opt/Scipion3/software/em/resmap-1.95"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_CONFIG="/opt/Scipion3/config/scipion.conf"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_CWD="/home/panos"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_DOMAIN="pwem"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_FONT_NAME="Helvetica"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_HOME="/opt/Scipion3"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_HOSTS="/opt/Scipion3/config/hosts.conf"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_LOCAL_CONFIG="/home/panos/.config/scipion/scipion.conf"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_LOG="/home/panos/ScipionUserData/logs/scipion.log"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_LOGO="scipion_logo.gif"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_LOGS="/home/panos/ScipionUserData/logs"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_NOTES_FILE="notes.txt"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_NOTIFY="True"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_PROTOCOLS="/opt/Scipion3/config/protocols.conf"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_SOFTWARE="/opt/Scipion3/software"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_SUPPORT_EMAIL="sc...@cn..."<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_TESTS="/opt/Scipion3/data/tests"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_TESTS_CMD="scipion3 tests"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_TESTS_OUTPUT="/home/panos/ScipionUserData/Tests"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_TMP="/home/panos/ScipionUserData/tmp"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_USER_DATA="/data1/ScipionUserData"<o:p></o:p></span></p><p><span style='color:red'>export SCIPION_VERSION="v3.0.7 - Eugenius"<o:p></o:p></span></p><p><span style='color:red'>export SIDESPLITTER_HOME="/opt/Scipion3/software/em/sidesplitter-1.2"<o:p></o:p></span></p><p><span style='color:red'>export SPIDER="spider_linux_mp_intel64"<o:p></o:p></span></p><p><span style='color:red'>export SPIDER_HOME="/opt/Scipion3/software/em/spider-26.06"<o:p></o:p></span></p><p><span style='color:red'>export SPIDER_MPI="spider_linux_mpi_opt64"<o:p></o:p></span></p><p><span style='color:red'>export TOPAZ_ENV_ACTIVATION="conda activate topaz-0.2.3"<o:p></o:p></span></p><p><span style='color:red'>export VMD_HOME="/usr/local/lib/vmd"<o:p></o:p></span></p><p><span style='color:red'>export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]"<o:p></o:p></span></p><p><span style='color:red'>export XMIPP2_HOME="/opt/Scipion3/software/em/Xmipp-2.4-src"<o:p></o:p></span></p><p><span style='color:red'>export XMIPP_HOME="/opt/Scipion3/software/em/xmipp"<o:p></o:p></span></p><p><span style='color:red'>[panos@cryoem01 ~]$<o:p></o:p></span></p><p class=MsoNormal><b><span style='background:yellow;mso-highlight:yellow'>scipion3 run printenv</span><o:p></o:p></b></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='color:red'>[panos@cryoem01 ~]$ scipion3 run printenv<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>Scipion v3.0.7 - Eugenius<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>** Running command: printenv <o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_VERSION=v3.0.7 - Eugenius<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_LOGO=scipion_logo.gif<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GAUTOMATCH_CUDA_LIB=/usr/local/cuda/lib64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>MAXIT_HOME=software/em/maxit-10.1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XDG_SESSION_ID=c3<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SSH_AGENT_PID=2160<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMOD_DIR=/usr/local/IMOD<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>HOSTNAME=cryoem01<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_FONT_NAME=Helvetica<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>RELION_CUDA_BIN=/usr/local/cuda/bin<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMSETTINGS_INTEGRATE_DESKTOP=yes<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XRDP_SOCKET_PATH=/run/xrdp<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOLO_GENERIC_DENOISED_MODEL=software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_TESTS_CMD=scipion3 tests<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>VTE_VERSION=5204<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XDG_MENU_PREFIX=gnome-<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SHELL=/bin/bash<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>TERM=xterm-256color<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SIDESPLITTER_HOME=software/em/sidesplitter-1.2<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>HISTSIZE=1000<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMOD_QTLIBDIR=/usr/local/IMOD/qtlib<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_NOTIFY=True<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_URL=http://scipion.cnb.csic.es/downloads/scipion<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CISTEM_HOME=software/em/cistem-1.0.0-beta<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SPIDER_HOME=software/em/spider-26.06<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_DOMAIN=pwem<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_USER_DATA=/data1/ScipionUserData<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOLO_GENERIC_MODEL=software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_TESTS_OUTPUT=/home/panos/ScipionUserData/Tests<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/409e3dd0_2aca_48db_a92c_2905ab5689a1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GJS_DEBUG_OUTPUT=stderr<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>DOGPICKER_HOME=software/em/dogpicker-0.2.1.1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_PROTOCOLS=/opt/Scipion3/config/protocols.conf<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CCP4_HOME=software/em/ccp4-7.0.056<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOASSESS_ENV_ACTIVATION=conda activate cryoassess-0.1.0<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>DYNAMO_HOME=software/em/dynamo-1.146<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>PHENIX_HOME=software/em/phenix-<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GJS_DEBUG_TOPICS=JS ERROR;JS LOG<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_HOSTS=/opt/Scipion3/config/hosts.conf<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GAUTOMATCH_HOME=software/em/gautomatch-0.56<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_PLUGIN_REPO_URL=http://scipion.i2pc.es/getplugins/<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOLO_NS_GENERIC_MODEL=software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GCTF_HOME=software/em/Gctf_v1.06<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>LC_ALL=en_US.UTF-8<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOASSESS_MODEL_MIC=software/em/cryoassess-models/micassess_051419.h5<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMSETTINGS_MODULE=none<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CUDA_HOME=/usr/local/cuda<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>USER=panos<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>LD_LIBRARY_PATH=/usr/local/cuda-10.0/lib64:/opt/Scipion3/software/lib<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_URL_TESTDATA=http://scipion.cnb.csic.es/downloads/scipion/data/tests<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>MOTIONCOR2_BIN=MotionCor2_1.3.2-Cuda100<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GNOME_TERMINAL_SERVICE=:1.103<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_SUPPORT_EMAIL=sc...@cn...<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GCTF=Gctf-v1.06_sm_30_cu8.0_x86_64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XMIPP_HOME=software/em/xmipp<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>FSC3D_HOME=software/em/fsc3D-3.0<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SSH_AUTH_SOCK=/tmp/ssh-ZJq5X9BOWO6G/agent.1847<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SPIDER_MPI=spider_linux_mpi_opt64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/1847,unix/unix:/tmp/.ICE-unix/1847<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOLO_ENV_ACTIVATION_CPU=conda activate cryoloCPU-1.7.6<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>EMPIAR_TOKEN=<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>VIRTUAL_ENV=/opt/Scipion3/.scipion3env<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XRDP_PULSE_SINK_SOCKET=xrdp_chansrv_audio_out_socket_10<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_CWD=/home/panos<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>PULSE_SCRIPT=/etc/xrdp/pulse/default.pa<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_TESTS=/opt/Scipion3/data/tests<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SPIDER=spider_linux_mp_intel64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GNOME_SHELL_SESSION_MODE=classic<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOSPARC_USER=ctueting<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>MAIL=/var/spool/mail/panos<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>PATH=/opt/Scipion3/.scipion3env/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/sbin:/bin:/usr/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_LOGS=/home/panos/ScipionUserData/logs<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_CONFIG=/opt/Scipion3/config/scipion.conf<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>QT_IM_MODULE=ibus<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>_=/bin/printenv<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOLO_ENV_ACTIVATION=conda activate cryolo-1.7.6<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>WIZARD_MASK_COLOR=[0.125, 0.909, 0.972]<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>ATSAS_HOME=software/em/atsas-3.0.1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>JANNI_GENERIC_MODEL=software/em/janni_model-20190703/gmodel_janni_20190703.h5<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>PWD=/home/panos<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XMODIFIERS=@im=ibus<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOLO_CUDA_LIB=/usr/local/cuda/lib64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>ETHAN_HOME=software/em/ethan-1.2<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GCTF_CUDA_LIB=/usr/local/cuda-8.0/lib64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>MOTIONCOR2_HOME=software/em/motioncor2-1.3.2<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XMIPP2_HOME=software/em/Xmipp-2.4-src<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>pkgdir=/usr/local/I-TASSER5.1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XRDP_SESSION=1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMOD_JAVADIR=/usr/local/java<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_SOFTWARE=/opt/Scipion3/software<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>LANG=en_US.UTF-8<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XRDP_PULSE_SOURCE_SOCKET=xrdp_chansrv_audio_in_socket_10<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_NOTES_FILE=notes.txt<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOASSESS_MODEL_2D=software/em/cryoassess-models/2dassess_062119.h5<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYOSPARC_HOME=/home/panos/software/cryosparc<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_URL_SOFTWARE=http://scipion.cnb.csic.es/downloads/scipion/software<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GAUTOMATCH=Gautomatch_v0.56_sm30-75_cu10.1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>RELION_CUDA_LIB=/usr/local/cuda/lib64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>LOADEDMODULES=<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>LOCSCALE_HOME=software/em/locscale-0.1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>FOR_DISABLE_STACK_TRACE=1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>EMFACILITIES_HOME=software/em/<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>ASCP=~/.aspera/connect/bin/ascp<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>RESMAP_HOME=software/em/resmap-1.95<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>HISTCONTROL=ignoredups<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>ASPERA_SCP_PASS=<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SHLVL=5<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>HOME=/home/panos<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CONDA_ACTIVATION_CMD=eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)"<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CTFFIND4_HOME=software/em/ctffind4-4.1.14<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>MOTIONCOR2_CUDA_LIB=/usr/local/cuda/lib64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_TMP=/home/panos/ScipionUserData/tmp<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>EMAN2_HOME=software/em/eman-2.31<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>GNOME_DESKTOP_SESSION_ID=this-is-deprecated<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CRYO_PROJECTS_DIR=/data1/ScipionUserData/projects/cryosparc_plugin<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMAGIC_HOME=software/em/imagic-190830<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_LOCAL_CONFIG=/home/panos/.config/scipion/scipion.conf<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>PYTHONPATH=:/opt/Scipion3/software/bindings<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>LOGNAME=panos<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>NOVACTF_HOME=software/em/novactf-master<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>BSOFT_HOME=software/em/bsoft-2.0.7<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-FKQakXHYCC,guid=649474707764c616b7441e9f60802f4a<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XDG_DATA_DIRS=/home/panos/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>MODULESHOME=/usr/share/Modules<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>MPI_HOME=/usr/local/mpich-3.2.1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>UID=1000<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CONTINUOUSFLEX_HOME=software/em/xmipp<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>LESSOPEN=||/usr/bin/lesspipe.sh %s<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMOD_CALIB_DIR=/usr/local/ImodCalib<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>JAVA_MAX_MEMORY=12<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>RESMAP=ResMap-1.95-cuda-Centos7x64<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>EMAN2SCRATCHDIR=/tmp<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_HOME=/opt/Scipion3<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>FSC3D_ACTIVATION_CMD=conda activate 3DFSC<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>RELION_HOME=software/em/relion-3.1.0<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>VMD_HOME=/usr/local/lib/vmd<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>VIEWERS={"Volume":["pwem.viewers.DataViewer"], "VolumeMask":["pwem.viewers.DataViewer"]}<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>DISPLAY=:10.0<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XDG_RUNTIME_DIR=/run/user/1000<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>SCIPION_LOG=/home/panos/ScipionUserData/logs/scipion.log<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>XDG_CURRENT_DESKTOP=GNOME<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>EM_ROOT=software/em<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>NMA_HOME=software/em/nma<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>COLORTERM=truecolor<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>CHIMERA_HOME=software/em/chimerax-1.1<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>EMXLIB_HOME=software/em/emx_export-1.0.0<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>IMOD_HOME=software/em/imod-4.10.42/IMOD<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>RESMAP_GPU_LIB=ResMap_krnl-cuda-V8.0.61-sm60_gpu.so<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>TOPAZ_ENV_ACTIVATION=conda activate topaz-0.2.3<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>}<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'>[panos@cryoem01 ~]$<o:p></o:p></span></p><p class=MsoNormal><span style='color:red'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:pc...@cn...">Pablo Conesa</a><br><b>Sent: </b>Wednesday, April 21, 2021 7:06 PM<br><b>To: </b><a href="mailto:sci...@li...">sci...@li...</a><br><b>Subject: </b>Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error</p></div><p class=MsoNormal><o:p> </o:p></p><p>You have eman2 acting as a conda manager, that is a problem.</p><p>At least the environment is not listed there. </p><p>Does the other plugins work? e.g. cryolo?</p><p>Can you send the output of:</p><p>scipion3 printenv </p><p>and </p><p>scipion3 run printenv</p><p>?</p><div><p class=MsoNormal>On 21/4/21 17:06, Dmitry Semchonok wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>Dear colleagues, <o:p></o:p></p><div><p class=MsoNormal>Just to add our current error from the xmipp deep learning installation.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Interestingly we almost fun to an end of this step but conda issue appeared.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Any suggestions?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>currentDir: /data1/ScipionUserData/projects/Image_processing_cn_10688</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00890: workingDir: Runs/007643_XmippProtScreenDeepLearning</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00891: runMode: Continue</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00892: MPI: 1</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00893: threads: 4</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00894: Starting at step: 3</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00895: Running steps</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00896: STARTED: predict, step 3, time 2021-04-20 11:08:26.633086</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00897: </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00898: $ /usr/local/EMAN_2.21/bin/conda info --env</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00899: # conda environments:</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00900: #</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00901: 3DFSC /home/panos/.conda/envs/3DFSC</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00902: cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00903: cryolo /home/panos/.conda/envs/cryolo</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00904: cryolo /usr/local/EMAN_2.21/envs/cryolo</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00905: cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00906: fsc /usr/local/EMAN_2.21/envs/fsc</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00907: topaz /usr/local/EMAN_2.21/envs/topaz</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00908: root * /usr/local/EMAN_2.21</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00909: </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00910: </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00911: >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00912: Traceback (most recent call last):</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00913: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00914: self._run()</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00915: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00916: resultFiles = self._runFunc()</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00917: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00918: return self._func(*self._args)</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00919: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deeplearning.py", line 319, in predict</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00920: env=self.getCondaEnv())</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00921: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00922: return CondaEnvManager.getCondaEnv(env, envName)</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00923: File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00924: envBin = os.path.join(environDir, "bin")</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00925: File "/usr/lib64/python3.6/posixpath.py", line 80, in join</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00926: a = os.fspath(a)</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00927: TypeError: expected str, bytes or os.PathLike object, not NoneType</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00928: Protocol failed: expected str, bytes or os.PathLike object, not NoneType</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00929: FAILED: predict, step 3, time 2021-04-20 11:08:27.020467</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00930: *** Last status is failed </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#0433FF'>00931: ------------------- PROTOCOL FAILED (DONE 3/4)</span><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thank you!<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Sincerely,<o:p></o:p></p></div><div><p class=MsoNormal>Dmitry<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p><div><p class=MsoNormal><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On 20. Apr 2021, at 11:25, Christian Tüting <<a href="mailto:chr...@bi...">chr...@bi...</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>Hi,<br><br>thank you for your response. I tried this twice. The first time, the<br>"_BACKUP2" folder was popping up again under .conda/envs, so I followed<br>your steps again, deleting the folder under software and removed the<br>conda enviroment, and now, no enviroment is generated at all. Logically,<br>running a job gives this error: ">>> 'xmipp_DLTK_v0.3' conda environment<br>not found... (check list above)". <br><br>Another long-term job is currently running, after this is done, we will<br>restart everything to have a clean system. But do you have any<br>additional tips?<br><br>Thanks in advance<br>Christian<br><br><br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>David Maluenda <<a href="mailto:dma...@ub...">dma...@ub...</a>> 20.04.21 10.02 Uhr >>><o:p></o:p></p></blockquote></blockquote></blockquote><p class=MsoNormal>Hi Christian,<br><br>If it already works, I would leave it as it is.<br><br>To make a clear installation, you don't need to reinstall the whole<br>xmipp. You can just reinstall the deepLearningToolkit by<br><br>rm -rf /opt/Scipion3/software/em/deepLearningToolkit<br>conda env remove --name xmipp_DLTK_v0.3_BACKUP2<br>scipion3 installb deepLearningToolkit<br><br><br>Cheers,<br><br><<a href="http://ucm.es/">http://ucm.es/</a>><br>_____<br>Dr. David Maluenda Niubó<br><a href="mailto:dma...@ub...">dma...@ub...</a><<a href="mailto:dma...@ub...">mailto:dma...@ub...</a>> - (+34) 619 029 310<br>Wavefront Engineering<br>Group<<a href="https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA">https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA</a>><br>Applied Physics - UB<<a href="https://www.ub.edu/portal/web/dp-fisica-aplicada">https://www.ub.edu/portal/web/dp-fisica-aplicada</a>><br><br>This email message and any documents attached to it may contain<br>confidential or legally protected material and are intended solely for<br>the use of the individual or organization to whom they are addressed. We<br>remind you that if you are not the intended recipient of this email<br>message or the person responsible for processing it, then you are not<br>authorized to read, save, modify, send, copy or disclose any of its<br>contents. If you have received this email message by mistake, we kindly<br>ask you to inform the sender of this and to eliminate both the message<br>and any attachments it carries from your account. Thank you for your<br>collaboration.<br><br><br><br>On Tue, Apr 20, 2021 at 9:53 AM Christian Tüting<br><<a href="mailto:chr...@bi...">chr...@bi...</a><<a href="mailto:chr...@bi...">mailto:chr...@bi...</a>>><br>wrote:<br>Hi Pablo,<br><br>I will take an eye on this. I have a question regarding dependencies:<br>tensorflow 1.15 requires keras-application>=1.0.8 and<br>keras-preprocessing>=1.0.5, but keras 2.2 requieres older versions<br>(1.0.2 and 1.0.1, respectivly).<br><br>Should we try to uninstall and a clean reinstall of xmipp, to resolve<br>all dependency issues?<br><br>Thank you for your support.<br><br>Best<br>Christian<br><br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>Pablo Conesa <<a href="mailto:pc...@cn...">pc...@cn...</a><<a href="mailto:pc...@cn...">mailto:pc...@cn...</a>>><o:p></o:p></p></blockquote></blockquote></blockquote><p class=MsoNormal>20.04.21 9.16 Uhr >>><br>Thanks Christian.<br><br>In theory, xmipp defines dependencies strictly<br>(<a href="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</a>)<br><br>I do not know how it ended up with higher versions, but something to<br>keep an eye on.<br><br>On 20/4/21 7:00, Christian Tüting wrote:<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>Hi all,<br><br>first the conda path looks actually very strange, and I fixed this<br>direclty. We had some other issues, which were tensorflow-related, but<br>this is fixed.<br><br><br>Just to comment on that, there were first an issue with the tensorflow<br>module. Installing the latest release (2.x) gives an error on "module<br>'tensorflow' has no attribute 'Session'". After fixing that by<br>downgrading, keras was giving an error, that the module does not have<o:p></o:p></p></blockquote><p class=MsoNormal>no<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>attribute "tf", which was also fixed by downgrading.<br><br><br><br>TL;DR Eventually, downgrading tensorflow to 1.15.0 and downgrading<o:p></o:p></p></blockquote><p class=MsoNormal>keras<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>to 2.2.4 (from 2.2.5) solved the issue<br><br><br>Best<br>Christian<br><br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>"Dmitry A. Semchonok"<o:p></o:p></p></blockquote></blockquote></blockquote></blockquote><p class=MsoNormal><<a href="mailto:sem...@gm...">sem...@gm...</a><<a href="mailto:sem...@gm...">mailto:sem...@gm...</a>>> 19.04.21 16.24 Uhr >>><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>Dear Carlos Oscar, Pablo, David, Ruben,<br><br><br>Thank you very much for your fast response.<br><br><br>Currently, deep learning is running.<br>A colleague of mine, Christian, kindly looked at the problem.<br><br><br>Let me, please post the errors we had and where we are now.<br>May be Christian can comment more on this issue.<br><br><br>Please see the errors here.<br><a href="https://yadi.sk/d/KlTeKv1O9UCTQg">https://yadi.sk/d/KlTeKv1O9UCTQg</a><br><br><br>Since> Sent: Monday, April 19, 2021 12:57 PM<br>To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David<br>Maluenda<br>Subject: Re: [scipion-users] deep consensus pickling error<br><br><br>Dear Dmitry,<br>let us see if David or Rubén knows where this environment is coming<br>from.<br>Kind regards, Carlos Oscar<br>El 19/04/2021 a las 9:37, Pablo Conesa escribió:<br><br>Hi Dmitry... you have no environment for xmipp_DLTK_v0.3.<br>You have a "weird" xmipp_DLTK_v0.3_BACKUP2<br>/home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2<br><br>On 17/4/21 8:56, Dmitry A. Semchonok wrote:<br><br>Dear colleagues,<br><br>During deep consensus pickling I received the following error<br><br>Any ideas?<br><br>Thank you<br><br>Sincerely,<br>Dmitry<br><br><br><br>[Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min<br>[Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min<br>[Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min<br>[Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min<br>[Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min<br>[Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min<br>[Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min<br>[Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min<br>[Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min<br>[Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min<o:p></o:p></p></blockquote><p class=MsoNormal>finished<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>[35mFINISHED[0m: extractParticles, step 12, time 2021-04-17<br>04:05:07.093613<br>[35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17<br>04:05:07.574152<br>[35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17<br>04:26:59.879548<br>[35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444<br>None None None None<br><br>$ /usr/local/EMAN_2.21/bin/conda info --env<br># conda environments:<br>#<br>3DFSC /home/panos/.conda/envs/3DFSC<br>cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0<br>cryolo /home/panos/.conda/envs/cryolo> cryolo <o:p></o:p></p></blockquote><p class=MsoNormal> /usr/local/EMAN_2.21/envs/cryolo<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4<br>fsc /usr/local/EMAN_2.21/envs/fsc<br>topaz /usr/local/EMAN_2.21/envs/topaz<br>root * /usr/local/EMAN_2.21<br><br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>'xmipp_DLTK_v0.3' conda environment not found... (check list above)<o:p></o:p></p></blockquote></blockquote></blockquote><p class=MsoNormal style='margin-bottom:12.0pt'>Traceback (most recent call last):<br> File<o:p></o:p></p></blockquote><p class=MsoNormal>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal style='margin-bottom:12.0pt'>line 189, in run<br> self._run()<br> File<o:p></o:p></p></blockquote><p class=MsoNormal>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal style='margin-bottom:12.0pt'>line 240, in _run<br> resultFiles = self._runFunc()<br> File<o:p></o:p></p></blockquote><p class=MsoNormal>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal style='margin-bottom:12.0pt'>line 236, in _runFunc<br> return self._func(*self._args)<br> File<br>"/opt/Scipion env=self.getCondaEnv())<br> File<o:p></o:p></p></blockquote><p class=MsoNormal>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py",<br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal style='margin-bottom:12.0pt'>line 204, in getCondaEnv<br> return CondaEnvManager.getCondaEnv(env, envName)<br> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in<br>getCondaEnv<br> envBin = os.path.join(environDir, "bin")<br> File "/usr/lib64/python3.6/posixpath.py", line 80, in join<br> a = os.fspath(a)<br>TypeError: expected str, bytes or os.PathLike object, not NoneType<br>[31mProtocol failed: expected str, bytes or os.PathLike object, not<br>NoneType[0m<br>[35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417<br>*** Last status is failed<br>Sent from Mail for Windows 10<br><br><br><br><br><br>_______________________________________________scipion-users mailing<o:p></o:p></p></blockquote><p class=MsoNormal><a href="mailto:lis...@li...https">lis...@li...https</a>://lists.sourceforge.net/lists/listinfo/scipion-users--<a href="http://lists.sourceforge.net/lists/listinfo/scipion-users--"><http://lists.sourceforge.net/lists/listinfo/scipion-users--></a><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal style='margin-bottom:12.0pt'><br>Pablo Conesa - Madrid Scipion team<br><br><br><br><br><br>_______________________________________________scipion-users mailing<o:p></o:p></p></blockquote><p class=MsoNormal><a href="mailto:lis...@li...https">lis...@li...https</a>:/><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal style='margin-bottom:12.0pt'><br><br><o:p></o:p></p></blockquote><p class=MsoNormal style='margin-bottom:12.0pt'>--<br>Pablo Conesa - *Madrid Scipion <<a href="http://scipion.i2pc.es">http://scipion.i2pc.es</a>> team*<br><br><br><br>Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir<br>informació confidencial o protegida legalment i s’adreça exclusivament a<br>la persona o entitat destinatària. Si no consteu com a destinatari final<br>o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo,<br>retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el<br>contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu<br>del sistema tant el missatge com els fitxers adjunts que hi pugui haver.<br><br>Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener<br>información confidencial o legalmente protegida y está exclusivamente<br>dirigido a la persona o entidad destinataria. Si usted no consta como<br>destinatario final ni es la persona encargada de recibirlo, no está<br>autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni<br>a revelar su contenido. Si lo ha recibido por error, informe de ello al<br>remitente y elimine del sistema tanto el mensaje como los ficheros<br>adjuntos que pueda contener.<br><br>This email message and any attachments it carries may contain<br>confidential or legally protected material and are intended solely for<br>the individual or organization to whom they are addressed. If you are<br>not the intended recipient of this message or the person responsible for<br>processing it, then you are not authorized to read, save, modify, send,<br>copy or disclose any part of it. If you have received the message by<br>mistake, please inform the sender of this and eliminate the message and<br>any attachments it carries from your account.<br><br><br>Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir<br>informació confidencial o protegida legalment i s’adreça exclusivament a<br>la persona o entitat destinatària. Si no consteu com a destinatari final<br>o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo,<br>retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el<br>contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu<br>del sistema tant el missatge com els fitxers adjunts que hi pugui haver.<br><br>Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener<br>información confidencial o legalmente protegida y está exclusivamente<br>dirigido a la persona o entidad destinataria. Si usted no consta como<br>destinatario final ni es la persona encargada de recibirlo, no está<br>autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni<br>a revelar su contenido. Si lo ha recibido por error, informe de ello al<br>remitente y elimine del sistema tanto el mensaje como los ficheros<br>adjuntos que pueda contener.<br><br>This email message and any attachments it carries may contain<br>confidential or legally protected material and are intended solely for<br>the individual or organization to whom they are addressed. If you are<br>not the intended recipient of this message or the person responsible for<br>processing it, then you are not authorized to read, save, modify, send,<br>copy or disclose any part of it. If you have received the message by<br>mistake, please inform the sender of this and eliminate the message and<br>any attachments it carries from your account.<o:p></o:p></p></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><br><br><br><o:p></o:p></p><pre>_______________________________________________</pre><pre>scipion-users mailing list</pre><pre><a href="mailto:sci...@li...">sci...@li...</a></pre><pre><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre></blockquote><p class=MsoNormal>-- <br>Pablo Conesa - <strong><span style='font-family:"Calibri",sans-serif'>Madrid <a href="http://scipion.i2pc.es">Scipion</a> team</span></strong><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Pablo C. <pc...@cn...> - 2021-04-21 17:05:52
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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 the folder under software and removed the >> conda enviroment, and now, no enviroment is generated at all. Logically, >> 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 A. Semchonok" >> <sem...@gm... >> <mailto:sem...@gm...><mailto:sem...@gm... >> <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(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 >>> >> 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 received the message by >> 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* |
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From: Dmitry S. <Sem...@gm...> - 2021-04-21 15:06:51
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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...> 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 the folder under software and removed the > conda enviroment, and now, no enviroment is generated at all. Logically, > 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...> 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/> > _____ > Dr. David Maluenda Niubó > dma...@ub...<mailto:dma...@ub...> - (+34) 619 029 310 > Wavefront Engineering > Group<https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA> > Applied Physics - UB<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...>> > 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...>> > 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) > > 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...<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 >> >> >> 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(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 >> > 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:/> >> >> >> > -- > Pablo Conesa - *Madrid Scipion <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 received the message by > mistake, please inform the sender of this and eliminate the message and > any attachments it carries from your account. > |
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From: Pablo C. <pc...@cn...> - 2021-04-20 10:31:35
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Yes, it should work. But in some cases (poor performance) there are reported issues associated "massive files deletion" when restarting a protocol or deleting it. And some sqlite access. In any case....the error you've reported might not e related.. Could you please post the whole stack trace? Cheers, Pablo. On 19/4/21 22:36, Kenneth Dalenberg wrote: > I have a user who is trying to open scipion projects on nfs mounts, > and they get this error when browsing to their stuff: > > AttributeError: 'NoneType' object has no attribute 'getCreationTime' > > The user running scipion has permission to the path, but when they try > to open they get the above. My question is, does scipion support > interacting with data stored on nfs mounts? > > > KEN DALENBERG > Unit Computing Manager, RCSB Protein Data Bank > Institute for Quantitative Biomedicine > Rutgers, The State University of New Jersey > 174 Frelinghuysen Road, Piscataway NJ 08854 > P: 848.445.4974 | E: kd...@iq... <mailto:kd...@iq...> > rcsb.org <http://rcsb.org> | iqb.rutgers.edu <http://iqb.rutgers.edu> > | facebook <https://www.facebook.com/RCSBPDB> | twitter > <https://twitter.com/buildmodels> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Christian T. <chr...@bi...> - 2021-04-20 09:26:18
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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 the folder under software and removed the conda enviroment, and now, no enviroment is generated at all. Logically, 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...> 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/> _____ Dr. David Maluenda Niubó dma...@ub...<mailto:dma...@ub...> - (+34) 619 029 310 Wavefront Engineering Group<https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA> Applied Physics - UB<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...>> 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...>> 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) 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...<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 > > > 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(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 > 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:/> > > > -- Pablo Conesa - *Madrid Scipion <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 received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account. |
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