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From: David M. <dma...@ub...> - 2021-04-20 08:02:57
|
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 > > > Sincerely, > Dmitry > > > > > > > > > Sent from Mail for Windows 10 > > From: Carlos Oscar Sorzano > Sent: Monday, April 19, 2021 12:57 PM > To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David > Maluenda > Subject: Re: [scipion-users] deep consensus pickling error > > > Dear Dmitry, > let us see if David or Rubén knows where this environment is coming > from. > Kind regards, Carlos Oscar > El 19/04/2021 a las 9:37, Pablo Conesa escribió: > > Hi Dmitry... you have no environment for xmipp_DLTK_v0.3. > You have a "weird" xmipp_DLTK_v0.3_BACKUP2 > /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 > > On 17/4/21 8:56, Dmitry A. Semchonok wrote: > > Dear colleagues, > > During deep consensus pickling I received the following error > > Any ideas? > > Thank you > > Sincerely, > Dmitry > > > > [Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min > [Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min > [Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min > [Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min > [Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min > [Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min > [Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min > [Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min > [Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min > [Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished > [35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 > 04:05:07.093613 > [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 > 04:05:07.574152 > [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 > 04:26:59.879548 > [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444 > None None None None > > $ /usr/local/EMAN_2.21/bin/conda info --env > # conda environments: > # > 3DFSC /home/panos/.conda/envs/3DFSC > cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 > cryolo /home/panos/.conda/envs/cryolo> 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://lists.sourceforge.net/lists/listinfo/scipion-users<http://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > -- 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. |
|
From: Christian T. <chr...@bi...> - 2021-04-20 07:53:39
|
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...> 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...> 19.04.21 16.24 Uhr >>> > Dear Carlos Oscar, Pablo, David, Ruben, > > > Thank you very much for your fast response. > > > Currently, deep learning is running. > A colleague of mine, Christian, kindly looked at the problem. > > > Let me, please post the errors we had and where we are now. > May be Christian can comment more on this issue. > > > Please see the errors here. > https://yadi.sk/d/KlTeKv1O9UCTQg > > > Sincerely, > Dmitry > > > > > > > > > Sent from Mail for Windows 10 > > From: Carlos Oscar Sorzano > Sent: Monday, April 19, 2021 12:57 PM > To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David > Maluenda > Subject: Re: [scipion-users] deep consensus pickling error > > > Dear Dmitry, > let us see if David or Rubén knows where this environment is coming > from. > Kind regards, Carlos Oscar > El 19/04/2021 a las 9:37, Pablo Conesa escribió: > > Hi Dmitry... you have no environment for xmipp_DLTK_v0.3. > You have a "weird" xmipp_DLTK_v0.3_BACKUP2 > /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 > > On 17/4/21 8:56, Dmitry A. Semchonok wrote: > > Dear colleagues, > > During deep consensus pickling I received the following error > > Any ideas? > > Thank you > > Sincerely, > Dmitry > > > > [Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min > [Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min > [Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min > [Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min > [Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min > [Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min > [Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min > [Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min > [Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min > [Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished > [35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 > 04:05:07.093613 > [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 > 04:05:07.574152 > [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 > 04:26:59.879548 > [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444 > None None None None > > $ /usr/local/EMAN_2.21/bin/conda info --env > # conda environments: > # > 3DFSC /home/panos/.conda/envs/3DFSC > cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 > cryolo /home/panos/.conda/envs/cryolo> 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-- > > Pablo Conesa - Madrid Scipion team > > > > > > _______________________________________________scipion-users mailing > lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2021-04-20 07:16:21
|
Thanks Christian. In theory, xmipp defines dependencies strictly (https://github.com/I2PC/xmipp/blob/devel/src/xmipp/bindings/python/xmipp_conda_envs.py) I do not know how it ended up with higher versions, but something to keep an eye on. On 20/4/21 7:00, Christian Tüting wrote: > Hi all, > > first the conda path looks actually very strange, and I fixed this > direclty. We had some other issues, which were tensorflow-related, but > this is fixed. > > > Just to comment on that, there were first an issue with the tensorflow > module. Installing the latest release (2.x) gives an error on "module > 'tensorflow' has no attribute 'Session'". After fixing that by > downgrading, keras was giving an error, that the module does not have no > attribute "tf", which was also fixed by downgrading. > > > > TL;DR Eventually, downgrading tensorflow to 1.15.0 and downgrading keras > to 2.2.4 (from 2.2.5) solved the issue > > > Best > Christian > > >>>> "Dmitry A. Semchonok" <sem...@gm...> 19.04.21 16.24 Uhr >>> > Dear Carlos Oscar, Pablo, David, Ruben, > > > Thank you very much for your fast response. > > > Currently, deep learning is running. > A colleague of mine, Christian, kindly looked at the problem. > > > Let me, please post the errors we had and where we are now. > May be Christian can comment more on this issue. > > > Please see the errors here. > https://yadi.sk/d/KlTeKv1O9UCTQg > > > Sincerely, > Dmitry > > > > > > > > > Sent from Mail for Windows 10 > > From: Carlos Oscar Sorzano > Sent: Monday, April 19, 2021 12:57 PM > To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David > Maluenda > Subject: Re: [scipion-users] deep consensus pickling error > > > Dear Dmitry, > let us see if David or Rubén knows where this environment is coming > from. > Kind regards, Carlos Oscar > El 19/04/2021 a las 9:37, Pablo Conesa escribió: > > Hi Dmitry... you have no environment for xmipp_DLTK_v0.3. > You have a "weird" xmipp_DLTK_v0.3_BACKUP2 > /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 > > On 17/4/21 8:56, Dmitry A. Semchonok wrote: > > Dear colleagues, > > During deep consensus pickling I received the following error > > Any ideas? > > Thank you > > Sincerely, > Dmitry > > > > [Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min > [Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min > [Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min > [Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min > [Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min > [Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min > [Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min > [Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min > [Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min > [Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished > [35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 > 04:05:07.093613 > [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 > 04:05:07.574152 > [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 > 04:26:59.879548 > [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444 > None None None None > > $ /usr/local/EMAN_2.21/bin/conda info --env > # conda environments: > # > 3DFSC /home/panos/.conda/envs/3DFSC > cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 > cryolo /home/panos/.conda/envs/cryolo > xmipp_DLTK_v0.3_BACKUP2 > /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 > cryolo /usr/local/EMAN_2.21/envs/cryolo > cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4 > fsc /usr/local/EMAN_2.21/envs/fsc > topaz /usr/local/EMAN_2.21/envs/topaz > root * /usr/local/EMAN_2.21 > > >>>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above) > Traceback (most recent call last): > File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 189, in run > self._run() > File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 240, in _run > resultFiles = self._runFunc() > File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 236, in _runFunc > return self._func(*self._args) > File > "/opt/Scipion env=self.getCondaEnv()) > File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", > line 204, in getCondaEnv > return CondaEnvManager.getCondaEnv(env, envName) > File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in > getCondaEnv > envBin = os.path.join(environDir, "bin") > File "/usr/lib64/python3.6/posixpath.py", line 80, in join > a = os.fspath(a) > TypeError: expected str, bytes or os.PathLike object, not NoneType > [31mProtocol failed: expected str, bytes or os.PathLike object, not > NoneType[0m > [35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417 > *** Last status is failed > Sent from Mail for Windows 10 > > > > > > _______________________________________________scipion-users mailing > lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users-- > > Pablo Conesa - Madrid Scipion team > > > > > > _______________________________________________scipion-users mailing > lis...@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 05:41:13
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Hi all, first the conda path looks actually very strange, and I fixed this direclty. We had some other issues, which were tensorflow-related, but this is fixed. Just to comment on that, there were first an issue with the tensorflow module. Installing the latest release (2.x) gives an error on "module 'tensorflow' has no attribute 'Session'". After fixing that by downgrading, keras was giving an error, that the module does not have no attribute "tf", which was also fixed by downgrading. TL;DR Eventually, downgrading tensorflow to 1.15.0 and downgrading keras to 2.2.4 (from 2.2.5) solved the issue Best Christian >>> "Dmitry A. Semchonok" <sem...@gm...> 19.04.21 16.24 Uhr >>> Dear Carlos Oscar, Pablo, David, Ruben, Thank you very much for your fast response. Currently, deep learning is running. A colleague of mine, Christian, kindly looked at the problem. Let me, please post the errors we had and where we are now. May be Christian can comment more on this issue. Please see the errors here. https://yadi.sk/d/KlTeKv1O9UCTQg Sincerely, Dmitry Sent from Mail for Windows 10 From: Carlos Oscar Sorzano Sent: Monday, April 19, 2021 12:57 PM To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David Maluenda Subject: Re: [scipion-users] deep consensus pickling error Dear Dmitry, let us see if David or Rubén knows where this environment is coming from. Kind regards, Carlos Oscar El 19/04/2021 a las 9:37, Pablo Conesa escribió: Hi Dmitry... you have no environment for xmipp_DLTK_v0.3. You have a "weird" xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 On 17/4/21 8:56, Dmitry A. Semchonok wrote: Dear colleagues, During deep consensus pickling I received the following error Any ideas? Thank you Sincerely, Dmitry [Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min [Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min [Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min [Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min [Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min [Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min [Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min [Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min [Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min [Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished [35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 04:05:07.093613 [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:05:07.574152 [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:26:59.879548 [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444 None None None None $ /usr/local/EMAN_2.21/bin/conda info --env # conda environments: # 3DFSC /home/panos/.conda/envs/3DFSC cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 cryolo /home/panos/.conda/envs/cryolo xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 cryolo /usr/local/EMAN_2.21/envs/cryolo cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4 fsc /usr/local/EMAN_2.21/envs/fsc topaz /usr/local/EMAN_2.21/envs/topaz root * /usr/local/EMAN_2.21 >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above) Traceback (most recent call last): File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run self._run() File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run resultFiles = self._runFunc() File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc return self._func(*self._args) File "/opt/Scipion env=self.getCondaEnv()) File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv return CondaEnvManager.getCondaEnv(env, envName) File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv envBin = os.path.join(environDir, "bin") File "/usr/lib64/python3.6/posixpath.py", line 80, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType [31mProtocol failed: expected str, bytes or os.PathLike object, not NoneType[0m [35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417 *** Last status is failed Sent from Mail for Windows 10 _______________________________________________scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users-- Pablo Conesa - Madrid Scipion team _______________________________________________scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Kenneth D. <kd...@iq...> - 2021-04-19 23:11:50
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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> |
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From: Grigory S. <sha...@gm...> - 2021-04-19 20:32:25
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Hi, have you tried to run your workflow (maybe with less particles) outside of Scipion with Relion GUI? If you cannot reproduce the problem there then I'll try to investigate further. For the "start from Relion protocol=no" option error you would need to contact Roberto Marabini who has implemented this option: ro...@cn... 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 Mon, Apr 19, 2021 at 9:57 AM Kumpula, Esa-Pekka < esa...@he...> wrote: > Hi again, > > > > We updated the Relion plugin on our system to 3.1.1, but unfortunately the > issue still persists. Subtract projection still outputs the wrong > orientations and shifts. It is not just a little bit off but completely > different values. I tried with and without centering but the results are > the same. I also tried running with the “Start from Relion protocol” set to > “no” even though it really is a Relion protocol, but there I got another > error that may or may not be linked with the problem at hand (see > attachment). > > > > Any suggestions? > > > > Cheers, > > Esa-Pekka > > > > > > -- > > Esa-Pekka Kumpula, PhD > > > > Postdoctoral Researcher > > Laboratory of Structural Biology > > Institute of Biotechnology > > Helsinki Institute of Life Science HiLIFE > > University of Helsinki > > > > www.helsinki.fi/lsb > > > > > > *From: *Grigory Sharov <sha...@gm...> > *Date: *Friday, 9 April 2021 at 11.39 > *To: *"Kumpula, Esa-Pekka" <esa...@he...> > *Cc: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] Assign alignment after Relion Subtract > Projection messes up orientations > > > > Hi, > > > > Relion plugin 3.1.1 is out now (just run "scipion installp -p > scipion-em-relion --noBin") > > > > Initial model is not related to this workflow but had the same problem. > > > > When you recenter the subtracted particles (by default = yes), the new > particles will have some remaining non-integer shifts but you can think of > it as zero shifts. The shifts that were required to recenter the particles > are not saved anywhere. So you will have a stack of subtracted particles > with no shifts (centered). > > > > Then if you do something with them (alignment etc) the new shifts are no > longer applicable to the original particles as you will be missing the part > that was used to recenter them. > > > > The centering is by default because it is default in Relion GUI as well. > My understanding is that the Relion subtraction job has the option to > revert to original particles - I'm not sure if this considers centering > shifts, I will ask Takanori. If yes, then indeed this is not implemented in > Scipion. So you will have to skip recentering in Scipion. > > > 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 Fri, Apr 9, 2021 at 8:55 AM Kumpula, Esa-Pekka < > esa...@he...> wrote: > > Hi Grigory, > > > > Thank you for a speedy fix! I’m curious: how does the initial model > protocol affect this workflow? It doesn’t appear in the workflow you sent > and it doesn’t appear on mine either. > > > > “PS. Also, don't forget if you are using recentering options in the > subtract protocol you cannot assign alignments later as this creates a new > set of shifted (centered) subtracted particles with (close to) zero shifts. > ” > > > > I suppose you mean that if I subtract particles using the recentering > option and then do assign alignment, the particle shifts will be applied > twice to those particles? I’m thinking this might be a part of my issue > too. I did the subtraction with recentering on (because it was the default > and I didn’t really know what I was doing). If I understand this correctly, > when I did assign alignment, it took not only the orientations but also the > particle shifts and re-applied them to the unsubtracted particles. Would it > make sense to have the default for recentering in subtract particles to be > set to no or to have an option in assign alignment that doesn’t assign > particle shifts, only orientations? > > > > Cheers, > > EP > > > > > > -- > > Esa-Pekka Kumpula, PhD > > > > Postdoctoral Researcher > > Laboratory of Structural Biology > > Institute of Biotechnology > > Helsinki Institute of Life Science HiLIFE > > University of Helsinki > > > > www.helsinki.fi/lsb > > > > > > *From: *Grigory Sharov <sha...@gm...> > *Date: *Thursday, 8 April 2021 at 22.27 > *To: *Mailing list for Scipion users <sci...@li...>, > "Kumpula, Esa-Pekka" <esa...@he...> > *Subject: *Re: [scipion-users] Assign alignment after Relion Subtract > Projection messes up orientations > > > > Hello again, > > > > I was able to find the problem: wrong particle shifts were saved by both > subtract and initial model protocol. I'll publish a new relion plugin > release tomorrow, which should fix this. > > > > PS. Also, don't forget if you are using recentering options in the > subtract protocol you cannot assign alignments later as this creates a new > set of shifted (centered) subtracted particles with (close to) zero shifts. > > > 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 Wed, Apr 7, 2021 at 9:53 PM Grigory Sharov <sha...@gm...> > wrote: > > Hi, > > > > I was able to reproduce the bug with the following workflow (attached), > indeed the "assign alignment" seems to be messing up the orientations as up > to that point reconstruct returns the correct map. > > > > I'll get back to you once I find the cause and release a fix. > > > > 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 Wed, Apr 7, 2021 at 3:25 PM Grigory Sharov <sha...@gm...> > wrote: > > Dear Esa-Pekka, > > > > Thank you for reporting this bug. > > > > I will try to reproduce your workflow but this will take quite some time > and I really have no other explanation except the one you suggested. > > > > > > 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 Wed, Apr 7, 2021 at 1:38 PM Kumpula, Esa-Pekka < > esa...@he...> wrote: > > Dear all, > > > > I’m running Scipion 3.0.7 and having the following issue: > > > > I have a set of particles refined by Relion autorefine. I have run a > Relion Subtract projection job on these particles and 3D classified them > using Relion’s 3D classifier and --relax_sym c2 and ended up with > asymmetric class averages, as expected. I then took the particles from one > of the classes and wanted to get the original, unsubtracted particles with > the new orientations from the classification. To this end I used the assign > alignment job using the subtracted particles from 3D classification as > input alignments and the full set of particles before subtraction as input > particles.* At this point I compare the particles by reconstructing using > Relion’s reconstruct plugin before and after assign alignment job. Before > assign alignment I get back the same map that I see in the 3D > classification results (obviously!), but after it seems that the > orientation information is lost and the map is just a sphere. I looked at > the transformation matrices of a few particles before and after assign > alignment but they are identical. > > > > * I also tried to do this by first taking particles from the whole > unsubtracted particle set using subset and then assigning the alignment > information to that set. Results were the same. > > > > Any ideas what might go wrong here and how to go about fixing it? Could it > be that subtract projection somehow messes the indices of the particles? At > least the indices change after the assign alignment job. > > > > Best, > > Esa-Pekka > > > > > > -- > > Esa-Pekka Kumpula, PhD > > > > Postdoctoral Researcher > > Laboratory of Structural Biology > > Institute of Biotechnology > > Helsinki Institute of Life Science HiLIFE > > University of Helsinki > > > > www.helsinki.fi/lsb > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Pablo C. <pc...@cn...> - 2021-04-19 14:16:03
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hehe, just a correction to the correction.... you've updated topaz <https://github.com/scipion-em/scipion-em-topaz/pull/19> some time ago to the latest version, in any case, Madrid's team is maintaining the plugin and responsible for any bugs! Please, do not bother Grigory with topaz issues, he is already maintaining many plugins. As usual you can report issues as described here: http://scipion.i2pc.es/contact NOTE: I just wanted to give credit to contributors. On 19/4/21 13:43, Grigory Sharov wrote: > Just a correction - I haven't done anything for this plugin ;) > > It's maintained by Scipion team > > 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 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Mon, Apr 19, 2021 at 12:39 PM Pablo Conesa <pc...@cn... > <mailto:pc...@cn...>> wrote: > > Dear users, we have released a new version of the topaz plugin. > > It installs 0.2.4 version of topaz and now has 3 protocols like > sphire/cryolo does: > > 1 to import a model > > 2 to train a model feeding an imported model or just coordinates > from a picking > > 3 to pick particles using a model. > > > Thanks to Grigory Sharov and Daniel del Hoyo for making this. > > All the best, Pablo. > > > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > 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... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry A. S. <sem...@gm...> - 2021-04-19 13:52:53
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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><div><p class=MsoNormal><span lang=EN-GB>Dear Carlos Oscar, Pablo, David, Ruben, <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 very much for your fast response.<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>Currently, deep learning is running.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>A colleague of mine, Christian, kindly looked at the problem.<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>Let me, please post the errors we had and where we are now.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>May be Christian can comment more on this issue.<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 errors here.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><a href="https://yadi.sk/d/KlTeKv1O9UCTQg">https://yadi.sk/d/KlTeKv1O9UCTQg</a><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>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Dmitry<o:p></o:p></span></p></div><p class=MsoNormal><span lang=EN-GB><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><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:co...@cn...">Carlos Oscar Sorzano</a><br><b>Sent: </b>Monday, April 19, 2021 12:57 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a>; <a href="mailto:pc...@cn...">Pablo Conesa</a>; <a href="mailto:rub...@gm...">Rubén Sánchez</a>; <a href="mailto:dma...@ub...">David Maluenda</a><br><b>Subject: </b>Re: [scipion-users] deep consensus pickling error</p></div><p class=MsoNormal><o:p> </o:p></p><p>Dear Dmitry,</p><p>let us see if David or Rubén knows where this environment is coming from.</p><p>Kind regards, Carlos Oscar</p><div><p class=MsoNormal>El 19/04/2021 a las 9:37, Pablo Conesa escribió:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Hi Dmitry... you have no environment for xmipp_DLTK_v0.3.</p><p>You have a "weird" xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2</p><p><o:p> </o:p></p><div><p class=MsoNormal>On 17/4/21 8:56, Dmitry A. 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><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>During deep consensus pickling I received the following error<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Any ideas?<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Thank you<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Sincerely,<o:p></o:p></p><p class=MsoNormal>Dmitry<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished<o:p></o:p></p><p class=MsoNormal>[35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 04:05:07.093613<o:p></o:p></p><p class=MsoNormal>[35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:05:07.574152<o:p></o:p></p><p class=MsoNormal>[35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:26:59.879548<o:p></o:p></p><p class=MsoNormal>[35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444<o:p></o:p></p><p class=MsoNormal>None None None None<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>$ /usr/local/EMAN_2.21/bin/conda info --env<o:p></o:p></p><p class=MsoNormal># conda environments:<o:p></o:p></p><p class=MsoNormal>#<o:p></o:p></p><p class=MsoNormal>3DFSC /home/panos/.conda/envs/3DFSC<o:p></o:p></p><p class=MsoNormal>cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0<o:p></o:p></p><p class=MsoNormal>cryolo /home/panos/.conda/envs/cryolo<o:p></o:p></p><p class=MsoNormal>xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2<o:p></o:p></p><p class=MsoNormal>cryolo /usr/local/EMAN_2.21/envs/cryolo<o:p></o:p></p><p class=MsoNormal>cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4<o:p></o:p></p><p class=MsoNormal>fsc /usr/local/EMAN_2.21/envs/fsc<o:p></o:p></p><p class=MsoNormal>topaz /usr/local/EMAN_2.21/envs/topaz<o:p></o:p></p><p class=MsoNormal>root * /usr/local/EMAN_2.21<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>>>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)<o:p></o:p></p><p class=MsoNormal>Traceback (most recent call last):<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run<o:p></o:p></p><p class=MsoNormal> self._run()<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run<o:p></o:p></p><p class=MsoNormal> resultFiles = self._runFunc()<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc<o:p></o:p></p><p class=MsoNormal> return self._func(*self._args)<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deepConsensus.py", line 948, in trainCNN<o:p></o:p></p><p class=MsoNormal> env=self.getCondaEnv())<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv<o:p></o:p></p><p class=MsoNormal> return CondaEnvManager.getCondaEnv(env, envName)<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv<o:p></o:p></p><p class=MsoNormal> envBin = os.path.join(environDir, "bin")<o:p></o:p></p><p class=MsoNormal> File "/usr/lib64/python3.6/posixpath.py", line 80, in join<o:p></o:p></p><p class=MsoNormal> a = os.fspath(a)<o:p></o:p></p><p class=MsoNormal>TypeError: expected str, bytes or os.PathLike object, not NoneType<o:p></o:p></p><p class=MsoNormal>[31mProtocol failed: expected str, bytes or os.PathLike object, not NoneType[0m<o:p></o:p></p><p class=MsoNormal>[35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417<o:p></o:p></p><p class=MsoNormal>*** Last status is failed<o:p></o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><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><div><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></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></blockquote><pre style='mso-margin-top-alt:0in;margin-right:.5in;margin-bottom:5.0pt;margin-left:.5in'><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p></div></body></html> |
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From: Grigory S. <sha...@gm...> - 2021-04-19 11:43:56
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Just a correction - I haven't done anything for this plugin ;) It's maintained by Scipion team 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 Mon, Apr 19, 2021 at 12:39 PM Pablo Conesa <pc...@cn...> wrote: > Dear users, we have released a new version of the topaz plugin. > > It installs 0.2.4 version of topaz and now has 3 protocols like > sphire/cryolo does: > > 1 to import a model > > 2 to train a model feeding an imported model or just coordinates from a > picking > > 3 to pick particles using a model. > > > Thanks to Grigory Sharov and Daniel del Hoyo for making this. > > All the best, Pablo. > > 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...> - 2021-04-19 11:38:57
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Dear users, we have released a new version of the topaz plugin. It installs 0.2.4 version of topaz and now has 3 protocols like sphire/cryolo does: 1 to import a model 2 to train a model feeding an imported model or just coordinates from a picking 3 to pick particles using a model. Thanks to Grigory Sharov and Daniel del Hoyo for making this. All the best, Pablo. Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Kumpula, Esa-P. <esa...@he...> - 2021-04-19 11:33:22
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Hi again, We updated the Relion plugin on our system to 3.1.1, but unfortunately the issue still persists. Subtract projection still outputs the wrong orientations and shifts. It is not just a little bit off but completely different values. I tried with and without centering but the results are the same. I also tried running with the “Start from Relion protocol” set to “no” even though it really is a Relion protocol, but there I got another error that may or may not be linked with the problem at hand (see attachment). Any suggestions? Cheers, Esa-Pekka -- Esa-Pekka Kumpula, PhD Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb> From: Grigory Sharov <sha...@gm...> Date: Friday, 9 April 2021 at 11.39 To: "Kumpula, Esa-Pekka" <esa...@he...> Cc: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] Assign alignment after Relion Subtract Projection messes up orientations Hi, Relion plugin 3.1.1 is out now (just run "scipion installp -p scipion-em-relion --noBin") Initial model is not related to this workflow but had the same problem. When you recenter the subtracted particles (by default = yes), the new particles will have some remaining non-integer shifts but you can think of it as zero shifts. The shifts that were required to recenter the particles are not saved anywhere. So you will have a stack of subtracted particles with no shifts (centered). Then if you do something with them (alignment etc) the new shifts are no longer applicable to the original particles as you will be missing the part that was used to recenter them. The centering is by default because it is default in Relion GUI as well. My understanding is that the Relion subtraction job has the option to revert to original particles - I'm not sure if this considers centering shifts, I will ask Takanori. If yes, then indeed this is not implemented in Scipion. So you will have to skip recentering in Scipion. 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<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Fri, Apr 9, 2021 at 8:55 AM Kumpula, Esa-Pekka <esa...@he...<mailto:esa...@he...>> wrote: Hi Grigory, Thank you for a speedy fix! I’m curious: how does the initial model protocol affect this workflow? It doesn’t appear in the workflow you sent and it doesn’t appear on mine either. “PS. Also, don't forget if you are using recentering options in the subtract protocol you cannot assign alignments later as this creates a new set of shifted (centered) subtracted particles with (close to) zero shifts.” I suppose you mean that if I subtract particles using the recentering option and then do assign alignment, the particle shifts will be applied twice to those particles? I’m thinking this might be a part of my issue too. I did the subtraction with recentering on (because it was the default and I didn’t really know what I was doing). If I understand this correctly, when I did assign alignment, it took not only the orientations but also the particle shifts and re-applied them to the unsubtracted particles. Would it make sense to have the default for recentering in subtract particles to be set to no or to have an option in assign alignment that doesn’t assign particle shifts, only orientations? Cheers, EP -- Esa-Pekka Kumpula, PhD Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb> From: Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> Date: Thursday, 8 April 2021 at 22.27 To: Mailing list for Scipion users <sci...@li...<mailto:sci...@li...>>, "Kumpula, Esa-Pekka" <esa...@he...<mailto:esa...@he...>> Subject: Re: [scipion-users] Assign alignment after Relion Subtract Projection messes up orientations Hello again, I was able to find the problem: wrong particle shifts were saved by both subtract and initial model protocol. I'll publish a new relion plugin release tomorrow, which should fix this. PS. Also, don't forget if you are using recentering options in the subtract protocol you cannot assign alignments later as this creates a new set of shifted (centered) subtracted particles with (close to) zero shifts. 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<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Apr 7, 2021 at 9:53 PM Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Hi, I was able to reproduce the bug with the following workflow (attached), indeed the "assign alignment" seems to be messing up the orientations as up to that point reconstruct returns the correct map. I'll get back to you once I find the cause and release a fix. 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<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Apr 7, 2021 at 3:25 PM Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Dear Esa-Pekka, Thank you for reporting this bug. I will try to reproduce your workflow but this will take quite some time and I really have no other explanation except the one you suggested. 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<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Apr 7, 2021 at 1:38 PM Kumpula, Esa-Pekka <esa...@he...<mailto:esa...@he...>> wrote: Dear all, I’m running Scipion 3.0.7 and having the following issue: I have a set of particles refined by Relion autorefine. I have run a Relion Subtract projection job on these particles and 3D classified them using Relion’s 3D classifier and --relax_sym c2 and ended up with asymmetric class averages, as expected. I then took the particles from one of the classes and wanted to get the original, unsubtracted particles with the new orientations from the classification. To this end I used the assign alignment job using the subtracted particles from 3D classification as input alignments and the full set of particles before subtraction as input particles.* At this point I compare the particles by reconstructing using Relion’s reconstruct plugin before and after assign alignment job. Before assign alignment I get back the same map that I see in the 3D classification results (obviously!), but after it seems that the orientation information is lost and the map is just a sphere. I looked at the transformation matrices of a few particles before and after assign alignment but they are identical. * I also tried to do this by first taking particles from the whole unsubtracted particle set using subset and then assigning the alignment information to that set. Results were the same. Any ideas what might go wrong here and how to go about fixing it? Could it be that subtract projection somehow messes the indices of the particles? At least the indices change after the assign alignment job. Best, Esa-Pekka -- Esa-Pekka Kumpula, PhD Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb> _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos O. S. <co...@cn...> - 2021-04-19 10:56:53
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Dear Dmitry, let us see if David or Rubén knows where this environment is coming from. Kind regards, Carlos Oscar El 19/04/2021 a las 9:37, Pablo Conesa escribió: > > Hi Dmitry... you have no environment for xmipp_DLTK_v0.3. > > You have a "weird" xmipp_DLTK_v0.3_BACKUP2 > /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 > > > On 17/4/21 8:56, Dmitry A. Semchonok wrote: >> >> Dear colleagues, >> >> During deep consensus pickling I received the following error >> >> Any ideas? >> >> Thank you >> >> Sincerely, >> >> Dmitry >> >> [Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min >> >> [Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min >> >> [Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min >> >> [Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min >> >> [Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min >> >> [Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min >> >> [Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min >> >> [Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min >> >> [Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min >> >> [Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished >> >> [35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 >> 04:05:07.093613 >> >> [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 >> 04:05:07.574152 >> >> [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 >> 04:26:59.879548 >> >> [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444 >> >> None None None None >> >> $ /usr/local/EMAN_2.21/bin/conda info --env >> >> # conda environments: >> >> # >> >> 3DFSC /home/panos/.conda/envs/3DFSC >> >> cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 >> >> cryolo /home/panos/.conda/envs/cryolo >> >> xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 >> >> cryolo /usr/local/EMAN_2.21/envs/cryolo >> >> cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4 >> >> fsc /usr/local/EMAN_2.21/envs/fsc >> >> topaz /usr/local/EMAN_2.21/envs/topaz >> >> root * /usr/local/EMAN_2.21 >> >> >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above) >> >> Traceback (most recent call last): >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", >> line 189, in run >> >> self._run() >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", >> line 240, in _run >> >> resultFiles = self._runFunc() >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", >> line 236, in _runFunc >> >> return self._func(*self._args) >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deepConsensus.py", >> line 948, in trainCNN >> >> 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 <https://go.microsoft.com/fwlink/?LinkId=550986> for >> Windows 10 >> >> >> >> _______________________________________________ >> 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 |
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From: Pablo C. <pc...@cn...> - 2021-04-19 07:37:59
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Hi Dmitry... you have no environment for xmipp_DLTK_v0.3. You have a "weird" xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 On 17/4/21 8:56, Dmitry A. Semchonok wrote: > > Dear colleagues, > > During deep consensus pickling I received the following error > > Any ideas? > > Thank you > > Sincerely, > > Dmitry > > [Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min > > [Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min > > [Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min > > [Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min > > [Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min > > [Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min > > [Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min > > [Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min > > [Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min > > [Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished > > [35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 > 04:05:07.093613 > > [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 > 04:05:07.574152 > > [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 > 04:26:59.879548 > > [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444 > > None None None None > > $ /usr/local/EMAN_2.21/bin/conda info --env > > # conda environments: > > # > > 3DFSC /home/panos/.conda/envs/3DFSC > > cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 > > cryolo /home/panos/.conda/envs/cryolo > > xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 > > cryolo /usr/local/EMAN_2.21/envs/cryolo > > cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4 > > fsc /usr/local/EMAN_2.21/envs/fsc > > topaz /usr/local/EMAN_2.21/envs/topaz > > root * /usr/local/EMAN_2.21 > > >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above) > > Traceback (most recent call last): > > File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 189, in run > > self._run() > > File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 240, in _run > > resultFiles = self._runFunc() > > File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 236, in _runFunc > > return self._func(*self._args) > > File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deepConsensus.py", > line 948, in trainCNN > > 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 <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > _______________________________________________ > 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 A. S. <sem...@gm...> - 2021-04-17 06:56:31
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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;} .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>Dear colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>During deep consensus pickling I received the following error</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Any ideas?</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you</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><o:p> </o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished</p><p class=MsoNormal>[35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 04:05:07.093613</p><p class=MsoNormal>[35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:05:07.574152</p><p class=MsoNormal>[35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:26:59.879548</p><p class=MsoNormal>[35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444</p><p class=MsoNormal>None None None None</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>$ /usr/local/EMAN_2.21/bin/conda info --env</p><p class=MsoNormal># conda environments:</p><p class=MsoNormal>#</p><p class=MsoNormal>3DFSC /home/panos/.conda/envs/3DFSC</p><p class=MsoNormal>cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0</p><p class=MsoNormal>cryolo /home/panos/.conda/envs/cryolo</p><p class=MsoNormal>xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2</p><p class=MsoNormal>cryolo /usr/local/EMAN_2.21/envs/cryolo</p><p class=MsoNormal>cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4</p><p class=MsoNormal>fsc /usr/local/EMAN_2.21/envs/fsc</p><p class=MsoNormal>topaz /usr/local/EMAN_2.21/envs/topaz</p><p class=MsoNormal>root * /usr/local/EMAN_2.21</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)</p><p class=MsoNormal>Traceback (most recent call last):</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run</p><p class=MsoNormal> self._run()</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run</p><p class=MsoNormal> resultFiles = self._runFunc()</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc</p><p class=MsoNormal> return self._func(*self._args)</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deepConsensus.py", line 948, in trainCNN</p><p class=MsoNormal> env=self.getCondaEnv())</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv</p><p class=MsoNormal> return CondaEnvManager.getCondaEnv(env, envName)</p><p class=MsoNormal> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv</p><p class=MsoNormal> envBin = os.path.join(environDir, "bin")</p><p class=MsoNormal> File "/usr/lib64/python3.6/posixpath.py", line 80, in join</p><p class=MsoNormal> a = os.fspath(a)</p><p class=MsoNormal>TypeError: expected str, bytes or os.PathLike object, not NoneType</p><p class=MsoNormal>[31mProtocol failed: expected str, bytes or os.PathLike object, not NoneType[0m</p><p class=MsoNormal>[35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417</p><p class=MsoNormal>*** Last status is failed</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></body></html> |
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From: helder v. <hel...@ho...> - 2021-04-16 11:19:39
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Hi! I have facing a similar problem with CUDA 11.2 . The problem is that $nvcc --version outputs the version at the last but one line instead of the last line as needed for xmipp code. Helder Ribeiro ________________________________ De: David <dst...@cn...> Enviado: sexta-feira, 16 de abril de 2021 02:31 Para: Carlos Oscar Sorzano <co...@cn...>; Mailing list for Scipion users <sci...@li...>; David Maluenda <dma...@ub...> Assunto: Re: [scipion-users] DeepLearning toolkit installation issue Hi, Yes, CUDA 11 is newly supported in the devel version of XMIPP. You can follow the Readme and wiki to install it: https://github.com/I2PC/xmipp https://scipion-em.github.io/docs/docs/scipion-modes/install-plugins-command-line.html#install-plugins-command-line However, I think that the main problem is here: nvccVersion = float(str(tokens[0] + '.' + tokens[1])) ValueError: could not convert string to float: 'Build cuda_11.0_bu' For some reason, we were not able to parse the CUDA version properly. Can you share with us you Python version used while running the 'scipion3 installb xmippSrc -j 8' and output of 'nvcc --version'? KR, David On 16/4/21 6:27, Carlos Oscar Sorzano wrote: It does now. It is in the development branch, you may have access to it if you install Xmipp from sources. Cheers, Carlos Oscar El 16/04/2021 a las 8:00, David Maluenda escribió: Yes, that's the problem. Xmipp is not installed since it is not supporting cuda11. To install cuda10, please check nvidia webpage. Then localize where cuda10 is installed (usually in /usr/local/cuda10). You can leave cuda11 as default on the system, while setting cuda10 just for xmipp. There are two possibilities to do that: 1. If <SCIPION_HOME>/config/scipion.conf exists, edit it to add XMIPP_CUDA_BIN=/usr/local/cuda10/bin XMIPP_CUDA_LIB=/usr/local/cuda10/lib and try again. If it does not exist, you can create it with just these two lines. 1. Alternatively, without editing the config file, you can run the following export XMIPP_CUDA_BIN=/usr/local/cuda10/bin export XMIPP_CUDA_LIB=/usr/local/cuda10/lib scipion3 installb xmippSrc check your cuda-bin and cuda-lib paths. _____ 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 Thu, Apr 15, 2021 at 11:18 PM Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Hi Dmitry, xmipp does not support cuda 11 yet. You need to use cuda 10 or older. 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<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Thu, Apr 15, 2021 at 3:46 PM Dmitry Semchonok <Sem...@gm...<mailto:Sem...@gm...>> wrote: Dear David, I did the steps and got the following error: [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb xmippSrc -j 8 Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building xmippSrc-3.20.07 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz mv -v /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz All targets exist. Skipping command: tar -xf xmippSrc-v3.20.07.tgz All targets exist. cd /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null Configuring ----------------------------------------- gcc detected g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include g++ -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ -I/home/user/.conda/envs/.scipion3env/include ./xmipp_test_opencv g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include OPENCV-2 detected without CUDA support rm -v xmipp_test_opencv* 'mpirun' detected. 'mpicc' detected. 'mpicxx' detected. Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 Traceback (most recent call last): File "./xmipp", line 1794, in <module> configDict = config() File "./xmipp", line 1151, in config configCuda(new_config_dict) File "./xmipp", line 942, in configCuda nvccVersion, nvccFullVersion = getCudaVersion(nvcc) File "./xmipp", line 1655, in getCudaVersion nvccVersion = float(str(tokens[0] + '.' + tokens[1])) ValueError: could not convert string to float: 'Build cuda_11.0_bu' Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') Error at main: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') [user@dataanalysisserver1 xmippSrc-v3.20.07]$ rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb deepLearningToolkit Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building deepLearningToolkit-0.2 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz All targets exist. cd /home/user/Data/Software/Scipion3/software/em tar -xf deepLearningToolkit.tgz cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi ls: cannot access /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: No such file or directory > Xmipp installation not found, please install it first (xmippSrc or xmippBin*). Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') Am I doing something wrong? Thank you Sincerely, Dmitry On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub...<mailto:dma...@ub...>> wrote: Hi Dimitry, It seems like Xmipp is not installed yet. I recommend you the following: scipion3 installb xmippSrc -j 8 rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit scipion3 installb deepLearningToolkit Hope it helps, _____ 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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok <Sem...@gm...<mailto:Sem...@gm...>> wrote: Dear colleagues, I received an error while trying to install DeepLearning toolkit on our server PC from the commandline scipion3 installb deepLearningToolkit Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building deepLearningToolkit-0.2 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz All targets exist. Skipping command: tar -xf deepLearningToolkit.tgz All targets exist. Skipping command: if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi All targets exist. cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'" Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base' Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') Any options? Thank you! Sincerely, Dmitry 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 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 _______________________________________________ scipion-users mailing list sci...@li...<mailto: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...<mailto: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...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Dmitry S. <Sem...@gm...> - 2021-04-16 09:03:37
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Dear David, My Pyton version is Python 2.7.5 [user@dataanalysisserver1 ~]$ nvcc --version nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2020 NVIDIA Corporation Built on Thu_Jun_11_22:26:38_PDT_2020 Cuda compilation tools, release 11.0, V11.0.194 Build cuda_11.0_bu.TC445_37.28540450_0 [user@dataanalysisserver1 ~]$ Sincerely, Dmitry > On 16. Apr 2021, at 09:31, David <dst...@cn...> wrote: > > Hi, > > > > Yes, CUDA 11 is newly supported in the devel version of XMIPP. > > You can follow the Readme and wiki to install it: > > https://github.com/I2PC/xmipp <https://github.com/I2PC/xmipp> > https://scipion-em.github.io/docs/docs/scipion-modes/install-plugins-command-line.html#install-plugins-command-line <https://scipion-em.github.io/docs/docs/scipion-modes/install-plugins-command-line.html#install-plugins-command-line> > > However, I think that the main problem is here: > > nvccVersion = float(str(tokens[0] + '.' + tokens[1])) > > ValueError: could not convert string to float: 'Build cuda_11.0_bu' > > > For some reason, we were not able to parse the CUDA version properly. > > Can you share with us you Python version used while running the 'scipion3 installb xmippSrc -j 8' and output of 'nvcc --version'? > > > > KR, > > > > David > > > > On 16/4/21 6:27, Carlos Oscar Sorzano wrote: >> It does now. It is in the development branch, you may have access to it if you install Xmipp from sources. >> >> Cheers, Carlos Oscar >> >> El 16/04/2021 a las 8:00, David Maluenda escribió: >>> Yes, that's the problem. Xmipp is not installed since it is not supporting cuda11. >>> >>> To install cuda10, please check nvidia webpage. Then localize where cuda10 is installed (usually in /usr/local/cuda10). >>> >>> You can leave cuda11 as default on the system, while setting cuda10 just for xmipp. There are two possibilities to do that: >>> >>> If <SCIPION_HOME>/config/scipion.conf exists, edit it to add >>> XMIPP_CUDA_BIN=/usr/local/cuda10/bin >>> XMIPP_CUDA_LIB=/usr/local/cuda10/lib >>> and try again. If it does not exist, you can create it with just these two lines. >>> >>> Alternatively, without editing the config file, you can run the following >>> export XMIPP_CUDA_BIN=/usr/local/cuda10/bin >>> export XMIPP_CUDA_LIB=/usr/local/cuda10/lib >>> scipion3 installb xmippSrc >>> check your cuda-bin and cuda-lib paths. >>> >>> >>> >>> _____ >>> 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 Thu, Apr 15, 2021 at 11:18 PM Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >>> Hi Dmitry, >>> >>> xmipp does not support cuda 11 yet. You need to use cuda 10 or older. >>> >>> 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 <tel:+44%201223%20267228> >>> e-mail: gs...@mr... <mailto:gs...@mr...> >>> >>> >>> On Thu, Apr 15, 2021 at 3:46 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>> Dear David, >>> >>> I did the steps and got the following error: >>> >>> >>> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb xmippSrc -j 8 >>> Scipion v3.0.7 - Eugenius >>> >>> >>> WARNING: Image library not found! >>> > Please install Xmipp to get full functionality. >>> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) >>> >>> >>> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >>> Building xmippSrc-3.20.07 ... >>> Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz <http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz> >>> mv -v /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz >>> All targets exist. >>> Skipping command: tar -xf xmippSrc-v3.20.07.tgz >>> All targets exist. >>> cd /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 >>> cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null >>> Configuring ----------------------------------------- >>> gcc detected >>> g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include >>> g++ -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ -I/home/user/.conda/envs/.scipion3env/include >>> ./xmipp_test_opencv >>> g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include >>> OPENCV-2 detected without CUDA support >>> rm -v xmipp_test_opencv* >>> 'mpirun' detected. >>> 'mpicc' detected. >>> 'mpicxx' detected. >>> Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 >>> Traceback (most recent call last): >>> File "./xmipp", line 1794, in <module> >>> configDict = config() >>> File "./xmipp", line 1151, in config >>> configCuda(new_config_dict) >>> File "./xmipp", line 942, in configCuda >>> nvccVersion, nvccFullVersion = getCudaVersion(nvcc) >>> File "./xmipp", line 1655, in getCudaVersion >>> nvccVersion = float(str(tokens[0] + '.' + tokens[1])) >>> ValueError: could not convert string to float: 'Build cuda_11.0_bu' >>> Traceback (most recent call last): >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> >>> main() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main >>> installPluginMethods() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods >>> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin >>> environment.execute() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute >>> self._executeTargets(targetList) >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets >>> tgt.execute() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute >>> command.execute() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute >>> assert glob(t), ("target '%s' not built (after " >>> AssertionError: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') >>> Error at main: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') >>> >>> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb deepLearningToolkit >>> Scipion v3.0.7 - Eugenius >>> >>> >>> WARNING: Image library not found! >>> > Please install Xmipp to get full functionality. >>> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) >>> >>> >>> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >>> Building deepLearningToolkit-0.2 ... >>> Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >>> mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >>> All targets exist. >>> cd /home/user/Data/Software/Scipion3/software/em >>> tar -xf deepLearningToolkit.tgz >>> cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>> if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi >>> ls: cannot access /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: No such file or directory >>> >>> > Xmipp installation not found, please install it first (xmippSrc or xmippBin*). >>> >>> Traceback (most recent call last): >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> >>> main() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main >>> installPluginMethods() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods >>> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin >>> environment.execute() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute >>> self._executeTargets(targetList) >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets >>> tgt.execute() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute >>> command.execute() >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute >>> assert glob(t), ("target '%s' not built (after " >>> AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') >>> Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') >>> >>> >>> Am I doing something wrong? >>> >>> Thank you >>> >>> Sincerely, >>> Dmitry >>> >>> >>> >>> >>>> On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub... <mailto:dma...@ub...>> wrote: >>>> >>>> Hi Dimitry, >>>> >>>> It seems like Xmipp is not installed yet. >>>> >>>> I recommend you the following: >>>> >>>> scipion3 installb xmippSrc -j 8 >>>> rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>>> scipion3 installb deepLearningToolkit >>>> >>>> >>>> Hope it helps, >>>> >>>> _____ >>>> 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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>>> <>Dear colleagues, >>>> >>>> >>>> I received an error while trying to install DeepLearning toolkit on our server PC from the commandline >>>> >>>> >>>> >>>> scipion3 installb deepLearningToolkit >>>> >>>> Scipion v3.0.7 - Eugenius >>>> >>>> >>>> >>> WARNING: Image library not found! >>>> >>>> > Please install Xmipp to get full functionality. >>>> >>>> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) >>>> >>>> >>>> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >>>> >>>> Building deepLearningToolkit-0.2 ... >>>> >>>> Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >>>> mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >>>> >>>> All targets exist. >>>> >>>> Skipping command: tar -xf deepLearningToolkit.tgz >>>> >>>> All targets exist. >>>> >>>> Skipping command: if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi >>>> >>>> All targets exist. >>>> >>>> cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>>> >>>> echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'" >>>> >>>> Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base' >>>> >>>> Traceback (most recent call last): >>>> >>>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> >>>> >>>> main() >>>> >>>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main >>>> >>>> installPluginMethods() >>>> >>>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods >>>> >>>> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >>>> >>>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin >>>> >>>> environment.execute() >>>> >>>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute >>>> >>>> self._executeTargets(targetList) >>>> >>>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets >>>> >>>> tgt.execute() >>>> >>>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute >>>> >>>> command.execute() >>>> >>>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute >>>> >>>> assert glob(t), ("target '%s' not built (after " >>>> >>>> AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') >>>> >>>> Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') >>>> >>>> >>>> Any options? >>>> >>>> >>>> Thank you! >>>> >>>> >>>> Sincerely, >>>> >>>> Dmitry >>>> >>>> >>>> >>>> >>>> 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> >>>> >>>> >>>> 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> >>> >>> _______________________________________________ >>> 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> >>> >>> >>> 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> >>> >>> >>> 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> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2021-04-16 08:12:17
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This is mine: usr/local/cuda-11/bin/nvcc --version nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2021 NVIDIA Corporation Built on Sun_Feb_14_21:12:58_PST_2021 Cuda compilation tools, release 11.2, V11.2.152 Build cuda_11.2.r11.2/compiler.29618528_0 I think, before, tweaking the xmipp script to expect this format xmipp (released code) was able to compile. On 16/4/21 9:31, David wrote: > > Hi, > > > Yes, CUDA 11 is newly supported in the devel version of XMIPP. > > You can follow the Readme and wiki to install it: > > https://github.com/I2PC/xmipp > > https://scipion-em.github.io/docs/docs/scipion-modes/install-plugins-command-line.html#install-plugins-command-line > > > However, I think that the main problem is here: > > nvccVersion = float(str(tokens[0] + '.' + tokens[1])) > > ValueError: could not convert string to float: 'Build cuda_11.0_bu' > > > For some reason, we were not able to parse the CUDA version properly. > > Can you share with us you Python version used while running the > 'scipion3 installb xmippSrc -j 8' and output of 'nvcc --version'? > > > KR, > > > David > > > On 16/4/21 6:27, Carlos Oscar Sorzano wrote: >> >> It does now. It is in the development branch, you may have access to >> it if you install Xmipp from sources. >> >> Cheers, Carlos Oscar >> >> El 16/04/2021 a las 8:00, David Maluenda escribió: >>> Yes, that's the problem. Xmipp is not installed since it is not >>> supporting cuda11. >>> >>> To install cuda10, please check nvidia webpage. Then localize where >>> cuda10 is installed (usually in |/usr/local/cuda10|). >>> >>> You can leave cuda11 as default on the system, while setting cuda10 >>> just for xmipp. There are two possibilities to do that: >>> >>> 1. If <SCIPION_HOME>/config/scipion.conf exists, edit it to add >>> >>> |XMIPP_CUDA_BIN=/usr/local/cuda10/bin >>> XMIPP_CUDA_LIB=/usr/local/cuda10/lib | >>> >>> and try again. If it does not exist, you can create it with just >>> these two lines. >>> >>> 2. Alternatively, without editing the config file, you can run the >>> following >>> >>> |export XMIPP_CUDA_BIN=/usr/local/cuda10/bin export >>> XMIPP_CUDA_LIB=/usr/local/cuda10/lib scipion3 installb xmippSrc | >>> >>> check your cuda-bin and cuda-lib paths. >>> >>> >>> >>> *_____ >>> 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 Thu, Apr 15, 2021 at 11:18 PM Grigory Sharov >>> <sha...@gm... <mailto:sha...@gm...>> wrote: >>> >>> Hi Dmitry, >>> >>> xmipp does not support cuda 11 yet. You need to use cuda 10 or >>> older. >>> >>> 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 <tel:+44%201223%20267228> >>> e-mail: gs...@mr... <mailto:gs...@mr...> >>> >>> >>> On Thu, Apr 15, 2021 at 3:46 PM Dmitry Semchonok >>> <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>> >>> Dear David, >>> >>> I did the steps and got the following error: >>> >>> >>> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 >>> installb xmippSrc -j 8 >>> Scipion v3.0.7 - Eugenius >>> >>> >>> WARNING: Image library not found! >>> > Please install Xmipp to get full functionality. >>> (Configuration->Plugins->scipion-em-xmipp -> expand, in >>> Scipion plugin manager window) >>> >>> >>> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >>> Building xmippSrc-3.20.07 ... >>> Skipping command: wget -nv -c -O >>> /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part >>> http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz >>> <http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz> >>> mv -v >>> /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part >>> /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz >>> All targets exist. >>> Skipping command: tar -xf xmippSrc-v3.20.07.tgz >>> All targets exist. >>> cd >>> /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 >>> cd . && ./xmipp config noAsk && ./xmipp check_config && >>> ./xmipp compileAndInstall N=8 && ln -srfn build >>> /home/user/Data/Software/Scipion3/software/em/xmipp && cd - >>> && touch installation_finished && rm bindings_linked 2> >>> /dev/null >>> Configuring ----------------------------------------- >>> gcc detected >>> g++ -c -w -mtune=native -march=native -std=c++11 -O3 >>> xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ >>> -I/home/user/.conda/envs/.scipion3env/include >>> g++ -w -mtune=native -march=native -std=c++11 -O3 >>> xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ >>> -I/home/user/.conda/envs/.scipion3env/include >>> ./xmipp_test_opencv >>> g++ -c -w -mtune=native -march=native -std=c++11 -O3 >>> xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ >>> -I/home/user/.conda/envs/.scipion3env/include >>> OPENCV-2 detected without CUDA support >>> rm -v xmipp_test_opencv* >>> 'mpirun' detected. >>> 'mpicc' detected. >>> 'mpicxx' detected. >>> Java detected at: >>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 >>> Traceback (most recent call last): >>> File "./xmipp", line 1794, in <module> >>> configDict = config() >>> File "./xmipp", line 1151, in config >>> configCuda(new_config_dict) >>> File "./xmipp", line 942, in configCuda >>> nvccVersion, nvccFullVersion = getCudaVersion(nvcc) >>> File "./xmipp", line 1655, in getCudaVersion >>> nvccVersion = float(str(tokens[0] + '.' + tokens[1])) >>> ValueError: could not convert string to float: 'Build >>> cuda_11.0_bu' >>> Traceback (most recent call last): >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >>> line 457, in <module> >>> main() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >>> line 297, in main >>> installPluginMethods() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>> line 259, in installPluginMethods >>> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>> line 166, in installBin >>> environment.execute() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 748, in execute >>> self._executeTargets(targetList) >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 690, in _executeTargets >>> tgt.execute() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 221, in execute >>> command.execute() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 161, in execute >>> assert glob(t), ("target '%s' not built (after " >>> AssertionError: target >>> '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' >>> not built (after running 'cd . && ./xmipp config noAsk && >>> ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln >>> -srfn build >>> /home/user/Data/Software/Scipion3/software/em/xmipp && cd - >>> && touch installation_finished && rm bindings_linked 2> >>> /dev/null') >>> Error at main: target >>> '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' >>> not built (after running 'cd . && ./xmipp config noAsk && >>> ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln >>> -srfn build >>> /home/user/Data/Software/Scipion3/software/em/xmipp && cd - >>> && touch installation_finished && rm bindings_linked 2> >>> /dev/null') >>> >>> [user@dataanalysisserver1 xmippSrc-v3.20.07]$rm -rf >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 >>> installb deepLearningToolkit >>> Scipion v3.0.7 - Eugenius >>> >>> >>> WARNING: Image library not found! >>> > Please install Xmipp to get full functionality. >>> (Configuration->Plugins->scipion-em-xmipp -> expand, in >>> Scipion plugin manager window) >>> >>> >>> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >>> Building deepLearningToolkit-0.2 ... >>> Skipping command: wget -nv -c -O >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz >>> <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >>> mv -v >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >>> All targets exist. >>> cd /home/user/Data/Software/Scipion3/software/em >>> tar -xf deepLearningToolkit.tgz >>> cd >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>> if ls >>> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >>> > /dev/null ; then touch xmippLibToken; echo ' > CUDA >>> support find. Driver version: 460' ; else echo ; echo ' > >>> Xmipp installation not found, please install it first >>> (xmippSrc or xmippBin*).';echo; fi >>> ls: cannot access >>> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: >>> No such file or directory >>> >>> > Xmipp installation not found, please install it first >>> (xmippSrc or xmippBin*). >>> >>> Traceback (most recent call last): >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >>> line 457, in <module> >>> main() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >>> line 297, in main >>> installPluginMethods() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>> line 259, in installPluginMethods >>> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>> line 166, in installBin >>> environment.execute() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 748, in execute >>> self._executeTargets(targetList) >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 690, in _executeTargets >>> tgt.execute() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 221, in execute >>> command.execute() >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 161, in execute >>> assert glob(t), ("target '%s' not built (after " >>> AssertionError: target >>> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' >>> not built (after running 'if ls >>> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >>> > /dev/null ; then touch xmippLibToken; echo ' > CUDA >>> support find. Driver version: 460' ; else echo ; echo ' > >>> Xmipp installation not found, please install it first >>> (xmippSrc or xmippBin*).';echo; fi') >>> Error at main: target >>> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' >>> not built (after running 'if ls >>> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >>> > /dev/null ; then touch xmippLibToken; echo ' > CUDA >>> support find. Driver version: 460' ; else echo ; echo ' > >>> Xmipp installation not found, please install it first >>> (xmippSrc or xmippBin*).';echo; fi') >>> >>> >>> Am I doing something wrong? >>> >>> Thank you >>> >>> Sincerely, >>> Dmitry >>> >>> >>> >>> >>>> On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub... >>>> <mailto:dma...@ub...>> wrote: >>>> >>>> Hi Dimitry, >>>> >>>> It seems like Xmipp is not installed yet. >>>> >>>> I recommend you the following: >>>> >>>> scipion3 installb xmippSrc -j 8 >>>> rm >>>> -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>>> scipion3 installb deepLearningToolkit >>>> >>>> >>>> Hope it helps, >>>> >>>> *_____* >>>> *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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok >>>> <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>>> >>>> Dear colleagues, >>>> >>>> >>>> I received an error while trying to >>>> install DeepLearning toolkit on our server PC from the >>>> commandline >>>> >>>> >>>> >>>> scipion3 installb deepLearningToolkit >>>> >>>> Scipion v3.0.7 - Eugenius >>>> >>>> >>>> >>> WARNING: Image library not found! >>>> >>>> > Please install Xmipp to get full functionality. >>>> >>>> (Configuration->Plugins->scipion-em-xmipp -> expand, in >>>> Scipion plugin manager window) >>>> >>>> >>>> Error retrieving plugin locscale >>>> binaries:'SCIPION_MPI_FLAGS' >>>> >>>> Building deepLearningToolkit-0.2 ... >>>> >>>> Skipping command: wget -nv -c -O >>>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz >>>> <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >>>> >>>> mv -v >>>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part >>>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >>>> >>>> All targets exist. >>>> >>>> Skipping command: tar -xf deepLearningToolkit.tgz >>>> >>>> All targets exist. >>>> >>>> Skipping command: if ls >>>> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >>>> > /dev/null ; then touch xmippLibToken; echo ' > CUDA >>>> support find. Driver version: 460' ; else echo ; echo ' >>>> > Xmipp installation not found, please install it first >>>> (xmippSrc or xmippBin*).';echo; fi >>>> >>>> All targets exist. >>>> >>>> cd >>>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>>> >>>> echo "Some error occurred when importing xmipp_base >>>> (from Xmipp binding): No module named 'xmipp_base'" >>>> >>>> Some error occurred when importing xmipp_base (from >>>> Xmipp binding): No module named 'xmipp_base' >>>> >>>> Traceback (most recent call last): >>>> >>>> File >>>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >>>> line 457, in <module> >>>> >>>> main() >>>> >>>> File >>>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >>>> line 297, in main >>>> >>>> installPluginMethods() >>>> >>>> File >>>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>>> line 259, in installPluginMethods >>>> >>>> pinfo.installBin({'args': [binTarget, '-j', >>>> numberProcessor]}) >>>> >>>> File >>>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>>> line 166, in installBin >>>> >>>> environment.execute() >>>> >>>> File >>>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>>> line 748, in execute >>>> >>>> self._executeTargets(targetList) >>>> >>>> File >>>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>>> line 690, in _executeTargets >>>> >>>> tgt.execute() >>>> >>>> File >>>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>>> line 221, in execute >>>> >>>> command.execute() >>>> >>>> File >>>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>>> line 161, in execute >>>> >>>> assert glob(t), ("target '%s' not built (after " >>>> >>>> AssertionError: target >>>> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >>>> not built (after running 'echo "Some error occurred >>>> when importing xmipp_base (from Xmipp binding): No >>>> module named 'xmipp_base'"') >>>> >>>> Error at main: target >>>> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >>>> not built (after running 'echo "Some error occurred >>>> when importing xmipp_base (from Xmipp binding): No >>>> module named 'xmipp_base'"') >>>> >>>> >>>> Any options? >>>> >>>> >>>> Thank you! >>>> >>>> >>>> Sincerely, >>>> >>>> Dmitry >>>> >>>> >>>> >>>> >>>> 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> >>>> >>>> >>>> >>>> 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> >>> >>> _______________________________________________ >>> 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> >>> >>> >>> >>> 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> >>> >>> >>> >>> 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 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: David <dst...@cn...> - 2021-04-16 07:32:08
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Hi, Yes, CUDA 11 is newly supported in the devel version of XMIPP. You can follow the Readme and wiki to install it: https://github.com/I2PC/xmipp https://scipion-em.github.io/docs/docs/scipion-modes/install-plugins-command-line.html#install-plugins-command-line However, I think that the main problem is here: nvccVersion = float(str(tokens[0] + '.' + tokens[1])) ValueError: could not convert string to float: 'Build cuda_11.0_bu' For some reason, we were not able to parse the CUDA version properly. Can you share with us you Python version used while running the 'scipion3 installb xmippSrc -j 8' and output of 'nvcc --version'? KR, David On 16/4/21 6:27, Carlos Oscar Sorzano wrote: > > It does now. It is in the development branch, you may have access to > it if you install Xmipp from sources. > > Cheers, Carlos Oscar > > El 16/04/2021 a las 8:00, David Maluenda escribió: >> Yes, that's the problem. Xmipp is not installed since it is not >> supporting cuda11. >> >> To install cuda10, please check nvidia webpage. Then localize where >> cuda10 is installed (usually in |/usr/local/cuda10|). >> >> You can leave cuda11 as default on the system, while setting cuda10 >> just for xmipp. There are two possibilities to do that: >> >> 1. If <SCIPION_HOME>/config/scipion.conf exists, edit it to add >> >> |XMIPP_CUDA_BIN=/usr/local/cuda10/bin >> XMIPP_CUDA_LIB=/usr/local/cuda10/lib | >> >> and try again. If it does not exist, you can create it with just >> these two lines. >> >> 2. Alternatively, without editing the config file, you can run the >> following >> >> |export XMIPP_CUDA_BIN=/usr/local/cuda10/bin export >> XMIPP_CUDA_LIB=/usr/local/cuda10/lib scipion3 installb xmippSrc | >> >> check your cuda-bin and cuda-lib paths. >> >> >> >> *_____ >> 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 Thu, Apr 15, 2021 at 11:18 PM Grigory Sharov >> <sha...@gm... <mailto:sha...@gm...>> wrote: >> >> Hi Dmitry, >> >> xmipp does not support cuda 11 yet. You need to use cuda 10 or older. >> >> 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 <tel:+44%201223%20267228> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Thu, Apr 15, 2021 at 3:46 PM Dmitry Semchonok >> <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> >> Dear David, >> >> I did the steps and got the following error: >> >> >> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 >> installb xmippSrc -j 8 >> Scipion v3.0.7 - Eugenius >> >> >>> WARNING: Image library not found! >> > Please install Xmipp to get full functionality. >> (Configuration->Plugins->scipion-em-xmipp -> expand, in >> Scipion plugin manager window) >> >> >> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >> Building xmippSrc-3.20.07 ... >> Skipping command: wget -nv -c -O >> /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part >> http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz >> <http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz> >> mv -v >> /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part >> /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz >> All targets exist. >> Skipping command: tar -xf xmippSrc-v3.20.07.tgz >> All targets exist. >> cd >> /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 >> cd . && ./xmipp config noAsk && ./xmipp check_config && >> ./xmipp compileAndInstall N=8 && ln -srfn build >> /home/user/Data/Software/Scipion3/software/em/xmipp && cd - >> && touch installation_finished && rm bindings_linked 2> /dev/null >> Configuring ----------------------------------------- >> gcc detected >> g++ -c -w -mtune=native -march=native -std=c++11 -O3 >> xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ >> -I/home/user/.conda/envs/.scipion3env/include >> g++ -w -mtune=native -march=native -std=c++11 -O3 >> xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ >> -I/home/user/.conda/envs/.scipion3env/include >> ./xmipp_test_opencv >> g++ -c -w -mtune=native -march=native -std=c++11 -O3 >> xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ >> -I/home/user/.conda/envs/.scipion3env/include >> OPENCV-2 detected without CUDA support >> rm -v xmipp_test_opencv* >> 'mpirun' detected. >> 'mpicc' detected. >> 'mpicxx' detected. >> Java detected at: >> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 >> Traceback (most recent call last): >> File "./xmipp", line 1794, in <module> >> configDict = config() >> File "./xmipp", line 1151, in config >> configCuda(new_config_dict) >> File "./xmipp", line 942, in configCuda >> nvccVersion, nvccFullVersion = getCudaVersion(nvcc) >> File "./xmipp", line 1655, in getCudaVersion >> nvccVersion = float(str(tokens[0] + '.' + tokens[1])) >> ValueError: could not convert string to float: 'Build >> cuda_11.0_bu' >> Traceback (most recent call last): >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 457, in <module> >> main() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 297, in main >> installPluginMethods() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >> line 259, in installPluginMethods >> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >> line 166, in installBin >> environment.execute() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 748, in execute >> self._executeTargets(targetList) >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 690, in _executeTargets >> tgt.execute() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 221, in execute >> command.execute() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 161, in execute >> assert glob(t), ("target '%s' not built (after " >> AssertionError: target >> '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' >> not built (after running 'cd . && ./xmipp config noAsk && >> ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln >> -srfn build >> /home/user/Data/Software/Scipion3/software/em/xmipp && cd - >> && touch installation_finished && rm bindings_linked 2> >> /dev/null') >> Error at main: target >> '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' >> not built (after running 'cd . && ./xmipp config noAsk && >> ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln >> -srfn build >> /home/user/Data/Software/Scipion3/software/em/xmipp && cd - >> && touch installation_finished && rm bindings_linked 2> >> /dev/null') >> >> [user@dataanalysisserver1 xmippSrc-v3.20.07]$rm -rf >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 >> installb deepLearningToolkit >> Scipion v3.0.7 - Eugenius >> >> >>> WARNING: Image library not found! >> > Please install Xmipp to get full functionality. >> (Configuration->Plugins->scipion-em-xmipp -> expand, in >> Scipion plugin manager window) >> >> >> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >> Building deepLearningToolkit-0.2 ... >> Skipping command: wget -nv -c -O >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz >> <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >> mv -v >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >> All targets exist. >> cd /home/user/Data/Software/Scipion3/software/em >> tar -xf deepLearningToolkit.tgz >> cd >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> if ls >> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >> > /dev/null ; then touch xmippLibToken; echo ' > CUDA support >> find. Driver version: 460' ; else echo ; echo ' > Xmipp >> installation not found, please install it first (xmippSrc or >> xmippBin*).';echo; fi >> ls: cannot access >> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: >> No such file or directory >> >> > Xmipp installation not found, please install it first >> (xmippSrc or xmippBin*). >> >> Traceback (most recent call last): >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 457, in <module> >> main() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 297, in main >> installPluginMethods() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >> line 259, in installPluginMethods >> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >> line 166, in installBin >> environment.execute() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 748, in execute >> self._executeTargets(targetList) >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 690, in _executeTargets >> tgt.execute() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 221, in execute >> command.execute() >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 161, in execute >> assert glob(t), ("target '%s' not built (after " >> AssertionError: target >> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' >> not built (after running 'if ls >> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >> > /dev/null ; then touch xmippLibToken; echo ' > CUDA support >> find. Driver version: 460' ; else echo ; echo ' > Xmipp >> installation not found, please install it first (xmippSrc or >> xmippBin*).';echo; fi') >> Error at main: target >> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' >> not built (after running 'if ls >> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >> > /dev/null ; then touch xmippLibToken; echo ' > CUDA support >> find. Driver version: 460' ; else echo ; echo ' > Xmipp >> installation not found, please install it first (xmippSrc or >> xmippBin*).';echo; fi') >> >> >> Am I doing something wrong? >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> >>> On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub... >>> <mailto:dma...@ub...>> wrote: >>> >>> Hi Dimitry, >>> >>> It seems like Xmipp is not installed yet. >>> >>> I recommend you the following: >>> >>> scipion3 installb xmippSrc -j 8 >>> rm >>> -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>> scipion3 installb deepLearningToolkit >>> >>> >>> Hope it helps, >>> >>> *_____* >>> *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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok >>> <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>> >>> Dear colleagues, >>> >>> >>> I received an error while trying to install DeepLearning >>> toolkit on our server PC from the commandline >>> >>> >>> >>> scipion3 installb deepLearningToolkit >>> >>> Scipion v3.0.7 - Eugenius >>> >>> >>> >>> WARNING: Image library not found! >>> >>> > Please install Xmipp to get full functionality. >>> >>> (Configuration->Plugins->scipion-em-xmipp -> expand, in >>> Scipion plugin manager window) >>> >>> >>> Error retrieving plugin locscale >>> binaries:'SCIPION_MPI_FLAGS' >>> >>> Building deepLearningToolkit-0.2 ... >>> >>> Skipping command: wget -nv -c -O >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz >>> <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >>> >>> mv -v >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >>> >>> All targets exist. >>> >>> Skipping command: tar -xf deepLearningToolkit.tgz >>> >>> All targets exist. >>> >>> Skipping command: if ls >>> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >>> > /dev/null ; then touch xmippLibToken; echo ' > CUDA >>> support find. Driver version: 460' ; else echo ; echo ' >>> > Xmipp installation not found, please install it first >>> (xmippSrc or xmippBin*).';echo; fi >>> >>> All targets exist. >>> >>> cd >>> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>> >>> echo "Some error occurred when importing xmipp_base >>> (from Xmipp binding): No module named 'xmipp_base'" >>> >>> Some error occurred when importing xmipp_base (from >>> Xmipp binding): No module named 'xmipp_base' >>> >>> Traceback (most recent call last): >>> >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >>> line 457, in <module> >>> >>> main() >>> >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >>> line 297, in main >>> >>> installPluginMethods() >>> >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>> line 259, in installPluginMethods >>> >>> pinfo.installBin({'args': [binTarget, '-j', >>> numberProcessor]}) >>> >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>> line 166, in installBin >>> >>> environment.execute() >>> >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 748, in execute >>> >>> self._executeTargets(targetList) >>> >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 690, in _executeTargets >>> >>> tgt.execute() >>> >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 221, in execute >>> >>> command.execute() >>> >>> File >>> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 161, in execute >>> >>> assert glob(t), ("target '%s' not built (after " >>> >>> AssertionError: target >>> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >>> not built (after running 'echo "Some error occurred when >>> importing xmipp_base (from Xmipp binding): No module >>> named 'xmipp_base'"') >>> >>> Error at main: target >>> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >>> not built (after running 'echo "Some error occurred when >>> importing xmipp_base (from Xmipp binding): No module >>> named 'xmipp_base'"') >>> >>> >>> Any options? >>> >>> >>> Thank you! >>> >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> >>> >>> 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> >>> >>> >>> >>> 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> >> >> _______________________________________________ >> 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> >> >> >> >> 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> >> >> >> >> 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 |
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From: Dmitry S. <Sem...@gm...> - 2021-04-16 06:49:01
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Thank you, David & Grigory & Carlos Oscar! Sincerely, Dmitry > On 16. Apr 2021, at 06:27, Carlos Oscar Sorzano <co...@cn...> wrote: > > It does now. It is in the development branch, you may have access to it if you install Xmipp from sources. > > Cheers, Carlos Oscar > > El 16/04/2021 a las 8:00, David Maluenda escribió: >> Yes, that's the problem. Xmipp is not installed since it is not supporting cuda11. >> >> To install cuda10, please check nvidia webpage. Then localize where cuda10 is installed (usually in /usr/local/cuda10). >> >> You can leave cuda11 as default on the system, while setting cuda10 just for xmipp. There are two possibilities to do that: >> >> If <SCIPION_HOME>/config/scipion.conf exists, edit it to add >> XMIPP_CUDA_BIN=/usr/local/cuda10/bin >> XMIPP_CUDA_LIB=/usr/local/cuda10/lib >> and try again. If it does not exist, you can create it with just these two lines. >> >> Alternatively, without editing the config file, you can run the following >> export XMIPP_CUDA_BIN=/usr/local/cuda10/bin >> export XMIPP_CUDA_LIB=/usr/local/cuda10/lib >> scipion3 installb xmippSrc >> check your cuda-bin and cuda-lib paths. >> >> >> >> _____ >> 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 Thu, Apr 15, 2021 at 11:18 PM Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >> Hi Dmitry, >> >> xmipp does not support cuda 11 yet. You need to use cuda 10 or older. >> >> 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 <tel:+44%201223%20267228> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Thu, Apr 15, 2021 at 3:46 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> Dear David, >> >> I did the steps and got the following error: >> >> >> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb xmippSrc -j 8 >> Scipion v3.0.7 - Eugenius >> >> >>> WARNING: Image library not found! >> > Please install Xmipp to get full functionality. >> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) >> >> >> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >> Building xmippSrc-3.20.07 ... >> Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz <http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz> >> mv -v /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz >> All targets exist. >> Skipping command: tar -xf xmippSrc-v3.20.07.tgz >> All targets exist. >> cd /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 >> cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null >> Configuring ----------------------------------------- >> gcc detected >> g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include >> g++ -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ -I/home/user/.conda/envs/.scipion3env/include >> ./xmipp_test_opencv >> g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include >> OPENCV-2 detected without CUDA support >> rm -v xmipp_test_opencv* >> 'mpirun' detected. >> 'mpicc' detected. >> 'mpicxx' detected. >> Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 >> Traceback (most recent call last): >> File "./xmipp", line 1794, in <module> >> configDict = config() >> File "./xmipp", line 1151, in config >> configCuda(new_config_dict) >> File "./xmipp", line 942, in configCuda >> nvccVersion, nvccFullVersion = getCudaVersion(nvcc) >> File "./xmipp", line 1655, in getCudaVersion >> nvccVersion = float(str(tokens[0] + '.' + tokens[1])) >> ValueError: could not convert string to float: 'Build cuda_11.0_bu' >> Traceback (most recent call last): >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> >> main() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main >> installPluginMethods() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods >> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin >> environment.execute() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute >> self._executeTargets(targetList) >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets >> tgt.execute() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute >> command.execute() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute >> assert glob(t), ("target '%s' not built (after " >> AssertionError: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') >> Error at main: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') >> >> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb deepLearningToolkit >> Scipion v3.0.7 - Eugenius >> >> >>> WARNING: Image library not found! >> > Please install Xmipp to get full functionality. >> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) >> >> >> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >> Building deepLearningToolkit-0.2 ... >> Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >> mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >> All targets exist. >> cd /home/user/Data/Software/Scipion3/software/em >> tar -xf deepLearningToolkit.tgz >> cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi >> ls: cannot access /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: No such file or directory >> >> > Xmipp installation not found, please install it first (xmippSrc or xmippBin*). >> >> Traceback (most recent call last): >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> >> main() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main >> installPluginMethods() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods >> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin >> environment.execute() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute >> self._executeTargets(targetList) >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets >> tgt.execute() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute >> command.execute() >> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute >> assert glob(t), ("target '%s' not built (after " >> AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') >> Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') >> >> >> Am I doing something wrong? >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> >>> On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub... <mailto:dma...@ub...>> wrote: >>> >>> Hi Dimitry, >>> >>> It seems like Xmipp is not installed yet. >>> >>> I recommend you the following: >>> >>> scipion3 installb xmippSrc -j 8 >>> rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>> scipion3 installb deepLearningToolkit >>> >>> >>> Hope it helps, >>> >>> _____ >>> 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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>> <>Dear colleagues, >>> >>> >>> I received an error while trying to install DeepLearning toolkit on our server PC from the commandline >>> >>> >>> >>> scipion3 installb deepLearningToolkit >>> >>> Scipion v3.0.7 - Eugenius >>> >>> >>> >>> WARNING: Image library not found! >>> >>> > Please install Xmipp to get full functionality. >>> >>> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) >>> >>> >>> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >>> >>> Building deepLearningToolkit-0.2 ... >>> >>> Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >>> mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >>> >>> All targets exist. >>> >>> Skipping command: tar -xf deepLearningToolkit.tgz >>> >>> All targets exist. >>> >>> Skipping command: if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi >>> >>> All targets exist. >>> >>> cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >>> >>> echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'" >>> >>> Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base' >>> >>> Traceback (most recent call last): >>> >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> >>> >>> main() >>> >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main >>> >>> installPluginMethods() >>> >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods >>> >>> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >>> >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin >>> >>> environment.execute() >>> >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute >>> >>> self._executeTargets(targetList) >>> >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets >>> >>> tgt.execute() >>> >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute >>> >>> command.execute() >>> >>> File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute >>> >>> assert glob(t), ("target '%s' not built (after " >>> >>> AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') >>> >>> Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') >>> >>> >>> Any options? >>> >>> >>> Thank you! >>> >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> >>> >>> 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> >>> >>> >>> 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> >> >> _______________________________________________ >> 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> >> >> >> 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> >> >> >> 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> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos O. S. <co...@cn...> - 2021-04-16 06:28:30
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It does now. It is in the development branch, you may have access to it if you install Xmipp from sources. Cheers, Carlos Oscar El 16/04/2021 a las 8:00, David Maluenda escribió: > Yes, that's the problem. Xmipp is not installed since it is not > supporting cuda11. > > To install cuda10, please check nvidia webpage. Then localize where > cuda10 is installed (usually in |/usr/local/cuda10|). > > You can leave cuda11 as default on the system, while setting cuda10 > just for xmipp. There are two possibilities to do that: > > 1. If <SCIPION_HOME>/config/scipion.conf exists, edit it to add > > |XMIPP_CUDA_BIN=/usr/local/cuda10/bin > XMIPP_CUDA_LIB=/usr/local/cuda10/lib | > > and try again. If it does not exist, you can create it with just these > two lines. > > 2. Alternatively, without editing the config file, you can run the > following > > |export XMIPP_CUDA_BIN=/usr/local/cuda10/bin export > XMIPP_CUDA_LIB=/usr/local/cuda10/lib scipion3 installb xmippSrc | > > check your cuda-bin and cuda-lib paths. > > > > *_____ > 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 Thu, Apr 15, 2021 at 11:18 PM Grigory Sharov > <sha...@gm... <mailto:sha...@gm...>> wrote: > > Hi Dmitry, > > xmipp does not support cuda 11 yet. You need to use cuda 10 or older. > > 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 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Apr 15, 2021 at 3:46 PM Dmitry Semchonok > <Sem...@gm... <mailto:Sem...@gm...>> wrote: > > Dear David, > > I did the steps and got the following error: > > > [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 > installb xmippSrc -j 8 > Scipion v3.0.7 - Eugenius > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in > Scipion plugin manager window) > > > Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' > Building xmippSrc-3.20.07 ... > Skipping command: wget -nv -c -O > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz> > mv -v > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.20.07.tgz > All targets exist. > cd /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 > cd . && ./xmipp config noAsk && ./xmipp check_config && > ./xmipp compileAndInstall N=8 && ln -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && > touch installation_finished && rm bindings_linked 2> /dev/null > Configuring ----------------------------------------- > gcc detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ > -I/home/user/.conda/envs/.scipion3env/include > g++ -w -mtune=native -march=native -std=c++11 -O3 > xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ > -I/home/user/.conda/envs/.scipion3env/include > ./xmipp_test_opencv > g++ -c -w -mtune=native -march=native -std=c++11 -O3 > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ > -I/home/user/.conda/envs/.scipion3env/include > OPENCV-2 detected without CUDA support > rm -v xmipp_test_opencv* > 'mpirun' detected. > 'mpicc' detected. > 'mpicxx' detected. > Java detected at: > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 > Traceback (most recent call last): > File "./xmipp", line 1794, in <module> > configDict = config() > File "./xmipp", line 1151, in config > configCuda(new_config_dict) > File "./xmipp", line 942, in configCuda > nvccVersion, nvccFullVersion = getCudaVersion(nvcc) > File "./xmipp", line 1655, in getCudaVersion > nvccVersion = float(str(tokens[0] + '.' + tokens[1])) > ValueError: could not convert string to float: 'Build > cuda_11.0_bu' > Traceback (most recent call last): > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 457, in <module> > main() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 297, in main > installPluginMethods() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 259, in installPluginMethods > pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && > ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln > -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && > touch installation_finished && rm bindings_linked 2> /dev/null') > Error at main: target > '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && > ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln > -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && > touch installation_finished && rm bindings_linked 2> /dev/null') > > [user@dataanalysisserver1 xmippSrc-v3.20.07]$rm -rf > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 > installb deepLearningToolkit > Scipion v3.0.7 - Eugenius > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in > Scipion plugin manager window) > > > Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' > Building deepLearningToolkit-0.2 ... > Skipping command: wget -nv -c -O > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> > mv -v > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz > All targets exist. > cd /home/user/Data/Software/Scipion3/software/em > tar -xf deepLearningToolkit.tgz > cd > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support > find. Driver version: 460' ; else echo ; echo ' > Xmipp > installation not found, please install it first (xmippSrc or > xmippBin*).';echo; fi > ls: cannot access > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: > No such file or directory > > > Xmipp installation not found, please install it first > (xmippSrc or xmippBin*). > > Traceback (most recent call last): > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 457, in <module> > main() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 297, in main > installPluginMethods() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 259, in installPluginMethods > pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' > not built (after running 'if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support > find. Driver version: 460' ; else echo ; echo ' > Xmipp > installation not found, please install it first (xmippSrc or > xmippBin*).';echo; fi') > Error at main: target > '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' > not built (after running 'if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support > find. Driver version: 460' ; else echo ; echo ' > Xmipp > installation not found, please install it first (xmippSrc or > xmippBin*).';echo; fi') > > > Am I doing something wrong? > > Thank you > > Sincerely, > Dmitry > > > > >> On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub... >> <mailto:dma...@ub...>> wrote: >> >> Hi Dimitry, >> >> It seems like Xmipp is not installed yet. >> >> I recommend you the following: >> >> scipion3 installb xmippSrc -j 8 >> rm >> -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> scipion3 installb deepLearningToolkit >> >> >> Hope it helps, >> >> *_____* >> *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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok >> <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> >> Dear colleagues, >> >> >> I received an error while trying to install DeepLearning >> toolkit on our server PC from the commandline >> >> >> >> scipion3 installb deepLearningToolkit >> >> Scipion v3.0.7 - Eugenius >> >> >> >>> WARNING: Image library not found! >> >> > Please install Xmipp to get full functionality. >> >> (Configuration->Plugins->scipion-em-xmipp -> expand, in >> Scipion plugin manager window) >> >> >> Error retrieving plugin locscale binaries:'SCIPION_MPI_FLAGS' >> >> Building deepLearningToolkit-0.2 ... >> >> Skipping command: wget -nv -c -O >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz >> <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >> >> mv -v >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >> >> All targets exist. >> >> Skipping command: tar -xf deepLearningToolkit.tgz >> >> All targets exist. >> >> Skipping command: if ls >> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >> > /dev/null ; then touch xmippLibToken; echo ' > CUDA >> support find. Driver version: 460' ; else echo ; echo ' > >> Xmipp installation not found, please install it first >> (xmippSrc or xmippBin*).';echo; fi >> >> All targets exist. >> >> cd >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> >> echo "Some error occurred when importing xmipp_base (from >> Xmipp binding): No module named 'xmipp_base'" >> >> Some error occurred when importing xmipp_base (from Xmipp >> binding): No module named 'xmipp_base' >> >> Traceback (most recent call last): >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 457, in <module> >> >> main() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 297, in main >> >> installPluginMethods() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >> line 259, in installPluginMethods >> >> pinfo.installBin({'args': [binTarget, '-j', >> numberProcessor]}) >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >> line 166, in installBin >> >> environment.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 748, in execute >> >> self._executeTargets(targetList) >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 690, in _executeTargets >> >> tgt.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 221, in execute >> >> command.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 161, in execute >> >> assert glob(t), ("target '%s' not built (after " >> >> AssertionError: target >> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >> not built (after running 'echo "Some error occurred when >> importing xmipp_base (from Xmipp binding): No module >> named 'xmipp_base'"') >> >> Error at main: target >> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >> not built (after running 'echo "Some error occurred when >> importing xmipp_base (from Xmipp binding): No module >> named 'xmipp_base'"') >> >> >> Any options? >> >> >> Thank you! >> >> >> Sincerely, >> >> Dmitry >> >> >> >> >> 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> >> >> >> >> 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> > > _______________________________________________ > 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> > > > > 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> > > > > 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: David M. <dma...@ub...> - 2021-04-16 06:18:33
|
Yes, that's the problem. Xmipp is not installed since it is not supporting cuda11. To install cuda10, please check nvidia webpage. Then localize where cuda10 is installed (usually in /usr/local/cuda10). You can leave cuda11 as default on the system, while setting cuda10 just for xmipp. There are two possibilities to do that: 1. If <SCIPION_HOME>/config/scipion.conf exists, edit it to add XMIPP_CUDA_BIN=/usr/local/cuda10/bin XMIPP_CUDA_LIB=/usr/local/cuda10/lib and try again. If it does not exist, you can create it with just these two lines. 1. Alternatively, without editing the config file, you can run the following export XMIPP_CUDA_BIN=/usr/local/cuda10/bin export XMIPP_CUDA_LIB=/usr/local/cuda10/lib scipion3 installb xmippSrc check your cuda-bin and cuda-lib paths. <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 Thu, Apr 15, 2021 at 11:18 PM Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Hi Dmitry, xmipp does not support cuda 11 yet. You need to use cuda 10 or older. 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<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Thu, Apr 15, 2021 at 3:46 PM Dmitry Semchonok <Sem...@gm...<mailto:Sem...@gm...>> wrote: Dear David, I did the steps and got the following error: [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb xmippSrc -j 8 Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building xmippSrc-3.20.07 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz mv -v /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz All targets exist. Skipping command: tar -xf xmippSrc-v3.20.07.tgz All targets exist. cd /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null Configuring ----------------------------------------- gcc detected g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include g++ -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ -I/home/user/.conda/envs/.scipion3env/include ./xmipp_test_opencv g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include OPENCV-2 detected without CUDA support rm -v xmipp_test_opencv* 'mpirun' detected. 'mpicc' detected. 'mpicxx' detected. Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 Traceback (most recent call last): File "./xmipp", line 1794, in <module> configDict = config() File "./xmipp", line 1151, in config configCuda(new_config_dict) File "./xmipp", line 942, in configCuda nvccVersion, nvccFullVersion = getCudaVersion(nvcc) File "./xmipp", line 1655, in getCudaVersion nvccVersion = float(str(tokens[0] + '.' + tokens[1])) ValueError: could not convert string to float: 'Build cuda_11.0_bu' Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') Error at main: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') [user@dataanalysisserver1 xmippSrc-v3.20.07]$ rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb deepLearningToolkit Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building deepLearningToolkit-0.2 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz All targets exist. cd /home/user/Data/Software/Scipion3/software/em tar -xf deepLearningToolkit.tgz cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi ls: cannot access /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: No such file or directory > Xmipp installation not found, please install it first (xmippSrc or xmippBin*). Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') Am I doing something wrong? Thank you Sincerely, Dmitry On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub...<mailto:dma...@ub...>> wrote: Hi Dimitry, It seems like Xmipp is not installed yet. I recommend you the following: scipion3 installb xmippSrc -j 8 rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit scipion3 installb deepLearningToolkit Hope it helps, <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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok <Sem...@gm...<mailto:Sem...@gm...>> wrote: Dear colleagues, I received an error while trying to install DeepLearning toolkit on our server PC from the commandline scipion3 installb deepLearningToolkit Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building deepLearningToolkit-0.2 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz All targets exist. Skipping command: tar -xf deepLearningToolkit.tgz All targets exist. Skipping command: if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi All targets exist. cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'" Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base' Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') Any options? Thank you! Sincerely, Dmitry 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 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 _______________________________________________ scipion-users mailing list sci...@li...<mailto: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...<mailto: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. |
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From: Grigory S. <sha...@gm...> - 2021-04-15 21:17:31
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Hi Dmitry, xmipp does not support cuda 11 yet. You need to use cuda 10 or older. 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 15, 2021 at 3:46 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear David, > > I did the steps and got the following error: > > > [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb xmippSrc > -j 8 > Scipion v3.0.7 - Eugenius > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin > manager window) > > > Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' > Building xmippSrc-3.20.07 ... > Skipping command: wget -nv -c -O > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz > mv -v > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.20.07.tgz > All targets exist. > cd /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 > cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp > compileAndInstall N=8 && ln -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null > Configuring ----------------------------------------- > gcc detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ > -I/home/user/.conda/envs/.scipion3env/include > g++ -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp > -o xmipp_test_opencv -I../ -I/home/user/.conda/envs/.scipion3env/include > ./xmipp_test_opencv > g++ -c -w -mtune=native -march=native -std=c++11 -O3 > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ > -I/home/user/.conda/envs/.scipion3env/include > OPENCV-2 detected without CUDA support > rm -v xmipp_test_opencv* > 'mpirun' detected. > 'mpicc' detected. > 'mpicxx' detected. > Java detected at: > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 > Traceback (most recent call last): > File "./xmipp", line 1794, in <module> > configDict = config() > File "./xmipp", line 1151, in config > configCuda(new_config_dict) > File "./xmipp", line 942, in configCuda > nvccVersion, nvccFullVersion = getCudaVersion(nvcc) > File "./xmipp", line 1655, in getCudaVersion > nvccVersion = float(str(tokens[0] + '.' + tokens[1])) > ValueError: could not convert string to float: 'Build cuda_11.0_bu' > Traceback (most recent call last): > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 457, in <module> > main() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 297, in main > installPluginMethods() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 259, in installPluginMethods > pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=8 && ln -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > Error at main: target > '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=8 && ln -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > > [user@dataanalysisserver1 xmippSrc-v3.20.07]$ rm -rf > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb > deepLearningToolkit > Scipion v3.0.7 - Eugenius > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin > manager window) > > > Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' > Building deepLearningToolkit-0.2 ... > Skipping command: wget -nv -c -O > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz > mv -v > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz > All targets exist. > cd /home/user/Data/Software/Scipion3/software/em > tar -xf deepLearningToolkit.tgz > cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver > version: 460' ; else echo ; echo ' > Xmipp installation not found, please > install it first (xmippSrc or xmippBin*).';echo; fi > ls: cannot access > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: No > such file or directory > > > Xmipp installation not found, please install it first (xmippSrc or > xmippBin*). > > Traceback (most recent call last): > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 457, in <module> > main() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 297, in main > installPluginMethods() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 259, in installPluginMethods > pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' > not built (after running 'if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver > version: 460' ; else echo ; echo ' > Xmipp installation not found, please > install it first (xmippSrc or xmippBin*).';echo; fi') > Error at main: target > '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' > not built (after running 'if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver > version: 460' ; else echo ; echo ' > Xmipp installation not found, please > install it first (xmippSrc or xmippBin*).';echo; fi') > > > Am I doing something wrong? > > Thank you > > Sincerely, > Dmitry > > > > > On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub...> wrote: > > Hi Dimitry, > > It seems like Xmipp is not installed yet. > > I recommend you the following: > > scipion3 installb xmippSrc -j 8 > rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > scipion3 installb deepLearningToolkit > > > Hope it helps, > > <http://ucm.es/> > *_____* > *Dr. David Maluenda Niubó* > 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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok <Sem...@gm...> > wrote: > >> Dear colleagues, >> >> >> I received an error while trying to install DeepLearning toolkit on our >> server PC from the commandline >> >> >> >> scipion3 installb deepLearningToolkit >> >> Scipion v3.0.7 - Eugenius >> >> >> >>> WARNING: Image library not found! >> >> > Please install Xmipp to get full functionality. >> >> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin >> manager window) >> >> >> Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' >> >> Building deepLearningToolkit-0.2 ... >> >> Skipping command: wget -nv -c -O >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part >> http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz >> >> mv -v >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >> >> All targets exist. >> >> Skipping command: tar -xf deepLearningToolkit.tgz >> >> All targets exist. >> >> Skipping command: if ls >> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > >> /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver >> version: 460' ; else echo ; echo ' > Xmipp installation not found, please >> install it first (xmippSrc or xmippBin*).';echo; fi >> >> All targets exist. >> >> cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> >> echo "Some error occurred when importing xmipp_base (from Xmipp binding): >> No module named 'xmipp_base'" >> >> Some error occurred when importing xmipp_base (from Xmipp binding): No >> module named 'xmipp_base' >> >> Traceback (most recent call last): >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 457, in <module> >> >> main() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 297, in main >> >> installPluginMethods() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >> line 259, in installPluginMethods >> >> pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >> line 166, in installBin >> >> environment.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 748, in execute >> >> self._executeTargets(targetList) >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 690, in _executeTargets >> >> tgt.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 221, in execute >> >> command.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 161, in execute >> >> assert glob(t), ("target '%s' not built (after " >> >> AssertionError: target >> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >> not built (after running 'echo "Some error occurred when importing >> xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') >> >> Error at main: target >> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >> not built (after running 'echo "Some error occurred when importing >> xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') >> >> >> Any options? >> >> >> Thank you! >> >> >> Sincerely, >> >> Dmitry >> >> >> >> 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 >> > > > 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 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2021-04-15 14:46:34
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Dear David, I did the steps and got the following error: [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb xmippSrc -j 8 Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building xmippSrc-3.20.07 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz mv -v /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz All targets exist. Skipping command: tar -xf xmippSrc-v3.20.07.tgz All targets exist. cd /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null Configuring ----------------------------------------- gcc detected g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include g++ -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ -I/home/user/.conda/envs/.scipion3env/include ./xmipp_test_opencv g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/user/.conda/envs/.scipion3env/include OPENCV-2 detected without CUDA support rm -v xmipp_test_opencv* 'mpirun' detected. 'mpicc' detected. 'mpicxx' detected. Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 Traceback (most recent call last): File "./xmipp", line 1794, in <module> configDict = config() File "./xmipp", line 1151, in config configCuda(new_config_dict) File "./xmipp", line 942, in configCuda nvccVersion, nvccFullVersion = getCudaVersion(nvcc) File "./xmipp", line 1655, in getCudaVersion nvccVersion = float(str(tokens[0] + '.' + tokens[1])) ValueError: could not convert string to float: 'Build cuda_11.0_bu' Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') Error at main: target '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') [user@dataanalysisserver1 xmippSrc-v3.20.07]$ rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 installb deepLearningToolkit Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building deepLearningToolkit-0.2 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz All targets exist. cd /home/user/Data/Software/Scipion3/software/em tar -xf deepLearningToolkit.tgz cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi ls: cannot access /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: No such file or directory > Xmipp installation not found, please install it first (xmippSrc or xmippBin*). Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' not built (after running 'if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi') Am I doing something wrong? Thank you Sincerely, Dmitry > On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub...> wrote: > > Hi Dimitry, > > It seems like Xmipp is not installed yet. > > I recommend you the following: > > scipion3 installb xmippSrc -j 8 > rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > scipion3 installb deepLearningToolkit > > > Hope it helps, > > <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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > <>Dear colleagues, > > > I received an error while trying to install DeepLearning toolkit on our server PC from the commandline > > > > scipion3 installb deepLearningToolkit > > Scipion v3.0.7 - Eugenius > > > >>> WARNING: Image library not found! > > > Please install Xmipp to get full functionality. > > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) > > > Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' > > Building deepLearningToolkit-0.2 ... > > Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> > mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz > > All targets exist. > > Skipping command: tar -xf deepLearningToolkit.tgz > > All targets exist. > > Skipping command: if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi > > All targets exist. > > cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > > echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'" > > Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base' > > Traceback (most recent call last): > > File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> > > main() > > File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main > > installPluginMethods() > > File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods > > pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) > > File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin > > environment.execute() > > File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute > > self._executeTargets(targetList) > > File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets > > tgt.execute() > > File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute > > command.execute() > > File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute > > assert glob(t), ("target '%s' not built (after " > > AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') > > Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') > > > Any options? > > > Thank you! > > > Sincerely, > > Dmitry > > > > > 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> > > > 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: David M. <dma...@ub...> - 2021-04-15 14:35:25
|
Hi Dimitry, It seems like Xmipp is not installed yet. I recommend you the following: scipion3 installb xmippSrc -j 8 rm -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit scipion3 installb deepLearningToolkit Hope it helps, <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 Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok <Sem...@gm...<mailto:Sem...@gm...>> wrote: Dear colleagues, I received an error while trying to install DeepLearning toolkit on our server PC from the commandline scipion3 installb deepLearningToolkit Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building deepLearningToolkit-0.2 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz All targets exist. Skipping command: tar -xf deepLearningToolkit.tgz All targets exist. Skipping command: if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi All targets exist. cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'" Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base' Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') Any options? Thank you! Sincerely, Dmitry 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 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: Dmitry S. <Sem...@gm...> - 2021-04-15 11:41:19
|
<>Dear colleagues, I received an error while trying to install DeepLearning toolkit on our server PC from the commandline scipion3 installb deepLearningToolkit Scipion v3.0.7 - Eugenius >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' Building deepLearningToolkit-0.2 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz All targets exist. Skipping command: tar -xf deepLearningToolkit.tgz All targets exist. Skipping command: if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 460' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi All targets exist. cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'" Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base' Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' not built (after running 'echo "Some error occurred when importing xmipp_base (from Xmipp binding): No module named 'xmipp_base'"') Any options? Thank you! Sincerely, Dmitry |
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