Re: [scipion-users] DeepLearning toolkit installation issue

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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>

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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

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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.

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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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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.

Re: [scipion-users] DeepLearning toolkit installation issue

Image processing framework to integrate EM software packages.

Re: [scipion-users] DeepLearning toolkit installation issue