Re: [scipion-users] deepLearning toolkit -- installation error

[Dmitry S. <Sem...@gm...>]

P.s.

And this is the error ( bit different)  on the other PC:


$ scipion3 installb deepLearningToolkit
Scipion v3.0.7 - Eugenius
WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
Error retrieving plugin relion binaries:  CUDA_LIB (or RELION_CUDA_LIB) is defined, but not CUDA_BIN (or RELION_CUDA_BIN), please execute scipion config --update
WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
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: 450' ; 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
export PYTHONPATH="" && eval "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22  -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml

CondaValueError: prefix already exists: /home/user/.conda/envs/xmipp_DLTK_v0.3

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/xmipp_DLTK_v0.3.yml' not built (after running 'export PYTHONPATH="" && eval "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22  -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml')
Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmipp_DLTK_v0.3.yml' not built (after running 'export PYTHONPATH="" && eval "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22  -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml')









> On 14. Dec 2020, at 16:04, Dmitry Semchonok <sem...@gm...> wrote:
> 
> Dear colleagues,
> 
> We are experiencing some issue with the installation of the deepLearning toolkit.
> 
> 
> While installing from the command line we have the following error:
> 
> 
> export PYTHONPATH="" && eval "$(/usr/local/EMAN_2.21/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22  -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml
> usage: conda [-h] [-V] command ...
> conda: error: argument command: invalid choice: u'/usr/local/EMAN_2.21/bin/conda' (choose from u'info', u'help', u'list', u'search', u'create', u'install', u'update', u'upgrade', u'remove', u'uninstall', u'config', u'clean', u'package')
> 
> CondaValueError: prefix already exists: /home/panos/.conda/envs/xmipp_DLTK_v0.3
> 
> 
> Could you please advice how to solve that ?
> 
> 
> Thank you 
> 
> 
> Sincerely,
> Dmitry
>