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Re: [scipion-users] deepLearning toolkit -- installation error
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From: Pablo C. <pc...@cn...> - 2020-12-15 08:33:46
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When this happens: WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH Conda related installations are probably not going to work. Set the CONDA_ACTIVATION_CMD variable in scipion.conf file. Here you can find some detailed descritpion: https://github.com/scipion-em/scipion-em-sphire#plugin-integration On 14/12/20 16:08, Dmitry Semchonok wrote: > 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 > 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 > "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create > --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 > scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 > scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && > pip install numpy==1.18.4 numpy==1.18.4 && conda env export > > xmipp_DLTK_v0.3.yml') > > > > > > > > > >> On 14. Dec 2020, at 16:04, Dmitry Semchonok <sem...@gm... >> <mailto:sem...@gm...>> wrote: >> >> Dear colleagues, >> >> We are experiencing some issue with the installation of the >> deepLearning toolkit. >> >> >> While installing from the command line we have the following error: >> >> >> export PYTHONPATH="" && eval "$(/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 >> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
