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Instructions from: https://medium.com/@danielwzou/installing-spacy-and-other-packages-without-sudo-or-root-privileges-using-anaconda-59571ec0ecad First, navigate to your home directory. module load anaconda/5.3.1py3 wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh sh Miniconda3-latest-Linux-x86_64.sh Now, we have a local installation of the Conda package manager at ~/miniconda3 Let’s add conda to our bash profile so that we can call it from the command line vim .bash_profile i Add this line to the file: export PATH=$HOME/miniconda3/bin:$PATH esc :wq Now, let’s reload our .bash_profile source .bash_profile And check that our installation was completed successfully which conda Which should return ~/miniconda3/bin/conda Now that Conda is installed, we can install Spacy or other Python packages conda install spacy python -m spacy download en Now, let’s make sure that Spacy is installed correctly python import spacy nlp = spacy.load('en') doc = nlp(u'Hello World!') print([w.lemma_ for w in doc]) Now that you have Conda installed, you can use it to install many packages locally. |
Anaconda on the new cluster
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module load anaconda3/2019.07py3 This should have packages like the tensorflow env. You can find with this: conda info --envs >>>>> conda info --envs # conda environments: # /sw/anaconda2/2019.07/envs/bio /sw/anaconda2/2019.07/envs/bioinfoPy27 base * /sw/anaconda3/2019.07 3point6 /sw/anaconda3/2019.07/envs/3point6 R /sw/anaconda3/2019.07/envs/R bioinformatics /sw/anaconda3/2019.07/envs/bioinformatics >>>>>>> This will give the packages in the base: conda list source activate 3point6 Next run: " conda list" This will list the packages installed in that environment. It shows among many others: pytorch 1.3.1 cuda100py36h53c1284_0 tensorboard 2.0.0 pyhb230dea_0 tensorflow 2.0.0 mkl_py36hef7ec59_0 tensorflow-base 2.0.0 mkl_py36h9204916_0 tensorflow-estimator 2.0.0 pyh2649769_0 termcolor 1.1.0 py_2 conda-forge theano 1.0.4 py36hf484d3e_1000 conda-forge Remember this cluster has no GPU (currently) |
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