Source /scratch/user/your_netid/pip_envs/Python/3.7.4-GCCcore-8.3.0/jupyterlab/bin/activate Here is an example of creating your own virtualenv on a login node. You must create your virtualenv using one of the Python modules listed on the JupyterLab HPRC portal webpage. You can create your own virtualenv to use with the JupyterLab portal app but in most cases the default virtualenv should work for you. If you get 'Server Connection Error' messages after restarting the kernel, stop all other notebooks you have running by clicking the 'Running Terminals and Kernels' button in the left panel menu and then 'SHUT DOWN' all other running KERNEL SESSIONS. in the top JupyterLab menu or click the 'Restart the kernel' icon at the top of the notebook. If you have already started your notebook before loading modules, you will need to restart the kernel in order for the loaded module to be available by clicking Kernel -> Restart Kernel. Search for modules with a compatible toolchain (such as TensorFlow/2.2.0-foss-2019b-Python-3.7.4) and click 'Load' once and wait for the LOADED MODULES section to refresh. To load additional software modules, click the 'Softwares' icon in the left most part of your JupyterLab notebook. Type 'toolchains' on the Terra command line to see a table of compatible toolchains. The default virtualenv has Jupyterlmod installed which allows you to load compatible software modules to use in your notebook. You can use the default virtualenv in the JupyterLab portal app by selecting Python/3.7.4-GCCcore-8.3.0 and leaving the 'Optional Conda Environment to be activated' field blank. NOTE: When using Anaconda3/2020.07 to create a virtualenv, the installation will add lines to your ~/.bashrc file that you should delete since these lines which automatically load your virtualenv which will interfere with other jobs and modules. In this example it will be /scratch/user/your_netid/Anaconda3/2020.07/envs/jupyterlab When using Anaconda3/2020.07, you must use the full path to the environment in the 'Optional Environment to be activated' field. Source activate /scratch/user/your_netid/Anaconda3/2020.07/envs/jupyterlab # > conda activate /scratch/user/your_netid/Anaconda3/2020.07/envs/jupyterlab You can use 'source activate' instead of 'conda activate' Mkdir -p /scratch/user/your_netid/Anaconda3/2020.07/envsĬonda create -prefix /scratch/user/your_netid/Anaconda3/2020.07/envs/jupyterlabĪfter your jupyterlab environment is created, you will see output on how to activate and use your jupyterlab environment. When using Anaconda3/2020.07, you will need to move your ~/.conda directory to $SCRATCH and make a symbolic link since Anaconda3 may fill up your $HOME disk quota: When using Anaconda/3-5.0.0.1, use just the environment name in the 'Optional Environment to be activated' field which in this example will be jupyterlab Custom Anaconda3/2020.07 conda environment To remove downloads after packages are installed. For example to install pandas version 1.1.3:Ĭonda install -c conda-forge pandas=1.1.3 You can specify a specific package version with the install command. Then you can install jupyterlab (specifying a version if needed) and add packages to your jupyterlab environmentĬonda install -c conda-forge package-name # To deactivate an active environment, use: To to create an Anaconda conda environment called jupyterlab, do the following on the command line:Īfter your jupyterlab environment is created, you will see output on how to activate and use your jupyterlab environment Notice that you will need to make sure you have enough available file quota (~30,000) since conda creates thousands of files. You can create your own JupyterLab conda environment using Anaconda for use on the HPRC portal but you must use one of the Anaconda versions that are on the JupyterLab HPRC portal webpage. The default environment for Anaconda3/2020.07 is /sw/hprc/sw/Anaconda3/2020.07/envs/jupyterlab_v2.2.9_R-3.6.1 which has the R console installed.Ĭustom Anaconda/3-5.0.0.1 conda environment The default environment for Anaconda/3-5.0.0.1 is jupyterlab-v1.2.3_R-3.6.1 which has the R console installed. You can use the default conda environment in the JupyterLab portal app by selecting Anaconda/3-5.0.0.1 or Anaconda3/2020.07 and leaving the 'Optional Conda Environment to be activated' field blank. JupyterLab Anaconda Default conda environment 1.1.3 Custom Anaconda3/2020.07 conda environment.1.1.2 Custom Anaconda/3-5.0.0.1 conda environment.
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