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Please note: additional packages should be installed within a user’s own directory.
Let’s now install the Deep Graph Library using pip.
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[jpf777@gadi-login-09 scr_fp0]$ export PYTHONPATH=/scratch/fp0/jpf777/EXTRA_PYTHON_LIBS/lib/python3.9/site-packages [jpf777@gadi-login-09 scr_fp0]$ python Python 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:24:11) [GCC 9.4.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import deepgraph >>> deepgraph.__file__ '/scratch/fp0/jpf777/EXTRA_PYTHON_LIBS/lib/python3.9/site-packages/deepgraph/__init__.py' >>> import dask >>> dask.__file__ '/opt/conda/lib/python3.9/site-packages/dask/__init__.py' >>> exit() |
Step 4:
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Setting PYTHONPATH to
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a PBS job script
If you want to add the Python packages installed in your own space to your job script, you will need to add in the PYTHONPATH which points to where you installed these packages:You can add your own Python package location to the environment variable PYTHONPATH in a PBS job script as below
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#!/bin/bash #PBS -N python-test #PBS -P <project code> #PBS -q normal #PBS -l walltime=5:00:00 #PBS -l ncpus=96 #PBS -l mem=384GB #PBS -l jobfs=100GB #PBS -l storage=gdata/dk92+scratch/<project code>+gdata/<project code> #PBS -v PYTHONPATH=<path to where you installed your Python packages> module use /g/data/dk92/apps/Modules/modulefiles module load NCI-data-analysis/2022.06 RUN_YOUR_OWN_PYTHON_SCRIPT |
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