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Jupyter_Lab_Poseidon
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Jupyter_Lab_Poseidon
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How to analyze data on Poseidon via python/jupyterlab/jupyter notebooks
Dependencies:
Need some version of python on Poseidon, my environment is based on Pangeo, named pangeox
You can follow these directions: https://ioos.github.io/ioos_code_lab/content/ioos_installation_conda.html
And it will comply with Poseidon python licensing issues (January 2022 email from Rich Signell)
Procedure:
1. Sign onto Poseidon
2. In your home directory - make folder called bin and change into that directory
a. “mkdir ~/bin” or “mkdir bin” in the ~/ folder
b. “cd bin” or “cd ~/bin”
3. Two files are needed in this directory - start_12 (start a 12 hour session) and start_jupyter_lab (creates session for your home browser) – see below
4. from poseidon terminal window type start_12 - this will give you a compute node node
a. “start_12”
b. Output:
(base) [scook@poseidon-l1 bin]$ start_12
(base) [scook@pn120 bin]$
5. Wait for the compute node to be allocated and from that terminal window type start_jupyter_lab - this will start a jupyter lab environment
a. “start_jupyter_lab”
b. Output:
(base) [scook@pn120 bin]$ start_jupyter_proj
ssh -N -L 8888:pn120:8888 -L 8787:pn120:8787 [email protected]
[I 19:38:28.045 LabApp] [nb_conda_kernels] enabled, 1 kernels found
[I 19:38:58.883 LabApp] JupyterLab extension loaded from /vortexfs1/home/scook/miniconda3/envs/pangeox/lib/python3.8/site-packages/jupyterlab
[I 19:38:58.883 LabApp] JupyterLab application directory is /vortexfs1/home/scook/miniconda3/envs/pangeox/share/jupyter/lab
[I 19:38:58.976 LabApp] Serving notebooks from local directory: /vortexfs1/home/scook
[I 19:38:58.976 LabApp] Jupyter Notebook 6.4.3 is running at:
[I 19:38:58.976 LabApp] http://pn120:8888/
[I 19:38:58.976 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
6. Once the jupyterlab session is started, copy the ssh'd output and paste to personal computer terminal window 7. In a browser window type http://localhost:8888/
start_12
-------------------------------------------------------------------------------------------------------------------------------
srun --qos=usgs -p usgs --ntasks-per-node=1 --mem=60G --time=12:00:00 --pty bash
-------------------------------------------------------------------------------------------------------------------------------
start_jupyter_lab
-------------------------------------------------------------------------------------------------------------------------------
source activate pangeox
cd /vortexfs1/home/scook
echo "ssh -N -L 8888:`hostname`:8888 -L 8787:`hostname`:8787 [email protected]"
jupyter lab --no-browser --ip=`hostname` --port=8888
pangeox = python environment on Poseidon
/vortexfs1/