Kerrie Geil

Kerrie Geil

Kerrie is an ARS SCINet postdoc in the research group of Dr. Deb Peters in Las Cruces, NM. Her M.S. and Ph.D. degrees are in Atmospheric Sciences and her research background is in climate modeling.

This page was modified from Session 3 of the SCINet Geospatial Workshop 2020. Ceres HPC Resources have been used to publish scientific papers:

Intro to Distributed Computing on the Ceres HPC System Using Python and Dask

This page contains all the info you need to participate in Session 3 of the SCINet Geospatial Workshop 2020.

A note about running this tutorial in your home directory: some participants got errors either downloading to or running the tutorial from their home directory because they did not have enough space free in their home directory. If this happens to you, download to and run the tutorial from a project directory. If you are a new HPC user and don’t yet have a project directory, you can request a small increase in space to your home directory from the SCINet VRSC at scinet_vrsc@usda.gov.


Learning Goals

  • data analysis technique for very large datasets (the tools in this tutorial are most appropriate for analysis of large earth-science-type datasets)
  • set up SLURM cluster to compute “in parallel”
  • scale clusters for heavy compute
  • use adaptive clusters to dynamically scale up and down your computing
  • view Dask diagnostics to visualize cluster computations in real time



Contents

How to Run the Tutorial on Ceres

View the Tutorial Online



How to Run the Tutorial on Ceres

Step 1: Login to your SCINet/Ceres account through the JupyterHub web interface

  • Go to https://jupyterhub.scinet.usda.gov
  • Login to the system with your SCINet credentials
  • Submit the Spawning Page with the following information (if not specified below, leave blank):
          Node Type: short
          Number of Cores: 4
          Job Duration: 02:00:00

These next two fields are important to enter correctly on the Spawning Page or you will not be able to run the tutorials once you are logged in. Please use copy/paste to avoid mistakes instead of typing these lines:

      Path to the container image: /lustre/project/geospatial_tutorials/wg_2020_ws/data_science_im_rs_vSCINetGeoWS_2020.sif
      Container Exec Args: --bind /etc/munge --bind /var/log/munge --bind /var/run/munge --bind /usr/bin/squeue --bind /usr/bin/scancel --bind /usr/bin/sbatch --bind /usr/bin/scontrol --bind /usr/bin/sinfo --bind /system/slurm:/etc/slurm --bind /run/munge --bind /usr/lib64/libslurm.so --bind /usr/lib64/libmunge.so.2 --bind /usr/lib64/slurm --bind /project --bind /lustre

After a few minutes, a JupyterLab instance running on the Ceres HPC should open in your browser. After several attempts, if the spawner fails and JupyterLab does not open correctly, please contact the SCINet Virtual Research Support Core (VRSC) for assistance at scinet_vrsc@usda.gov.

Step 2: Copy the tutorial jupyter notebook file into your home directory

From inside JupyterLab File > New > Terminal to open a terminal tab.

At the command line

cp /project/shared_files/GEOSPATIAL_WORKSHOP/session3-intro-to-python-dask-on-ceres.ipynb .

Note: The original method listed here for accessing our tutorials (from GitHub) was not working for some participants. It will be easiest to copy the files from the shared folder on Ceres as above… but an alternate method you can try is to download the tutorial material from the workshop GitHub repo.

  • Open a terminal: File–>New–>terminal (alternatively, click the “+” icon (launcher) on the left and then choose the “terminal” icon on the launcher screen)
  • Download the tutorials to your home directory
git clone --single-branch https://github.com/kerriegeil/SCINET-GEOSPATIAL-RESEARCH-WG.git

Step 3: Run a notebook

  • You should now see the file session3-intro-to-python-dask-on-ceres.ipynb (in the file system extension on the left hand side of JupyterLab, you may have to click the refresh icon in JupyterLab)
  • Double click the session3 file to open it
  • Select the py_geo kernel (upper right corner in the notebook)

  • Execute blocks of script by clicking the “play” icon in the notebook or typing Shift+Enter

  • If you used git clone to get the tutorial Navigate to ~/SCINET-GEOSPATIAL-RESEARCH-WG/tutorials/session3-intro-to-python-dask-on-ceres.ipynb



View the Tutorial Online

If you are not running the tutorial on Ceres during the session you can view a static version of it at https://kerriegeil.github.io/SCINET-GEOSPATIAL-RESEARCH-WG/html-tutorials/session3-intro-to-python-dask-on-ceres.html