HPC MUSE2022 Workshop1: Difference between revisions

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= MUSE HPC 2022 Workshop #1 =
= MUSE HPC 2022 Workshop #1 =
== HPC Tutorials ==
== HPC Hands-On Labs ==
=== Tutorial #1 ===
=== Hands-On Lab #1 - Logging into Open OnDemand ===
# Login to ELSA's Open OnDemand web portal with your TCNJ login and password
# Login to ELSA's Open OnDemand web portal with your TCNJ login and password
#* Open browser and go to https://ondemand.hpc.tcnj.edu/
#* Open browser and go to https://ondemand.hpc.tcnj.edu/
#* Create your home directory if necessary
#* Create your home directory if necessary by following the on-screen instructions
Additional help for this tutorial can be found at [https://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Getting_Started#Accessing_the_Cluster_via_Open_OnDemand Accessing the Cluster via Open OnDemand]
Additional help for this tutorial can be found at [https://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Getting_Started#Accessing_the_Cluster_via_Open_OnDemand Accessing the Cluster via Open OnDemand]
=== Tutorial #2 - Open a Terminal in Open OnDemand ===
 
=== Hands-On Lab #2 - Open a Terminal in Open OnDemand ===
# Login to the Open OnDemand port if you're not already logged in
# Login to the Open OnDemand port if you're not already logged in
# Using the Open OnDemand menu, go to <code>Clusters</code> and choose <code>_ELSA OpenHPC Cluster Shell Access</code>
# Using the Open OnDemand menu, go to <code>Clusters</code> and choose <code>_ELSA OpenHPC Cluster Shell Access</code>
# When you are done with the terminal, type <code>exit</code> at the command prompt and close the browser tab.
# Execute Linux commands at the terminal prompt, e.g. <code>ls</code>
# When you are done with the terminal, type <code>exit</code> at the command prompt and close the browser tab
Additional help for this tutorial can be found at [https://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Getting_Started#Open_OnDemand Accessing the Cluster via SSH using Open OnDemand]
 
=== Hands-On Lab #3 - Running a Cluster Job ===
# Open a terminal shell
# Add the ELSA tutorial module <code>module add elsa-tutorial</code>
# Run the ELSA tutorial setup script <code>elsa-tutorial-setup.sh</code>
# Change to elsa-tutorial directory <code>cd elsa-tutorial</code>
# Look at the a submit scripts <code>cat submit-serial.sh</code>
# Look at the other two submit scripts in the tutorial directory using either <code>cat</code> or the Open OnDemand file manager
# Edit the three submit scripts to change the email address to your email address. Use either <code>nano</code> or the Open OnDemand edit file option in the file manager
# Run the serial job <code>sbatch submit-serial.sh</code> (this one can take 2-3 minutes to complete)
# Review the job.'''jobnumber'''.out file <code>cat job.####.out</code> or use the Open OnDemand file manager to view the contents
# Run the other two jobs (these run much faster)
# Review the job output files for these jobs
Additional help for this tutorial can be found at [https://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Job_Scheduler#Submitting_Your_First_HPC_Job Submitting Your First HPC Job]


=== Tutorial #3 ===
=== Hands-On Lab #4 - The Final Exam ===
=== Tutorial #4 ===
# Download the zip file from [https://owd.tcnj.edu/~ssivy/muse2022/another-pi.zip Another Pi Implementation] to your computer
=== Tutorial #5 ===
# Unpack the zip on your local machine
# Make a new folder in your ELSA cluster home directory (e.g. <code>workshop1</code>)
# Upload at least the <code>mpi-pi-numinteg</code> program (optionally upload the other files) to the folder you created above
# Copy the <code>submit-mpi.sh</code> script from the <code>elsa-tutorial</code> folder
# Edit the copy to make any necessary changes
#* Change the command to run from <code>mdart 50000 10000</code> to <code>./mpi-pi-numinteg</code>
#* Use 2 nodes with 16 ntasks
# Change permissions on the <code>mpi-pi-numinteg</code> program while in the Linux shell to make it executable
#* <code>chmod +x mpi-pi-numinteg</code>
# Run the job by submitting it from the Linux shell
# Review the job.''jobnumber''.out file

Latest revision as of 19:46, 9 June 2023

MUSE HPC 2022 Workshop #1

HPC Hands-On Labs

Hands-On Lab #1 - Logging into Open OnDemand

  1. Login to ELSA's Open OnDemand web portal with your TCNJ login and password

Additional help for this tutorial can be found at Accessing the Cluster via Open OnDemand

Hands-On Lab #2 - Open a Terminal in Open OnDemand

  1. Login to the Open OnDemand port if you're not already logged in
  2. Using the Open OnDemand menu, go to Clusters and choose _ELSA OpenHPC Cluster Shell Access
  3. Execute Linux commands at the terminal prompt, e.g. ls
  4. When you are done with the terminal, type exit at the command prompt and close the browser tab

Additional help for this tutorial can be found at Accessing the Cluster via SSH using Open OnDemand

Hands-On Lab #3 - Running a Cluster Job

  1. Open a terminal shell
  2. Add the ELSA tutorial module module add elsa-tutorial
  3. Run the ELSA tutorial setup script elsa-tutorial-setup.sh
  4. Change to elsa-tutorial directory cd elsa-tutorial
  5. Look at the a submit scripts cat submit-serial.sh
  6. Look at the other two submit scripts in the tutorial directory using either cat or the Open OnDemand file manager
  7. Edit the three submit scripts to change the email address to your email address. Use either nano or the Open OnDemand edit file option in the file manager
  8. Run the serial job sbatch submit-serial.sh (this one can take 2-3 minutes to complete)
  9. Review the job.jobnumber.out file cat job.####.out or use the Open OnDemand file manager to view the contents
  10. Run the other two jobs (these run much faster)
  11. Review the job output files for these jobs

Additional help for this tutorial can be found at Submitting Your First HPC Job

Hands-On Lab #4 - The Final Exam

  1. Download the zip file from Another Pi Implementation to your computer
  2. Unpack the zip on your local machine
  3. Make a new folder in your ELSA cluster home directory (e.g. workshop1)
  4. Upload at least the mpi-pi-numinteg program (optionally upload the other files) to the folder you created above
  5. Copy the submit-mpi.sh script from the elsa-tutorial folder
  6. Edit the copy to make any necessary changes
    • Change the command to run from mdart 50000 10000 to ./mpi-pi-numinteg
    • Use 2 nodes with 16 ntasks
  7. Change permissions on the mpi-pi-numinteg program while in the Linux shell to make it executable
    • chmod +x mpi-pi-numinteg
  8. Run the job by submitting it from the Linux shell
  9. Review the job.jobnumber.out file
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