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New User Training

This page mirrors and expands upon the content provided in the HiPerGator User Training in Canvas.

HiPerGator User Training Registration

The HiPerGator User Training is offered through UF’s Professional and Workforce Development site.

REGISTER HERE: https://go.ufl.edu/hpg-training.

The course is free.

Expand for full registration details

After navigating to https://go.ufl.edu/hpg-training

  • Click the + to expand the only section of the course, and click “Add to Cart.”
  • In your cart, click “Checkout.”
  • When signing in, users with a GatorLink account should sign in with their GatorLink. Federated users may select from the other options to sign in.
  • After completing the checkout process (no payment will be required), users will get two confirmation emails from Matt Gitzendanner (magitz@ufl.edu).

  • For UF users, the course should be available in your Canvas dashboard. All users can also follow the information below:

    1. Follow this link: https://elearning.ufl.edu/
    2. Click the blue "Log in to continuing education" button
    3. Login with the same account you used to register.

A more in-depth guide to accesing courses can be found here

Taking the Course is Required

While this page mirrors the content, to get credit for taking the training, you must complete the training and pass the final quiz in the Canvas course.

Training Objectives

  1. Recognize the role of UFIT Research Computing.
  2. Understand Research Computing's investment model for resource allocation.
  3. Understand different mechanisms to access HiPerGator.
  4. Describe the appropriate use of the login servers and how to request resources for work beyond those limits.
  5. Understand the primary resources tracked by the Slurm scheduler.
  6. Understand how to log in to HiPerGator using an SSH client.
  7. Understand several common mistakes HiPerGator users make and how to avoid them.

Module 1: Introduction to Research Computing and HiPerGator

HiPerGator

  • About 60,000 cores Racks of the HiPerGator 4th Generation B200 Servers
  • 504 B200 and 600 L4 GPUs
  • 11 Petabytes of all-flash, high-performance storage (Blue storage)
  • 32 Petabytes of capacity storage (Orange storage)

The HiPerGator page has updated information on the current hardware, and the History page provides historical information.

Summary

HiPerGator is a large, high-performance compute cluster capable of tackling some of the largest computational challenges, but users need to understand how to use the resources responsibly and efficiently.

Investor Supported

HiPerGator is heavily subsidized by the university, but researchers need to make investments for access to resources. Research Computing sells three main products:

  1. Compute: NCUs (Normalized Compute Units) An image highlighing a CPU, a DDN storage cabinet and an NVIDIA A100 front plate
    • 1 CPU core and 7.8 GB of RAM (as of Jan 2021)
  2. Storage:
    • Blue: High-performance storage for most data during analyses. Filesystem: /blue
    • Orange: Intended for long-term storage, raw data, and archival use. Not intended for regular job input/output (I/O). Filesystem: /orange
  3. GPUs: NGUs (Normalized Graphic Units)
    • Sold in units of GPU cards
    • An NCU investment is required to make use of GPU(s)

Investments can be categorized as hardware investments, with a fixed 5-year term and no indirect costs (IDC), or service investments, with flexible investment durations of 1 month or longer and IDC.

Module 2: Accessing HiPerGator and Running Jobs

Cluster Components

Accessing HiPerGator

Proper use of Login Nodes

  • Generally speaking, interactive work other than managing jobs and data is discouraged on the login nodes.
  • Login nodes are intended for file and job management, and short-duration testing and development. See more information here Acceptable login node use limits graphic - 16 cores, 10 minutes, 64 GB memory

Login server acceptable use limits

  • No more than 16-cores
  • No longer than 10 minutes (wall time)
  • No more than 64 GB of RAM

For users of VSCode and other IDEs with SSH connections

As outlined in the Common mistakes section below, many popular IDEs have SSH extensions that will connect to a login server.

Most of these will consume large amounts of CPU resources and violate acceptable use of the login servers, risking having your account suspended.

It is generally not recommended to use these applications on a login server.

Resources for Scheduling a Job

For use beyond what is acceptable on the login servers, you can request resources on development servers, GPUs servers, through JupyterHub, Galaxy, Graphical User Interface servers via open on demand or submit batch jobs. All of these services work with the scheduler to allocate your requested resources so that your computations run efficiently and do not impact other users.

Scheduling a Job

  1. Understand the resources that your analysis will use:
    • CPUs: Can your job use multiple CPU cores? Does it scale?
    • Memory: How much RAM will it use? Requesting more will not make your job run faster!
    • GPUs: Does your application use GPUs?
    • Time: How long will it run?
  2. Request those resources:
    • Sample Slurm Scripts
    • Watch the HiPerGator: Slurm Submission Scripts training video. This video is approximately 35 minutes long and includes a demonstration Play Video
    • Watch the HiPerGator: Slurm Submission Scripts for MPI Jobs training video. This video is approximately 25 minutes long and includes a demonstration Play Video
    • Open on Demand, JupyterHub and Galaxy all have other mechanisms to request resources as Slurm needs this information to schedule your job.
  3. Submit the Job
    • Either using the sbatch JOB_SCRIPT command or through on of the interfaces
    • Once your job is submitted, Slurm will check that there are resources available in your group and schedule the job to run
  4. Run
    • Slurm will work through the queue and run your job

Locations for Storage

The storage systems are reviewed on the storage page. Photo of the Blue storage racks

Note

In the examples below, the text in all-caps (e.g. USER) indicates example text for user-specific information (e.g. /home/albertgator)

  1. Home Storage: /home/USER
    • Each user has 40GB of space.
    • Good for scripts, code and compiled applications.
    • Do not use for job input/output (I/O).
    • Snapshots are available for a month.
  2. Blue Storage: /blue/GROUP
    • Our highest-performance filesystem.
    • All I/O from jobs should go here.
  3. Orange Storage: /orange/GROUP
    • Slower than /blue
    • Not intended for large I/O for jobs.
    • Primarily for archival purposes.

Backup and Quotas

No Storage Backup by Default

No backups graphic Unless purchased separately, nothing is backed up on HiPerGator!!

Without backup, accidental file erasure is unrecoverable. People can and do lose valuable research data. You are responsible for protecting your data.

  • The Data Protection page describes the tape backup options and costs.
  • Orange and Blue storage quotas are at the group level and based on investment.
  • The blue_quota and orange_quota commands will show your group's current quota and use.
  • The home_quota command will show your home directory quota and use.

Automounting of Directories

Directory Automounting

  • Directories on the Orange and Blue filesystems are automounted--they are only added when accessed.
  • Your group's directory may not appear until you access it.

A GIF displaying how a directory is automounted upon access

As you can see in the gif above, an ls in /blue does not show the group directory for ufhpc. After a cd into the directory, and back out, it does show. This shows how the directory is automounted on access. Of course, it would be easier to just go directly without stopping in /blue first.

Remember

  • Directories may not show up in an ls of /blue or /orange
  • If you cd to /blue and type ls, you will likely not see your group directory. You also cannot tab-complete the path to your group's directory. However, if you add the name of the group directory (e.g., cd /blue/GROUP/ the directory becomes available and tab-completion functions.
  • Of course, there is no need to change directories one step at a time...cd /blue/GROUP, will get there in one command.
  • You may need to type the path in SFTP clients or Globus for your group directory to appear
  • You cannot always use tab completion in the shell

Important user profile files

  • Do not remove files necessary for your account to function normally, such as the ~/.ssh directory or your entire /home directory.
  • Keep permissions on your home and ~/.ssh directories as they are.
    • Making your ~/.ssh directory readable to others can prevent user login.
    • Making your home directory accessible to others is a bad security practice.

Environment Modules System

  • HiPerGator uses the Lmod Environment Modules System to hide application installation complexity and make it easy to use the installed applications.
  • For applications, compilers or interpreters, load the corresponding module
  • See a list of all Installed Applications

Module 3: Common Mistakes and Getting Support

Common Mistakes

  1. Running resource intensive applications on the login nodes
  2. Using IDE SSH connections
    • VSCode, Spyder, and PyCharm all have SSH extensions. These will connect you to a login server, not a job running on HiPerGator.
    • Running applications using these often violates the acceptable use of login nodes.
    • Opening a folder with many files starts a recurring process to check for file modifications. With millions of files to check, this can quickly consume large amounts of CPU resources and impact the filesystem.
    • Use the VSCode Remote Tunnel extension as documented here.
  3. Writing to /home or /orange during batch job execution
  4. Wasting resources
    • Understand CPU and memory needs of your application
    • Over-requesting resources generally does not make your application run faster--it prevents other users from accessing resources.
  5. Blindly copying scripts from colleagues
    • Make sure you understand what borrowed scripts do
    • Many users copy previous labmate scripts, but do not understand the details
    • This often leads to wasted resources
  6. Misunderstanding the group investment limits and the burst QOS
    • Each group has specific limits
    • Burst jobs are run as idle resources are available
      • The slurmInfo command can show your group's investment and current use. See qos limits for more information.
  7. When using our Python environment modules, attempting to install new Python packages may not work because incompatible packages may get installed into the ~/.local folder and result in errors at run time. If you need to install packages, create a personal or project-specific Conda environment or request the addition of new packages in existing environment modules via the RC Support System.

See the FAQ page for these and more hints, answers, and potential pitfalls that you may want to avoid.

How to get Help

See the Get Help page for more details. In general,

  • Submit support requests via the UFRC Support System
  • For problems with running jobs, provide:
  • JobID number(s)
  • Filesystem path(s) to job scripts and job logs
  • As much detailed information as you can about your problem
  • For requests to install an application, provide:
  • Name of application
  • URL to download the application

Additional information for students using the cluster for courses

  • The instructor will provide a list of students enrolled in the course.
  • Course group names will be in the format pre1234 with the 3-letter department prefix and 4-digits course code.
  • All sections of a course will typically use the same group name, so the name may be different from the specific course you are enrolled in.
  • In the documentation below, substitute the generic pre1234 with your particular group name.
  • Students who do not have a HiPerGator Account will have one created for them.

  • Students who already have a HiPerGator Account will be added to the course group (as a secondary group).

    • You can create a folder in the class's /blue/pre1234 folder with your GatorLink username.

    • To use the resources of the class rather than your primary group, use the --account and --qos flags, in the submit script, in the sbatch command or in the boxes in the Open onDemand interface.

      1. In your submit script, add these lines: 

        #SBATCH --account=pre1234
#SBATCH --qos=pre1234

      2. In the sbatch command: sbatch --account=pre1234 --qos=pre1234 my_script.sh

      3. Using Open onDemand: Open OnDemand Account and QOS session configuration page

      JupyterHub Primary Group Only

      JupyterHub can only use your primary group's resources and cannot be used for accessing secondary group resources. To use Jupyter using your secondary group, please use Open onDemand.

  • Using your account implies agreeing to the Acceptable use policy.

  • Students understand that no restricted data should be used on HiPerGator.
  • Classes are typically allocated 32-cores, 112GB RAM and 2TB of storage
    • Instructors should keep this in mind when designing exercises and assignments.
    • Students should understand that these are shared resources: use them efficiently, share them fairly and know that if everyone waits until the last minute, there may not be enough resources to run all jobs.
  • All storage should be used for research and coursework only.
  • Accounts created for the class and the contents of the class /blue/pre1234 folder will be deleted at the end of the semester. Please copy anything you want to keep off of the cluster before the end of the semester.
  • Students should consult with their professor or TA rather than opening a support request.
    • Only the professor or TA should open support requests if needed.