Difference between revisions of "Getting Started"

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[[Category:Essentials]]
 
[[Category:Essentials]]
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__NOTOC__
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Welcome to UF Research Computing! This page is intended to help new clients getting started on HiPerGator use.
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Welcome to UF Research Computing! This page is intended to help new clients get started on HiPerGator.
 
  
 
Note that new users are highly encouraged to take the [[New_user_training|New User Training]] course to familiarize themselves with using a supercomputer for research, save time, and avoid many beginner mistakes.
 
Note that new users are highly encouraged to take the [[New_user_training|New User Training]] course to familiarize themselves with using a supercomputer for research, save time, and avoid many beginner mistakes.
  
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=Introduction to Using HiPerGator=
 
  
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To use HiPerGator or HiPerGator-AI you need three basic parts
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=From Zero to HiPerGator=
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===[[HPG Interfaces | Interfaces]]===
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===Initial Consult===
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You use Interfaces to interact with the system, manage data, initialize computation, and view the results. The main categories of interfaces 'Command-Line' also known as Terminal, Graphical User Interfaces, and Web Interfaces or applications for more specialized use. Some distinctions here are blurred because, for example, you can open a Terminal while using a Web Interface like [[Jupyter#JupyterHub|JupyterHub]] or [[Open OnDemand]], but mostly you use a command-line Terminal interface through SSH connections (see below).
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If a face-to-face discussion about the group's needs is needed you can [https://outlook.office365.com/owa/calendar/UFITResearchComputingSupport@uflorida.onmicrosoft.com/bookings/ schedule an appointment] to [https://www.rc.ufl.edu/get-support/walk-in-support/ meet with one of the UF Research Computing Facilitators] face-to-face or virtually, or [https://support.rc.ufl.edu/ submit a support request to start the conversation].
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===[[HPG Data Management | Data Management]]===
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To perform research analyses you need to [[Transfer_Data|upload]] and [[Storage|manage]] data. Note that misuse of the storage systems is the second main reason for account suspension after running analyses on login nodes.
 
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===[[HPG Computation | Computation]]===
 
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'''Warning:''' do not run full-scale (normal) analyses on login nodes. [[Development and Testing]] is required reading. The main approach to run computational analyses is through writing [[Sample SLURM Scripts|job scripts]] and sending them to the [[SLURM_Commands|scheduler]] to run. Some interfaces like [[Open OnDemand]], [[Jupyter#JupyterHub|JupyterHub]], and [[Galaxy]] can manage job scheduling behind the scenes and may be more convenient than job submission from the command-line when appropriate.
 
  
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For more information about on how to get started using HiPerGator visit our Wiki category  [https://help.rc.ufl.edu/doc/Category:Essentials Essentials], where you can find additional instructions, training, and tutorial videos.
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For the initial interview we recommend prospective users to be ready to answer questions such as:
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===[[HPG Scheduling | Scheduling]]===
 
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You may want to run multiple jobs or the same job repeatedly, [[Slurm|SLURM]] allows you to schedule these jobs and allocate resources to them.
 
  
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==From Zero to HiPerGator==
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* Does the data fall under FERPA, HIPAA, or another restricted classification?
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===Initial Consult===
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* Explain in simple words what your research is about.
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If a face-to-face discussion about the group's needs is needed you can [https://www.rc.ufl.edu/get-support/walk-in-support/ meet one of the UF Research Computing Facilitators] face-to-face or virtually or [https://support.rc.ufl.edu/ submit a support request to start the conversation].
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* What file types will be processed initially?
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** Input files, average size of individual files, total amount of data in Gb/Tb, etc.
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* What software or pipeline is needed to process the files?
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Define success for you:
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* What is the expected output?
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** Expected results, output file types and individual file size, amount of data produced after processing in Gb/Tb.
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* Do you have any estimations on compute needs?
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* Are you or will you be working with external collaborators?
  
 
===HiPerGator Accounts===
 
===HiPerGator Accounts===
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Group's sponsor has to be the first person to [https://www.rc.ufl.edu/access/account-request/ request a HiPerGator account] indicating that they are a new sponsor. In the process we will create their sponsored group.
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====Sponsor Username and Group Creation====
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The group's sponsor has to be the first person to [https://www.rc.ufl.edu/access/account-request/ request a HiPerGator account] indicating that they are a new sponsor. In the process we will create their sponsored group.
  
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Afterwards, group members will be able to [https://www.rc.ufl.edu/access/account-request/ submit HiPerGator account requests] indicating their PI as the sponsor. Once approved, their linux accounts will be created.
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====User Account Creation====
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Group members will be able to [https://www.rc.ufl.edu/access/account-request/ submit HiPerGator account requests] indicating their PI as the sponsor. Once approved, their HPG Linux accounts will be created.
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====Joining a Group====
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Once their HPG username is created users must [https://support.rc.ufl.edu submit a request] to be added to a sponsor's group. Once the sponsor or an assigned manager replies to the request with approval, the user is added to the requested group. Accounts can only be added to groups with active resource allocations (see below for details).
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[https://support.rc.ufl.edu Request to be added to a group]:
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* Include the following in the Summary line: "Add [username] to [groupname] group".
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* Include the reason in the request's description.
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* If possible, add your sponsor's email to the ticket's CC list.
  
 
===Trial Allocation===
 
===Trial Allocation===
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'''At this point a group is established on HiPerGator and can continue their computational work. See below for more details on the basic use.'''
 
'''At this point a group is established on HiPerGator and can continue their computational work. See below for more details on the basic use.'''
  
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==Getting help==
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=Using HiPerGator=
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To use HiPerGator or HiPerGator-AI you must have basic understanding the following concepts:
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* Use the various [[HPG Interfaces]] to connect to the system.
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* See [[HPG Computation]] for an overview of running analyses on HiPerGator.
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* Read [[HPG Scheduling]] for an overview of managing resources in jobs.
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* Learn how to manage data on the filesystems in [[Storage]] and how to transfer it in or out in [[HPG Data Management]].
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Click on the buttons below to explore.
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<div style = 'text-align: center;'>
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[[Image:Interface.png|frameless|upright=1| link=HPG Interfaces]]
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[[Image:Computation.png|frameless|upright=1|link=HPG Computation]]
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[[Image:Scheduling.png|frameless|upright=1|link=HPG Scheduling]]
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[[Image:Storage.png|frameless|upright=1|link=HPG Data Management]]
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</div>
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=Getting help=
 
If you are having problems using the UFRC system, try our resources at [https://help.rc.ufl.edu/doc/Category:Help Help] or let our staff know by submitting a [http://support.rc.ufl.edu support request].
 
If you are having problems using the UFRC system, try our resources at [https://help.rc.ufl.edu/doc/Category:Help Help] or let our staff know by submitting a [http://support.rc.ufl.edu support request].

Latest revision as of 17:56, 19 August 2024

Welcome to UF Research Computing! This page is intended to help new clients getting started on HiPerGator use.

Note that new users are highly encouraged to take the New User Training course to familiarize themselves with using a supercomputer for research, save time, and avoid many beginner mistakes.


From Zero to HiPerGator

Initial Consult

If a face-to-face discussion about the group's needs is needed you can schedule an appointment to meet with one of the UF Research Computing Facilitators face-to-face or virtually, or submit a support request to start the conversation.


For the initial interview we recommend prospective users to be ready to answer questions such as:

  • Does the data fall under FERPA, HIPAA, or another restricted classification?
  • Explain in simple words what your research is about.
  • What file types will be processed initially?
    • Input files, average size of individual files, total amount of data in Gb/Tb, etc.
  • What software or pipeline is needed to process the files?

Define success for you:

  • What is the expected output?
    • Expected results, output file types and individual file size, amount of data produced after processing in Gb/Tb.
  • Do you have any estimations on compute needs?
  • Are you or will you be working with external collaborators?

HiPerGator Accounts

The group's sponsor has to be the first person to request a HiPerGator account indicating that they are a new sponsor. In the process we will create their sponsored group.

User Account Creation

Group members will be able to submit HiPerGator account requests indicating their PI as the sponsor. Once approved, their HPG Linux accounts will be created.

Joining a Group

Once their HPG username is created users must submit a request to be added to a sponsor's group. Once the sponsor or an assigned manager replies to the request with approval, the user is added to the requested group. Accounts can only be added to groups with active resource allocations (see below for details).

Request to be added to a group:

  • Include the following in the Summary line: "Add [username] to [groupname] group".
  • Include the reason in the request's description.
  • If possible, add your sponsor's email to the ticket's CC list.

Trial Allocation

We recommend that the group's sponsor request a free trial allocation for storage and computational resources to get the group started on HiPerGator. Group members can then use HiPerGator for the 3 month duration of the trial allocation to figure out what resources and applications they really need.

Purchasing Resources

After or while the group uses a trial allocation to determine the computational and storage resources it needs the group's sponsor can submit a purchase request for hardware (5-years) or services (3-months to longer) to invest into the resources to cover the group's HiPerGator use.

Some groups may have access to shared departmental allocations. In this case, instead of purchasing resources, group members can request to be added to the departmental group to gain access to the shared resources.

Some examples of departments with shared allocations include the Genetics Institute, Emerging Pathogens Institute, Statistics Department, Biostatistics Department, Center for Compressible Multiphase Turbulence (CCMT), Cognitive Aging and Memory Clinical Translational Research Program (CAMCTRP), Center for Molecular Magnetic Quantum Materials, Physics Department, and Plant Pathology Department. In addition, several research groups working on collaborative projects have shared allocations accessible to members of those projects.

At this point a group is established on HiPerGator and can continue their computational work. See below for more details on the basic use.

Using HiPerGator

To use HiPerGator or HiPerGator-AI you must have basic understanding the following concepts:

Click on the buttons below to explore.

Interface.png Computation.png Scheduling.png Storage.png

Getting help

If you are having problems using the UFRC system, try our resources at Help or let our staff know by submitting a support request.

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Getting_Started&oldid=29039"