Difference between revisions of "Getting Started"

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[[Category:Essentials]]
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Welcome to UF Research Computing! This page is intended to help new clients get started on HiPerGator.
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Welcome to UF Research Computing! This page is intended to help new or uninitiated users understand and user HiPerGator. Be sure to check out [https://wiki.rc.ufl.edu/doc/Training our training schedule] if you'd like help getting started in person!
 
==Account creation==
 
To get an account at the UF Research Computing, you need to read [https://www.rc.ufl.edu/about/policies/account/ UFRC Account Policy] and then [https://www.rc.ufl.edu/help/account-request/ submit an account request].
 
  
==Logging in==
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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 for any given command, <code><your_username></code> should be replaced with your GatorLink username.
 
  
For example, if your are referencing the command <code>ssh <your_username>@hpg2.rc.ufl.edu</code> and your Gatorlink username is '''smith''', you would use the command:
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=Introduction to Using HiPerGator=
<pre style="width:80%;">ssh smith@hpg2.rc.ufl.edu</pre>
 
  
===Windows===
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To use HiPerGator or HiPerGator-AI you need 4 basic parts, learn about them below!
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 2px groove black;">
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<div style = 'text-align: center;'>
''Expand this section to view instructions for logging in with Windows.''
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[[Image:Interface.png|frameless|upright=1| link=HPG Interfaces]]
<div class="mw-collapsible-content" style="padding: 5px;">
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[[Image:Computation.png|frameless|upright=1|link=HPG Computation]]
Since Microsoft Windows does not come with a built-in SSH client, you must download a client from the web.
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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]]
UFRC recommends using [http://www.chiark.greenend.org.uk/~sgtatham/putty PuTTY] or [http://mobaxterm.mobatek.net/ MobaXterm].
 
 
 
'''PuTTY'''
 
* [http://www.chiark.greenend.org.uk/~sgtatham/putty Download PuTTY] to your local machine and start the program
 
* Configure PuTTY using the [[PuTTY|configuration instructions for UFRC]] .
 
* Select the connection you created in the previous step and click "Open"
 
* At the login prompt, enter your username (this should be the same as your GatorLink username)
 
* Enter your password when prompted. You are now connected and ready to work!
 
 
 
'''MobaXterm'''
 
* [http://mobaxterm.mobatek.net/ Download MobaXterm] to your local machine and start the program.
 
* Click "Start local terminal"
 
* Open a terminal and run <code>ssh <your_username>@hpg2.rc.ufl.edu</code>
 
* Enter your password when prompted. You are now connected and ready to work!
 
</div>
 
</div>
 
 
 
===Linux / Unix===
 
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 2px groove black;">
 
''Expand this section to view instructions for logging in with Linux/Unix.''
 
<div class="mw-collapsible-content" style="padding: 5px;">
 
Open a terminal and run
 
ssh <your_username>@hpg2.rc.ufl.edu
 
 
 
Enter your password when the prompt appears. You are now connected and ready to work!
 
</div>
 
</div>
 
 
 
===OS X===
 
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 2px groove black;">
 
''Expand this section to view instructions for logging in with OS X.''
 
<div class="mw-collapsible-content" style="padding: 5px;">
 
For OS X users, connection instructions are very similar to those for Linux users.
 
 
 
'''Terminal''', the terminal emulation application for OS X, is located in the folder Applications/Utilities.
 
 
 
Start the Terminal application and run
 
ssh <your_username>@hpg2.rc.ufl.edu
 
 
 
Enter your password when the prompt appears. You are now connected and ready to work!
 
</div>
 
 
</div>
 
</div>
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==From Zero to HiPerGator==
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===Initial Consult===
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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].
  
==Transferring your files==
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===HiPerGator Accounts===
SFTP and Rsync file transfers should use the servers dedicated to these transfer types, which are <code>sftp.rc.ufl.edu</code> and <code>rsync.rc.ufl.edu</code> respectively.
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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.
 
 
If the above methods seem unfamiliar or intimidating, you probably want to use a graphical file transfer client. UF Research Computing recommends:
 
* [https://filezilla-project.org/download.php?show_all=1 FileZilla] (Windows & OS X)
 
* [http://winscp.net/eng/index.php WinSCP] (Windows)
 
* [http://cyberduck.ch/ Cyberduck] (OS X)
 
 
 
After downloading, configure the client to connect to <code>sftp.rc.ufl.edu</code>, using your username and password to log in.  
 
  
Globus is another mechanism for transferring data to and from HiPerGator. [[Globus|See the Globus page]] for setup and configuration information.  
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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.
  
==Editing your files==
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'''Note:''' accounts can only be added to groups with allocations either trial or purchased.
Several methods exist for editing your files on the cluster.
 
===Native Editors===
 
* '''vi''' - The visual editor (vi) is the traditonal Unix editor; however, it is not necessarily the most intuitive editor. [http://www.eng.hawaii.edu/Tutor/vi.html View a tutorial for using vi]
 
* '''emacs''' - Emacs is a much heavier duty editor, but again has the problem of having commands that are non-intuitive. [http://www2.lib.uchicago.edu/~keith//tcl-course/emacs-tutorial.html View a tutorial for using emacs]
 
* '''pico''' - While pico is not installed on the system, nano is installed, and is a pico work-a-like.
 
* '''nano''' - Nano has a good bit of on-screen help to make it easier to use.
 
  
===External Editors===
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===Trial Allocation===
You can also use your favorite editor on your local machine, and then transfer the files to the cluster afterwards. One caveat to this is that files created on Windows machines usually contain unprintable characters, which may be misinterpreted by Linux command interpreters (shells). If this happens, there is a utility called <code>dos2unix</code> that you can use to convert the text file from DOS/Windows formatting to Linux formatting.
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We recommend that the group's sponsor [https://gravity.rc.ufl.edu/access/request-trial-allocation/ 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.
  
==Using installed software==
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===Purchasing Resources===
We use [[Modules|Environment Modules]] to provide access to the installed software. Read about the [[Modules_Basic_Usage|basic usage of environment modules]] for information on loading software.
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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 [https://gravity.rc.ufl.edu/access/purchase-request/hpg-hardware/ hardware (5-years)] or [https://gravity.rc.ufl.edu/access/purchase-request/hpg-service/ services (3-months to longer)] to invest into the resources to cover the group's HiPerGator use.
  
==Running graphical programs==
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Some groups may have access to shared departmental allocations. In this case, instead of purchasing resources, group members can [https://support.rc.ufl.edu/ request] to be added to the departmental group to gain access to the shared resources.  
Please see the [[GUI_Programs|Gui Programs]] page for information on running graphical user interface applications at UFRC.
 
  
==Running jobs using SLURM==
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Some examples of departments with shared allocations include the [http://ufgi.ufl.edu/ Genetics Institute], [http://epi.ufl.edu/ Emerging Pathogens Institute], [https://stat.ufl.edu/ Statistics Department], [http://biostat.ufl.edu/ Biostatistics Department], [https://www.eng.ufl.edu/ccmt/ Center for Compressible Multiphase Turbulence (CCMT)], [https://chp.phhp.ufl.edu/research/affiliated-centers/center-for-cognitive-aging-memory-cam/ Cognitive Aging and Memory Clinical Translational Research Program (CAMCTRP)], [https://efrc.ufl.edu/ Center for Molecular Magnetic Quantum Materials], [https://www.phys.ufl.edu/ Physics Department], and [https://plantpath.ifas.ufl.edu/ Plant Pathology Department]. In addition, several research groups working on collaborative projects have shared allocations accessible to members of those projects.
See [[Sample_SLURM_Scripts]] for a simple SLURM job script example.
 
  
To submit a job script from one of login nodes via hpg2.rc.ufl.edu, you would use the following command:
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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.'''
<pre>
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==Using HiPerGator==
$ sbatch <your_job_script>
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* Use the various [[HPG Interfaces]] to connect to the system.
</pre>
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* See [[HPG Computation]] for an overview of running analyses on HiPerGator.
To check the status of running jobs, you would use the following command:
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* Read [[HPG Scheduling]] for an overview of managing resources in jobs.
<pre>
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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]].
$ squeue [-u <your_username>]
 
</pre>
 
  
View [[SLURM_Commands]] for more useful SLURM commands.
 
 
==Getting help==
 
==Getting help==
If you are having problems using the UFRC system, please let the UFRC Staff know by submitting a [http://support.rc.ufl.edu support request].
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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 18:06, 16 April 2024

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 course to familiarize themselves with using a supercomputer for research, save time, and avoid many beginner mistakes.

Introduction to Using HiPerGator

To use HiPerGator or HiPerGator-AI you need 4 basic parts, learn about them below!

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

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.

HiPerGator Accounts

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.

Afterwards, group members will be able to submit HiPerGator account requests indicating their PI as the sponsor. Once approved, their linux accounts will be created.

Note: accounts can only be added to groups with allocations either trial or purchased.

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

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.