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!

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

Use the various HPG Interfaces to connect to the system.
See HPG Computation for an overview of running analyses on HiPerGator.
Read HPG Scheduling for an overview of managing resources in jobs.
Learn how to manage data on the filesystems in Storage and how to transfer it in or out in HPG Data Management.

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.

@@ Line 1: / Line 1: @@
-{|align=right
+[[Category:Essentials]]
-  |__TOC__
+Welcome to UF Research Computing! This page is intended to help new clients get started on HiPerGator.
-  |}
-==Getting an account==
-To get an account at the UF HPC Center, you need to read the HPC Center [http://www.hpc.ufl.edu/users/accounts.php Policies] and then put a request in at our request page. That page is [http://www.hpc.ufl.edu/support/acctrqst/ located here].
-==Login==
+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.
-===Linux / Unix===
-Open a terminal and run
- ssh -Y <YOUR_USERNAME>@submit.hpc.ufl.edu
-where <code><YOUR_USERNAME></code> is your HPC Center username, which was sent to you when you got your HPC Center account.
-The command <code>ssh -Y <YOUR_USERNAME>@submit.hpc.ufl.edu</code> is what you would type in at a command prompt on your system.  After this, it asks you for a password, which you type in. After that, you are logged in and ready to work.  As a concrete example, if your HPC Center username is "smith", you would use the command <code>ssh smith@submit.hpc.ufl.edu</code> to log into the HPC Center.
+=Introduction to Using HiPerGator=
-The <code>-Y</code> option is used to indicate that X11 forwarding should be enabled on the connection.  If your desktop supports an X Windows server, X11 forwarding will allow you to run X Windows clients on the HPC Center's interactive servers and view the display on your desktop.  Otherwise, the <code>-Y</code> option is not necessary.
+To use HiPerGator or HiPerGator-AI you need 4 basic parts, learn about them below!
+<div style = 'text-align: center;'>
+[[Image:Interface.png|frameless|upright=1| link=HPG Interfaces]]
+[[Image:Computation.png|frameless|upright=1|link=HPG Computation]]
+[[Image:Scheduling.png|frameless|upright=1|link=HPG Scheduling]]
+[[Image:Storage.png|frameless|upright=1|link=HPG Data Management]]
+</div>
+==From Zero to HiPerGator==
+===Initial Consult===
+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].
-===Windows===
+===HiPerGator Accounts===
-Microsoft Windows does not come with a built-in SSH client. You have to download a client from the web. We recommend the following software:
+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.
-* SSH client - [http://www.chiark.greenend.org.uk/~sgtatham/putty Putty]
-** [[PuTTY|configuration instructions for UF HPC]]
-* Graphical file transfer clients:
-** [http://filezilla-project.org/download.php?type=client FileZilla]. See our [[FileZilla|tutorial on transferring files to UF HPC using FileZilla]].
-** [http://winscp.net/eng/index.php WinSCP]
-====X Windows for MS Windows====
-For Windows users who would like to run [http://en.wikipedia.org/wiki/X_Window_System X Windows] applications, there are several X Windows servers available for the MS Windows operating system.
-* [http://mobaxterm.mobatek.net/ MobaXterm]
+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.
-* [http://www.straightrunning.com/XmingNotes/ Xming] ([http://sourceforge.net/projects/xming/files/Xming/6.9.0.31/Xming-6-9-0-31-setup.exe/download download])
-* [http://connectivity.opentext.com/products/exceed.aspx Xceed]
-===MacOS===
+'''Note:''' accounts can only be added to groups with allocations either trial or purchased.
-For MacOS users, the connection instructions are very similar to those for Linux/Unix users.
-''Terminal'', the terminal emulation application under MacOS is located in Applications/Utilities.
+===Trial Allocation===
+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.
-Both [http://filezilla-project.org/download.php?type=client FileZilla] and [http://cyberduck.ch/ Cyberduck] are available for MacOS if you prefer a graphical interface for transferring files.
+===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 [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.
-==Getting Help==
+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.
-If you are having problems connecting to the HPC system, please let the HPC Staff know by submitting a [http://support.hpc.ufl.edu Support Request].
-==Interactive work under Linux==
+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.
-Once you are logged in to an HPC Center server, you will find yourself at a Linux command line prompt. That may be daunting at first. However, you only need to know a small subset of Linux commands to accomplish most tasks. There are many Linux "Getting Started" guides online and in print.  Below are just a few possibilities.  Many more are easily found via a Google search.
-* [http://www.tldp.org/LDP/intro-linux/html/ Introduction to Linux]
+'''At this point a group is established on HiPerGator and can continue their computational work. See below for more details on the basic use.'''
-* [http://www.linux.org/tutorial/view/beginners-level-course Linux for Beginners]
+==Using HiPerGator==
-* [http://www.tutorialized.com/tutorial/Basic-Linux-Shell-commands/21596 Basic Linux Shell Commands]
+* Use the various [[HPG Interfaces]] to connect to the system.
+* See [[HPG Computation]] for an overview of running analyses on HiPerGator.
+* Read [[HPG Scheduling]] for an overview of managing resources in jobs.
+* Learn how to manage data on the filesystems in [[Storage]] and how to transfer it in or out in [[HPG Data Management]].
-==A Few Basic Commands==
+==Getting help==
-While it is advantageous to have a working knowledge of the most common Linux commands, it is not a requirement.  For the uninitiated, the following information may be useful as well as a good "Introduction to Using Linux" book.
+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].
-{| border=1
-|-
-! Command !! Description
-|-
-| ls || List files in the current directory
-|-
-| cd || Change directory
-|-
-| more || View a file's contents
-|-
-| mkdir <dir> || Create a directory
-|-
-| cp file1 file2 || Copy a file
-|-
-| mv file1 file2 || Move (i.e. rename) a file
-|-
-| rm file || Delete a file
-|-
-| rmdir dir || Delete an ''empty'' directory
-|}
-==Editing==
-Editing files on the cluster can be done through a couple of different methods...
-===Native Editors===
-* '''vi''' - The visual editor (vi) is the traditonal Unix editor. However, it is not necessarily the most intuitive editor.  That being the case, if you are unfamiliar with it, the following tutorial may be useful.
-** [http://www.eng.hawaii.edu/Tutor/vi.html VI Tutorial]
-** Another resource for vi is [[vi | right here]] on our wiki.
-** There is also a vi tutorial, '''vimtutor'''. Once logged in, simply type "<code>vimtutor</code>" at the command line to start the tutorial.
-* '''emacs''' - Emacs is a much heavier duty editor, but again has the problem of having commands that are non-intuitive. Again, we have provided a link to a tutorial for this editor.
-** [http://www2.lib.uchicago.edu/~keith//tcl-course/emacs-tutorial.html Emacs Tutorial]
-* '''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===
-You can also use your favorite editor on your local machine and then transfer the files over to the HPC Center afterwards. One caveat to this is that with 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.
-==Running Jobs==
-====Trivial Example====
-{|
-|-valign="top"
-|
-<pre>
-#! /bin/sh
-#PBS -N testjob
-#PBS -o testjob.out
-#PBS -e testjob.err
-#PBS -M <INSERT EMAIL HERE>
-#PBS -r n
-#PBS -l walltime=00:01:00
-#PBS -l nodes=1:ppn=1
-#PBS -l pmem=100mb
-date
-hostname
-module load python
-python -V
-</pre>
-||
-To submit this job from [[submit.hpc.ufl.edu]], you would use the following command:
-<pre>
-$ qsub <your job script>
-</pre>
-To check the status of running jobs, you would use the following command:
-<pre>
-$ qstat [-u <username>]
-</pre>
-or [http://www.hpc.ufl.edu/ HPC] --> Utilization --> [http://www.hpc.ufl.edu/index2.php?body=queue2 Torque Queue Status]
-|}
-'''Notes: '''
-* More [[Sample Scripts]] for more information on PBS scripts.
-* See [[Modules]] for more information on using the installed software via the environment modules system.
-====Notes on Batch Scripts====
-* The script can handle only one set of directives. '''Do not submit a script that has more than one set of directives''' included in it.
-* For more info on '''advanced directives''' see [[PBS_Directives]]
-* For a more detailed explanation of what is going on in a [[Batch Script Explanation | batch script]]

Difference between revisions of "Getting Started"