Difference between revisions of "Getting Started"

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{|align=right
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[[Category:Essentials]]
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  |__TOC__
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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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  |}
 
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==Getting an account==
 
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To get an account at the UF Research Computing, you need to read [http://www.hpc.ufl.edu/about/policies/account/] and then put a request in at our request page. That page is [http://www.hpc.ufl.edu/support/acctrqst/ located here].
 
  
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==Login==
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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.
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NOTE: If you are using UF's Visitor Wireless, you will not be able to login to our systems using SSH. You will need to arrange for access using some other network.
 
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===Linux / Unix===
 
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Open a terminal and run
 
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ssh <YOUR_USERNAME>@gator.hpc.ufl.edu
 
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where <code><YOUR_USERNAME></code> is your Research Computing username, which was sent to you when you got your Research Computing account.
 
  
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The command <code>ssh <YOUR_USERNAME>@gator.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 Research Computing username is "smith", you would use the command <code>ssh smith@gator.hpc.ufl.edu</code> to log into the Research Computing.
 
  
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===Windows===
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=From Zero to HiPerGator=
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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:
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===Initial Consult===
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* SSH client - [http://www.chiark.greenend.org.uk/~sgtatham/putty Putty]
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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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** [[PuTTY|configuration instructions for UFRC]]
 
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* Graphical file transfer clients:
 
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** [http://filezilla-project.org/download.php?type=client FileZilla]. See our [[FileZilla|tutorial on transferring files to UFRC using FileZilla]].
 
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** [http://winscp.net/eng/index.php WinSCP]
 
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===MacOS===
 
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For MacOS users, the connection instructions are very similar to those for Linux/Unix users.
 
  
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''Terminal'', the terminal emulation application under MacOS is located in Applications/Utilities.
 
  
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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.
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For the initial interview we recommend prospective users to be ready to answer questions such as:
  
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==Running Graphical Programs==
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* Does the data fall under FERPA, HIPAA, or another restricted classification?
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See the [[GUI_Programs|Gui Programs]] page for information on running graphical user interface applications at UFRC.
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* Explain in simple words what your research is about.
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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?
  
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==Getting Help==
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===HiPerGator Accounts===
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If you are having problems connecting to the UFRC system, please let the UFRC Staff know by submitting a [http://support.rc.ufl.edu Support Request].
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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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==Interactive work under Linux==
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====User Account Creation====
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Once you are logged in to a Research Computing 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.
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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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* [http://www.tldp.org/LDP/intro-linux/html/ Introduction to Linux]
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====Joining a Group====
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* [http://www.linux.org/tutorial/view/beginners-level-course Linux for Beginners]
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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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* [http://www.tutorialized.com/tutorial/Basic-Linux-Shell-commands/21596 Basic Linux Shell Commands]
 
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* [[Getting_Started_on_Linux]]
 
  
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==A Few Basic Commands==
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[https://support.rc.ufl.edu Request to be added to a group]:
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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.
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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.
  
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{| border=1
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===Trial Allocation===
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|-
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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.
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! Command !! Description
 
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|-
 
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| ls || List files in the current directory
 
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|-
 
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| cd || Change directory
 
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|-
 
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| more || View a file's contents
 
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|-
 
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| mkdir <dir> || Create a directory
 
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|-
 
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| cp file1 file2 || Copy a file
 
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|-
 
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| mv file1 file2 || Move (i.e. rename) a file
 
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|-
 
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| rm file || Delete a file
 
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|-
 
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| rmdir dir || Delete an ''empty'' directory
 
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|}
 
  
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==Editing==
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===Purchasing Resources===
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Editing files on the cluster can be done through a couple of different methods...
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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.
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===Native Editors===
 
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* '''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.
 
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** [http://www.eng.hawaii.edu/Tutor/vi.html VI Tutorial]
 
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** Another resource for vi is [[vi | right here]] on our wiki.
 
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** There is also a vi tutorial, '''vimtutor'''. Once logged in, simply type "<code>vimtutor</code>" at the command line to start the tutorial.
 
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* '''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.
 
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** [http://www2.lib.uchicago.edu/~keith//tcl-course/emacs-tutorial.html Emacs Tutorial]
 
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* '''pico''' - While pico is not installed on the system, [[nano]] is installed, and is a pico work-a-like.
 
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* '''nano''' - Nano has a good bit of on-screen help to make it easier to use.
 
  
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===External Editors===
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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.  
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You can also use your favorite editor on your local machine and then transfer the files over to the Research Computing 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.
 
  
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==Running Jobs==
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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.
  
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====Trivial Example====
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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.'''
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{|
 
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|-valign="top"
 
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|
 
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<pre>
 
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#! /bin/sh
 
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#PBS -N testjob
 
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#PBS -o testjob.out
 
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#PBS -e testjob.err
 
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#PBS -M <INSERT EMAIL HERE>
 
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#PBS -r n
 
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#PBS -l walltime=00:01:00
 
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#PBS -l nodes=1:ppn=1
 
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#PBS -l pmem=100mb
 
  
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date
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=Using HiPerGator=
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hostname
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To use HiPerGator or HiPerGator-AI you must have basic understanding the following concepts:
 +
* 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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module load python
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Click on the buttons below to explore.
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python -V
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<div style = 'text-align: center;'>
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</pre>
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[[Image:Interface.png|frameless|upright=1| link=HPG Interfaces]]
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||
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[[Image:Computation.png|frameless|upright=1|link=HPG Computation]]
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To submit this job from gator.hpc.ufl.edu, you would use the following command:
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[[Image:Scheduling.png|frameless|upright=1|link=HPG Scheduling]]
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<pre>
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[[Image:Storage.png|frameless|upright=1|link=HPG Data Management]]
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$ qsub <your job script>
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</div>
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</pre>
 
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To check the status of running jobs, you would use the following command:
 
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<pre>
 
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$ qstat [-u <username>]
 
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</pre>
 
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|}
 
  
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=Getting help=
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'''Notes: '''
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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].
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* See [[Modules]] for more information on using the installed software via the environment modules system.
 
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====DRMAA====
 
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It's possible to submit jobs by using the scheduler API via the DRMAA library. A python example that uses our installed Python DRMAA library can be found in [[Example_pbs-drmaa_python_script]].
 
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====Notes on Batch Scripts====
 
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* 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.
 
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* For more info on '''advanced directives''' see [[PBS_Directives]].
 
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* Please see our [[Batch Script Explanation | annotated submission script]].
 
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===Scratch Storage===
 
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See [[Scratch]] for notes on the main high-performance storage.
 

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"