Difference between revisions of "Getting Started"

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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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Welcome to UF Research Computing! This page is intended to help new and uninitiated users understand and use UFRC resources. Be sure to check out [https://wiki.rc.ufl.edu/doc/Training our training schedule] if you'd like help getting started in person!
 
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==Overview==
 
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The diagram below shown a high-level overview of HiPerGator use. We will go over each part in sections below
 
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[[file:HiPerGator.png|800px]]
 
  
 +
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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==Creating an Account==
 
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To be able to do ''anything'' on HiPerGator you need a UF Research Computing account. Later on we will switch to using GatorLink. At this time we use the same account names that GatorLink uses, but the passwords are different. To create an account with UF Research Computing, you must read the [https://www.rc.ufl.edu/about/policies/account/ UFRC Account Policy]. After you have reviewed the policy, go to [https://www.rc.ufl.edu/help/account-request/ to submit an account request]. You will have to tell us the name of the Principal Investigator who sponsors the access of the group. If you are a PI you'll have to indicate it, so we could create a new group for you. Please note that to do useful work your group will have to [https://www.rc.ufl.edu/services/rates/ invest into computational resources] or you will have to join a departmental group with a shared allocation.
 
  
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==Connecting to HiPerGator==
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=From Zero to HiPerGator=
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To work on HiPerGator you will have to connect to it from your local computer either via SSH (terminal session) or via one of the web/application interfaces we provide such as [[Galaxy]] or Matlab (for Matlab distributed computing toolbox pilot project we are testing).
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===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].
  
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''Note about using this guide:'' for any given command, <code><username></code> should be replaced with the UFRC username (same as your GatorLink username).
 
  
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For example, if you are referencing the command <code>ssh <username>@hpg2.rc.ufl.edu</code> and your Gatorlink username is '''smith''', you would use the command:
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For the initial interview we recommend prospective users to be ready to answer questions such as:
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<pre style="width:75%;">ssh smith@hpg2.rc.ufl.edu</pre>
 
  
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===Connecting from Windows===
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* Does the data fall under FERPA, HIPAA, or another restricted classification?
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<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
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* Explain in simple words what your research is about.
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''Expand this section to view instructions for logging in with Windows.''
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* What file types will be processed initially?
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<div class="mw-collapsible-content" style="padding: 5px;">
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** Input files, average size of individual files, total amount of data in Gb/Tb, etc.
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Since Microsoft Windows does not come with a built-in SSH client, you must download a client from the web.  
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* 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?
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* Are you or will you be working with external collaborators?
  
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UFRC recommends using [http://www.chiark.greenend.org.uk/~sgtatham/putty PuTTY] or [http://mobaxterm.mobatek.net/ MobaXterm].  
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===HiPerGator Accounts===
 +
====Sponsor Username and Group Creation====
 +
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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'''PuTTY'''
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====User Account Creation====
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* [http://www.chiark.greenend.org.uk/~sgtatham/putty Download PuTTY] to your local machine and start the program
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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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* Configure PuTTY using the [[PuTTY|configuration instructions for UFRC]] .
 
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* Select the connection you created in the previous step and click "Open"
 
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* At the login prompt, enter your username (this should be the same as your GatorLink username)
 
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* Enter your password when prompted. You are now connected and ready to work!
 
  
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'''MobaXterm'''
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====Joining a Group====
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* [http://mobaxterm.mobatek.net/ Download MobaXterm] to your local machine and start the program.
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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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* Click "Start local terminal"
 
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* Open a terminal and run <code>ssh <username>@hpg2.rc.ufl.edu</code>
 
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* Enter your password when prompted. You are now connected and ready to work!
 
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</div>
 
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</div>
 
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===Connecting from Linux===
 
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<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
 
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''Expand this section to view instructions for logging in with Linux/Unix.''
 
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<div class="mw-collapsible-content" style="padding: 5px;">
 
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Open a terminal and run
 
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ssh <username>@hpg2.rc.ufl.edu
 
  
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Enter your password when the prompt appears. You are now connected and ready to work!
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[https://support.rc.ufl.edu Request to be added to a group]:
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</div>
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* Include the following in the Summary line: "Add [username] to [groupname] group".
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</div>
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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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===Connecting from MacOS X===
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===Trial Allocation===
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<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
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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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''Expand this section to view instructions for logging in with OS X.''
 
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<div class="mw-collapsible-content" style="padding: 5px;">
 
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For OS X users, connection instructions are very similar to those for Linux users.
 
  
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'''Terminal''', the terminal emulation application for OS X, is located in the folder Applications/Utilities.
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===Purchasing Resources===
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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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Start the Terminal application and run
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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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ssh <username>@hpg2.rc.ufl.edu
 
  
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Enter your password when the prompt appears. You are now connected and ready to work!
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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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</div>
 
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</div>
 
  
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==Transferring Data==
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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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If you need to transfer datasets to or from HiPerGator and your local computer or another external location you have to pick the appropriate transfer mechanism.
 
  
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===Samba===
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=Using HiPerGator=
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Samba service, also known as a '<code>network share</code>' or '<code>mapped drive</code>' provides you with an ability to connect to some HiPerGator filesystems as locally mapped drives (or mount points on Linux or MacOS X). Once you connected to a share this mechanism provides you with a file transfer option that allows you to use your client computer's native file manager to access and manage your files. Samba works best for moving smaller files, like job scripts, to and from the system. You must be connected to the UF network (either on-campus or through the [[VPN]]) to connect to Samba shares.
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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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* [[Samba_Access|See the page on accessing Samba]] for setup information specific to your computer's operating system.
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Click on the buttons below to explore.
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<div style = 'text-align: center;'>
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===SFTP===
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[[Image:Interface.png|frameless|upright=1| link=HPG Interfaces]]
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SFTP, or secure file transfer, works well for small to mediaum data transfers and is appropriate for both small and large data files.
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[[Image:Computation.png|frameless|upright=1|link=HPG Computation]]
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===Graphical file transfer client===
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[[Image:Scheduling.png|frameless|upright=1|link=HPG Scheduling]]
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For many users, a graphical file transfer client is the simplest method of file transfer. UFRC recommends:  
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[[Image:Storage.png|frameless|upright=1|link=HPG Data Management]]
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* [https://filezilla-project.org/download.php?show_all=1 FileZilla] (Windows, OS X)
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</div>
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* [http://winscp.net/eng/index.php WinSCP] (Windows)
 
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* [http://cyberduck.ch/ Cyberduck] (OS X)
 
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After you have chosen and downloaded a client, configure the client to connect to <code>sftp.rc.ufl.edu</code>, specifying port number 22. Use your username and password to log in.
 
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===GatorBox===
 
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GatorBox uses the ownCloud storage platform (similar to Dropbox) to provide a different option for file management. GatorBox can be accessed through the web interface (gatorbox.rc.ufl.edu) or by downloading the ownCloud client. To access storage purchased from UFRC, the user must first set up their UFRC storage as an external storage option within GatorBox.
 
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* [[GatorBox|See the GatorBox page]] for more information on this service.
 
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* [[GatorBox:_Adding_external_storage|See the page on adding external storage to GatorBox]] for detailed instructions on adding your UFRC storage to GatorBox.
 
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===Rsync===
 
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Rsync is a incremental file transfer utility that minimizes network usage. It does so by transmitting only the differences in sequential data, rather than transmitting the complete file. Rsync is best used for tasks like synchronizing files stored across multiple subdirectories, or updating large data sets.
 
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* [[Rsync|See the Rsync page]] for instructions on using rsync.
 
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===Globus===
 
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Globus is another mechanism for file transfer. Globus works especially well for transferring large files or data sets
 
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* [[Globus|See the Globus page]] for setup and configuration information.
 
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==Editing your files==
 
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Several methods exist for editing your files on the cluster.
 
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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. [http://www.eng.hawaii.edu/Tutor/vi.html View a tutorial for using vi]
 
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* '''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]
 
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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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You can also use your favorite file editor on your local machine, and then transfer the files to the cluster afterwards. A 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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==Using installed software==
 
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The full list of software available for use can be viewed on the [[Installed_Software|Installed Software]] page. Access to installed software is provided through [[Modules|Environment Modules]].
 
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The following command can be used to browse the full list of available modules, along with short descriptions of the applications they make available:
 
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<pre>
 
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module spider
 
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</pre>
 
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To load a module, use the following command:
 
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<pre>
 
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load module <module_name>
 
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</pre>
 
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For more information on loading modules to access software, view the page on the [[Modules_Basic_Usage|basic usage of environment modules]].
 
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==Running graphical programs==
 
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It is possible to run programs that use a graphical user interface (GUI) on the system. However, doing so requires installation of and configuration of additional software on the client computer.
 
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Please see the [[GUI_Programs|GUI Programs]] page for information on running graphical user interface applications at UFRC.
 
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==Scheduling jobs using SLURM==
 
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UFRC uses the Simple Linux Utility for Resource Management, or '''SLURM''', to allocate resources and schedule jobs. Users can create SLURM job scripts to submit jobs to the system. These scripts can, and should, be modified in order to control several aspects of your job, like resource allocation, email notifications, or output destination.
 
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* See the [[Annotated_SLURM_Script|Annotated SLURM Script]] for a walk-through of the basic components of a SLURM job script
 
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* See the [[Sample_SLURM_Scripts|Sample SLURM Scripts]] for several SLURM job script examples
 
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To submit a job script from one of login nodes via hpg2.rc.ufl.edu, use the following command:
 
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<pre>
 
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$ sbatch <your_job_script>
 
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</pre>
 
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To check the status of submitted jobs, use the following command:
 
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<pre>
 
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$ squeue -u <username>
 
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</pre>
 
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View [[SLURM_Commands]] for more useful SLURM commands.
 
  
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==Getting help==
+
=Getting help=
−
If you are having problems using the UFRC system, please 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"